Biomark & EP1 Publications

Introduced in 2006 and updated in 2011, Biomark HD stands alone in the world of analytical instrumentation as a multiapplication platform without compromise, providing high quality results for every experimental approach. Using a wide variety of sample types and chemistry choices to accommodate the most genomic applications, Biomark HD lets users run entire projects from research to validation to routine screening on a single system with the flexibility and consistency necessary for today’s biological research.

Browse our catalog of related publications to learn how Biomark empowers researchers across a range of genomic fields.

• Overview

  Number of papers per research area as of September, 2021

  Number of cumulative papers as of September, 2021

• Recent

  • Whole blood stabilization for the microfluidic isolation and molecular characterization of circulating tumor cells
    Wong, K.H.K., Tessier, S.N., Miyamoto, D.T. et al. Nature Communications (2017): 1,733
  • Role of epithelial to mesenchymal transition associated genes in mammary gland regeneration and breast tumorigenesis
    Sikandar, S.S., Kuo, A.H., Kalisky, T. et al. Nature Communications (2017): 1,669
  • Frequency of canine nt230(del4) MDR1 mutation in prone pure breeds, their crosses and mongrels in Israel - insights from a worldwide comparative perspective
    Dekel, Y., Machluf, Y., Stoler, A. et al. BMC Veterinary Research (2017): 333
  • Inhibition of the H3K9 methyltransferase G9A attenuates oncogenicity and activates the hypoxia signaling pathway
    Ho, J.C., Abdullah, L.N., Pang, Q.Y. et al. PLoS One (2017): e0188051
  • IL-2 imprints human naive B cell fate towards plasma cell through ERK/ELK1-mediated BACH2 repression
    Hipp, N., Symington, H., Pastoret, C. et al. Nature Communications (2017): 1,443

• Research Areas

  • Biomarker Screening

    • Risk of Type 1 Diabetes Progression in Islet Autoantibody-Positive Children Can Be Further Stratified Using Expression Patterns of Multiple Genes Implicated in Peripheral Blood Lymphocyte Activation and Function
      Jin, Y., Sharma, A., Bai, S. et al. Diabetes (2014): 2,506–15
    • Huntington's disease biomarker progression profile identified by transcriptome sequencing in peripheral blood
      Mastrokolias, A., Ariyurek, Y., Goeman, J.J. et al. European Journal of Human Genetics (2015): 1349–56
    • Profiles of serum microRNAs; miR-125b-5p and miR223-3p serve as novel biomarkers for HBV-positive hepatocellular carcinoma
      Giray, B.G., Emekdas, G., Tezcan, S. et al. Molecular Biology Reports (2014): 4513–9
    • Multiple Recurrent De Novo CNVs, Including Duplications of the 7q11.23 Williams Syndrome Region, Are Strongly Associated with Autism
      Sanders, S.J., Ercan-Sencicek, A.G., Hus, V. et al. Neuron (2011): 863–85
    • Evaluation of Nanofluidics Technology for High-Throughput SNP Genotyping in a Clinical Setting
      Chan, M., Chan, M.W., Loh, T.W. et al. Journal of Molecular Diagnostics (2011): 305–12
    • Temporal transcriptomics suggest that twin-peaking genes reset the clock
      Pembroke, W.G., Babbs, A., Davies, K.E. et al. eLife (2015): e10518
    • Regulation of alternative splicing at the single‐cell level
      Faigenbloom, L., Rubinstein, N.D., Kloog, Y. et al. Molecular Systems Biology (2015): 845
    • Role of the transient receptor potential (TRP) channel gene expressions and TRP melastatin (TRPM) channel gene polymorphisms in obesity-related metabolic syndrome
      Tabur, S., Oztuzcu, S, Duzen, I.V. et al. European Review for Medical and Pharmacological Sciences (2015): 1,388–97
    • Influence of pharmacogenetic variability on the pharmacokinetics and toxicity of the aurora kinase inhibitor danusertib
      Steeghs, N., Mathijssen, R.H.J., Wessels, J.A.M. et al. Investigational New Drugs (2011): 953–62
    • Arteriolar Function in Visceral Adipose Tissue Is Impaired in Human Obesity
      Farb, M.G., Ganley-Leal, L., Mott, M. et al. Arteriosclerosis, Thrombosis, and Vascular Biology (2011): 467–73
    • A Plasmablast Biomarker for Nonreponse to Antibody Therapy to CD20 in Rheumatoid Arthritis
      Owczarczyk, K., Lal, P., Abbas, A.R. et al. Science Translational Medicine (2011): 101ra92
    • A genome-wide association study identifies two new risk loci for Graves' disease
      Chu, X., Pan, C.M., Zhao, S.X. et al. Nature Genetics (2011): 897–901
    • Reduced Adiposed Tissue Inflammation Represents an Intermediate Cardiometabolic Phenotype in Obesity
      Farb, M.G., Bigornia, S., Mott, M. et al. Journal of the American College of Cardiology (2011): 232–7
    • Genetic dissection of a major mouse obesity QTL (Carfhg2): integration of gene expression and causality modeling
      Farber, C.R., Aten, J.E., Farber, E.A. et al. Physiological Genomics (2009): 294–302
    • Further Improvement in Quanitfying Male Fetal DNA in Maternal Plasma
      Jin, S., Lin, X.M., Law, H. et al. Clinical Chemistry (2012): 465–8
    • Strain-specific modifier genes of Cecr2-associated exencephaly in mice: genetic analysis and identification of differentially expression candidate genes
      Kooistra, M.K., Leduc, R.Y.M., Dawe, C.E. et al. Physiological Genomics (2011): 35–46
    • Differential effects of macronutrient content in 2 energy risk factors and adipose tissue cell size in moderately obese individual: a radnomized controlled trial
      Rizkalla, S.W., Prifti, E., Cotillard, A. et al. The American Journal of Clinical Nutrition (2012): 49–63
    • A comparative analysis of high-throughput platforms for validation of a circulating microRNA signature in diabetic retinopathy
      Farr, R.J., Januszewski, A.S., Joglekar, M.V. et al. Scientific Reports (2015): 10,375
    • Identification of cardiomyopathy associated circulating miRNA biomarkers in patients with muscular dystrophy using a complementary cardiovascular magnetic resonance and plasma profiling approach
      Becker, S., Florian, A., Patrascu, A. et al. Journal of Cardiovascular Magnetic Resonance (2016): 25
    • Discordant Expression of Circulating microRNA from Cellular and Extracellular Sources
      Shah, R., Tanriverdi, K., Levy, D. et al. PLoS One (2016): e0153691
    • A Systems Approach Identifies Essential FOXO3 Functions at Key Steps of Terminal Erythropoiesis
      Liang, R., Campreciós, G., Kou, Y. et al. PLoS Genetics (2015): e1005526
    • A whole blood gene expression-based signature for smoking status
      Beineke, P., Fitch, K., Tao, H. et al. BMC Medical Genomics (2012): 58
    • Catecholaminergic Gene Polymorphisms Are Associated with GI Symptoms and Morphological Brain Changes in Irritable Bowel Syndrome
      Orand, A., Gupta, A., Shih, W. et al. PLoS One (2015): e0135910
    • Circulating Cell and Plasma microRNA Profiles Differ between Non-ST-Segment and ST-Segment-Elevation Myocardial Infarction
      Ward, J.A., Esa, N., Pidikiti, R. et al. Family Medicine and Medical Science Research (2013): 108
    • Transcriptional profiling in facioscapulohumeral muscular dystrophy to identify candidate biomarkers
      Rahimov, F., King, O.D., Leung, D.G. et al.. Proceedings of the National Academy of Sciences (2012): 16,234–9
    • Genome-Wide Characterization and Expression Profiling of the AUXIN RESPONSE FACTOR (ARF) Gene Family in Eucalyptus grandis
      Yu, H., Soler, M., Mila, I. et al. PLoS One (2014): e0108906
    • Genome-wide Identification of microRNA Expression Quantitative Trait Loci
      Huan, T., Rong, J., Liu, C. et al. Nature Communications (2015): 6,601
    • Integrated Genome-wide association and hypothalamus eQTL studies indicate a link between the circadian rhythm-related gene PER1 and coping behavior
      Ponsuksili, S., Zebunke, M., Murani, E. et al. Scientific Reports (2015): 16,264
    • Targeted biomarker profiling of matched primary and metastatic estrogen receptor positive breast cancers
      Schleifman, E.B., Desai, R., Spoerke, J.M. et al. PLoS One (2014): e88401
    • FOXO3-mTOR Metabolic Cooperation in the Regulation of Erythroid Cell Maturation and Homeostasis
      Zhang, X., Campreciós, G., Rimmelé, P. et al. American Journal of Hematology (2014): 954–63
    • Transcriptomics of Maternal and Fetal Membranes Can Discriminate between Gestational-Age Matched Preterm Neonates with and without Cognitive Impairment Diagnosed at 18–24 Months
      Pappas, A., Chaiworapongsa, T., Romero, R. et al. PLoS One (2015): e0118573
    • A Prospective Study of Leukocyte Telomere Length and Risk of Type 2 Diabetes in Postmenopausal Women
      You, N.Y., Chen, B.H., Song, Y. et al. Diabetes (2012): 2,998–3,004
    • Analytical and Clinical Validation of a Prostate Cancer-Enhanced messenger RNA Detection Assay in Whole Blood as a Prognostic Biomarker for Survival
      Danila, D.C., Anand, A., Schultz, N. et al. European Urology (2014): 1,191–7
    • Chronic psychosocial stressors and salivary biomarkers in emerging adults
      Bergen, A.W., Mallick, A., Nishita, D. et al. Psychoneuroendocrinology (2012): 1,158–70
    • Low HERV-K(C4) Copy Number Is Associated With Type 1 Diabetes
      Mason, M.J., Speake, C., Gersuk, V.H. et al. Diabetes (2014): 1,789–95
    • Molecular characterization of corona radiata cells from patients with diminished ovarian reserve using microarry and microfluidic based gene expression profiling
      May-Panloup, P., Ferré-L'Hôtellier, V., Morinière, C. et al. Human Reproduction (2012): 829–43
    • Noninvasive urinary miRNA biomarkers for early detection of pancreatic adenocarcinoma
      Debernardi, S., Massat, N.J., Radon, T.P. et al. American Journal of Cancer Research (2015): 3,455–66
    • Expression patterns of cardiac aging in Drosophila
      Cannon, L., Zambon, A.C., Cammarato, A. et al. Aging Cell (2017): 82–92
    • A Flowering Locus C Homolog Is a Vernalization-Regulated Repressor in Brachypodium and Is Cold Regulated in Wheat
      Sharma, N., Ruelens, P., D'hauw, M. et al. Plant Physiology (2017): 1,301–15
    • Association between IRAK1 rs3027898 and miRNA-499 rs3746444 polymorphisms and rheumatoid arthritis: A case control study and meta-analysis
      Yang, X.K., Li, P., Zhang, C. et al. Zeitschrift für Rheumatologie (2016): 622–9
    • Cystatin D (CST5): An ultra-early inflammatory biomarker of traumatic brain injury
      Hill, L.J., Di Pietro, V., Hazeldine, J. et al. Scientific Reports (2017): 5,002
    • Elevation of brain-enriched miRNAs in cerebrospinal fluid of patients with acute ischemic stroke
      Sørensen, S.S., Nygaard, A.B., Carlsen, A.L. et al. Biomarker Research (2017): 24
    • Muscle transcriptome analysis reveals molecular pathways and biomarkers involved in extreme ultimate pH and meat defect occurrence in chicken
      Beauclercq, S., Hennequet-Antier, C., Praud, C. et al. Scientific Reports (2017): 6,447
    • Identification of SNPs associated with muscle yield and quality traits using allelic-imbalance analyses of pooled RNA-Seq samples in rainbow trout
      Al-Tobasei, R., Ali, A., Leeds, T.D. et al. BMC Genomics (2017): 582
    • New Genetic Loci Associated with Preharvest Sprouting and Its Evaluation Based on the Model Equation in Rice
      Lee, G.A., Jeon, Y.A., Lee, H.S. et al. Frontiers in Plant Science (2017): 1,393
    • Development of a Genetic Map for Onion (Allium cepa L.) Using Reference-Free Genotyping-by-Sequencing and SNP Assays
      Jo, J., Purushotham, P.M., Han, K. et al. Frontiers in Plant Science (2017): 1,606
    • Quantifying engineered nanomaterial toxicity: comparison of common cytotoxicity and gene expression measurements
      Atha, D.H., Nagy, A., Steinbrück, A. et al. Journal of Nanobiotechnology (2017): 79
    • Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids
      Saski, C.A., Scheffler, B.E., Hulse-Kemp, A.M. et al. Scientific Reports (2017): 15,274
    • Frequency of canine nt230(del4) MDR1 mutation in prone pure breeds, their crosses and mongrels in Israel - insights from a worldwide comparative perspective
      Dekel, Y., Machluf, Y., Stoler, A. et al. BMC Veterinary Research (2017): 333
    • Coronary artery disease-associated genetic variants and biomarkers of inflammation
      Christiansen, M.K., Larsen, S.B., Nyegaard, M. et al. PLoS One (2017): doi: 10.1371/journal.pone.0180365
    • Candidate gene analyses of 3-dimensional dentoalveolar phenotypes in subjects with malocclusion
      Weaver, C.A., Miller, S.F., da Fontoura, C.S.G. et al. American Journal of Orthodontics and Dentofacial Orthopedics (2017): 539–58
    • Inflammatory markers in late pregnancy in association with postpartum depression-A nested case-control study
      Bränn, E., Papadopoulos, F., Fransson, E. et al. Psychoneuroendocrinology (2017): 146–59
    • Single-Cell Resolution of Temporal Gene Expression during Heart Development
      DeLaughter, D.M., Bick, A.G., Wakimoto, H. et al. Developmental Cell (2016): 480–90
    • Cytoplasmic FMR1-Interacting Protein 2 is a Major Genetic Factor Underlying Binge Eating
      Kirkpatrick, S.L., Goldberg, L.R., Yazdani, N. et al. Biological Psychiatry (2016): 757–69
    • Novel sex-dependent differentially methylated regions are demethylated in adult male mouse livers
      Ito, S., Hirabayashi, K., Moriishi, K. et al. Biochemical and Biophysical Research Communications (2015): 332–8
    • Biophysical and Population Genetic Models Predict the Presence of “Phantom” Stepping Stones Connecting Mid-Atlantic Ridge Vent Ecosystems
      Breusing, C., Biastoch, A., Drews, A. et al. Current Biology (2016): 2,257–67
    • Diets enriched in trans-11 vaccenic acid alleviate ectopic lipid accumulation in a rat model of NAFLD and metabolic syndrome
      Jacome-Sosa, M.M., Borthwick, F., Mangat, R. et al. Journal of Nutritional Biochemistry (2014): 692–701
    • A multispecies Lactobacillus- and Bifidobacterium-containing probiotic mixture attenuates body weight gain and insulin resistance after a short-term challenge with a high-fat diet in C57/BL6J mice
      Holowacz, S., Guigné, C., Chêneb, G. et al. PharmaNutrition (2015): 101–7
    • Chronic venlafaxine treatment fails to alter the levels of galanin system transcripts in normal rats
      Petschner, P., Juhasz, G., Tamasi, V. et al. Neuropeptides (2016): 65–70
    • A common variant near BDNF is associated with dietary calcium intake in adolescents
      Dušátková, L., Zamrazilová, H., Aldhoon-Hainerová, I. et al. Nutrition Research (2015): 766–73
    • Effects of a meal rich in medium-chain saturated fat on postprandial lipemia in relatives of type 2 diabetics
      Pietraszek, A., Hermansen, K., Pedersen, S.B. et al. Nutrition (2013): 7–8
    • Gene profiling in the avian embryo using laser capture microdissection and RT-qPCR
      Morrison, J.A., Bailey, C.M., Kulesa, P.M. Cold Spring Harbor Protocols (2012): doi: https://doi.org/10.1101/pdb.prot072140
    • Lineage tracing of cells involved in atherosclerosis
      Albarrán-Juárez, J., Kaur, H., Grimm, M. et al. Atherosclerosis (2016): 445–53
    • Association between renin and atherosclerotic burden in subjects with and without type 2 diabetes
      Gonçalves, I., Edsfeldt, A., Colhoun, H.M., et al. BMC Cardiovascular Disorders (2016): 171
    • Distinct functional responses to stressors of bone marrow derived dendritic cells from diverse inbred chicken lines
      Van Goor, A., Slawinska, A., Schmidt, C.J., Lamont, S.J. Developmental & Comparative Immunology (2016): 96–110
    • Converting Human Skin Cells to Neurons: A New Tool to Study and Treat Brain Disorders?
      Kim, K.S. Cell Stem Cell (2011): 179–81
    • Sox9 Activation Highlights a Cellular Pathway of Renal Repair in the Acutely Injured Mammalian Kidney
      Kumar, S., Liu, J., Pang, P. et al. Cell Reports (2015): 1,325–38
    • Proteomic and transcriptomic analysis of rice tranglutaminase and chloroplast-related proteins
      Campos, N., Torné, J.M., Bleda, M.J. et al. Plant Science (2014): 142–53
    • Toward Novel Diagnostics for Primary Open-Angle Glaucoma? An Association Study of Polymorphic Variation in Ras Homolog Family Member (A, B, C, D) Genes RHOA, RHOB, RHOC, and RHOD
      Saracaloglu, A., Demiryürek, S., Okumus, S. et al. OMICS: A Journal of Integrative Biology (2016): 290–5
    • Expression-based GWAS identifies variants, gene interactions and key regulators affecting intramuscular fatty acid content and composition in porcine meat
      Puig-Oliveras, A., Revilla, M., Castelló, A. et al. Scientific Reports (2016): 31,803
    • Postnatal Pancreas of Mice Contains Tripotent Progenitors Capable of Giving Rise to Duct, Acinar, and Endocrine Cells In Vitro
      Ghazalli, N., Mahdavi, A., Feng, T. et al. Stem Cells and Development (2015): 1,995–2,008
    • Toxicogenomics-based identification of mechanisms for direct immunotoxicity
      Shao, J., Katika, M.R., Schmeits, P.C. et al. Toxicological Sciences (2013): 328–46
    • Retinal toxicity, in vivo and in vitro, associated with inhibition of nicotinamide phosphoribosyltransferase
      Zabka, T.S., Singh, J. et al. Toxicological Sciences (2015): 163–72
    • Certified DNA Reference Materials to Compare HER2 Gene Amplification Measurements Using Next-Generation Sequencing Methods
      Lih, C.J., Si, H., Das, B. et al. Journal of Molecular Diagnostics (2016): 753–61
    • Discovery of New Risk Markers for Ischemic Stroke Using a Novel Targeted Proteomics Chip
      Lind, L., Siegbahn, A., Lindahl, B. et al. Stroke (2015): 3,340–7
    • Identification and isolation of a dermal lineage with intrinsic fibrogenic potential
      Rinkevich Y., Walmsley, G.G., Hu, M.S. et al. Science (2015): aaa2151
    • A common missense variant in the neuregulin 1 gene is associated with both schizophrenia and sudden cardiac death
      Huertas-Vazquez, A., Teodorescu, C., Reinier, K. et al. Heart Rhythm (2013): 994–8
    • A Genome-wide Association Study of Nonsyndromic Cleft Palate Identifies an Etiologic Missense Variant in GRHL3
      Leslie, E.J., Liu, H., Carlson, J.C. et al. American Journal of Human Genetics (2016): 744–54
    • Hematopoietic Reprogramming In Vitro Informs In Vivo Identification of Hemogenic Precursors to Definitive Hematopoietic Stem Cells
      Pereira, C.F., Chang, B., Gomes, A. et al. Developmental Cell (2016): 525–39
    • Oncostatin M regulates SOCS3 mRNA stability via the MEK–ERK1/2-pathway independent of p38MAPK/MK2
      Ehlting, C., Böhmer, O., Hahnel, M.J. et al. Cellular Signalling (2015): 555–67
    • Genomewide comparison of the inducible transcriptomes of nuclear receptors CAR, PXR and PPARα in primary human hepatocytes
      Kandel, B.A., Thomas, M., Winter, S. et al. Biochimica et Biophysica Acta (2016): 1,218–27
    • Abnormal Endogenous Repression of GA Signaling in a Seedless Table Grape Cultivar with High Berry Growth Response to GA Application
      Acheampong, A.K., Zheng, C., Halay, T. et al. Frontiers in Plant Science (2017): 850
    • MicroRNA-223 coordinates cholesterol homeostasis
      Vickers, K.C., Landstreet, S.R., Levin, M.G. et al. Proceedings of the National Academy of Sciences (2014): 14,518–23
    • Regulation of gene expression by the BLM helicase correlates with the presence of G-quadruplex DNA motifs
      Nguyen, G.H., Tang, W., Robles, A.I. et al. Proceedings of the National Academy of Sciences (2014): 9,905–10
    • Impact of Body Mass Index, Age, Prostate Volume, and Genetic Polymorphisms on Prostate-specific Antigen Levels in a Control Population
      Cornu, J.N., Cancel-Tassin, G., Cox, D.G. et al. European Urology (2016): 6–8
    • Loss of Iroquois homeobox transcription factors 3 and 5 in osteoblasts disrupts cranial mineralization
      Cain, C.J., Gaborit, N., Lwin, W. et al. Bone Reports (2016): 86–95
    • The molecular basis for sonographic cervical shortening at term: identification of differentially expressed genes and the epithelial-mesenchymal transition as a function of cervical length
      Hassan, S.S., Romero, R., Tarca, A.L. et al. American Journal of Obstetrics and Gynecology (2010): 4723.e1–e14
    • Effect of zearalenone on reproductive parameters and expression of selected testicular genes in mice
      Zatecka, E., Ded, L., Elzeinova, F. et al. Reproductive Toxicology (2014): 20–30
    • Regulation of the Probability of Mouse Odorant Receptor Gene Choice
      Khan, M., Vaes, E., Mombaerts, P. Cell (2011): 907–21
    • REST represses a subset of the pancreatic endocrine differentiation program
      Martin, D., Kim, Y.H., Sever, D. et al.. Developmental Biology (2015): 316–27
    • CYP gene expressions in obesity-associated metabolic syndrome
      Tabur, S., Oztuzcu, S., Oguz, E. et al. Obesity Research and Clinical Practice (2016): 719–23
    • Association between Rho-kinase (ROCK2) gene polymorphisms and Behçet's disease
      Oguz, E., Alasehirli, B., Pehlivan, Y. et al. Translational Research (2012): 428–34
    • Two miRNA clusters, miR-34b/c and miR-449, are essential for normal brain development, motile ciliogenesis, and spermatogenesis
      Wu, J., Bao, J., Kim, M. et al. Proceedings of the National Academy of Sciences (2014): E2851–7
    • A five-gene expression signature to predict progression in T1G3 bladder cancer
      Van der Heijden, A.G., Mengual, L., Lozano, J.J. et al. European Journal of Cancer (2016): 127–36
    • Hypothermia inhibits osteoblast differentiation and bone formation but stimulates osteoclastogenesis
      Patel, J.J., Utting, J.C., Key, M.L. et al. Experimental Cell Research (2012): 2,237–44
    • Comparison of plasma MicroRNA levels in drug naive, first episode depressed patients and healthy controls
      Camkurt, M.A., Acar, Ş., Coşkun, S. et al. Journal of Psychiatric Research (2015): 67–71
    • Corticotropin-releasing hormone receptor 1 (CRH-R1) polymorphisms are associated with irritable bowel syndrome and acoustic startle response
      Orand, A., Naliboff, B., Gadd, M. et al. Psychoneuroendocrinology (2016): 133–41
    • Association of type 2 diabetes GWAS loci and the risk of Parkinson's and Alzheimer's diseases
      Chung, S.J., Kim, M.J., Kim, J. et al. Parkinsonism & Related Disorders (2015): 1,435–40
    • Association of Rho-kinase Gene Polymorphisms with Respiratory Distress Syndrome in Preterm Neonates
      Kaya, G., Sivasli, E., Oztuzcu, S. et al. Pediatrics and Neonatology (2017): 36–42
    • Suppressing Farnesyl diphosphate synthase alters chloroplast development and triggers sterol-dependent induction of JA and Fe-related responses
      Manzano, D., Andrade, P., Caudepon, D. et al. Plant Physiology (2016): 16.​00431
    • MicroRNA network changes in the brain stem underlie the development of hypertension
      DeCicco, D., Zhu, H., Brureau, A. et al. Physiological Genomics (2015): 388–99
    • Novel epigenetic changes in CDKN2A are associated with progression of cervical intraepithelial neoplasia
      Wijetunga, N.A., Belbin, T.J., Burk, R.D. et al. Gynecologic Oncology (2016): 566–73
    • Direct transcriptional regulation of human hepatic cytochrome P450 3A4 (CYP3A4) by peroxisome proliferator-activated receptor alpha (PPARα)
      Thomas, M., Burk, O., Klumpp, B. et al. Molecular Pharmacology (2013): 709–18
    • Keratin 23 is a stress-inducible marker of mouse and human ductular reaction in liver disease
      Guldiken, N., Kobazi Ensari, G., Lahiri, P. et al. Journal of Hepatology (2016): 552–9
    • Activating and Inhibitory Functions of WNT/β-Catenin in the Induction of Cytochromes P450 by Nuclear Receptors in HepaRG Cells
      Thomas, M., Bayha, C., Vetter, S. et al. Molecular Pharmacology (2015): 1,013–20
    • The body mass index (BMI) is significantly correlated with levels of cytokines and chemokines in cerebrospinal fluid
      Larsson, A., Carlsson, L., Lind, A.L. et al. Cytokine (2015): 514–8
    • No activation of human pregnane X receptor by hyperforin-related phloroglucinols
      Kandel, B.A., Ekins, S., Leuner, K. et al. The Journal of Pharmacology and Experimental Therapeutics (2014): 393–400
    • Differential Editosome Protein Function between Life Cycle Stages of Trypanosoma brucei
      McDermott, S.M., Guo, X., Carnes, J., Stuart, K. Journal of Biological Chemistry (2015): 24,914–31
    • Gene variants associated with age at menopause are also associated with polycystic ovary syndrome, gonadotrophins and ovarian volume
      Saxena, R., Bjonnes, A.C., Georgopoulos, N.A. et al. Human Reproduction (2015): 1,697–703
    • Relationship between diminished ovarian reserve and mitochondrial biogenesis in cumulus cells
      Boucret, L., Chao de la Barca, J.M., Morinière, C. et al. Human Reproduction (2015): 1,653–64
    • Functional evaluation of genetic variants associated with endometriosis near GREB1
      Fung, J.N., Holdsworth-Carson, S.J., Sapkota, Y. et al. Human Reproduction (2015): 1,263–75
    • A multi-ethnic genome-wide association study identifies novel loci for non-syndromic cleft lip with or without cleft palate on 2p24.2, 17q23 and 19q13
      Leslie, E.J., Carlson, J.C., Shaffer, J.R. et al. Human Molecular Genetics (2016): 2,862–72
    • Limited effects of preterm birth and the first enteral nutrition on cerebellum morphology and gene expression in piglets
      Bergström, A., Kaalund, S.S., Skovgaard, K. et al. Physiological Reports (2016): e12871
    • Association of Polymorphisms within the Serotonin Receptor Genes 5-HTR1A, 5-HTR1B, 5-HTR2A and 5-HTR2C and Migraine Susceptibility in a Turkish Population
      Yücel, Y., Coşkun, S., Cengiz, B. et al. Clinical Psychopharmacology and Neuroscience (2016): 250–5
    • A mouse GM-CSF receptor antibody attenuates neutrophilia in mice exposed to cigarette smoke
      Botelho, F.M., Nikota, J.K., Bauer, C. et al. European Respiratory Journal (2011): 285–94
    • Cell adhesion molecules and cathelicidin in mice model of hypersensitivity pneumonitis
      Lemieszek, M., Wielscher, M., Golec, M. et al. European Respiratory Journal (2014): P3913
    • Longitudinal analysis of sarcoidosis blood transcriptomic signatures and disease outcomes
      Su, R., Li, M.M., Bhakta, N.R. et al. European Respiratory Journal (2014): 985–93
    • Is idiopathic hirsutism (IH) really idiopathic? mRNA expressions of skin steroidogenic enzymes in women with IH
      Taheri, S., Zararsiz, G., Borlu, M. et al. European Journal of Endocrinology (2015): 447–54
    • Expression Variability of Absorption, Distribution, Metabolism, Excretion–Related MicroRNAs in Human Liver: Influence of Nongenetic Factors and Association with Gene Expression
      Rieger, J.K., Klein, K., Winter, S., Zanger, U.M. Drug Metabolism and Disposition (2013): 1,752–62
    • Inflammation-Associated MicroRNA-130b Down-Regulates Cytochrome P450 Activities and Directly Targets CYP2C9
      Rieger, J.K., Reutter, S., Hofmann, U., Schwab, M., Zanger, U.M. Drug Metabolism and Disposition (2015): 884–8
    • Comparative Analysis and Functional Characterization of HC-AFW1 Hepatocarcinoma Cells: Cytochrome P450 Expression and Induction by Nuclear Receptor Agonists
      Braeuning, A., Thomas, M., Hofmann, U., Vetter, S. et al. Drug Metabolism and Disposition (2015): 1,781–7
    • A gene-based map of the Nod factor-independent Aeschynomene evenia sheds new light on the evolution of nodulation and legume genomes
      Chaintreuil, C., Rivallan, R., Bertioli, D.J. et al. DNA Research (2016): 365–76
    • Developmental fate and lineage commitment of singled mouse blastomeres
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      Golden, T.R., Hubbard, A., Dando, C., Herren, M.A., Melov, S. Aging Cell (2008): 850–65
    • Cell-Free DNA in Maternal Plasma: Has the Size-Distribution Puzzle Been Solved?
      Hahn, S., Zimmermann, B.G. Clinical Chemistry (2010): 1210–1

  • Carrier Screening

    • High-throughput beta-thalassemia carrier screening by allele-specific Q-primer real-time polymerase chain reaction
      Liu, X., Law, H.Y., Tan, Y.M., Hong, Y. Analytical Biochemistry (2010): 97–9
    • Organophosphate Pesticide Exposures, Nitric Oxide Synthase Gene Variants, and Gene–Pesticide Interactions in a Case–Control Study of Parkinson’s Disease, California (USA)
      Paul, K.C., Sinsheimer, J.S., Rhodes, S.L., Cockburn, M., Bronstein, J., Ritz, B. Environmental Health Perspectives (2016): 570–7
    • Association transient receptor potential melastatin channel gene polymorphism with primary open angle glaucoma
      Okumus, S., Demiryürek, S., Gürler, B., Coskun, E., Bozgeyik, İ., Oztuzcu, S., Kaydu, E., Celik, O., Erbagcı, İ., Demiryürek, A.T. Molecular Vision (2013): 1,852-8
    • Single molecule detection in nanofluidic digital array enables accurate measurement of DNA copy number
      Bhat, S., Herrmann, J., Armishaw, P., Corbisier, P., Emslie, K.R. Analytical and Bioanalytical Chemistry (2009): 457–67
    • Association of TALS Developmental Disorder with Defect in Minor Splicing Cmponent U4atac snRNA
      Edery, P., Marcaillou, C., Sahbatou, M., Labalme, A., Chastang, J., Touraine, R., Tubacher, E., Senni, F., Bober, M.B., Nampoothiri, S., Jouk, P.S., Steichen, E., Berland, S., Toutain, A., Wise, C.A., Sanalville, D., Rousseau, F., Clerget-Darpoux, F., Leutenegger, A.L. Science (2011): 240–3

  • Fingerprinting/Sample ID

    • Human Biosample Authentication Using the High-Throughput, Cost-Effective SNPtrace™ System
      Liang-Chu, M.M.Y., Yu, M., Haverty, P.M. et al. PLoS One (2015): e0116218
    • A genetic basis for the variation in the vulnerability of cancer to DNA damage
      Yard, B.D., Adams, D.J., Chie, E.K. et al. Nature Communications (2016): 11,428
    • Characterization of CD8+ T Cell Differentiation following SIVΔnef Vaccination by Transcription Factor Expression Profiling
      Billingsley, J.M., Rajakumar, P.A., Connole, M.A. et al. PLoS Pathogens (2015): e1004740
    • The selective estrogen receptor downregulator GDC-0810 is efficacious in diverse models of ER+ breast cancer
      Joseph, J.D., Darimont, B., Zhou, W. et al. eLife (2016): e15828
    • Transcriptional Profiling of Human Familial Longevity Indicates a Role for ASF1A and IL7R
      Passtoors, W.M., Boer, J.M., Goeman, J.J. et al. PLoS One (2012): e27759
    • Proceedings of the 1st Puerto Rico Biobanking Workshop
      Mora, E., Robb, J.A., Stefanoff, G., et al. Reviews on Recent Clinical Trials (2014): 233–44
    • Partial Genome Assembly for a Candidate Division OP11 Single Cell from an Anoxic Spring (Zodletone Spring, Oklahoma)
      Youssef, N.H., Blainey, P.C., Quake, S.R., Elshahed, M.S. Applied and Environmental Microbiology (2011): 7,804–14
    • Parallel genome-scale loss of function screens in 216 cancer cell lines for the identification of context-specific genetic dependencies
      Cowley, G.S., Weir, B.A., Vazquez, F., et al. Scientific Data (2014): 140,035
    • Integrated genetic and pharmacologic interrogation of rare cancers
      Hong, A.L., Tseng, Y.Y., Cowley, G.S., et al. Nature Communcations (2016): 11,987
    • Metabolite profiling stratifies pancreatic ductal adenocarcinomas into subtypes with distinct sensitivities to metabolic inhibitors
      Daemen, A., Peterson, D., Sahu, N., et al. Proceedings of the National Academy of Sciences of the United States of America (2015): E4,410–7
    • Heritability and Genomics of Gene Expression in Peripheral Blood
      Wright, F.A., Sullivan, P.F., Brooks, A.I., et al. Nature Genetics (2014): 430–7
    • Accurate Determination of Genetic Identity for a Single Cacao Bean, Using Molecular Markers with a Nanofluidic System, Ensures Cocoa Authentication
      Fang, W., Meinhardt, L.W., Mischke, S., Bellato, C.M., Motila, L., Zhang, D. Journal of Agricultural and Food Chemistry (2013): 481–7
    • The Effect of Input DNA Copy Number on Genotype Call and Characterising SNP Markers in the Humpback Whale Genome Using a Nanofluidic Array
      Bhat, S., Polanowski, A.M., Double, M.C., Jarman, S.N., Emslie, K.R. PLoS One (2012): e39181
    • Development of a Novel Reference Plasmid for Accurate Quantification of Genetically Modified Kefeng6 Rice DNA in Food and Feed Samples
      Li, L., Zhang, X., Wan, Y., Jin, W. BioMed Research International (2013): 134,675

  • HLA Typing

    • VAV1 and BAFF, via NFκB pathway, are genetic risk factors for myasthenia gravis
      Avidan, N., Le Panse, R., Harbo, H.F., et al. Annals of Clinical and Translational Neurology (2014): 329–39
    • Universal noninvasive detection of solid organ transplant rejection
      Snyder, T.M., Khush, K.K., Valantine, H.A., Quake, S.R. Proceedings of the National Academy of Sciences (2011): 6229–34

  • Immuno-oncology

    • Inhibition of the H3K9 methyltransferase G9A attenuates oncogenicity and activates the hypoxia signaling pathway
      Ho, J.C., Abdullah, L.N., Pang, Q.Y. et al. PLoS One (2017): e0188051
    • RSPO3 antagonism inhibits growth and tumorigenicity in colorectal tumors harboring common Wnt pathway mutations
      Fischer, M.M., Yeung, V.P., Cattaruzza, F. et al. Scientific Reports (2017): 15,270
    • Role of epithelial to mesenchymal transition associated genes in mammary gland regeneration and breast tumorigenesis
      Sikandar, S.S., Kuo, A.H., Kalisky, T. et al. Nature Communications (2017): 1,669
    • EINCR1 is an EGF inducible lincRNA overexpressed in lung adenocarcinomas
      Nowicki-Osuch, K., Li, Y., Challinor, M. et al. PLoS One (2017): doi: 10.1371/journal.pone.0181902
    • Genome-wide association and expression quantitative trait loci studies identify multiple susceptibility loci for thyroid cancer
      Son, H.Y., Hwangbo, Y., Yoo, S.K. et al. Nature Communications (2017): doi: 10.1038/ncomms15966
    • Expression of CCL21 in Ewing sarcoma shows an inverse correlation with metastases and is a candidate target for immunotherapy
      Sand, L.G.L., Berghuis, D., Szuhai, K., Hogendoom, P.C.W. Cancer Immunology, Immunotherapy (2016): 995–1,002
    • Characterization of the first-in-class T-cell-engaging bispecific single-chain antibody for targeted immunotherapy of solid tumors expressing the oncofetal protein claudin 6
      Stadler, C.R., Bähr-Mahmud, H., Plum, L.M., et al. Oncoimmunology (2016): e1091555
    • SITC/iSBTc Cancer Immunotherapy Biomarkers Resource Document: Online resources and useful tools - a compass in the land of biomarker discovery
      Bedognetti, D., Balwit, J.M., Wang, E., et al. Journal of Translational Medicine (2011): 155
    • Novel technologies and emerging biomarkers for personalized cancer immunotherapy
      Yuan, J., Hegde, P.S., Clynes, R., Foukas, P.G., Harari, A., Kleen, T.O., Kvistborg, P., Maccalli, C., Maecker, H.T., Page, D.B., et al Journal for ImmunoTherapy of Cancer (2016): 3

  • Immunology

    • Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation
      Prospero, V., Piccolo, A., Haim-Vilmovsky, L. et al. Genome Biology (2016): 103
    • Expression of Mitochondrial-Encoded Genes in Blood Differentiate Acute Renal Allograft Rejection
      Roedder, S., Sigdel, T., Hsieh, S.C. et al. Frontiers in Medicine (2017): doi: 10.3389/fmed.2017.00185
    • Poly-β-hydroxybutyrate administration during early life: effects on performance, immunity and microbial community of European sea bass yolk-sac larvae
      Franke, A., Roth, O., De Schryver, P. et al. Scientific Reports (2017): 15,022
    • IL-2 imprints human naive B cell fate towards plasma cell through ERK/ELK1-mediated BACH2 repression
      Hipp, N., Symington, H., Pastoret, C. et al. Nature Communications (2017): 1,443
    • PRR2, a pseudo-response regulator, promotes salicylic acid and camalexin accumulation during plant immunity
      Cheval, C., Perez, M., Leba, L.J. et al. Scientific Reports (2017): doi: 10.1038/s41598-017-07535-8
    • A data-driven modeling approach to identify disease-specific multi-organ networks driving physiological dysregulation
      Anderson, W.D., DeCicco, D., Schwaber, J.S. et al. PLoS Computational Biology (2017): doi: 10.1371/journal.pcbi.1005627
    • Combined single-cell quantitation of host and SIV genes and proteins ex vivo reveals host-pathogen interactions in individual cells
      PLoS Pathogens (2017): doi: 10.1371/journal.ppat.1006445
    • Loss of prion protein induces a primed state of type I interferon-responsive genes
      Malachin, G., Reiten, M.R., Salvesen, Ø. et al. PLoS One (2017): doi: 10.1371/journal.pone.0179881
    • Technical note: Evaluation of endogenous control gene expression in bovine neutrophils by reverse-transcription quantitative PCR using microfluidics gene expression arrays
      Crookenden, M.A., Walker, C.G., Kuhn-Sherlock, B. et al. Journal of Dairy Science (2017): 6,763–71
    • Trans‐generational plasticity in response to immune challenge is constrained by heat stress
      Roth, O., Landis, S.H. Evolutionary Applications (2017): 514–28
    • A combined biomarker and clinical panel for chronic graft versus host disease diagnosis
      Pidala, J., Sigdel, T.K., Wang, A. et al. Journal of Pathology (2017): 3–16
    • The Heterogeneity of Ly6Chi Monocytes Controls Their Differentiation into iNOS+ Macrophages or Monocyte-Derived Dendritic Cells
      Menezes, S., Melandri, D., Anselmi, G. et al. Immunity (2017): 1,205–18
    • Deformation-induced transitional myofibroblasts contribute to compensatory lung growth
      Bennett, R.D., Ysasi, A.B., Wagner, W.L. et al. American Journal of Physiology: Lung Cellular and Molecular Physiology (2017): L79–88
    • Associations Between Macrophage Colony‐Stimulating Factor and Monocyte Chemotactic Protein 1 in Plasma and First‐Time Coronary Events: A Nested Case–Control Study
      Schiopu, A., Bengtsson, E., Gonçalves, I. et al. Journal of the American Heart Association (2016): e002851
    • Antigen exposure shapes the ratio between antigen-specific Tregs and conventional T cells in human peripheral blood
      Su, L.F., del Alcazar, D., Stelekati, E. et al. Proceedings of the National Academy of Sciences of the United States of America (2016): E6192–8
    • Evaluation of Innate Immune Gene Expression Following HDAC Inhibitor Treatment by High Throughput qPCR and PhosFlow Cytometry
      Olagnier, D., Chiang, C., Hiscott, J. Methods in Molecular Biology (2016): 245–55
    • Gene expression profiling in single cells from the pancreatic islets of Langerhans reveals lognormal distribution of mRNA levels
      Bengtsson, M., Ståhlberg, A., Rorsman, P. et al. Genome Research (2005): 1,388–92
    • Retinoblastoma protein potentiates the innate immune response in hepatocytes: significance to hepatocellular carcinoma
      Hutcheson, J., Bourgo, R.J., Balaji, U. et al. Hepatology (2014): 1,231–40
    • Tissue damage drives co-localization of NF-κB, Smad3, and Nrf2 to direct Rev-erb sensitive wound repair in mouse macrophages
      Eichenfield, D.Z., Troutman, T.D., Link, V.M. et al. eLife (2016): e13024
    • Enhanced Reconstitution of Human Erythropoiesis and Thrombopoiesis in an Immunodeficient Mouse Model with KitWv Mutations
      Yurino, A., Takenaka, K., Yamauchi, T., et al. Stem Cell Reports (2016): 425–38
    • Potential of DNA methylation in rectal cancer as diagnostic and prognostic biomarkers
      Exner, R., Pulverer, W., Diem, M. et al. British Journal of Cancer (2015): 1,035–45
    • Chronic exposure to trichloroethylene increases DNA methylation of the Ifng promoter in CD4+ T cells
      Gilbert, K.M., Blossom, S.J., Erickson, S.W. et al. Toxicology Letters (2016): 1–7
    • Synergistic Actions of Blocking Angiopoietin-2 and Tumor Necrosis Factor-α in Suppressing Remodeling of Blood Vessels and Lymphatics in Airway Inflammation
      Le, C.T., Laidlaw, G., Morehouse, C.A. et al. The American Journal of Pathology (2015): 2,949–68
    • Émergence de plasmocytes à longue durée de vie autoréactifs spléniques dans l’anémie hémolytique auto-immune à auto-anticorps chauds chez les patients en échec de rituximab
      Mahevas, M., Michel, M., Vingert, B. et al. La Revue de Médecine Interne (2014): A35
    • Association of TRPM Channel Gene Polymorphisms with Systemic Sclerosis
      Oztuzcu, S., Onat, A.M., Pehlivan, Y. et al. In Vivo (2015): 763–70
    • Integrative analysis of methylome and transcriptome in human blood identifies extensive sex- and immune cell-specific differentially methylated regions.
      Mamrut, S., Avidan, N., Staun-Ram, E. et al. Epigenetics (2015): 943–57
    • Toll-like receptors in maraena whitefish: Evolutionary relationship among salmonid fishes and patterns of response to Aeromonas salmonicida
      Altmann, S., Korytář, T., Kaczmarzyk, D. et al. Fish & Shellfish Immunology (2016): 391–401
    • Evaluation of reference genes for expression studies in leukocytes from term human pregnancy
      Vega-Sanchez, R., Arenas-Hernandez, M., Vazquez-Perez, J.A., Moreno-Valencia, Y., Gomez-Lopez, N. Placenta (2015): 240–5
    • Specific autoantibody profiles and disease subgroups correlate with circulating micro-RNA in systemic sclerosis
      Wuttge, D.M., Carlsen, A.L., Teku, G. et al. Rheumatology (2015): 2,100–7
    • Silymarin Suppresses Cellular Inflammation By Inducing Reparative Stress Signaling
      Lovelace, E.S., Wagoner, J., MacDonald, J. et al. Journal of Natural Products (2015): 1,990–2,000
    • Distinct NF-κB and MAPK Activation Thresholds Uncouple Steady-State Microbe Sensing from Anti-pathogen Inflammatory Responses
      Gottschalk, R.A., Martins, A.J., Angermann, B.R. et al. Cell Systems (2016): 378–90
    • Emergence of long-lived autoreactive plasma cells in the spleen of primary warm auto-immune hemolytic anemia patients treated with rituximab
      Mahévas, M., Michel, M., Vingert, B. et al. Journal of Autoimmunity (2015): 22–30
    • Circulating HIV-Specific Interleukin-21+CD4+ T Cells Represent Peripheral Tfh Cells with Antigen-Dependent Helper Functions
      Schultz, B.T., Teigler, J.E., Pissani, F. et al. Immunity (2016): 167–78
    • Successful immunotherapy induces previously unidentified allergen-specific CD4+ T-cell subsets
      Ryan, J.F., Hovde, R., Glanville, J. et al. Proceedings of the National Academy of Sciences (2016): E1286–95
    • The effects of age and gender on plasma levels of 63 cytokines
      Larsson, A., Carlsson, L., Gordh, T. et al. Journal of Immunological Methods (2015): 58–61
    • Exploring the immune signalling pathway-related genes of the cattle tick Rhipicephalus microplus: From molecular characterization to transcriptional profile upon microbial challenge
      Rosa, R.D., Capelli-Peixoto, J., Mesquita, R.D. et al. Developmental and Comparative Immunology (2016): 1–14
    • High polymorphism in big defensin gene expression reveals presence-absence gene variability (PAV) in the oyster Crassostrea gigas
      Rosa, R.D., Alonso, P., Santini, A. et al. Developmental and Comparative Immunology (2015): 231–8
    • Biparental immune priming in the pipefish Syngnathus typhle
      Beemelmanns, A., Roth, O. Zoology (2016): 262–72
    • IL-12 drives functional plasticity of human group 2 innate lymphoid cells
      Lim, A.I., Menegatti, S., Bustamante, J. et al. Journal of Experimental Medicine (2016): 569–83
    • Rheumatoid arthritis-associated RBPJ polymorphism alters memory CD4+ T cells
      Orent, W., Mchenry, A.R., Rao, D.A. et al. Human Molecular Genetics (2016): 404–17
    • Invariant NKT Cell Activation Induces Late Preterm Birth That Is Attenuated by Rosiglitazone
      St Louis, D., Romero, R., Plazyo, O. et al. The Journal of Immunology (2016): 1,044–59
    • Type I IFNs Regulate Inflammation, Vasculopathy, and Fibrosis in Chronic Cutaneous Graft-versus-Host Disease
      Delaney, T.A., Morehouse, C., Brohawn, P.Z. et al. The Journal of Immunology (2016): 42–50
    • Model-Based Characterization of Inflammatory Gene Expression Patterns of Activated Macrophages
      Rex, J., Albrecht, U., Ehlting, C. et al. PLoS Computational Biology (2016): e1005018
    • The autophagy gene Atg16l1 differentially regulates Treg and TH2 cells to control intestinal inflammation
      Kabat, A.M., Harrison, O.J., Riffelmacher, T. et al. eLife (2016): e12444
    • Immunological effects of reduced mucosal integrity in the early life of BALB/c mice
      Bendtsen, K.M., Hansen, C.H.F., Krych, L. et al. PLoS One (2017): e0176662
    • Longitudinal dynamics of the HIV-specific B cell response during intermittent treatment of primary HIV infection
      de Bree, G.J., Wheatley, A.K., Lynch, R.M. et al. PLoS One (2017): e0173577
    • A Three-Gene Assay for Monitoring Immune Quiescence in Kidney Transplantation
      Roedder, S., Li, L., Alonso, M.N. et al. Journal of the American Society of Nephrology (2015): 2,042–53
    • Regulation of Activation-associated MicroRNA Accumulation Rates during Monocyte-to-macrophage Differentiation
      Eigsti, R.L., Sudan, B., Wilson, M.E. et al. Journal of Biological Chemistry (2014): 28,433–47
    • Next-Generation qPCR for the High-Throughput Measurement of Gene Expression in Multiple Leukocyte Subsets
      Adamski, M.G., Li, Y., Wagner, E. et al. Journal of Biomolecular Screening (2013): 1,008–17
    • The Impact of Staphylococcus aureus Concentration on the Development of Pulmonary Lesions and Cytokine Expression After Intravenous Inoculation of Pigs
      Soerensen, K.E., Skovgaard, K., Heegaard, P.M.H. et al. Veterinary Pathology (2012): 950–62
    • Expression of innate immune genes, proteins and microRNAs in lung tissue of pigs infected experimentally with influenza virus (H1N2)
      Skovgaard, K., Cirera, S., Vasby, D. et al. Innate Immunity (2013): 531–44
    • Single-cell analysis reveals new subset markers of murine peritoneal macrophages and highlights macrophage dynamics upon Staphylococcus aureus peritonitis
      Accarias, S., Genthon, C., Rengel, D. et al. Innate Immunity (2016): 382–92
    • Small nucleolar RNA expression profiling identifies potential prognostic markers in peripheral T-cell lymphoma
      Valleron, W., Ysebaert, L., Berquet, L. et al. Blood (2012): 3,997–4,005
    • Multiparameter single-cell profiling of human CD4+FOXP3+ regulatory T-cell populations in homeostatic conditions and during graft-versus-host disease
      Dong, S., Maiella, S., Xhaard, A. et al. Blood (2013): 1,802–12
    • Cytokine response to the RSV antigen delivered by dendritic cell-directed vaccination in congenic chicken lines
      Mucksová, J., Plachý, J., Staněk, O. et al. Veterinary Research (2017): DOI 10.1186/s13567-017-0423-8
    • Selective induction of alternatively spliced FynT isoform by TNF facilitates persistent inflammatory responses in astrocytes
      Lee, C., Low, C.Y.B., Wong, S.Y. et al. Scientific Reports (2017): 43,651
    • Polyfunctional and IFN-γ monofunctional human CD4⁺ T cell populations are molecularly distinct
      Burel, J.G., Apte, S.H., Groves, P.L. et al. JCI Insight (2017): e87499
    • TCR-CD3ζ gene polymorphisms and expression profile in rheumatoid arthritis.
      Li, P., Wang, X., Zhao, M.Q., et al. Autoimmunity (2016): 466–71
    • Bacterial Internalization, Localization, and Effectors Shape the Epithelial Immune Response during Shigella flexneri Infection
      LIppmann, J., Gwinner, F., Rey, C., et al. Infection and Immunity (2015): 3,624–37
    • The EPIICAL project: an emerging global collaboration to investigate immunotherapeutic strategies in HIV-infected children
      Palma, P., Foster, C., Rojo, P., et al. Journal of Virus Eradication (2015): 134–9
    • Monocytic MKP-1 Is a Sensor of the Metabolic Environment and Regulates Function and Phenotypic Fate of Monocyte-Derived Macrophages in Atherosclerosis
      Kim, H.S., Tavakoli, S., Piefer, L.A. et al. Scientific Reports (2016): 34,223
    • Grandparental immune priming in the pipefish Syngnathus typhle
      Beemelmanns, A., Roth, O. BMC Evolutionary Biology (2017): 44
    • Cytotoxic CD4 T Cells—Friend or Foe during Viral Infection?
      Juno, J.A., van Bockel, D., Kent, S.J. et al. Frontiers in Immunology (2017): 19
    • Physiological evidence for diversification of IFNα- and IFNβ-mediated response programs in different autoimmune diseases
      de Jong, T.D., Vosslamber, S., Mantel, E., et al. Arthritis Research and Therapy (2016): 49
    • Late regulation of immune genes and microRNAs in circulating leukocytes in a pig model of influenza A (H1N2) infection
      Brogaard, L., Heegaard, P.M.H., Larsen, L.E., et al. Scientific Reports (2016): 21,812
    • Serological and Genetic Evidence for Altered Complement System Functionality in Systemic Lupus Erythematosus: Findings of the GAPAID Consortium
      Prechl, J., Papp, K., Hérincs, Z., et al. PLoS One (2016): e0150685
    • Single cell analysis defines the divergence between the innate lymphoid cell and lymphoid tissue inducer lineages
      Ishizuka, I.E., Chea, S., Gudjonson, H., et al. Nature Immunology (2016): 269–76
    • The IL17A and IL17F loci have divergent histone modifications and are differentially regulated by prostaglandin E2 in Th17 cells
      Adamik, J., Henkel, M., Ray, A., et al. Cytokine (2013): 404–12
    • Temporal changes in innate immune signals in a rat model of alcohol withdrawal in emotional and cardiorespiratory homeostatic nuclei
      Freeman, K., Brureau, A., Vadigepalli, R., et al. Journal of Neuroinflammation (2012): 97
    • Small-molecule screening identifies inhibition of salt-inducible kinases as a therapeutic strategy to enhance immunoregulatory functions of dendritic cells
      Sundberg, T.B., Choi, H.G., Song, J.H., et al. Proceedings of the National Academy of Sciences of the United States of America (2014): 12,468–73
    • Single-cell NF-κB dynamics reveal digital activation and analog information processing in cells
      Tay, S., Hughley, J.J., Lee, T.K., et al. Nature (2010): 267–71
    • Protein-poor diet reduces host-specific immune gene expression in Bombus terrestris
      Brunner, F.S., Schmitd-Hempel, P., Barribeau, S.M. Proceedings of the Royal Society B: Biological Sciences (2014):
    • Protective effects of matrix metalloproteinase-12 following corneal injury
      Chan, M.F., Li, J., Bertrand, A., et al. Journal of Cell Science (2013): 3,948–60
    • Peripheral CD300a+CD8+ T Lymphocytes with a Distinct Cytotoxic Molecular Signature Increase in Pregnant Women with Chronic Chorioamnionitis
      Xu, Y., Tarquini, F., Romero, R., et al. American Journal of Reproductive Immunology (2012): 184–97
    • Lymphotoxin-LIGHT Pathway Regulates the Interferon Signature in Rheumatoid Arthritis
      Bienkowska, J., Allaire, N., Thai, A., et al. PLoS One (2014): e112545
    • Intra-graft expression of genes involved in iron homeostasis predicts the development of operational tolerance in human liver transplantation
      Bohne, F., Martínez-Llordella, M., Lozano, J.J., et al. Journal of Clinical Investigation (2012): 368–82
    • Inflammation and Immune-Related Candidate Gene Associations with Acute Lung Injury Susceptibility and Severity: A Validation Study
      O'Mahony, D.S., Glavan, B.J., Holden, T.D., et al. PLoS One (2012): e51104
    • Immune-Related Functions of the Hivep Gene Family in East African Cichlid Fishes
      Diepeveen, E.T., Roth, O., Salzburger, W. G3 (2013): 2,205–17
    • HIV-Infected Spleens Present Altered Follicular Helper T Cell (Tfh) Subsets and Skewed B Cell Maturation
      Colineau, L., Rouers, A., Yamamoto, T., et al. PLoS One (2015): e0140978
    • Genetic inference of immune responsiveness of melanoma cancer patients to TIL therapy
      Sommariva, M., Cheung, F., Chen, J., et al. Journal for ImmunoTherapy of Cancer (2013): P63
    • Exploring the Mode of Action of Bioactive Compounds by Microfluidic Transcriptional Profiling in Mycobacteria
      Murima, P., de Sessions, P.F., Lim, V., et al. PLoS One (2013): e69191
    • Spatiotemporal control of interferon-induced JAK/STAT signalling and gene transcription by the retromer complex
      Chmiest, D., Sharma, N., Zanin, N. et al. Nature Communications (2016): 13,476
    • Adaptively introgressed Neandertal haplotype at the OAS locus functionally impacts innate immune responses in humans
      Sams, A.J., Dumaine, A., Nédélec, Y. et al. Genome Biology (2016): 246
    • Progestin-Containing Contraceptives Alter Expression of Host Defense-Related Genes of the Endometrium and Cervix
      Goldfien, G.A., Barragan, F., Chen, J. et al. Reproductive Sciences (2015): 814–28
    • Mesenchymal Stromal Cells Derived From Crohn's Patients Deploy Indoleamine 2,3-dioxygenase-mediated Immune Suppression, Independent of Autophagy
      Chinnadurai, R., Copland, I.B., Ng, S. et al. Molecular Therapy (2015): 1,248–61
    • Crosstalk between human DC subsets promotes antibacterial activity and CD8+ T-cell stimulation in response to bacille Calmette-Guérin
      Lozza, L., Farinacci, M., Faé, K. et al. European Journal of Immunology (2014): 80–92
    • Corticosteroids for Dengue – Why Don't They Work?
      Nguyen, T.H.T., Nguyen, T.H.Q., Vu, T.T. et al. PLoS Neglected Tropical Diseases (2013): e2592
    • Coordinated Changes in AHRR Methylation in Lymphoblasts and Pulmonary Macrophages from Smokers
      Monick, M.M., Beach, S.R.H., Plume, J. et al. American Journal of Medical Genetics Part B (2012): 141–51
    • Mature Cystic Fibrosis Airway Neutrophils Suppress T-Cell Function: Evidence for a Role of Arginase 1, But Not Programmed Death-Ligand 1
      Ingersoll, S.A., Laval, J., Forrest, O.A. et al. Journal of Immunology (2015): 5,520–8
    • Impact of Chronic HIV/SIV Infection on T Follicular Helper Cell Subsets and Germinal Center Homeostasis
      Graff-Dubois, S., Rouers, A., Moris, A. Frontiers in Immunology (2016): 501
    • A transcriptome-based model of central memory CD4 T cell death in HIV infection
      Olvera-Garcia, G., Aguilar-García, T., Gutiérrez-Jasso, F. et al. BMC Genomics (2016): 956
    • High-throughput gene-expression quantification of grapevine defense responses in the field using microfluidic dynamic arrays
      Dufour, M.C., Magnin, N., Dumas, B. et al. BMC Genomics (2016): 957
    • Widely Divergent Transcriptional Patterns Between SLE Patients of Different Ancestral Backgrounds in Sorted Immune Cell Populations
      Sharma, S., Jin, Z., Rosenzweig, E. et al. Journal of Automimmunity (2015): 51–8
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    • Heat Stress and Lipopolysaccharide Stimulation of Chicken Macrophage-Like Cell Line Activates Expression of Distinct Sets of Genes
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    • CD40 is required for protective immunity against liver stage Plasmodium infection
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    • Reduced BMPR2 expression induces GM-CSF translation and macrophage recruitment in humans and mice to exacerbate pulmonary hypertension
      Sawada, H., Saito, T., Nickel, N.P., Alastalo, T.P., Glotzbach, J.P., Chan, R., Haghighat, L., Fuchs, G., Januszyk, M., Cao, A., Lai, Y.J., de Jesus Perez, V., Kim, Y.M., Wang, L., Chen, P.I., Spiekerkoetter, E., Mitani, Y., Gurtner, G.C., Sarnow, P., Rabinovitch, M. Journal of Experimental Medicine (2014): 263–80
    • The Transcription Factor ARID3a Is Important for In Vitro Differentiation of Human Hematopoietic Progenitors
      Ratliff, M.L., Mishra, M., Frank, M.B., Guthridge, J.M., Webb, C.F. The Journal of Immunology (2016): 614–23
    • Histone Deacetylase Inhibitor Romidepsin Inhibits De Novo HIV-1 Infections
      Jønsson, K.L., Tolstrup, M., Vad-Nielsen, J., Kjær, K., Laustsen, A., Andersen, M.N., Rasmussen, T.A., Søgaard, O.S., Østergaard, L., Denton, P.W., Jakobsen, M.R. Antimicrobial Agents and Chemotherapy (2015): 3,984–94
    • High-Throughput Single-Cell Analysis for Wound Healing Applications
      Januszyk, M., Gurtner, G.C. Advances in Wound Care (2013): 457–69
    • Parturition in dairy cows temporarily alters the expression of genes in circulating neutrophils
      Crookenden, M.A., Heiser, A., Murray, A., Dukkipati, V.S., Kay, J.K., Loor, J.J., Meier, S., Mitchell, M.D., Moyes, K.M., Walker, C.G., Roche, J.R. Journal of Dairy Science (2016): doi: 10.3168/jds.2015-10877
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      Lee, J.H., Romero, R., Chaiworapongsa, T., Dong, Z., Tarca, A.L., Xu, Y., Chiang, P.J., Kusanovic, J.P., Hassan, S.S., Yeo, L., Than, N.G., Kim, C.J. American Journal of Reproductive Immunology (2013): 265–84
    • B cell depletion in immune thrombocytopenia reveals splenic long-lived plasma cells
      Mahévas, M., Patin, P., Huetz, F., Descatoire, M., Cagnard, N., Bole-Feysot, C., Le Gallou, S., Khellaf, M., Fain, O., Boutboul, D., Galicier, L., Ebbo, M., Lambotte, O., Hamidou, M., Bierling, P., Godeau, B., Michel, M., Weill, J.C., Reynaud, C.A. Journal of Clinical Investigation (2013): 432–42
    • Antigen-specific memory in B-1a and its relationship to natural immunity
      Yang, Y., Ghosn, E.E.B., Cole, L.E., Obukhanych, T.V., Sadate-Ngatchou, P., Vogel, S.N., Herzenberg, L.A., Herzenberg, L.A. Proceedings of the National Academy of Sciences of the United States of America (2012): 5,388–93
    • Antigen-specific antibody responses in B-1a and their relationship to natural immunity
      Yang, Y., Ghosn, E.E.B., Cole, L.E., Obukhanych, T.V., Sadate-Ngatchou, P., Vogel, S.N., Herzenberg, L.A., Herzenberg, L.A. Proceedings of the National Academy of Sciences of the United States of America (2012): 5,382–7
    • Airway Epithelial miRNA Expression Is Altered in Asthma
      Solberg, O.D., Ostrin, E.J., Love, M.I., Peng, J.C., Bhakta, N.R., Hou, L., Nguyen, C., Solon, M., Nguyen, C., Barczak, A.J., Zlock, L.T., Blagev, D.P., Finkbeiner, W.E., Ansel, K.M., Arron, J.R., Erle, D.J., Woodruff, P.G. American Journal of Respiratory and Critical Care Medicine (2012): 965–74
    • Adjuvant-specific regulation of long-term antibody responses by ZBTB20
      Wang, Y., Bhattacharya, D. Journal of Experimental Medicine (2014): 841–56
    • A Rapid Noninvasive Assay for the Detection of Renal Transplant Injury
      Sigdel, T.K., Vitalone, M.J., Tran, T.Q., Dai, H., Hsieh, S.C., Salvatierra, O., Sarwal, M.M. Transplantation (2013): 97–101
    • Diversity of viruses in Ixodes ricinus, and characterization of a neurotropic strain of Eyach virus
      Moutailler, S., Popovici, I., Devillers, E., Vayssier-Taussat, M., Eloit, M. New Microbes and New Infections (2016): 71–81
    • Innate immune response to homologous rotavirus infection in the small intestinal villous epithelium at single-cell resolution
      Sen, A., Rothenberg, M.E., Mukherjee, G., Feng, N., Kalisky, T., Nair, N., Johnstone, I.M., Clarke, M.F., Greenberg, H.B. Proceedings of the National Academy of Sciences of the United States of America (2012): 20,667–72
    • Immune gene expression in the spleen of chickens experimentally infected with Ascaridia galli
      Dalgaard, T.S., Skovgaard, K., Norup, L.R., Pleidrup, J., Permin, A., Schou, T.W., Vadekær, D.F., Jungersen, G., Juul-Madsen, H.R. Veterinary Immunology and Immunopathology (2015): 79–86
    • Type I interferon: potential therapeutic target for psoriasis?
      Yao, Y., Richman, L., Morehouse, C., de los Reyes, M., Higgs, B.W., Boutrin, A., White, B., Coyle, A., Krueger, J., Kiener, P.A., Jallal, B. PLoS One (2008): e2737
    • Single-cell gene profiling analysis of human regulatory T cell subsets
      Maiella, S., Dong, S., Becavin, C., Coffre, M., Placek, K., Bianchi, E., Benecke, A., Rogge, L. Journal of Translational Medicine (2010): P3
    • Single-cell analysis techniques reveal a striking heterogeneity of human CD4+ T cell subsets
      Coffre, M., Placek, K., Maiella, S., Bianchi, E., Rogge, L. Journal of Translational Medicine (2010): O5
    • Infectious disease, shifting climates, and opportunistic predators: cumulative factors potentially impacting wild salmon declines
      Miller, K.M., Teffer, A., Tucker, S., Li, S., Schulze, A.D., Trudel, M., Juanes, F., Tabata, A., Kaukinen, K.H., Ginther, N.G., et al Evolutionary Applications (2014): 812-55
    • HTLV-1 Tax-Mediated Inhibition of FOXO3a Activity Is Critical for the Persistence of Terminally Differentiated CD4+ T Cells
      Olagnier, D., Sze, A., Hadj, S.B., Chiang, C., Steel, C., Han, X., Routy, J.P., Lin, R., Hiscott, J., van Grevenynghe, J. PLoS Pathogens (2014): e1004575
    • Foliar treatments with Gaultheria procumbens essential oil induce defense responses and resistance against a fungal pathogen in Arabidopsis
      Vergnes, S., Ladouce, N., Fournier, S., Ferhout, H., Attia, F., Dumas, B. Frontiers in Plant Science (2014): 477
    • A common rejection module (CRM) for acute rejection across multiple organs identifies novel therapeutics for organ transplantation
      Khatri, P., Roedder, S., Kimura, N., De Vusser, K., Morgan, A.A., Gong, Y., Fischbein, M.P., Robbins, R.C., Naesens, M., Butte, A.J., Sarwal, M.M. Journal of Experimental Medicine (2013): 2,205–21
    • Early Preservation of CXCR5+ PD-1+ Helper T Cells and B Cell Activation Predict the Breadth of Neutralizing Antibody Responses in Chronic HIV-1 Infection
      Cohen, K., Altfeld, M., Alter, G., Stamatatos, L. Journal of Virology (2014): 13,310–21
    • γδ T cells recognize a microbial encoded B cell antigen to initiate a rapid antigen specific Interleukin 17 response
      Zeng, X., Wei, Y.L., Huang, J., Newell, E.W., Yu, H., Kidd, B.A., Kuhns, M.S., Waters, R.W., Davis, M.M., Weaver, C.T., Chien, Y.H. Immunity (2012): 524-34
    • Trained immunity in newborn infants of HBV-infected mothers
      Hong, M., Sandalova, E., Low, D., Gehring, A.J., Fieni, S., Amadei, B., Urbani, S., Chong, Y.S., Guccione, E., Bertoletti, A. Nature Communications (2015): 6,588
    • The Influence of Immunization Route, Tissue Microenvironment, and Cytokine Cell Milieu on HIV-Specific CD8+ T Cells Measured Using Fluidigm Dynamic Arrays
      Trivedi, S., Ranasinghe, C. PLoS One (2015): e0126487
    • Tacrolimus Inhibits the Revascularization of Isolated Pancreatic Islets
      Nishimura, R., Nishioka, S., Fujisawa, I., Shiku, H., Shimada, M., Sekiguchi, S., Fujimori, K., Ushiyama, A., Matsue, T., Ohuchi, N., Satomi, S., Goto, M. PLoS One (2013): e56799
    • Single cell transcriptional analysis reveals novel innate immune cell types
      Kippner, L.E., Kim, J., Gibson, G., Kemp, M.L. PeerJ (2014): e452
    • Significance and Suppression of Redundant IL17 Responses in Acute Allograft Rejection by Bioinformatics Based Drug Repositioning of Fenofibrate
      Roedder, S., Kimura, N., Okamura, H., Hsieh, S.C., Gong, Y., Sarwal, M.M. PLoS One (2013): e56657
    • Sequence-Specific Modifications Enhance the Broad-Spectrum Antiviral Response Activated by RIG-I Agonists
      Chiang, C.,Beljanski, V.,Yin, K., Olagnier, D., Yebdri, F.B., Steel, C., Goulet, M.L., DeFilippis, V.R., Streblow, D.N., Haddad, E.K., Trautmann, L., Ross, T., Lin, R., Hiscott, J. Journal of Virology (2015): 8,011–25
    • Reversible Reprogramming of Circulating Memory T Follicular Helper Cell Function during Chronic HIV Infection
      Cubas, R., van Grevenynghe, J., Wills, S., Kardava, L., Santich, B.H., Buckner, C.M., Muir, R., Tardif, V., Nichols, C., Procopio, F., He, Z., Metcalf, T., Ghneim, K., Locci, M., Ancuta, P., Routy, J.P., Trautmann, L., Li, Y., McDermott, A.B., Koup, R.A., Petrovas, C., Migueles, S.A., Connors, M., Tomaras, G.D., Moir, S., Crotty, S., Haddad, E.K. Journal of Immunology (2015): 5,625-36
    • Pre-Existing Hypertension Dominates γδT Cell Reduction in Human Ischemic Stroke
      Adamski, M.G., Wagner, E., Yu, H., Seales-Bailey, C., Durkin, H., Hao, Q., Soper, S.A., Murphy, M., Baird, A.E. PLoS One (2014): e97755
    • No monkey business: why studying NK cells in non-human primates pays off
      Hong, H.S., Rajakumar, P.A., Billingsley, J.M., Reeves, R.K., Johnson, R.P. Frontiers in Immunology (2013): 32
    • Multifaceted Activities of Type I Interferon Are Revealed by a Receptor Antagonist
      Levin, D., Schneider, W.M., Hoffman, H.H., Yarden, G., Busetto, A.G., Manor, O., Sharma, N., Rice, C.M., Schreiber, G. Science Signaling (2014): ra50
    • Microdevices for examining immunological responses of single cells to HIV
      Choi, J., Jeong, Y., Han, H.S., Lee, K.H. Bioscience Reports (2014): e00134
    • Immune Gene Expression in Bombus terrestris: Signatures of Infection Despite Strong Variation among Populations, Colonies, and Sister Workers
      Brunner, F.S., Schmid-Hempel, P., Barribeau, S.M. PLoS One (2013): e68181
    • Early specification of CD8+ T lymphocyte fates during adaptive immunity revealed by single-cell gene expression analyses
      Arsenio, J., Kakaradov, B., Metz, P.J., Kim, S.H., Yeo, G.W., Chang, J.T. Nature Immunology (2014): 365–72
    • Germinal Center B Cell Depletion Diminishes CD4+ Follicular T Helper Cells in Autoimmune Mice
      Yusuf, I., Stern, J., McCaughtry, T.M., Gallagher, S., Sun, H., Gao, C., Tedder, T., Carlesso, G., Carter, L., Herbst, R., Wang, Y. PLoS One (2014): e102791
    • Generation of IL-8 and IL-9 Producing CD4+ T Cells Is Affected by Th17 Polarizing Conditions and AHR Ligands
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    • Gamma delta T cells recognize haptens and mount a hapten-specific response
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    • Functional genomics identifies negative regulatory nodes controlling phagocyte oxidative burst
      Nature Communications (2015): 7,838
    • Fine Tuning of a Type 1 Interferon Antagonist
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    • Evaluation of the Plasma Micro RNA Expression Levels in Secondary Hemophagocytic Lymphohistiocytosis
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    • Development of Potential Pharmacodynamic and Diagnostic Markers for Anti-IFN-α Monoclonal Antibody Trials in Systemic Lupus Erythematosus
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    • Development and Function of Invariant Natural Killer T Cells Producing TH2- and TH17-Cytokines
      Watari, H., Sekine-Kondo, E., Shigeura, T., Motomura, Y., Yasuda, T., Satoh, R., Yoshida, H., Kubo, M., Kawamoto, H., Koseki, H., Taniguchi, M. PLoS Biology (2012): e1001255
    • Coordinating Role of RXRα in Downregulating Hepatic Detoxification during Inflammation Revealed by Fuzzy-Logic Modeling
      Keller, R., Klein, M., Thomas, M., Dräger, A., Metzger, U., Templin, M.F., Joos, T.O., Thasler, W.E., Zell, A., Zanger, U.M. PLoS Computational Biology (2016): e1004431
    • A miRNA upregulated in asthma airway T cells promotes TH2 cytokine production
      Simpson, L.J., Patel, S., Bhakta, N.R., Choy, D.F., Brightbill, H.D., Ren, X., Wang, Y., Pua, H.H., Baumjohann, D., Montoya, M.M., Panduro, M., Remedios, K.A., Huang, X., Fahy, J.V., Arron, J.R., Woodruff, P.G., Ansel, K.M. Nature Immunology (2015): 1,162–70
    • An integrated nano-scale approach to profile miRNAs in limited clinical samples
      Seumois, G., Vijayanand, P., Eisley, C.J., Omran, N., Kalinke, L., North, M., Ganesan, A.P., Simpson, L.J., Hunkapiller, N., Moltzahn, F., Woodruff, P.G., Fahy, J.V., Erle, D.J., Djukanovic, R., Blelloch, R., Ansel, K.M. American Journal of Clinical and Experimental Immunology (2012): 70-89
    • Altered Methylation Profile of Lymphocytes Is Concordant with Perturbation of Lipids Metabolism and Inflammatory Response in Obesity
      Jacobsen, M.J., Mentzel, C.M.J., Olesen, A.S., Huby, T., Jørgensen, C.B., Barrès, R., Fredholm, M., Simar, D. Journal of Diabetes Research (2015): 8,539,057
    • Adipose-derived mesenchymal stromal cells modulate tendon fibroblast responses to macrophage-induced inflammation in vitro
      Manning, C.N., Martel, C., Sakiyama-Elbert, S.E., Silva, M.J., Shah, S., Gelberman, R.H., Thomopoulos, S. Stem Cell Research and Therapy (2015): 74
    • A varying T cell subtype explains apparent tobacco smoking induced single CpG hypomethylation in whole blood
      Bauer, M., Linsel, G., Fink, B., Offenberg, K., Hahn, A.M., Sack, U., Knaack, H., Eszlinger, M., Herberth, G. Clinical Epigenetics (2015): 81
    • A Systematic Approach to Identify Markers of Distinctly Activated Human Macrophages
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    • A depauperate immune repertoire precedes evolution of sociality in bees
      Barribeau, S.M., Sadd, B.M., du Plessis, L., Brown, M.J.F., Beuchel, S.D., Cappelle, K., Carolan, J.C., Christiaens, O., Colgan, T.J., Erler, S., Evans, J., Helbing, S., Karaus, E., Lattorff, H.M.G., Meeus, I., Näpflin, K., Niu, J., Schmid-Hempel, R., Smagghe, G., Waterhouse, R.M., Yu, N., Zdobnov, E.M., Schmid-Hempel, P. Genome Biology (2015): 83
    • Detecting Antigen-Specific T Cell Responses: From Bulk Populations to Single Cells
      Phetsouphanh, C., Zaunders, J.J., Kelleher, A.D. International Journal of Molecular Sciences (2015): 18,878–93
    • Distinct Roles of Type I and Type III Interferons in Intestinal Immunity to Homologous and Heterologous Rotavirus Infections
      Lin, J.D., Feng, N., Sen, A., Balan, M., Tseng, H.C., McElrath, C., Smirnov, S.V., Peng, J., Yasukawa, L.L., Durbin, R.K., Durbin, J.E., Greenberg, H.B., Kotenko, S.V. PLoS Pathogens (2016): e1005600
    • Correlation of Gene Expression and Genome Mutation in Single B-Cells
      Weinstein, J.A., Zeng, x., Chien, Y.H., Quake, S.R. PLoS One (2013): e67624
    • Shifting of Immune Reposiveness to House Dust Mite by Influenza A Infection: Genomic Insights
      Al-Garawi, A., Husain, M., Ilieva, D., Humbles, A.A., Kolbeck, R., Stampfli, M.R., O’Byrne, P.M., Coyle, A.J., Jordana, M. The Journal of Immunology (2011): 832–43
    • A Common peripheral blood gene set for diagnosis of operational tolerance in pediatric and adult liver transplantation
      Li, L., Wozniak, L.J., Rodder, S., Heish, S., Talisetti, A. Wang, Q., Esquivel, C., Cox, K., Chen, R., McDiarmid, S.V., Sarwal, M.M. American Journal of Transplantation (2012): 1218–28
    • The earliest thymic T cell progenitors sustain B cell and myeloid lineage potential
      Luc, S., Luis, T.C., Boukarabila, H., Macaulay, I.C., Buza-Vidas, N., Bouriez-Jones, T., Lutteropp, M., Woll, P.S., Loughran, S.J., Mead, A.J., Hultquist, A., Brown, J., Mizukami, T., Matsuoka, S., Ferry, H., Anderson, K., Duarte, S., Atkinson, D., Soneji, S., Domanski, A., Farley, A., Sanjuan-Pla, A., Carella, C., Patient, R., de Bruijn, M., Enver, T., Nerlov, C., Blackburn, C., Godin, I., Jacobsen, S.E.W. Nature Immunology (2012): 412–9
    • A mouse GM-CSF receptor antibody attenuated neutrophilia in mice exposed to cigarette smoke
      Botelho, F.M., Nikota, J.K., Bauer, C., Davis, N.H.E., Cohen, E.S., Anderson, I.K., Coyle, A.J., Kolbeck, R., Humbles, A.A., Stampfli, M.R., Sleeman, M.A. European Respiratory Journal (2011): 285–94
    • Single-cell NF-kB dynamics reveal digital activation and analouge information processing
      Tay, S., Hughey, J.J., Lee, T.K., Lipniacki, T., Quake, S.R., Covert, M.W. Nature (2010): 267–71
    • Single-cell gene-expression profiling reveals qualitatively distinct CD8 T cells elicited by different gene-based vaccines
      Flatz, L., Roychoudhuri, R., Honda, M., Filali-Mouhim, A., Goulet, J.P., Kettaf, N., Lin, M., Roederer, M., Haddad, E.K., Sékaly, R.P., Nabel, G.J. Proceedings of the National Academy of Sciences (2011): 5724–9
    • Evaluation of Replication of Variants Associated with Genetic Risk of Otitis Media
      Allen, E.K., Manichaikul, A., Chen, W.M., Rich, S.S., Daly, K.A., Sale, M.M. PLoS One (2014): e104212
    • Microfluidic high-throughput RT-qPCR measurements of the immune response of primary bovine mammary epithelial cells cultured from milk to mastitis pathogens
      Sorg, D., Danowski, K., Korenkova, V., Rusnakova, V., Küffner, R., Zimmer, R., Meyer, H.H., Kliem, H. Animal (2012): 799–805
    • Genetic analysis of the pathogenic molecular sub-phenotype interferon-alpha identifies multiple novel loci involved in systemic lupus erythematosus
      Kariuki, S.N., Ghodke-Puranik, Y., Dorschner, J.M., Chrabot, B.S., Kelly, J.A., Tsao. B.P., Kimberly, R.P., Alarcón-Riquelme, M.E., Jacob, C.O., Criswell, L.A., Sivils, K.L., Langefeld, C.D., Harley. J.B., Skol, A.D., Niewold, T.B. Genes and Immunity (2014): 15–23
    • Pyroptosis of resident macrophages differentially orchestrates inflammatory responses to Staphylococcus aureus in resistant and susceptible mice
      Accarias, S., Lugo-Villarino, G., Foucras, G., Neyrolles, O., Boullier, S., Tabouret, G. European Journal of Immunology (2015): 794–806

  • Immunophenotyping

    • MicroRNA expression profiling of porcine mammary epithelial cells after challenge with Escherichia coli in vitro
      Jaeger, A., Hadlich, F., Kemper, N. et al. BMC Genomics (2017): doi: 10.1186/s12864-017-4070-2
    • Comparative gut microbiota and resistome profiling of intensive care patients receiving selective digestive tract decontamination and healthy subjects
      Buelow, E., Bello González, T.d.j., Fuentes, S. et al. Microbiome (2017): doi: 10.1186/s40168-017-0309-z
    • Physiological and pathophysiological control of synaptic GluN2B-NMDA receptors by the C-terminal domain of amyloid precursor protein
      Pousinha, P.A., Mouska, X., Raymond, E.F. et al. eLife (2017): doi: 10.7554/eLife.25659
    • Mucosal BCG Vaccination Induces Protective Lung-Resident Memory T Cell Populations against Tuberculosis
      Perdomo, C., Zedler, U., Kühl, A.A. et al. mBio (2016): e01686–16
    • CD4-Transgenic Zebrafish Reveal Tissue-Resident Th2- and Regulatory T Cell–like Populations and Diverse Mononuclear Phagocytes
      Dee, C.T., Nagaraju, R.T., Athanasiadis, E.I. et al. Journal of Immunology (2016): 3,520–30
    • Synovium-Derived MicroRNAs Regulate Bone Pathways in Rheumatoid Arthritis
      Maeda, Y., Farina, N.H., Matzelle, M.M. et al. Journal of Bone and Mineral Research (2017): 461–72
    • Dynamic regulatory network controlling Th17 cell differentiation
      Yosef, N., Shalek, A.K., Gaublomme, J.T. et al. Nature (2013): 461–8
    • Interferon-Stimulated Gene 15 (ISG15) Conjugates Proteins in Dermatomyositis Muscle with Perifascicular Atrophy
      Salajegheh, M., Kong, S.W., Pinkus, J.L., Walsh, R.J., Liao, A., Nazareno, R., Amato, A.A., Krastins, B., Morehouse, C., Higgs, B.W., Jallal, B., Yao, Y., Sarracino, D.A., Parker, K., Greenberg, S.A. Annals of Neurology (2010): 53–63
    • Single-cell profiling of human megakaryocyte-erythroid progenitors identifies distinct megakaryocyte and erythroid differentiation pathways
      Psaila, B., Barkas, N., Iskander, D., Roy, A., Anderson, S., Ashley, N., Caputo, V.S., Lichtenberg, J., Loaiza, S., Bodine, D.M., Karadimitris, A., Mead, A.J., Roberts, I. Genome Biology (2016): 83
    • Regulation of IFN response gene activity during infliximab treatment In rheumatoid arthritis is associated with clinical response to treatment
      van Baarsen, L.G.M., Wijbrandts, C.A., Rustenburg, F., Cantaert, T., van der Pouw Kraan, T.C.T.M., Baeten, D.L., Dijkmans, B.A.C., Tak, P.P., Verweij, C.L. Arthritis Research and Therapy (2010): R11

  • Inherited Disease

    • Transcriptional profiling of single fiber cells in a transgenic paradigm of an inherited childhood cataract reveals absence of molecular heterogeneity
      Bhat, S.P., Gangalum, R.K., Kim, D. et al. Journal of Biological Chemistry (2019): https://www.ncbi.nlm.nih.gov/pubmed/31243103
    • Association of long noncoding RNAs expression levels and their gene polymorphisms with systemic lupus erythematosus
      Li, J., Wu, G.C., Zhang, T.P. et al. Scientific Reports (2017): 15,119
    • The atopic dermatitis blood signature is characterized by increases in inflammatory and cardiovascular risk proteins
      Brunner, P.M., Suárez-Fariñas,M., He, H. et al. Scientific Reports (2017): doi: 10.1038/s41598-017-09207-z
    • Single nucleotide polymorphisms associated with P2X7R function regulate the onset of gouty arthritis
      Tao, J.H., Cheng, M., Tang, J.P. et al. PLoS One (2017): doi: 10.1371/journal.pone.0181685
    • RNAseq based transcriptomics study of SMCs from carotid atherosclerotic plaque: BMP2 and IDs proteins are crucial regulators of plaque stability
      Alloza, I., Goikuria, H., Idro, J.L. et al. Scientific Reports (2017): 3,470
    • Quantitative trait loci at the 11q23.3 chromosomal region related to dyslipidemia in the population of Andhra Pradesh, India
      Pranavchand, R., Reddy, B.M. Lipids in Health and Disease (2017): 116
    • A Point Mutation in a lincRNA Upstream of GDNF Is Associated to a Canine Insensitivity to Pain: A Spontaneous Model for Human Sensory Neuropathies
      Plassais, J., Lagoutte, L., Correard, S. et al. PLoS Genetics (2016): e1006482
    • Cumulative Impact of Polychlorinated Biphenyl and Large Chromosomal Duplications on DNA Methylation, Chromatin, and Expression of Autism Candidate Genes
      Dunaway, K.W., Islam, M.S., Coulson, R.L. et al. Cell Reports (2016): 3,035–48
    • Long-Term Quercetin Dietary Enrichment Partially Protects Dystrophic Skeletal Muscle
      Spaulding, H.R., Ballmann, C.G., Quindry, J.C. et al. PLoS One (2016): e0168293
    • Joint Profiling of miRNAs and mRNAs Reveals miRNA Mediated Gene Regulation in the Göttingen Minipig Obesity Model
      Junker Mentzel, C.M., Alkan, F., Keinicke, H. et al. PLoS One (2016): e0167285
    • Genetic variant of IL-10RA and susceptibility to rheumatoid arthritis in a Chinese population
      Yang, X.K., Li, P., Li, S. et al. Clinical Rheumatology (2016): 825–30
    • Reconstructing blood stem cell regulatory network models from single-cell molecular profiles
      Hamey, F.K., Nestorowa, S., Kinston, S.J. et al. Proceedings of the National Academy of Sciences of the United States of America (2017): 5,822–9
    • Pridopidine activates neuroprotective pathways impaired in Huntington Disease
      Geva, M., Kusko, R., Soares, H. et al. Human Molecular Genetics (2016): 3,975–87
    • A deleterious Nav1.1 mutation selectively impairs telencephalic inhibitory neurons derived from Dravet Syndrome patients
      Sun, Y., Paşca, S.P., Portmann, T. et al. eLife (2016): e13073
    • Association Studies and Direct DNA Sequencing Implicate Genetic Susceptibility Loci in the Etiology of Nonsyndromic Orofacial Clefts in Sub-Saharan African Populations
      Gowans, L.J.J., Adeyemo, W.L., Eshete, M. et al. Journal of Dental Research (2016): 1,245–56
    • The first hundred families diagnosed with familial hypercholesterolaemia in two lipid clinics in lothian
      Finnie, R.M., Bell, C., Bloomfield, P. et al. British Journal of Diabetes and Vascular Disease (2012): 243–7
    • Inefficient Reprogramming of Fibroblast into Cardiomyocytes Using Gata4, Mef2c, and Tbx5
      Chen, J.X., Krane, M., Deutsch, M.A. et al. Circulation Research, American Heart Association (2012): 50–5
    • A Genome-Wide Association Study Identifies Variants in Casein Kinase II (CSNK2A2) to be Associated with Leukocyte Telomere Length in a Punjabi Sikh Diabetic Cohort
      Saxena, R., Bjonnes, A., Prescott, J. et al. Circulation: Cardiovascular Genetics 287–95
    • Genomic Characteristics of Genetic Creutzfeldt-Jakob Disease Patients with V180I Mutation and Associations with Other Neurodegenerative Disorders
      Lee, S.M., Chung, M., Hyeon, J.W. et al. PLoS One (2016): e0157540
    • Transcriptome Analysis of Ullrich Congenital Muscular Dystrophy Fibroblasts Reveals a Disease Extracellular Matrix Signature and Key Molecular Regulators
      Paco, S., Casserras, T., Rodríguez, M.A., et al. PLoS One (2015): e0145107
    • Telomere Position Effect (TPE) Regulates DUX4 in Human Facioscapulohumeral Muscular Dystrophy (FSHD)
      Stadler, G., Rahimov, F., King, O.D., et al. Nature Structural and Molecular Biology (2013): 671–8
    • Resequencing and clinical associations of the 9p21.3 region: a comprehensive investigation in the Framingham Heart Study
      Johnson, A.D., Hwang, S.J., Voorman, A., et al. Circulation (2013): 799–810
    • Non-exomic and synonymous variants in ABCA4 are an important cause of Stargardt disease
      Braun, T.A., Mullins, R.F., Wagner, A.H., et al. Human Molecular Genetics (2013): 5,136–45
    • Type I interferon response gene expression in established rheumatoid arthritis is not associated with clinical parameters
      de Jong, T.D., Blits, M., de Ridder, S. et al. Arthritis Research and Therapy (2016): 290
    • PARP9 and PARP14 cross-regulate macrophage activation via STAT1 ADP-ribosylation
      Iwata, H., Goettsch, C., Sharma, A. et al. Nature Communications (2016): 12,849
    • High-Throughput Carrier Screening Using TaqMan Allelic Discrimination
      Fedick, A., Su, J., Jalas, C., Northrop, L., Devkota, B., Ekstein, J., Treff, N.R. PLoS One (2013): e59722
    • Age-dependent expression of osteochondrosis-related genes in equine leukocytes
      Mendoza, L., Piquemal, D., Lejeune, J.P., Vander Heyden, L., Noguier, F., Bruno, R., Sandersen, C., Serteyn, D. Veterinary Record Open (2015): e000058
    • Comparision of microfluidic digital PCR and conventional quantitative PCR for measuring copy number variation
      Whale, A.S., Huggett, J.F., Cowen, S., Speirs, V., Shaw, J., Ellison, S., Foy, C.A., Scott, D.J. Nucleic Acids Research (2012): e82
    • Detection of aneuploidy with digital polymerase chain reaction
      Fan, H.C., Quake, S.R. Analytical Chemistry (2007): 7576–9
    • Role of Cdx2 and cell polarity in cell allocation and specification of trophectoderm and inner cell mass in the mouse embryo
      Jedrusik, A., Parfitt, D.E., Guo, G., Skamagki, M., Grabarek, J.B., Johnson, M.H., Robson, P., Zernicka-Goetz, M. Genes & Development (2008): 2692–706
    • Digital PCR: a powerful new tool for noninvasive prenatal diagnosis?
      Zimmermann, B.G., Grill, S., Holzgreve, W., Zhong, X.Y., Jackson, L.G., Hahn, S. Prenatal Diagnosis (2008): 1087–93
    • A novel and critical role for Oct4 as a regulator of the maternal-embryonic transition
      Foygel, K., Choi, B., Jun, S., Leong, D.E., Lee, A., Wong, C.C., Zuo, E., Eckart, M., Reijo Pera, R.A., Wong, W.H., Yao, M.W. PLoS One (2008): e4109
    • Microfluidic digital PCR enables rapid prenatal diagnosis of fetal aneuploidy
      Fan, H.C., Blumenfeld, Y.J., El-Sayed, Y.Y., Chueh, J., Quake, S.R. American Journal of Obstetrics and Gynecology (2009): 543-e1
    • Single-molecule sequencing of an individual human genome
      Pushkarev, D., Neff, N.F., Quake, S.R. Nature Biotechnology (2009): 847–50
    • Noninvasive prenatal detection of trisomy 21 by an epigenetic-genetic chromosome-dosage approach
      Tong, Y.K., Jin, S., Chiu, R.W., Ding, C., Chan, K.C., Leung, T.Y., Yu, L., Lau, T.K., Lo, Y.M. Clinical Chemistry (2009): 90–8
    • Residual Electroretinograms in Young Leber Congenital Amaurosis Patients with Mutation of AIPL1
      Pennesi, M.E., Stover, N.B., Stone, E.M., Chiang, P.W., Weleber, R.G. Investigative Ophthalmology & Visual Science (2011): 8166–73
    • 136 use of nanofluidic rt quantitative polymerase chain reaction to study variation in gene expression between single bovine oocyte and blastocyst samples
      Morrill, B.H., Sessions, B.R., White, K.L., Isom, S.C. Reproduction,Fertility and Development (2011): 180–1
    • Breast, Skin, Soft Tissue and Bone: Accurate quantification of dystrophin mRNA and exon skipping levels in Duchenne Muscular Dystrophy
      Spitali, P., Heemskerk, H., Vossen, R.H., Ferlini, A., den Dunnen, J.T., 't Hoen, P.A.C., Aartsma-Rus, A. Laboratory Investigation (2010): 1396–402
    • Relation of platelet and leukocyte inflammatory transcripts to body mass index in the Framingham heart study
      Freedman, J.E., Larson, M.G., Tanriverdi, K., O'Donnell, C.J., Morin, K., Hakanson, A.S., Vasan, R.S., Johnson, A.D., Iafrati, M.D., Benjamin E.J. Circulation (2010): 119–29
    • Experimental Generation of SNP Haplotype Signature in Patients with Sickle Cell Anaemia
      Menzel, S., Qin, J., Vasavda, N., Thein, S.L., Ramakrishnan, R. PLoS One (2010): e13004
    • Digital PCR Analysis of Maternal Plasma for Noninvasive Detection of Sickle Cell Anemia
      Barrett, A.N., McDonnell, T.C., Chan, K.C., Chitty, L.S. Clinical Chemistry (2012): 1026–32
    • A unique library of myogenic cells from facioscapulohumeral muscular dystrophy subjects and unaffected relatives: family, diease, and cell function
      Homma, S., Chen, J.C., Rahimov, F., Beermann, M.L., Hanger, K., Bibat, G.M., Kunkel, L.M., Emerson, C.P.Jr, Miller, J.B. European Journal of Human Genetics (2011): 404–10
    • Microfluidic single-cell real-time PCR for comparative analysis of gene expression patterns
      Sanches-Freire, V., Ebert, A.D., Kalisky, T., Quake, S.R., Wu, J.C. Nature Protocols (2012): 829–38
    • Beneficial effect of a high number of copies of salivary amylase AMY1 gene on obesity risk in Mexican children
      Mejía-Benítez, M.A., Bonnefond, A., Yengo, L., Huyvaert, M., Dechaume, A., Peralta-Romero, J., Klünder-Klünder, M., García Mena, J., El-Sayed Moustafa, J.S., Falchi, M., Cruz, M., Frogue, P. Diabetologia (2014): 290–4

  • Liquid Biopsy

    • Diurnal Variations of Human Circulating Cell-Free Micro-RNA
      Heegaard, N.H.H., Carlsen, A.L., Lilje, B. et al. PLOS One (2016): e0160577
    • An Immunofluorescence-Assisted Microfluidic Single Cell Quantitative Reverse Transcription Polymerase Chain Reaction Analysis of Tumour Cells Separated from Blood
      Hoshino, K., Chung, H.W., Wu, C.H. et al. Journal of Circulating Biomarkers (2015): 11
    • Noninvasive prenatal diagnosis of hemophilia by microfluidics digital PCR analysis of maternal plasma DNA
      Tsui, N., Kadir, R.A., Chan, K.C. et al. Blood (2012): 3,684–91
    • Impact of Intratumoral Expression Levels of Fluoropyrimidine-Metabolizing Enzymes on Treatment Outcomes of Adjuvant S-1 Therapy in Gastric Cancer
      Kim, J.Y., Shin, E., Kim, J.W. et al. PLoS One (2015): e0120324
    • Multiplexed Homogenous Proximity Ligation Assays for High-throughput Protein Biomarker Research in Serological Material
      Lundberg, M., Thorsen, S.B., Assarsson, E. et al. Molecular & Cellular Proteomics (2011): M110-004978
    • The kSORT Assay to Detect Renal Transplant Patients at High Risk for Acute Rejection: Results of the Multicenter AART Study
      Roedder, S., Sigdel, T., Salomonis, N., et al. PLoS Medicine (2014): e1001759
    • The distribution of circulating microRNA and their relation to coronary disease
      Freedman, J.E., Ercan, B., Morin, et al. F1000 Research (2012): 50
    • Relations between circulating microRNAs and atrial fibrillation: data from the Framingham Offspring Study
      McManus, D.D., Lin, H., Tanriverdi, K., et al. Heart Rhythm (2014): 663–9
    • Quantification and Dynamic Monitoring of EGFR T790M in Plasma Cell-Free DNA by Digital PCR for Prognosis of EGFR-TKI Treatment in Advanced NSCLC
      Wang, Z., Chen, R., Wang, S., et al. PLoS One (2014): e110780
    • Reproducibility of Circulating MicroRNAs in Stored Plasma Samples
      Bertoia, M.L., Bertrand, K.A., Sawyer, S.J., et al. PLoS One (2015): e0136665
    • Noninvasive prenatal diagnosis of monogenic diseases by digital size selection and relative mutation dosage on DNA in maternal plasma
      Fun, F.M.F., Tsui, N.B.Y., Chan, K.C.A., et al. Proceedings of the National Academy of Sciences of the United States of America (2008): 19,920–5
    • Noninvasive in vivo monitoring of tissue-specific global gene expression in humans
      Koh, W., Pan, W., Gawad, C., et al. Proceedings of the National Academy of Sciences of the United States of America (2014): 7,361–6
    • Insights Into Fetal and Neonatal Development Through Analysis of Cell-Free RNA in Body Fluids
      Bianchi, D.W., Maron, J.L., Johnson, K.L. Early Human Development (2010): 747–52
    • Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood
      Fan, H.C., Blumenfeld, Y.J., Chitkara, U., Hudgins, L., Quake, S.R. Proceedings of the National Academy of Sciences (2008): 16266–71
    • Analysis of the size distributions of fetal and maternal cell-free DNA by paired-end sequencing
      Fan, H.C., Blumenfeld, Y.J., Chitkara, U., Hudgins, L., Quake, S.R. Clinical Chemistry (2010): 1279–86
    • Preconceptional paternal glycidamide exposure affects embryonic gene expression: single embryo gene expression study following in vitro fertilization
      Brevik, A., Rusnakova, V., Duale, N., Slagsvold, H.H., Olsen, A.K., Storeng, R., Kubista, M., Brunborg, G., Lindeman, B. Reproductive Toxicology (2011): 463–71
    • Implementing Prenatal Diagnosis Based on Cell-Free Fetal DNA: Accurate Identification of Factors Affecting Fetal DNA Yield
      Barrett, A.N., Zimmermann, B.G., Wang, D., Holloway, A., Chitty, L.S. PLoS One (2011): e25202
    • Prenatal diagnosis of fetal anueploidies: post-genomic developments
      Hahn, S., Jackson, L.G., Zimmerman, B.G. Genome Medicine (2010): 50

  • Marker Assisted Breeding

    • Identification of the varietal origin of processed loose-leaf tea based on analysis of a single leaf by SNP nanofluidic array
      Fanga, W., Meinhardtb, L.W., Tana, H. et al. The Crop Journal (2016): 304–12
    • Association of MC1R genotypes with shank color traits in Korean native chicken
      Jina, S., Park, H.B., Seo, D.W. et al. (2014): 1–7
    • Dietary β-glucan (MacroGard®) enhances survival of first feeding turbot (Scophthalmus maximus) larvae by altering immunity, metabolism and microbiota
      Miest, J.J., Arndt, C., Adamek, M., Steinhagen, D., Reusch, T.B. Fish & Shellfish Immunology (2016): 94–104
    • Amplifying recombination genome-wide and reshaping crossover landscapes in Brassicas
      Pelé,A., Falque,M., Trotoux, G. et al. PLoS Genetics (2017): e1006794
    • Dietary methionine level affects growth performance and hepatic gene expression of GH-IGF system and protein turnover regulators in rainbow trout (Oncorhynchus mykiss) fed plant protein-based diets
      Rolland, M., Dalsgaard, J., Holm, J. et al. Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology (2015): 33–41
    • Identification and functional analysis of novel facial patterning genes in the duplicated beak chicken embryo
      Nimmagadda, S., Buchtová, M., Fu, K. et al. Developmental Biology (2015): 275–88
    • Different secretory repertoires control the biomineralization processes of prism and nacre deposition of the pearl oyster shell
      Marie, B., Joubert, C., Tayalé, A. et al. Proceedings of the National Academy of Sciences (2012): 20,986–91
    • A MYB/ZML Complex Regulates Wound-Induced Lignin Genes in Maize
      Vélez-Bermúdez, I.C., Salazar-Henao, J.E., Fornalé, S. et al. The Plant Cell (2015): 3,245–59
    • Reference genes for high-throughput quantitative reverse transcription-PCR analysis of gene expression in organs and tissues of Eucalyptus grown in various environmental conditions
      Cassan-Wang, H., Soler, M,. Yu H, Camargo, E.L. et al. Plant & Cell Physiology (2012): 2,101–16
    • Comprehensive genome-wide analysis of the Aux/IAA gene family in Eucalyptus: evidence for the role of EgrIAA4 in wood formation
      Yu, H., Soler, M., San Clemente, H. et al. Plant & Cell Physiology (2015): 700–14
    • Genome-Wide Transcriptome Analysis During Anthesis Reveals New Insights into the Molecular Basis of Heat Stress Responses in Tolerant and Sensitive Rice Varieties
      González-Schain, N., Dreni, L., Lawas, L.M. et al. Plant & Cell Physiology (2016): 57–68
    • QTL analyses of general compound, color, and pH traits in breast and thigh muscles in Korean native chicken
      Seo, D.W., Park, H.B., Jung, S. et al. Livestock Science (2015): 145–50
    • Silencing of the potato StNAC103 gene enhances the accumulation of suberin polyester and associated wax in tuber skin
      Verdaguer, R., Soler, M., Serra, O. et al. Journal of Experimental Biology (2016): 5,415–27
    • Transposon Insertions, Structural Variations, and SNPs Contribute to the Evolution of the Melon Genome
      Sanseverino, W., Hénaff, E., Vives, C. et al. Molecular Biology and Evolution (2015): 2,760–74
    • The Diversity in Performance of Commercial Olive Clones Selected from the Autochthonous cv. Souri Population for Intensive Irrigated Cultivation
      Biton, I., Mani, Y., Avidan, B. HortScience (2014): 425–9
    • Temporal Genetic Variance and Propagule-Driven Genetic Structure Characterize Naturalized Rainbow Trout (Oncorhynchus mykiss) from a Patagonian Lake Impacted by Trout Farming
      Benevente, J.N., Seeb, L.W., Seeb, J.E. et al. PLoS One (2015): e0142040
    • Second generation physical and linkage maps of yellowtail (Seriola quinqueradiata) and comparison of synteny with four model fish
      Aoki, J., Kai, W., Kawabata, Y. et al. BMC Genomics (2016): 406
    • Transcriptional analysis of defense mechanisms in upland tetraploid switchgrass to greenbugs
      Donze-Reiner, T., Palmer, N.A., Scully, E.D. et al. BMC Plant Biology (2017): 46
    • Development and validation of allele-specific SNP/indel markers for eight yield-enhancing genes using whole-genome sequencing strategy to increase yield potential of rice, Oryza sativa L.
      Kim, S.R., Ramos, J., Ashikari, M., et al. Rice (2016): 12
    • Transcriptomic analysis comparing stay-green and senescent Sorghum bicolor lines identifies a role for proline biosynthesis in the stay-green trait
      Johnson, S.M., Cummins, I., Lim, F.L., et al. Journal of Experimental Botany (2015): 7,061–73
    • AUXIN RESPONSE FACTOR 2 Intersects Hormonal Signals in the Regulation of Tomato Fruit Ripening
      Breitel, D.A., Chappell-Maor, L., Meir, S., et al. PLoS Genetics (2016): e1005903
    • Genetic Control of Water and Nitrate Capture and Their Use Efficiency in Lettuce (Lactuca sativa L.)
      Kerbiriou, P.J., Maliepaard, C.A., Stomph, T.J., et al. Frontiers in Plant Science (2016): 343
    • Outlier Loci Detect Intraspecific Biodiversity amongst Spring and Autumn Spawning Herring across Local Scales
      Bekkevold, D., Gross, R., Arula, T., et al. PLoS One (2016): e0148499
    • Varietal identification of tea (Camellia sinensis) using nanofluidic array of single nucleotide polymorphism (SNP) markers
      Fang, W.P., Meinhardt, L.W., Tan, H.W., et al. Horticulture Research (2014): 14,035
    • Variance Component Quantitative Trait Locus Analysis for Body Weight Traits in Purebred Korean Native Chicken
      Cahyadi, M., Park, H.B., Seo, D.W., et al. Asian-Australian Journal of Animal Sciences (2016): 43–50
    • Transcriptome sequencing of different narrow-leafed lupin tissue types provides a comprehensive uni-gene assembly and extensive gene-based molecular markers
      Kamphuis, L.G., Hane, J.K., Nelson, M.N. et al. Plant Biotechnology Journal (2015): 14–25
    • The Yield of Essential Oils in Melaleuca alternifolia (Myrtaceae) Is Regulated through Transcript Abundance of Genes in the MEP Pathway
      Webb, H., Lanfear, R., Hamill, J., et al. PLoS One (2013): e60631
    • The mQTL hotspot on linkage group 16 for phenolic compounds in apple fruits is probably the result of a leucoanthocyanidin reductase gene at that locus
      Khan, S.A., Schaart, J.G., Beekwilder, J., et al. BMC Research Notes (2012): 618
    • The construction of a high-density linkage map for identifying SNP markers that are tightly linked to a nuclear-recessive major gene for male sterility in Cryptomeria japonica D. Don
      Moriguchi, Y., Ujino-Ihara, T., Uchiyama, K., et al. BMC Genomics (2012): 95
    • Temporal transcriptome changes induced by MDV in marek's disease-resistant and -susceptible inbred chickens
      Yu, Y., Luo, J., Mitra, A., et al. BMC Genomics (2011): 501
    • Single nucleotide polymorphism-based dispersal estimates using noninvasive sampling
      Norman, A.J., Spong, G. Ecology and Evolution (2015): 3,056–65
    • Single nucleotide polymorphism discovery in cutthroat trout subspecies using genome reduction, barcoding, and 454 pyro-sequencing
      Houston, D.D., Elzinga, D.B., Maughan, P.J., et al. BMC Genomics (2012): 724
    • Signatures of natural selection among lineages and habitats in Oncorhynchus mykiss
      Limborg, M.T., Blankenship, S.M., Young, S.F., et al. Ecology and Evolution (2012): 1–18
    • Post-weaning blood transcriptomic differences between Yorkshire pigs divergently selected for residual feed intake
      Liu, H., Nguyen, Y.T., Nettleton, D., et al. BMC Genomics (2016): 73
    • Nutrigenomic and Nutritional Analyses Reveal the Effects of Pelleted Feeds on Asian Seabass (Lates calcarifer)
      Ngoh, S.Y., Tan, D., Shen, X., et al. PLoS One (2015): e0145456
    • New insight into the SSC8 genetic determination of fatty acid composition in pigs
      Revilla, M., Ramayo-Caldas, Y., Castelló, A., et al. Genetics Selection Evolution (2014): 28
    • Drought susceptibility of modern rice varieties: an effect of linkage of drought tolerance with undesirable traits
      Vikram, P., Swamy, B.P.M., Dixit, S., et al. Scientific Reports (2015): 14,799
    • Draft Genome Sequence, and a Sequence-Defined Genetic Linkage Map of the Legume Crop Species Lupinus angustifolius L
      Yang, H., Tao, Y., Zheng, Z., et al. PLoS One (2013): e64799
    • Developing single nucleotide polymorphism (SNP) markers from transcriptome sequences for identification of longan (Dimocarpus longan) germplasm
      Wang, B., Tan, H.W., Meinhardt, L.W. et al. Horticulture Research (2015): 14,065
    • Developing molecular tools and insights into the Penstemon genome using genomic reduction and next-generation sequencing
      Dockter, R.B., Elzinga, D.B., Geary, B. et al. BMC Genetics (2013): 66
    • Genetic diversity and population structure analysis to construct a core collection from a large Capsicum germplasm
      Lee, H.Y., Ro, N.Y., Jeong, H.J. et al. BMC Genomics (2016): 142
    • Whole Genome Sequencing of Elite Rice Cultivars as a Comprehensive Information Resource for Marker Assisted Selection
      Duitama, J., Silva, A., Sanabria, Y. et al. PLoS One (2015): e0124617
    • Development and mapping of SNP assays in allotetraploid cotton
      Byers, R.L., Harker, D.B., Yourstone, S.M., Maughan, P.J., Udall, J.A. Theoretical and Applied Genetics (2012): 1,201–14
    • The ambiguous ripening nature of the fig (Ficus carica L.) fruit: a gene-expression study of potential ripening regulators and ethylene-related genes
      Freiman, Z.E., Rosianskey, Y., Dasmohapatra, R., Kamara, I., Flaishman, M.A. Journal of Experimental Biology (2015): 3,309–24
    • Linkage Mapping Reveals Strong Chiasma Interference in Sockeye Salmon: Implications for Interpreting Genomic Data
      Limborg, M.T., Waples, R.K., Allendorf, F.W., Seeb, J.E. G3 (2015): 2,463–73
    • The environment exerts a greater influence than the transgene on the transcriptome of field-grown wheat expressing the Pm3b allele
      Quijano, C.D., Brunner, S., Keller, B., Gruissem, W., Sautter, C. Transgenic Research (2014): 87–97
    • Small-scale transcriptomics reveals differences among gonadal stages in Asian seabass (Lates calcarifer)
      Ravi, P., Jiang, J., Liew, W.C., Orbán, L. Reproductive Biology and Endocrinology (2014): 5
    • Pectinmethylesterases (PME) and Pectinmethylesterase Inhibitors (PMEI) Enriched during Phloem Fiber Development in Flax (Linum usitatissimum)
      Pinzon-Latorre, D., Deyholos, M.K. PLoS One (2014): e105386
    • Genomic and expression analysis of the flax (Linum usitatissimum) family of glycosyl hydrolase 35 genes
      Hobson, N., Deyholos, M.K. BMC Genomics (2013): 344
    • Developing single nucleotide polymorphism markers for the identification of pineapple (Ananas comosus) germplasm
      Zhou, L., Matsumoto, T., Tan, H.W., Meinhardt, L.W., Mischke, S., Wang, B., Zhang, D. Horticulture Research (2015): 15,056
    • A Transcript Profiling Approach Reveals an Abscisic Acid-Specific Glycosyltransferase (UGT73C14) Induced in Developing Fiber of Ligon lintless-2 Mutant of Cotton (Gossypium hirsutum L.)
      Gilbert, M.K., Bland, J.M., Shockey, J.M., Cao, H., Hinchliffe, D.J., Fang, D.D., Naoumkina, M. PLoS One (2013): e75268
    • Genes involved in floral meristem in tomato exhibit drastically reduced genetic diversity and signature of selection
      Bauchet, G., Munos, S., Sauvage, C., Bonnet, J., Grivet, L., Causse, M. BMC Plant Biology (2014): 279
    • The regulation of quantitative variation of foliar terpenes in medicinal tea tree Melaleuca alternifolia
      Webb, H., Carsten, K., Rob, L., Hamill, J., Foley, W. BMC Proceedings (2011): O20
    • The effects of phytochrome-mediated light signals on the developmental acquisition of photoperiod sensitivity in rice
      Yoshitake, Y., Yokoo, T., Saito, H., Tsukiyama, T., Quan, X., Zikihara, K., Katsura, H., Tokutomi, S., Aboshi, T., Mori, N., Inoue, H., Nishida, H., Kohchi, T., Teraishi, M., Okumoto, Y., Tanisaka, T. Scientific Reports (2015): 7,709
    • Source-Sink Estimates of Genetic Introgression Show Influence of Hatchery Strays on Wild Chum Salmon Populations in Prince William Sound, Alaska
      Jasper, J.R., Habicht, C., Moffitt, S., Brenner, R., Marsh, J., Lewis, B., Fox, E.C., Grauvogel, Z., Olive, S.D.R., Grant, W.S. PLoS One (2013): e0081916
    • Meiotic maps of sockeye salmon derived from massively parallel DNA sequencing
      Everett, M.V., Miller, M.R., Seeb, J.E. BMC Genomics (2012): 521
    • How Stock of Origin Affects Performance of Individuals across a Meta-Ecosystem: An Example from Sockeye Salmon
      Griffiths, J.R., Schindler, D.E., Seeb, L.W. PLoS One (2013): e58584
    • Expression profiling of genes involved in drought stress and leaf senescence in juvenile barley
      Wehner, G., Balko, C., Humbeck, K., Zyprian, E., Ordon, F. BMC Plant Biology (2016): 3
    • Archived DNA reveals fisheries and climate induced collapse of a major fishery
      Bonanomi, S., Pellissier, L., Therkildsen, N.O., Hedeholm, R.B., Retzel, A., Meldrup, D., Olsen, S.M., Nielsen, A., Pampoulie, C., Hemmer-Hansen, J., Wisz, M.S., Grønkjær, P., Nielsen, E.E. Scientific Reports (2015): 15,395
    • A Gene-Phenotype Network Based on Genetic Variability for Drought Responses Reveals Key Physiological Processes in Controlled and Natural Environments
      Rengel, D., Arribat, S., Maury, P., Martin-Magniette, M.L., Hourlier, T., Laporte, M., Varès, D., Carrère, S., Grieu, P., Balzergue, S., Gouzy, J., Vincourt, P., Langlade, N.B. PLoS One (2012): e45249
    • Loss of DNA methylation affects the recombination landscape in Arabidopsis
      Mirouze, M., Liberman-Lazarovich, M., Aversano, R., Bucher, E., Nicolet, J., Reinders, J., Paszkowshi, J. Proceedings of the National Academy of Sciences (2012): 5880–5
    • Absolute quantification of genetically modified MON810 maise (Zea mays L.) by digital polymerase chain reaction
      Corbisier, P., Bhat, S., Partis, L., Xie, V.R., Emslie, K.R. Analytical and Bioanalytical Chemistry (2010): 2143–50
    • The applicability of digital PCR for the assessment of detection limits in GMO analysis
      Burns, M.J., Burrell, A.M., Foy, C.A. European Food Research and Technology (2010): 353–62
    • Expression levels of 25 genes in liver and testis located in a QTL region for androstenone on SSC7q1.2
      Robic, A., Fève, K., Larzul, C., Billon, Y., van Son, M., Liaubet, L., Sarry, J., Milan, D., Grindflek, E., Bidanel, J.P., Riquet, J. Animal Genetics (2011): 662–5
    • Controlling rice bacterial blight in Africa: needs and prospects
      Verdier, V., Vera Cruz, C., Leach, J.E. Journal of Biotechnology (2011): 320–8
    • Gene expression analysis by quantitative real-time PCR for floral tissues
      Bustamante, M., Jin, J., Casagran, O., Nolan, T., Riechmann, J.L. Methods in Molecular Biology (2013): 363–82
    • Construction of a radiation hybrid panel and the first yellowtail (Seriola quinqueradiata) radiation hybrid map using a nanofluidic dynamic array
      Aoki, J.Y., Kai, W., Kawabata, Y., Ozaki, A., Yoshida, K., Tsuzaki, T., Fuji, K., Koyama, T., Sakamoto, T., Araki, K. BMC Genomics (2014): 165
    • Post-season Stock Composition Analysis of Upper Cook Inlet Sockeye Salmon Harvest, 2005-2007
      Habicht, C., Templin, W.D., Willette, T.M., Fair, L.F., Raborn, S.W., Seeb, L.W. Alaska Department of Fish and Game, Fishery Manuscript No.07-07, Anchorage (2008):

  • Method Development

    • A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications
      Haque, A., Engel, J., Teichmann, S.A. et al. Genome Medicine (2017): 75
    • NGS-Logistics: federated analysis of NGS sequence variants across multiple locations
      Ardeshirdavani, A., Souche, E., Dehaspe, L. et al. Genome Medicine (2014): 71
    • Monitoring and manipulating cellular crosstalk during kidney fibrosis inside a 3D in vitro co-culture
      Nugraha, B., Mohr, M.A., Ponti, A. et al. Scientific Reports (2017): 14,490
    • Whole blood stabilization for the microfluidic isolation and molecular characterization of circulating tumor cells
      Wong, K.H.K., Tessier, S.N., Miyamoto, D.T. et al. Nature Communications (2017): 1,733
    • Strategies for profiling single mouse intestinal epithelial cells by targeted gene expression
      McDowell, W., Box, A., Staehling, K. et al. Journal of Biomolecular Techniques (2014): S26–7
    • Quantitative assessment of single-cell RNA-sequencing methods
      Wu, A.R., Neff, N.F., Kalisky, T. et al. Nature Methods (2014): 41–6
    • Microfluidics-based digital quantitative PCR for single-cell small RNA quantification
      Yu, T., Tang, C., Zhang, Y. et al. Biology of Reproduction (2017): 490-6
    • Single Cell Gene Expression Profiling of Skeletal Muscle-Derived Cells
      Gatto, S., Puri, P.L., Malecova, B. Methods in Molecular Biology (2017): 191–219
    • Multiplexed locus-specific analysis of DNA methylation in single cells
      Cheow, L.F., Quake, S.R., Burkholder, W.F. et al. Nature Protocols (2015): 619–31
    • Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method
      Livak, K.J., Schmittgen, T.D. Methods (2001): 402–8
    • Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes
      Vandesompele, J., De Preter, K., Pattyn, F. et al. Genome Biology (2002): research0034.1–11
    • Two methods for full-length RNA sequencing for low quantities of cells and single cells
      Pan, X., Durrett, R.E., Zhu, H. et al. Proceedings of the National Academy of Sciences of the United States of America (2013): 594–9
    • Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments
      McDavid, A., Finak, G., Chattopadyay, P.K. et al. Bioinformatics (2013): 461–7
    • Validation of high-throughput single cell analysis methodology
      Devonshire, A.S., Baradez, M.O., Morley, G. et al. Analytical Biochemistry (2014): 103–13
    • High-throughput microfluidic single-cell analysis pipeline for studies of signaling dynamics
      Kellogg, R.A., Gómez-Sjöberg, R., Leyrat, A.A. et al. Nature Protocols (2014): 1,713–26
    • Quantitative single cell gene expression profiling in the avian embryo
      Morrison, J.A., Box, A.C., McKinney, M.C. et al. Developmental Dynamics (2015): 774–84
    • Influence of primer & probe chemistry and amplification target on reverse transcription digital PCR quantification of viral RNA
      Van Heuverswyn, F., Karczmarczyk, M., Schimmel, H., et al. Biomolecular Detection and Quantification (2016): 20–8
    • Validation of a digital PCR method for quantification of DNA copy number concentrations by using a certified reference material
      Deprez, L., Corbisier, P., Kortekaas, A.M., et al. Biomolecular Detection and Quantification (2016): 29–39
    • A superior strategy for single-cell mutational screening via multiplex-targeted QPCR using the BioMark HD microfluidic platform
      Li, G., Teng. L. Future Oncology (2014): 507–10
    • Proximity assays for sensitive quantification of proteins
      Greenwood, C., Ruff, D., Kirvell, S. et al. Biomolecular Detection and Quantification (2015): 10–6
    • Cryopreservation and recovery of human endometrial epithelial cells with high viability, purity, and functional fidelity
      Chen, J.C., Hoffman, J.R., Arora, R. et al. Fertility and Sterility (2016): 501–10.e1
    • Digital polymerase chain reaction for characterisation of DNA reference materials
      Bhat, S., Emslie, K.R. Biomolecular Detection and Quantification (2016): 47–9
    • Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape
      Marco, E., Karp, R.L., Guo, G. et al. Proceedings of the National Academy of Sciences (2014): E5643–50
    • Global preamplification simplifies targeted mRNA quantification
      Kroneis, T., Jonasson, E., Andersson, D. et al. Scientific Reports (2017): 45,219
    • Creatine reduces hepatic TG accumulation in hepatocytes by stimulating fatty acid oxidation
      da Silva, R.P., Kelly, K.B., Leonard, K.A., Jacobs, R.L. Biochimica et Biophysica Acta (2014): 1,639–46
    • Comparison of RNA isolation and associated methods for extracellular RNA detection by high-throughput quantitative polymerase chain reaction
      Tanriverdi, K., Kucukural, A., Mikhalev, E. et al. Analytical Biochemistry (2016): 66–74
    • Development and application of absolute quantitative detection by duplex chamber-based digital PCR of genetically modified maize events without pretreatment steps
      Zhu, P., Fu, W., Wang, C. et al. Analytica Chimica Acta (2016): 60–6
    • Novel approach to PET probe synthesis involving a microfluidic coin-shaped reactor
      Elizarov. A., Kolb. H., van Dam, M. et al. The Journal of Nuclear Medicine (2006): 538P
    • Human satellite-III non-coding RNAs modulate heat shock-induced transcriptional repression
      Goenka, A., Sengupta, S., Pandey, R. et al. Journal of Cell Science (2016): 3,541–52
    • High purity galacto-oligosaccharides (GOS) enhance specific Bifidobacterium species and their metabolic activity in the mouse gut microbiome
      Monteagudo-Mera, A., Arthur, J.C., Jobin, C. et al. Beneficial Microbes (2016): 247–64
    • The Digital MIQE Guidelines: Minimum Information for Publication of Quantitative Digital PCR Experiments
      Huggett, J.F., Foy, C.A., Benes, V. et al. Clinical Chemistry (2013): 892–902
    • quantGenius: implementation of a decision support system for qPCR-based gene quantification
      Baebler, S., Svalina, M., Petek, M. et al. BMC Informatics (2017): 276
    • Extending digital PCR analysis by modelling quantification cycle data
      Wilson, P.J., Ellison, S.L.R. BMC Bioinformatics (2016): 421
    • A Novel Pretreatment-Free Duplex Chamber Digital PCR Detection System for the Absolute Quantitation of GMO Samples
      Zhu, P., Wang, C., Huang, K. et al. International Journal of Molecular Sciences (2016): 402
    • Multi-Platform Analysis of MicroRNA Expression Measurements in RNA from Fresh Frozen and FFPE Tissues
      Kolbert, C.P., Feddersen, R.M., Rakhshan, F. et al. PLoS One (2013): e52517
    • An integrated microfluidic device for two-dimensional combinatorial dilution
      Jang, Y.H., Hancock, M.J., Kim, S.B. et al. Lab on a Chip (2011): 3,277-86
    • Homogenous 96-Plex PEA Immunoassay Exhibiting High Sensitivity, Specificity, and Excellent Scalability
      Assarsson, E., Lundberg, M., Holmquist, G. et al. PLoS One (2014): e0095192
    • Evaluation of Digital PCR for Absolute RNA Quantification
      Sanders, R., Mason, D.J., Foy, C.A. et al. PLoS One (2013): e75296
    • Multiplex Quantitative Measurement of mRNAs from Fixed Tissue Microarray Sections
      Armani, M., Tangrea, M., Yang, B. et al. Applied Immunohistochemistry and Molecular Morphology (2015): 323-30
    • In vivo quantitation of glucose metabolism in mice using small-animal PET and a microfluidic device.
      Wu, H.M., Sui, G., Lee, C.C. et al. The Journal of Nuclear Medicine (2007): 837–45
    • The focus on sample quality: Influence of colon tissue collection on reliability of qPCR data
      Korenkova, V., Slyskova, J., Novosadova, V. et al. Scientific Reports (2016): 29,023
    • Chemically Defined and Small Molecule-Based Generation of Human Cardiomyocytes
      Burridge, P.W., Matsa, E., Shukla, P. et al. Nature Methods (2014): 855-60
    • Measuring Signaling and RNA-Seq in the Same Cell Links Gene Expression to Dynamic Patterns of NF-κB Activation
      Lane, K., Van Valen, D., DeFelice, M.M. et al. Cell Systems (2017): S2,405-12
    • Cell Cycle and Cell Size Dependent Gene Expression Reveals Distinct Subpopulations at Single-Cell Level
      Dolatabadi, S., Candia, J., Akrap, N. et al. Frontiers in Genetics (2017): 1
    • Combined RT-qPCR of mRNA and microRNA Targets within One Fluidigm Integrated Fluidic Circuit
      Baldwin, D.A., Horan, A.D., Hesketh, P.J., Mehta, S. Journal of Biomolecular Techniques (2016): 75–83
    • Reference-free detection of isolated SNPs
      Uricaru, R., Rizk, G., Lacroix, V., et al. Nucleic Acids Research (2015): e11
    • Reduction of Systematic Bias in Transcriptome Data from Human Peripheral Blood Mononuclear Cells for Transportation and Biobanking
      Ohomo, H., Hachiya, T., Shiwa, Y., et al. PLoS One (2014): e104283
    • One Bacterial Cell, One Complete Genome
      Woyke, T., Tighe, D., Mavromatis, K., et al. PLoS One (2010): e10314
    • Next-Generation Sequencing for Cancer Diagnostics: a Practical Perspective
      Meldrum, C., Doyle, M.A., Tothill, R.W. Clinical Biochemist Reviews (2011): 177–95
    • Multi-platform assessment of transcriptional profiling technologies utilizing a precise probe mapping methodology
      Yu, J., Cliften, P.F., Juehne, T.I., et al. BMC Genomics (2015): 710
    • Highly sensitive amplicon-based transcript quantification by semiconductor sequencing
      Zhang, J.D., Schindler, T., Küng, E., et al. BMC Genomics (2014): 565
    • Micro Total Analysis Systems: Fundamental Advances and Applications in the Laboratory, Clinic, and Field
      Kovarik, M.L., Ornoff, D.M., Melvin, A.T., et al. Analytical Chemistry (2013): 451–72
    • Micro Total Analysis Systems for Cell Biology and Biochemical Assays
      Kovarik, M.L., Gach, P.C., Ornoff, D.M., et al. Analytical Chemistry (2012): 516–40
    • Methods for Multiplex Template Sampling in Digital PCR Assays
      Petriv, O.I., Heyries, K.A., VanInsberghe, M., et al. PLoS One (2014): e98341
    • Methodological approaches to cytochrome P450 profiling in embryos
      Goldstone, J.V., Stegeman, J.J. Methods in Molecular Biology (2012): 265–75
    • Meeting report: discussions and preliminary findings on extracellular RNA measurement methods from laboratories in the NIH Extracellular RNA Communication Consortium
      Laurent, L.C., Abdel-Mageed, A.B., Adelson, P.D., et al. Journal of Extracellular Vesicles (2015): 26,533
    • LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets
      Wilm, A., Aw, P.P.K., Bertrand, D., et al. Nucleic Acids Research (2012): 11,189–201
    • In Vivo Zonal Variation and Liver Cell-Type Specific NF-κB Localization after Chronic Adaptation to Ethanol and following Partial Hepatectomy
      Nilakantan, H., Kuttippurathu, L., Parrish, A., et al. PLoS One (2015): e0140236
    • High Throughput MicroRNA Profiling: Optimized Multiplex qRT-PCR at Nanoliter Scale on the Fluidigm Dynamic ArrayTM IFCs
      Moltzahn, F., Hunkapiller, N., Mir, A.A., et al. Journal of Visualized Experiments (2011): 2,552
    • Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes
      Shiroguchi, K., Jia, T.Z., Sims, P.A., Xie, X.S. Proceedings of the National Academy of Sciences of the United States of America (2012): 1,347–52
    • An international comparability study on quantification of mRNA gene expression ratios: CCQM-P103.1
      Devonshire, A.S., Sanders, R., Whale, A.S. et al. Biomolecular Detection and Quantification (2016): 15–28
    • Inflammatory Serum Protein Profiling of Patients with Lumbar Radicular Pain One Year after Disc Herniation
      Moen, A., Lind, A.L., Thulin, M. et al. International Journal of Inflammation (2016): 3,874,964
    • The correlation between expression profiles measured in single cells and in traditional bulk samples
      Dzamba, D., Valihrach, L., Kubista, M. et al. Scientific Reports (2016): 37,022
    • Comparison of microfluidic digital PCR and conventional quantitative PCR for measuring copy number variation
      Whale, A.S., Huggett, J.F., Cowen, S. et al. Nucleic Acids Research (2012): e82
    • Multiplex quantification of four DNA targets in one reaction with Bio-Rad droplet digital PCR system for GMO detection
      Dobnik, D., Štebih, D., Blejec, A. et al. Scientific Reports (2016): 35,451
    • Combinatorial labeling of single cells for gene expression cytometry.
      Fan, H.C., Fu, G.K., Fodor, S.P. Science (2015): 1,258,367
    • Quantitative miRNA Expression Analysis Using Fluidigm Microfluidics Dynamic Arrays
      Jang, J.S., Simon, V., Feddersen, R., Rakhshan, F., Schultz, D., Zschunke, M., Lnigle, W., Kolbert, C., Jen, J. BMC Genomics (2011): 144
    • Robust Inference of Cell-to-Cell Expression Variations from Single- and K-Cell Profiling
      Narayanan, M., Martins, A.J., Tsang, J.S. PLoS Computational Biology (2016): e1005016
    • A microfluidic device for multiplexed protein detection in nano-liter volumes
      Diercks, A.H., Ozinsky, A., Hansen, C.L., Spotts, J.M., Rodriguez, D.J., Aderem, A. Analytical Biochemistry (2009): 30–5
    • A Bead-Based Microfluidic Approach to Integrated Single-Cell Gene Expression Analysis by Quantitative RT-PCR
      Sun, H., Olsen, T., Zhu, J., Tao, J., Ponnaiya, B., Amundson, S.A., Brenner, D.J., Lin, Q. RSC Advances (2014): 4,886–93
    • SCExV: a webtool for the analysis and visualisation of single cell qRT-PCR data
      Lang, S., Ugale, A., Erlandsson, E., Karlsson, G., Bryder, D., Soneji, S. BMC Bioinformatics (2015): 320
    • Accurate quantification of supercoiled DNA by digital PCR
      Dong, L., Yoo, H.B., Wang, J., Park, S.R. Scientific Reports (2016): 24,230
    • Validating single cell genomics for the study of renal development
      Jain, S., Noordam, M.J., Hoshi, M., Vallania, F.L., Conrad, D.F. Kidney International (2014): 1,049–55
    • Methods for Applying Accurate Digital PCR Analysis on Low Copy DNA Samples
      Whale, A.S., Cowen, S., Foy, C.A., Huggett, J.F. PLoS One (2013): e58177
    • LEMming: A Linear Error Model to Normalize Parallel Quantitative Real-Time PCR (qPCR) Data as an Alternative to Reference Gene Based Methods
      Vlaic, S., Arlt, J., Sawodny, O., Dahmaen, U., Zanger, U.M., Thomas, M. PLoS One (2015): e0135852
    • Intracellular expression profiles measured by real-time PCR tomography in the Xenopus laevis oocyte
      Sindelka, R., Jonak, J., Hands, R., Bustin, S.A., Kubista, M. Nucleic Acids Research (2008): 387–92
    • High throughput nano-liter RT-qPCR to classify soil contamination using a soil arthropod
      de Boer, M.E., Berg, S., Timmermans, M.J.T.N., den Dunnen, J.T., van Straalen, N.M., Ellers, J., Roelofs, D. BMC Molecular Biology (2011): 11
    • Genotyping of DNA Samples Isolated from Formalin-Fixed Paraffin-Embedded Tissues Using Preamplification
      Baak-Pablo, R., Dezentje, V., Guchelaar, H.J., van der Straaten, T. Journal of Molecular Diagnostics (2010): 746–9
    • Fluidigm Dynamic Arrays provide a platform for single-cell gene expression analysis
      Pieprzyk, M., High, H. Nature Methods (2009):
    • Establishment of single-cell screening system for the rapid identification of transcriptional modulators involved in direct cell reprogramming
      Shin, J.W., Suzuki, T., Ninomiya, N., Kishima, M., Hasegawa, Y., Kubosaki, A., Yabukami, H., Hayashizaki, Y., Suzuki, H. Nucleic Acids Research (2012):
    • DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLight
      Weisenberger, D.J., Trinh, B.N., Campan, M., Sharma, S., Long, T.I., Ananthnarayan, S., Liang, G., Esteva, F.J., Hortobagyi, G.N., McCormick, F., et al Nucleic Acids Research (2008): 4,689–98
    • DNA copy number concentration measured by digital and droplet digital quantitative PCR using certified reference materials
      Corbisier, P., Pinheiro, L., Mazoua, S., Kortekaas, A.M., Chung, P.Y., Gerganova, T., Roebben, G., Emons, H., Emslie, K. Analytical and Bioanalytical Chemistry (2015): 1,831–40
    • DAG Expression: High-Throughput Gene Expression Analysis of Real-Time PCR Data Using Standard Curves for Relative Quantification
      Ballester, M., Cordón, R., Folch, J.M. PLoS One (2013): e80385
    • Single Cell Transcriptional Profiling of Adult Mouse Cardiomyocytes
      Flynn, J.M., Santana, L.F., Melov, S. Journal of Visualized Experiments (2011): 3,302
    • Properties of targeted preamplification in DNA and cDNA quantification
      Andersson, D., Akrap, N., Svec, D., Godfrey, T.E., Kubista, M., Landberg, G., Ståhlberg, A. Expert Review of Molecular Diagnostics (2015): 1,085-100
    • Methods for qPCR gene expression profiling applied to 1440 lymphoblastoid single cells
      Livak, K.J., Wills, Q.F., Tipping, A.J., Datta, K., Mittal, R., Goldson, A.J., Sexton, D.W., Holmes, C.C. Methods (2013): 71–9
    • Evaluation of extraction kits and RT-qPCR systems adapted to high-throughput platform for circulating miRNAs
      Tan, G.W., Khoo, A.S.B., Tan, L.P. Scientific Reports (2015): 9,430
    • Chip in a lab: Microfluidics for next generation life science research
      Streets, A.M., Huang, Y. Biomicrofluidics (2013): 011,302
    • Analysis of Extracellular RNA by Digital PCR
      Takahashi, K., Yan, I.K., Kim, C., Kim, J., Patel, T. Frontiers in Oncology (2014): 129
    • Assessment of the real-time PCR and different digital PCR platforms for DNA quantification
      Jernej Pavšič, J., Žel, J., Milavec, M. Analytical and Bioanalytical Chemistry (2015): 107–21
    • A Method for Quantitative Analysis of Standard and High-Throughput qPCR Expression Data Based on Input Sample Quantity
      Adamski, M.G., Gumann, P., Baird, A.E. PLoS One (2014): e103917
    • Microfluidics for single cell analysis
      Yin, H., Marshall, D. Current Opinion in Biotechnology (2012): 110–9
    • New bandwidth selection criterion for Kernel PCA: Approach to dimensionality reduction and classification problems
      Thomas, M., De Brabanter, K., De Moor, B. BioMed Central Bioinformatics (2014): 137
    • Problems with the nested granularity of feature domains in bioinformatics: the eXtasy case
      Popovic, D., Sifrim, A., Davis, J., Moreau, Y., De Moor, B. BMC Bioinformatics (2015): S2
    • Highly multiplexed quantitation of gene expression on single cells
      Dominguez, M.H., Chattopadhyay, P.K., Ma, S., Lamoreaux, L., McDavid, A., Finak, G., Gottardo, R., Koup, R.A., Roederer, M. Journal of Immunological Methods (2013): doi: 10.1016/j.jim.2013.03.002
    • A stochastic model dissects cell states in biological transition processes
      Armond, J.W., Saha, K., Rana, A.A., Oates, C.J., Jaenisch, R., Nicodemi, M., Mukherjee, S. Scientific Reports (2014): 3692
    • Probabilistic PCA of censored data: accounting for uncertainties in the visualization of high-throughput single-cell qPCR data
      Buettner, F., Moignard, V., Göttgens, B., Theis, F.J. Bioinformatics (2014): 1867–75
    • Product Focus: Analytical and Preparative Instrumentation
      Taylor, P. Journal of Biomolecular Sceening (2012): 121–3
    • High throughput gene expression measurement with real time PCR in a microfluidic dynamic array
      Spurgeon, S.L., Jones, R.C., Ramakrishnan, R. PLoS One (2008): e1662
    • Mathematical analysis of copy number variation in a DNA sample using digital PCR on a nanofluidic device
      Dube, S., Qin, J., Ramakrishnan, R. PLoS One (2008): e2876
    • Studying copy number variations using a nanofluidic platform
      Qin, J., Jones, R.C., Ramakrishnan, R. Nucleic Acids Research (2008): e116
    • Go with the (micro) flow
      Chang, C., Nagel, D., Zaghloul, M. IEEE Potentials (2008): 17–25
    • Digital PCR provides sensitive and absolute calibration for high throughput sequencing
      White, R.A. 3rd, Blainey, P.C., Fan, H.C., Quake, S.R. BMC Genomics (2009): 116
    • High-throughput single nucleotide polymorphism genotyping using nanofluidic Dynamic Arrays
      Wang, J., Lin, M., Crenshaw, A., Hutchinson, A., Hicks, B., Yeager, M., Berndt, S., Huang, W.Y., Hayes, R., Chanock, S., Jones, R., Ramakrishnan, R. BMC Genomics (2009): 561
    • Megapixel digital PCR
      Heyries, K.A., Tropini, C., Van Insberghe, M., Doolin, C., Petriv, O.I., Singhal, A., Leung, K., Hughesman, C.B., Hansen, C. L. Nature Methods (2011): 649–51
    • Taking qPCR to a higher level: Analysis of CNV reveals the power of high throughput qPCR to enhance quantitative resolution
      Weaver, S., Dube, S., Mir, A., Qin, J., Sun, G., Ramakrishnan, R., Jones, R.C., Livak, K.J. Methods (2010): 271–6
    • Product Focus: High-Content Screening and Imaging Instrumentation, Analysis, and Applications
      Hart, C.P. Journal of Biomolecular Sceening (2010): 584–9
    • Digital MDA for enumeration of total nucleic acid contamination
      Blainey, P., Quake, S. Nucleic Acids Research (2010): e19
    • Applicability of RNA standards for evaluating RT-qPCR assays and platforms
      Devonshire, A.S., Elaswarapu, R., Foy, C.A. BMC Genomics (2011): 118
    • Comparasion of reverse transcription-quantitative polymerase chain reaction methods and platforms for single cell gene expression analysis
      Fox, B.C., Devonshire, A.S., Baradez, M.O., Marshall, D., Foy, C.A. Analytical Biochemistry (2013): 178–86
    • A duck RH panel and its potential for assisting NGS genome assembly
      Rao, M., Morisson, M., Faraut, T., Bardes, S., Fève, K., Labarthe, E., Fillon, V., Huang, Y., Li, N., Vignal, A. BMC Genomics (2012): 513
    • Single-cell PCR profiling of gene expression in hematopoiesis
      Teles, J., Enver, T., Pina, C. Methods in Molecular Biology (2014): 21–42
    • Self-Digitization Microfluidic Chip for Absolute Quantification of mRNA in Single Cells
      Thompson, A.M., Gansen, A., Paguirigan, A.L., Kreutz, J.E., Radich, J.P., Chiu, D.T. Analytical Chemistry (2014): 12308–14
    • Comparative study of sensitivity, linearity, and resistance to inhibition of digital and nondigital polymerase chain reaction and loop mediated isothermal amplification assays for quantification of human cytomegalovirus
      Nixon, G., Garson, J.A., Grant, P., Nastouli, E., Foy, C.A., Huggett, J.F. Analytical Chemistry (2014): 4387–94
    • Pre-amplification in the context of high-throughput qPCR gene expression experiment.
      BMC Molecular Biology (2015): 5

  • Microbiology/Pathogen Detection (viral)

    • Association between selected antimicrobial resistance genes and antimicrobial exposure in Danish pig farms
      Birkegård, A.C., Halasa, T., Græsbøll, K. et al. Scientific Reports (2017): doi: 10.1038/s41598-017-10092-9
    • Molecular indices of viral disease development in wild migrating salmon
      Miller, K.M., Günther, O.P., Li, S. et al. Conservation Physiology (2017): doi: 10.1093/conphys/cox036
    • In vivo cleavage specificity of Trypanosoma brucei editosome endonucleases
      Carnes, J., McDermott, S., Anupama, A. et al. Nucleic Acids Research (2017): 4,667–86
    • Focused human gene expression profiling using dual-color reverse transcriptase multiplex ligation-dependent probe amplification
      Haks, M.C., Goeman, J.J., Magis-Escurra, C. et al. Vaccine (2016): 5,282–8
    • Novel HIV IL-4R antagonist vaccine strategy can induce both high avidity CD8 T and B cell immunity with greater protective efficacy
      Jackson, R.J., Worley, M., Trivedi, S. et al. Vaccine (2014): 5,703–14
    • Wind and sunlight shape microbial diversity in surface waters of the North Pacific Subtropical Gyre
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      Coudray-Meunier, C., Fraisse, A., Martin-Latil, S., Delannoy, S., Fach, P., Perelle, S. PLoS One (2016): DOI: 10.1371/journal.pone.0147832
    • A Functional Tricarboxylic Acid Cycle Operates during Growth of Bordetella pertussis on Amino Acid Mixtures as Sole Carbon Substrates
      Izac, M., Garnier, D., Speck, D., Lindley, N.D. PLoS One (2015): e0145251
    • Characterization of Shiga Toxin Subtypes and Virulence Genes in Porcine Shiga Toxin-Producing Escherichia coli
      Baranzoni, G.M., Fratamico, P.M., Gangiredla, J., Patel, I., Bagi, L.K., Delannoy, S., Fach, P., Boccia, F., Anastasio, A., Pepe, T. Frontiers in Microbiology (2016): 574
    • Microfluidic digital PCR enables multigene analysis of individual environmental bacteria
      Ottesen, E.A., Hong, J.W., Quake, S.R., Leadbetter, J.R. Science (2006): 1464–7
    • Digital PCR provides absolute quantitation of viral load for an occulate RNA virus
      White, R.A. 3rd, Quake, S.R., Curr, K. Journal of Virological Methods (2011): 45–50
    • Identification of Genetic Markers for Differentiation of Shiga Toxin-Producing , Enteropathogenic, and Avirulent Strains of Escherichia coli O26
      Bugarel, M., Beutin, L., Scheutz, F., Loukiadis, E., Fach, P. Appplied and Environmental Microbiology (2011): 2275–81
    • The multibasic cleavage site of the hemagglutinin of highly pathogenics A/Vietnam/1203/2004 (h5N1) avian influenza virus acts as a virulence factor in a host-specific manner in mammals
      Suguitan, A.L.Jr, Matsuoka, Y., Lau, Y.F., Santos, C.P., Vogel, L., Cheng, L.I., Orandle, M., Subbarao, K. Journal of Virology (2011): 2706–14
    • A novel high-throughput method for molecular serotyping and serotype-specific quantification of Streptococcus pneumoniae using a nanofluidic real-time PCR system
      Dhoubhadel, B.G., Yasunami, M., Thi, T.H., Thi, T.A., Watanabe, K., Suzuki, M., Morimoto, K., Dang, D.A., Ariyoshi, K. Journal of Medical Microbiology (2014): 528–39
    • Standardization of Nucleic Acid Tests for Clinical Measurements of Bacteria and Viruses
      Pavšič, J., Devonshire, A.S., Parkes, H., Schimmel, H., Foy, C.A., Karczmarczyk, M., Gutiérrez-Aguirre, I., Honeyborne, I., Huggett, J.F., McHugh, T.D., Milavec, M., Zeichhardt, H., Žel, J. Journal of Clinical Microbiology (2014): 2008–14

  • Neurology

    • Heterogeneity of astrocytes: from development to injury—single cell gene expression
      Rusnakova, V., Honsa, P., Dzamba, D. et al. PLoS One (2013): e69734
    • Evidence linking microRNA suppression of essential prosurvival genes with hippocampal cell death after traumatic brain injury
      Boone, D.K., Weisz, H.A., Bi, M. et al. Scientific Reports (2017): doi: 10.1038/s41598-017-06341-6
    • Hierarchical prediction errors in midbrain and septum during social learning
      Diaconescu, A.O., Mathys, C., Weber, L.A.E. et al. Social Cognitive and Affective Neuroscience (2017): 618Stat5 deficiency decreases transcriptional heterogeneity and supports emergence of hematopoietic sub-populations34
    • Nogo receptor blockade overcomes remyelination failure after white matter stroke and stimulates functional recovery in aged mice
      Sozmen, E.G., Rosenzweig, S., Llorente, I.L. et al. Proceedings of the National Academy of Sciences of the United States of America (2016): E8453–62
    • Developmental epigenetic modification regulates stochastic expression of clustered protocadherin genes, generating single neuron diversity
      Toyoda, S., Kawaguchi, M., Kobayashi, T. et al. Neuron (2014): 94–108
    • Autism-Associated Neuroligin-3 Mutations Commonly Impair Striatal Circuits to Boost Repetitive Behaviors
      Fuccillo, M.V., Rothwell, P.E., Maxeiner, S. et al. Cell (2014): 198–212
    • Increased expression of hyperpolarization-activated cyclic nucleotide-gated (HCN) channels in reactive astrocytes following ischemia
      Honsa, P., Pivonkova, H., Harantova, L. et al. Glia (2014): 2,004–21
    • Intrathecal somatic hypermutation of IgM in multiple sclerosis and neuroinflammation
      Beltrán, E., Obermeier, B., Moser, M. et al. Brain (2014): 2,703–14
    • Multipotent caudal neural progenitors derived from human pluripotent stem cells that give rise to lineages of the central and peripheral nervous system
      Denham, M., Hasegawa, K., Menheniott, T. et al. Stem Cells (2015): 1,759–70
    • Single-cell analysis reveals transcriptional heterogeneity of neural progenitors in human cortex
      Johnson, M.B., Wang, P.P., Atabay, K.D. et al. Nature Neuroscience (2015): 637–46
    • Quantitative Analysis of Glutamate Receptors in Glial Cells from the Cortex of GFAP/EGFP Mice Following Ischemic Injury: Focus on NMDA Receptors
      Dzamba, D., Honsa, P., Valny, M. et al. Cellular and Molecular Neurobiology (2015): 1,187–202
    • Diversity of Transgenic Mouse Models for Selective Targeting of Midbrain Dopamine Neurons
      Lammel, S., Steinberg, E.E., Földy, C. et al. Neuron (2015): 429–38
    • Lack of BDNF expression through promoter IV disturbs expression of monoamine genes in the frontal cortex and hippocampus
      Sakata, K., Duke, S.M. Neuroscience (2014): 265–75
    • Antibody-Mediated Targeting of Tau In Vivo Does Not Require Effector Function and Microglial Engagement
      Lee, S.H., Le Pichon, C.E., Adolfsson, O. et al. Cell Reports (2016): 1,690–700
    • Comprehensive Analysis of Transcription Dynamics from Brain Samples Following Behavioral Experience
      Turm, H., Mukherjee, D., Haritan, D., Tahor, M., Citri, A. Journal of Visualized Experiments (2014): 51,642
    • Bullous Pemphigoid, Neurodegenerative Disease, and Hippocampal BP180 Expression: A Retrospective Postmortem Neuropathologic Study
      Barrick. B.J., Ida, C.M., Laniosz, V. et al. Journal of Investigative Dermatology (2016): 2,090–2
    • New tools for studying microglia in the mouse and human CNS
      Bennett, M.L., Bennett, F.C., Liddelow, S.A. et al. Proceedings of the National Academy of Sciences (2016): E1738–46
    • Transcriptional Profiling of a Selective CREB Binding Protein Bromodomain Inhibitor Highlights Therapeutic Opportunities
      Chekler, E.L., Pellegrino, J.A., Lanz, T.A. et al. Chemistry & Biology (2015): 1,588–96
    • Rescue of gene-expression changes in an induced mouse model of spinal muscular atrophy by an antisense oligonucleotide that promotes inclusion of SMN2 exon 7
      Staropoli, J.F., Li, H., Chun, S.J. et al. Genomics (2015): 220–8
    • Single-Cell Gene Expression Analyses Reveal Heterogeneous Responsiveness of Fetal Innate Lymphoid Progenitors to Notch Signaling
      Chea, S., Schmutz, S., Berthault, C. et al. Cell Reports (2016): 1,500–16
    • CR1, ABCA7, and APOE genes affect the features of cognitive impairment in Alzheimer's disease
      Chung, S.J., Kim, M.J., Kim, Y.J. et al. Journal of the Neurological Sciences (2014): 91–6
    • A subpopulation of itch‐sensing neurons marked by Ret and somatostatin expression
      Stantcheva, K.K., Iovino, L., Dhandapani, R. et al. EMBO Reports (2016): 585–600
    • Building an RNA Sequencing Transcriptome of the Central Nervous System
      Dong, X., You, Y., Wu, J.Q. Neuroscientist (2015): 579–92
    • An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex
      Zhang, Y., Chen, K., Sloan, S.A. et al. Journal of Neuroscience (2014): 11,929–47
    • A large genome scan for rare CNVs in amyotrophic lateral sclerosis
      Blauw, H.M., Al-Chalabi, A., Andersen, P.M. et al. Human Molecular Genetics (2010): 4091–9
    • Characteristics and Predictive Value of Blood Transcriptome Signature in Males with Autism Spectrum Disorders
      Kong, S.W., Collins, C.D., Shimizu-Motohashi, Y. et al. PLoS One (2012): e49475
    • Utilization of Super BAC Pools and Fluidigm Access Array Platform for High-Throughput BAC Clone Identification: Proof of Concept
      Gomez-Ospina, N., Panagiotakos, G., Portmann, T. et al. PLoS One (2013): e60526
    • Investigating the Role of Surface Materials and Three Dimensional Architecture on In Vitro Differentiation of Porcine Monocyte-Derived Dendritic Cells
      Hartmann, S.B., Mohanty, S., Skovgaard, K. et al. PLoS One (2016): e0158503
    • CCR4 promotes medullary entry and thymocyte–dendritic cell interactions required for central tolerance
      Hu, Z., Lancaster, J.N., Sasiponganan, C., Ehrlich, L.I.R. The Journal of Experimental Medicine (2015): 1,947–65
    • Untangling the brain's neuroinflammatory and neurodegenerative transcriptional responses
      Srinivasan, K., Friedman, B.A., Larson, J.L., et al. Nature Communications (2016): 11,295
    • Single-Cell mRNA Profiling Reveals Cell-Type Specific Expression of Neurexin Isoforms
      Fuccillo, M.V., Földy, C., Gökce, O., et al. Neuron (2015): 326–40
    • Transcriptional profiling at whole population and single cell levels reveals somatosensory neuron molecular diversity
      Chiu, I.M., Barrett, L.B., Williams, E.K., et al. eLife (2014): e04660
    • Rapid temporal changes in the expression of a set of neuromodulatory genes during alcohol withdrawal in the dorsal vagal complex: molecular evidence of homeostatic disturbance
      Freeman, K., Staehle, M.M., Gümüş, Z.H., et al. Alcoholism Clinical and Experimental Research (2012): 1,688–1,700
    • Membrane-Tethered Monomeric Neurexin LNS-Domain Triggers Synapse Formation
      Gokce, O., Südhof, T.C. Journal of Neuroscience (2013): 14,617–28
    • Human Plasmacytoid Dendritic Cell Accumulation Amplifies Their Type 1 Interferon Production
      Liao, A.P., Salajegheh, M., Morehouse, C., et al. Clinical Immunology (2010): 130–8
    • Human induced pluripotent stem cell derived neurons as a model for Williams-Beuren syndrome
      Khattak, S., Brimble, E., Zhang, W., et al. Molecular Brain (2015): 77
    • Genome-Wide Gene Expression Profiling of Nucleus Accumbens Neurons Projecting to Ventral Pallidum Using both Microarray and Transcriptome Sequencing
      Chen, H., Liu, Z., Gong, S., et al. Frontiers in Neuroscience (2011): 98
    • Generation of Human Striatal Neurons by MicroRNA-Dependent Direct Conversion of Fibroblasts
      Victor, M.B., Richner, M., Hermanstyne, T.O., et al. Neuron (2014): 311–23
    • Differential Transcriptional Profiling of Damaged and Intact Adjacent Dorsal Root Ganglia Neurons in Neuropathic Pain
      Reinhold, A.K., Batti, L., Bilbao, D., et al. PLoS One (2015): e0123342
    • Single-Cell Transcriptional Analysis Reveals Novel Neuronal Phenotypes and Interaction Networks Involved in the Central Circadian Clock
      Park, J., Zhu, H., O'Sullivan, S. et al. Frontiers in Neuroscience (2016): 481
    • Protease-degradable PEG-maleimide coating with on-demand release of IL-1Ra to improve tissue response to neural electrodes
      Gutowski, S.M., Shoemaker, J.T., Templeman, K.L., Wei, Y., Latour Jr., R.A., Bellamkonda, R.V., LaPlaca, M.C., García, A.J. Biomaterials (2015): 55–70
    • MECP2e1 isoform mutation affects the form and function of neurons derived from Rett syndrome patient iPS cells
      Djuric, U., Cheung, A.Y.L., Zhang, W., Mok, R.S., Lai, W., Piekna, A., Hendry, J.A., Ross, P.J., Pasceri, P., Kim, D.S., Salter, M.W., Ellis, J. Neurology of Disease (2015): 37–45
    • Using iPS cell-derived neurons to uncover cellular phenotypes associated with Timothy Syndrome
      Paşca, S.P., Portmann, T., Voineagu, I., Yazawa, M., Shcheglovitov, O., Paşca, A.M., Cord, B., Palmer, T.D., Chikahisa, S., Seiji, N., Bernstein, J.A., Hallmayer, J., Geschwind, D.H., Dolmetsch, R.E. Nature Medicine (2011): 1,657–62
    • Synaptotagmin-1 and -7 Trigger Synchronous and Asynchronous Phases of Neurotransmitter Release
      Bacaj, T., Wu, D., Yang, X., Morishita, W., Zhou, P., Xu, W., Malenka, R.C., Südhof, T.C. Neuron (2013): 947–59
    • LRRK2 Mutant iPSC-Derived DA Neurons Demonstrate Increased Susceptibility to Oxidative Stress
      Nguyen, H.N., Byers, B., Cord, B., Shcheglovitov, A., Byrne, J., Gujar, P., Kee, K., Schüle, B., Dolmetsch, R.E., Langston, W., Palmer, T., Pera, R.R. Cell Stem Cell (2011): 267–80
    • Distinct circuit-dependent functions of presynaptic neurexin-3 at GABAergic and glutamatergic synapses
      Aoto, J., Földy, C., Ilcus, S.M.C., Tabuchi, K., Südhof, T.C. Nature Neuroscience (2015): 997–1,007
    • BDNF May Play a Differential Role in the Protective Effect of the mGluR2/3 Agonist LY379268 on Striatal Projection Neurons in R6/2 Huntington's Disease Mice
      Reiner, A., Wang, H.B., Del Mar, N., Sakata, K., Yoo, W., Deng, Y.P. Brain Research (2014): 161–72
    • Association of the CHRNA4 Neuronal Nicotinic Receptor Subunit Gene with Frequency of Binge Drinking in Young Adults
      Coon, H., Piasecki, T.M., Cook, E.H., Dunn, D., Mermelstein, R.J., Weiss, R.B., Cannon, D.S. Alcoholism, Clinical and Experimental Research (2014): 930–7
    • Assessing the Accuracy of Quantitative Molecular Microbial Profiling
      O'Sullivan, D.M., Laver, T., Temisak, S., Redshaw, N., Harris, K.A., Foy, C.A., Studholme, D.J., Huggett, J.F. International Journal of Molecular Sciences (2014): 21,476–91
    • APOE, MAPT, SNCA, and Cognitive Performance in Parkinson Disease
      JAMA Neurology (2014): 1,405–12
    • Aldehyde dehydrogenase variation enhances effect of pesticides associated with Parkinson disease
      Fitzmaurice, A.G., Rhodes, S.L., Cockburn, M., Ritz, B., Bronstein, J.M. Neurology (2014): 419–26
    • Aberrant Dopamine D2-Like Receptor Function in a Rodent Model of Schizophrenia
      Perez, S.M., Lodge, D.J. Journal of Pharmacology and Experimental Therapeutics (2012): 288–95
    • Neuronal Rac1 Is Required for Learning-Evoked Neurogenesis
      Haditsch, U., Anderson, M. P., Freewoman, J., Cord, B., Babu, H., Brakebusch, C., Palmer, T. D. Journal of Neuroscience (2013): 12,229–41
    • Identifying Functional Gene Regulatory Network Phenotypes Underlying Single Cell Transcriptional Variability
      Park, J., Ogunnaike, B., Schwaber, J., Vadigepalli, R. Progress in Biophysics and Molecular Biology (2015): 87–98
    • A Promoter in the Coding Region of the Calcium Channel Gene CACNA1C Generates the Transcription Factor CCAT
      Gomez-Ospina, N., Panagiotakos, G., Portmann, T., Pasca, S.P., Rabah, D., Budzillo, A., Kinet, J.P., Dolmetsch, R.E. PLoS One (2013): e0060526
    • TrkB/BDNF signalling patterns the sympathetic nervous system
      Kasemeier-Kulesa, J.C., Morrison, J.A., Lefcort, F., Kulesa, P.M. Nature Communications (2015): 8,281
    • Inputs drive cell phenotype variability
      Park, J., Brureau, A., Kernan, K., Starks, A., Gulati, S., Ogunnaike, B., Schwaber, J., Vadigepalli, R. Genome Research (2014): 930–41
    • DNA methylation profile dynamics of tissue-dependent and differentially methylated regions during mouse brain development
      Hirabayashi, K., Shiota, K., Yagi, S. BMC Genomics (2013): 82
    • Comprehensive qPCR profiling of gene expression in single neuronal cells
      Citri, A., Pang, Z.P., Sudhof, T.C., Wernig, M., Malenka, R.C. Nature Protocols (2011): 118-27
    • Generation of Induced Neuronal Cells by the Single Reprogramming Factor ASCL1
      Chanda, S., Ang, C.E., Davila, J., Pak, C.H., Mall, M., Lee, Q.Y., Ahlenius, H., Jung, S.W., Südhof, T.C., Wernig, M. Stem Cell Reports (2014): 282–96
    • Pumilio-2 Function in the Mouse Nervous System
      Siemen, H., Colas, D., Heller, H.C., Brüstle, O., Reijo Pera, R.A. PLoS One (2011): e25932
    • Gene Expression Profiling of Dendritic Cells Reveals Important Mechanisms Associated with Predisposition to Staphylococcus Infections
      Toufeer, M., Bonnefont, C.M.D., Foulon, E., Caubet, C., Tasca, C., Aurel, M.R., Robert-Granié, C., Rupp, R., Foucras, G. PLoS One (2011): e22147
    • Defining midbrain dopaminergic neuron diversity by single-cell gene profiling
      Poulin, J.F., Zou, J., Drouin-Ouellet, J., Kim, K.Y.A., Cicchetti, F., Awatramani, R.B. Cell Reports (2014): 930-43
    • Association of Thymidylate Synthase Polymorphisms with Acute Pancreatitis and/or Peripheral Neuropathy in HIV-Infected Patients on Stavudine-Based Therapy
      Domingo, P., del Carmen Cabeza, M., Torres, F., Salazar, J., del Mar Gutierrez, M., Mateo, M.G., Martinez, E., Domingo, J.C., Fernandez, I., Villarroya, F., Ribera, E., Vidal, F., Baiget, M. PLoS One (2013): e57347
    • Analysis of Adult Neurogenesis: Evidence for a Prominent “Non-Neurogenic” DCX-Protein Pool in Rodent Brain
      Kremer, T., Jagasia, R., Hermann, A., Matile, H., Borroni, E., Francis, F., Kuhn, H.G., Czech, C. PLoS One (2014): e59269
    • Age-related micro-RNA abundance in individual C. elegans
      Lucanic, M., Graham, J., Scott, G., Bhaumik, D., Benz, C.C., Hubbard, A., Lithgow, G.J., Melov, S. Impact Journal on Aging (2013): 394-411
    • Lola regulates Drosophila olfactory projection neuron identity and targeting specificity
      Spletter, M.L., Liu, J., Su, H., Giniger, E., Komiyama, T., Quake, S., Luo, L. Neural Development (2007): 14
    • Adpative transcriptional dynamics of A2 neurons and central cardiovascular control pathways
      Vadigepalli, R., Gonye, G.E., Paton, J.F., Schwaber, J.S. Experimental Physiology (2011): 462–8
    • Intergrative Gene Regulatory Network Analysis Reveals Light-Induced Regional Gene Expression Phase Shift Program
      Zhu, H., Vadigepalli, R., Rafferty, R., Gonye, G.E., Weaver, D.R., Schwaber, J.S. PLoS One (2012): e37833
    • Role of common and rare APP DNA sequence variants in Alzheimer disease
      Hooli, B.V., Mohapatra, G., Mattheisen, M., Parrado, A.R., Roehr, J.T., Shen, Y., Gusella, J.F., Moir, R., Saunders, A.J., Lange, C., Tanzi, R.E., Bertram, L. Neurology (2012): 1250–7

  • Oncology

    • "Stealth dissemination" of macrophage-tumor cell fusions cultured from blood of patients with pancreatic ductal adenocarcinoma
      Clawson, G.A., Matters, G.L., Xin, P. et al. PLoS One (2017): e0184451
    • Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells
      Kim, K.T., Lee, H.W., Lee, H.O. et al. Genome Biology (2015): 127
    • Histone Deacetylase Inhibitors Potentiate Vesicular Stomatitis Virus Oncolysis in Prostate Cancer Cells by Modulating NF-κB-Dependent Autophagy
      Shulak, L.,Beljanski, V., Chiang, C. et al. Journal of Virology (2014): 2,927–40
    • Impaired PRC2 activity promotes transcriptional instability and favors breast tumorigenesis
      Wassef, M., Rodilla, V., Teissandier, A. et al. Genes & Development (2015): 2,547–62
    • Granulocyte colony-stimulating factor prevents loss of spermatogenesis after sterilizing busulfan chemotherapy
      Benavides-Garcia, R., Joachim, R., Pina, N.A. et al. Fertility and Sterility (2015): 270–80
    • Single-cell analysis of targeted transcriptome predicts drug sensitivity of single cells within human myeloma tumors
      Mitra, A.K., Mukherjee, U.K., Harding, T. et al. Leukemia (2016): 1,094–102
    • Liquid biopsies in lung cancer—time to implement research technologies in routine care?
      Köhn, L., Johansson, M., Grankvist, K. et al. Annals of Translational Medicine (2017): doi: 10.21037/atm.2017.04.12
    • Characterization of MicroRNA-200 pathway in ovarian cancer and serous intraepithelial carcinoma of fallopian tube
      Yang, J., Zhou, Y., Ng, S.K. et al. BMC Cancer (2017): 422
    • Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia
      Wang, L., Fan, J., Georghiou, G. et al. Genome Research (2017): 1,300–11
    • Most T790M mutations are present on the same EGFR allele as activating mutations in patients with non–small cell lung cancer
      Hidaka, N., Iwama, E., Kubo, N. et al. Lung Cancer (2017): 75–82
    • Enrichment and Molecular Analysis of Breast Cancer Disseminated Tumor Cells from Bone Marrow Using Microfiltration
      Pillai, S.G., Zhu, P., Siddappa, C.M. et al. PLoS One (2017): e0170761
    • RAD51 Is a Selective DNA Repair Target to Radiosensitize Glioma Stem Cells
      King, H.O., Brend, T., Payne, H.L. et al. Stem Cell Reports (2017): 125–39
    • Exploratory Analysis of TP53 Mutations in Circulating Tumour DNA as Biomarkers of Treatment Response for Patients with Relapsed High-Grade Serous Ovarian Carcinoma: A Retrospective Study
      Parkinson, C.A., Gale, D., Piskorz, A.M. et al. PLoS One (2017): e1002198
    • Development and Application of a Microfluidics-Based Panel in the Basal/Luminal Transcriptional Characterization of Archival Bladder Cancers
      Kim, D., Choi, Y.J., Ireland, J. et al. PLoS One (2016): e0165856
    • Diagnostic value of microRNAs in prostate cancer patients with prostate specific antigen (PSA) levels between 2, and 10 ng/mL
      Akbayır, S., Muşlu, N., Erden, S. et al. Turkish Journal of Urology (2016): 247–55
    • Transcriptional Landscape of Human Tissue Lymphocytes Unveils Uniqueness of Tumor-Infiltrating T Regulatory Cells
      De Simone, M., Arrigoni, A., Rossetti, G. et al. Immunity (2016): 1,135–47
    • Vitamin D Receptor Gene Polymorphism and the Risk of Colorectal Cancer: A Nested Case-Control Study
      Budhathoki, S., Yamaji, T., Iwasaki, M. et al. PLoS One (2016): e0164648
    • In pursuit of synergy: An investigation of the PI3K/mTOR/MEK co-targeted inhibition strategy in NSCLC
      Heavey, S., Cuffe, S., Finn, S. et al. Oncotarget (2016): 79,526–43
    • Patient survival and tumor characteristics associated with CHEK2:p.I157T – findings from the Breast Cancer Association Consortium
      Muranen, T.A., Blomqvist, C., Dörk, T. et al. Breast Cancer Research (2016): 98
    • Pharmacogenetics of the DNA repair pathways in advanced non-small cell lung cancer patients treated with platinum-based chemotherapy
      Sullivan, I., Salazar, J., Majem, M. et al. Cancer Letters (2014): 160–6
    • 3000 Chemo-radiation (CRT) and mutation profile in stage III Non Small Cell Lung Cancer (NSCLC): An analysis of the prognostic value
      Boros, A., Lacroix, L., Lacas, B. et al. European Journal of Cancer (2015): S595
    • Detection of Novel Cancer Subpopulations Through Integration of Public Microarray Data with Single Cell Gene Expression Profiling
      Januszyk, M., Jahchan, N., Purvesh, K. et al. Plastic and Reconstructive Surgery (2015): 120–1
    • Single-cell genetic analysis reveals the composition of initiating clones and phylogenetic patterns of branching and parallel evolution in myeloma
      Melchor, L., Brioli, A., Wardell, C.P. et al. Leukemia (2014): 1,705–15
    • Polymorphisms in the MTHFR gene are associated with recurrence risk in lymph node-positive breast cancer patients
      Suner, A., Buyukhatipoglu, H., Aktas, G. et al. OncoTargets and Therapy (2016): 5,603–9
    • Breast cancer risk variants at 6q25 display different phenotype associations and regulate ESR1, RMND1 and CCDC170
      Dunning, A.M., Michailidou, K., Kuchenbaecker, K.B., et al. Nature Genetics (2016): 374–86
    • Functional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast-ovarian cancer susceptibility locus
      Lawrenson, K., Kar, S., McCue, K. et al. Nature Communications (2016): 12,675
    • Atezolizumab in combination with bevacizumab enhances antigen-specific T-cell migration in metastatic renal cell carcinoma
      Wallin, J.J., Bendell, J.C., Funke, R., et al. Nature Communications (2016): 12,624
    • Noninvasive monitoring of the genetic evolution of EGFR-mutant non-small-cell lung cancer by analyzing circulating tumor DNA during combination chemotherapy with gefitinib and pemetrexed or S-1
      Nakahara, Y., Takagi, Y., Hosomi, Y., et al. OncoTargets and Therapy (2016): 5,287–95
    • HER2 drives Mucin-like 1 to control proliferation in breast cancer cells
      Conley, S.J., Bosco, E.E., Tice, D.A., et al. Oncogene (2016): 4,225–34
    • Enhanced MAPK signaling drives ETS1-mediated induction of miR-29b leading to downregulation of TET1 and changes in epigenetic modifications in a subset of lung SCC.
      Taylor, MA., Wappett, M., Delpuech, O., et al. Oncogene (2016): 4,345–57
    • High-throughput screening of Sirtuin family of genes in breast cancer
      Igci, M., Kalender, M.E., Borazan, E. et al. Gene (2016): 123–8
    • BRCA1/2 mutations and expression: response to platinum chemotherapy in patients with advanced stage epithelial ovarian cancer
      Dann, R.B., DeLoia, J.A., Timms, K.M. et al. Gynecologic Oncology (2012): 677–82
    • MYCN controls an alternative RNA splicing program in high-risk metastatic neuroblastoma
      Zhang, S., Wei, J.S., Li, S.Q. et al. Cancer Letters (2016): 214–24
    • SND1 overexpression deregulates cholesterol homeostasis in hepatocellular carcinoma
      Navarro-Imaz, H., Rueda, Y., Fresnedo, O. Biochimica et Biophysica Acta (BBA)—Molecular and Cell Biology of Lipids (2016): 988–96
    • Modelling the in-utero initation of ETV6-RUNX1 in childhood acute lymphoblastic leukaemia using human pluripotent stem cells
      Richardson, S., Böiers,C., Zriwil, A. et al. The Lancet (2016): S86
    • Polymorphism of CYP3A4 and ABCB1 genes increase the risk of neuropathy in breast cancer patients treated with paclitaxel and docetaxel
      Kus, T., Aktas, G., Kalender, M.E., Demiryurek, A.T. et al. OncoTargets and Therapy (2016): 5,073–80
    • TGF-β1 and TGF-β2 abundance in liver diseases of mice and men
      Dropmann, A., Dediulia, T., Breitkopf-Heinlein, K. et al. Oncotarget (2016): 19,499–518
    • Analysis of dysplasia in patients with Barrett's esophagus based on expression pattern of 90 genes
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    • Stemness of the hybrid Epithelial/Mesenchymal State in Breast Cancer and Its Association with Poor Survival
      Grosse-Wilde, A., d’Hérouël, A.F., McIntosh, E., Ertaylan, G., Skupin, A., Kuestner, R.E., del Sol, A., Walters, K.A., Huang, S. PLoS One (2015): e0126522
    • Salivary MicroRNA in Pancreatic Cancer Patients
      Humeau, M., Vignolle-Vidoni, A., Sicard, F., Martins, F., Bournet, B., Buscail, L., Torrisani, J., Cordelier, P. PLoS One (2015): e0130996
    • RNA-Seq Differentiates Tumour and Host mRNA Expression Changes Induced by Treatment of Human Tumour Xenografts with the VEGFR Tyrosine Kinase Inhibitor Cediranib
      Bradford, J.R., Farren, M., Powell, S.J., Runswick, S., Weston, S.L., Brown, H., Delpuech, O., Wappett, M., Smith, N.R., Carr, T.H., Dry, J.R., Gibson, N.J., Barry, S.T. PLoS One (2013): e0066003
    • Next Generation MUT-MAP, a High-Sensitivity High-Throughput Microfluidics Chip-Based Mutation Analysis Panel
      Schleifman, E.B., Tam, R., Patel, R., Tsan, A., Sumiyoshi, T., Fu, T., Desai, R., Schoenbrunner, N., Myers, T.W., Bauer, K., Smith, E., Raja, R. PLoS One (2014): e90761
    • Molecular characteristics of mismatch repair genes in sporadic colorectal tumors in Czech patients
      Vymetalkova, V.P., Slyskova, J., Korenkova, V., Bielik, L., Langerova, L., Prochazka, P., Rejhova, A., Schwarzova, L., Pardini, B., Naccarati, A., Vodicka, P. BMC Medical Genetics (2014): 17
    • Molecular and In Vivo Characterization of Cancer-Propagating Cells Derived from MYCN-Dependent Medulloblastoma
      Ahmad, Z., Jasnos, L., Gil, V., Howell, L., Hallsworth, A., Petrie, K., Sawado, T., Chesler, L. PLoS One (2015): e0119834
    • Mesenchymal Stem/Progenitors and Other Endometrial Cell Types From Women With Polycystic Ovary Syndrome (PCOS) Display Inflammatory and Oncogenic Potential
      Piltonen, T.T., Chen, J., Erikson, D.W., Spitzer, T.L.B., Barragan, F., Rabban, J.T., Huddleston, H., Irwin, J.C., Guidice, L.C. Journal of Clinical Endocrinology and Metabolism (2013): 3,765-75
    • Ionizing radiations sustain glioblastoma cell dedifferentiation to a stem-like phenotype through survivin: possible involvement in radioresistance
      Dahan, P., Gala, J.M., Delmas, C., Monferran, S., Malric, L., Zentowski, D., Lubrano, V., Toulas, C., Moyal, E.C.J., Lemarie, A. Cell Death and Disease (2014): e1543
    • CXorf61 is a target for T cell based immunotherapy of triple-negative breast cancer
      Paret, C., Simon, P., Vormbrock, K., Bender, C., Kölsch, A., Breitkreuz, A., Yildiz, Ö., Omokoko, T., Hubich-Rau, S., Hartmann, C., Häcker, S., Wagner, M., Roldan, D.B., Selmi, A., Türeci, Ö., Sahin, U. Oncotarget (2015): 25,356–67
    • Evaluation of current methods used to analyze the expression profiles of ABC transporters yields an improved drug-discovery database
      Orina, J.N., Calcagno, A.M., Wu, C.P., Varma, S., Shih, J., Lin, M., Eichler, G., Weinstein, J.N., Pommier, Y., Ambudkar, S.V., Gottesman, M.M., Gillet, J.P. Molecular Cancer Therapeutics (2009):
    • Enriched Bone Marrow Derived Disseminated Neuroblastoma Cells Can Be a Reliable Source for Gene Expression Studies—A Validation Study
      Rifatbegovic, F., Abbasi, M.R., Taschner-Mandl, S., Kauer, M., Weinhäusel, A., Handgretinger, R., Ambros, P.F. PLoS One (2015): e0137995
    • Downregulation of CXCR4 in Metastasized Breast Cancer Cells and Implication in Their Dormancy
      Nobutani, K., Shimono, Y., Mizutani, K., Ueda, Y., Suzuki, T., Kitayama, M., Minami, A., Momose, K., Miyawaki, K., Akashi, K., Azuma, T., Takai, Y. PLoS One (2015): e0130032
    • Diurnal suppression of EGFR signalling by glucocorticoids and implications for tumour progression and treatment
      Lauriola, M., Enuka, Y., Zeisel, A., D'Uva, G., Roth, L., Sharon-Sevilla, M., Lindzen, M., Sharma, K., Nevo, N., Feldman, M., Carvalho, S., Cohen-Dvashi, H., Kedmi, M., Ben-Chetrit, N., Chen, A., Solmi, R., Wiemann, S., Schmitt, F., Domany, E., Yarden, Y. Nature Communications (2014): 5,073
    • Discrepant NOXA (PMAIP1) transcript and NOXA protein levels: a potential Achilles' heel in mantle cell lymphoma
      Dengler, M.A., Weilbacher, A., Gutekunst, M., Staiger, A.M., Vöhringer, M.C., Horn, H., Ott, G., Aulitzky, W.E., van der Kuip, H. Cell Death and Disease (2014): e1013
    • Current status and future potential of somatic mutation testing from circulating free DNA in patients with solid tumours
      Aung, K.L., Board, R.E., Ellison, G., Donald, E., Ward, T., Clack, G., Ranson, M., Hughes, A., Newman, W., Dive, C. Hugo Journal (2011): 11-21
    • Copy number alterations and allelic ratio in relation to recurrence of rectal cancer
      Goossens-Beumer, I.J., Oosting, J., Corver, W.E., Janssen, M.J.F.W., Janssen, B., van Workum, W., Zeestraten, E.C.M., van de Velde, C.J.H., Morreau, H., Kuppen, P.J.K., van Wezel, T. BMC Genomics (2015): 438
    • Common Oncogene Mutations and Novel SND1-BRAF Transcript Fusion in Lung Adenocarcinoma from Never Smokers
      Jang, J.S., Lee, A., Li, J., Liyanage, H., Yang, Y., Guo, L., Asmann, Y.W., Li, P.W., Erickson-Johnson, M., Sakai, Y., Sun, Z.F., Jeon, H.S., Hwang, H., Bungum, A.O., Edell, E.S., Simon, V.A., Kopp, K.J., Eckloff, B., Oliveira, A.M., Wieben, E., Aubry, M.C., Yi, E., Wigle, D., Diaso, R.B., Yang, P., Jen, J. Scientific Reports (2015): 9,755
    • Circulating Tumor Cells: Application as a Biomarker for Molecular Characterization and Predictor of Survival in an All-Comer Solid Tumor Phase I Clinical Study
      Bao, H., Burke, P.A., Huang, J., Chen, X., Brohawn, P.Z., Yao, Y., Lechleider, R.J., Sikorski, R.S., Buzoianu, M., Zhang, J., Shi, X., Richman, L.K., LaVallee, T.M. PLoS One (2013): e58557
    • Chordoma Characterization of Significant Changes of the DNA Methylation Pattern
      Rinner, B., Weinhaeusel, A., Lohberger, B., Froelich, E.V., Pulverer, W., Fischer, C., Meditz, K., Scheipl, S., Trajanoski, S., Guelly, C., Leithner, A., Liegl, B. PLoS One (2013): e56609
    • Cell type specific gene expression analysis of prostate needle biopsies resolves tumor tissue heterogeneity
      Krönig, M., Walter, M., Drendel, V., Werner, M., Jilg, C.A., Richter, A.S., Backofen, R., McGarry, D., Follo, M., Schultze-Seemann, W., Schüle. R. Oncotarget (2014): 1,302-14
    • Capturing complex tumour biology in vitro: histological and molecular characterisation of precision cut slices
      Davies, E.J., Dong, M., Gutekunst, M., Närhi, K., van Zoggel, H.J.A.A., Blom, S., Nagaraj, A., Metsalu, T., Oswald, E., Erkens-Schulze, S., Delgado San Martin, J.A., Turkki, R., Wedge, S.R., af Hällström, T.M., Schueler, J., van Weerden, W.M., Verschuren, E.W., Barry, S.T., van der Kuip, H., Hickman, J.A. Scientific Reports (2015): 17,187
    • Biomarkers of Residual Disease, Disseminated Tumor Cells, and Metastases in the MMTV-PyMT Breast Cancer Model
      Franci, C., Zhou, J., Jiang, Z., Modrusan, Z., Good, Z., Jackson, E., Kouros-Mehr, H. PLoS One (2013): e58183
    • Bioinformatic construction of the human cell surfaceome
      da Cunha, J.P., Galante, P.A., de Souza, J.E., de Souza, R.F., Carvalho, P.M., Ohara, D.T., Moura, R.P., Oba-Shinja, S.M., Marie, S.K., Silva, W.A. Jr., Perez, R.O., Stransky, B., Pieprzyk, M., Moore, J., Caballero, O., Gama-Rodrigues, J., Habr-Gama, A., Kuo, W.P., Simpson, A.J., Camargo, A.A., Old, L.J., de Souza, S.J. Proceedings of the National Academy of Sciences (2009): 16,752–7
    • Autophagy limits proliferation and glycolytic metabolism in acute myeloid leukemia
      Watson, A.S., Riffelmacher, T., Stranks, A., Williams, O., De Boer, J., Cain, K., MacFarlane, M., McGouran, J., Kessler, B., Khandwala, S., Chowdhury, O., Puleston, D., Phadwal, K., Mortensen, M., Ferguson, D., Soilleux, E., Woll, P., Jacobsen, S.E.W., Simon, A.K. Cell Death Discovery (2015): 15,008
    • Advances in the Molecular Detection of ABC Transporters Involved in Multidrug Resistance in Cancer
      Gillet, J.P., Gottesman, M.M. Current Pharmaceutical Biotechnology (2011): 686–92
    • Single-cell mutational profiling and clonal phylogeny in cancer
      Potter, N.E., Ermini, L., Papaemmanuil, E., Cazzaniga, G., Vijayaraghavan, G., Titley, I., Ford, A., Campbell, P., Kearney, L., Greaves, M. Genome Research (2013): 2,115–25
    • Antibody-independent isolation of circulating tumor cells by continuous-flow dielectrophoresis
      Shim, S., Stemke-Hale, K., Tsimberidou, A.M., Noshari, J., Anderson, T.E., Gascoyne, P.R.C. Biomicrofluidics (2013): 011807
    • ANKS1B is a smoking-related molecular alteration in clear cell renal cell carcinoma
      Eckel-Passow, J.E., Serie, D.J., Bot, B.M., Joseph, R.W., Cheville, J.C., Parker, A.S. BMC Urology (2014): 14
    • Altered Expression of Insulin Receptor Isoforms in Breast Cancer
      Huang, J., Morehouse, C., Streicher, K., Higgs, B.W., Gao, J., Czapiga, M., Boutrin, A., Zhu, W., Brohan, P., Chang, Y., Viner, J., LaVallee, T., Richman, L., Jallal, B., Yao, Y. PLoS One (2011): e26177
    • Adrenomedullin in Ovarian Cancer: Foe In Vitro and Friend In Vivo?
      Baranello, C., Mariani, M., Andreoli, M., Fanelli, M., Martinelli, E., Ferrandina, E., Ferrandina, G., Scambia, G., Shahabi, S., Ferlini, C. PLoS One (2012): e40678
    • A Synthetic Lethality Screen Using a Focused siRNA Library to Identify Sensitizers to Dasatinib Therapy for the Treatment of Epithelial Ovarian Cancer
      Pathak, H.B., Zhou, Y., Sethi, G., Hirst, J., Schilder, R.J., Golemis, E.A., Godwin, A.K. PLoS One (2015): e0144126
    • A novel multiplexed immunoassay identifies CEA, IL-8 and prolactin as prospective markers for Dukes’ stages A-D colorectal cancers
      Mahboob, S., Ahn, S.B., Cheruku, H.R., Cantor, D., Rennel, E., Fredriksson, S., Edfeldt, G., Breen, E.J., Khan, A., Mohamedali, A., Muktadir, M.G., Rangathan, S., Tan, S.H., Nice, E., Baker, M.S. Clinical Proteomics (2015): 10
    • Tumor Content Chart-Assisted HER2/CEP17 Digital PCR Analysis of Gastric Cancer Biopsy Specimens
      Matsusaka, K., Ishikawa, S., Nakayama, A., Ushiku, T., Nishimoto, A., Urabe, M., Kaneko, N., Kunita, A., Kaneda, A., Aburatani, H., Fujishiro, M., Seto, Y., Fukayama, M. PLoS One (2016): e0154430
    • A Common Cancer Risk-Associated Allele in the hTERT Locus Encodes a Dominant Negative Inhibitor of Telomerase
      Killedar, A., Stutz, M.D., Sobinof, A.P., Tomlinson, C.G., Bryan, T.M., Beesley, J., Chenevix-Trench, G., Reddel, R.R., Pickett, H.A. PLoS Genetics (2015): e1005286
    • A colorectal cancer prediction model using traditional and genetic risk scores in Koreans
      Jung, K.J., Won, D., Kim, S., Kim, T.I., Jee, S.H., Beaty, T.H. BMC Genetics (2015): 49
    • Characterizing heterogeneity in leukemic cells using single-cell gene expression analysis
      Saadatpour, A., Guo, G., Orkin, S.H., Yuan, G.C. Genome Biology (2014): 525
    • Evaluation of current methods used to analyze the expression profiles of ATP-binding cassette transporters yields an improved drug-discovery database
      Orina, J.N., Calcagno, A.M., Wu, C.P., Varma, S., Shih, J., Lin, M., Eichler, G., Weinstein, J.N., Pommier, Y., Ambudkar, S.V., Gottesman, M.M., Gillet, J.P. Molecular Cancer Therapeutics (2009): 2057–66
    • An Integrative Analysis of PIK3CA Mutation, PTEN, and INPP4B Expression in Terms of Trastuzumab Efficacy in HER2-Positive Breast Cancer
      Sueta, A., Yamamoto, Y., Yamamoto-Ibusuki, M., Hayashi, M., Takeshita, T., Yamamoto, S., Iwase, H. PLoS One (2014): e116054
    • A Mammary Stem Cell Population Identified and Characterized in Late Embryogenesis Reveals Similarities to Human Breast Cancer
      Spike, B.T., Engle, D.D., Lin, J.C., Cheung, S.K., La, J., Wahl, G.M. Cell Stem Cell (2012): 183–97
    • Molecular and cellular effects of oncogene cooperation in a genetically accurate AML mouse model
      Reckzeh, K., Bereshchenko, O., Mead, A., Rehn, M., Kharazi, S., Jacobsen, S-E., Nerlov, C., Cammenga, J. Leukemia (2012): 1527–36
    • Identification of a cKit+ Colonic Crypt Base Secretory Cell That Supports Lgr5+ Stem Cells in Mice
      Rothenberg, M.E., Nusse, Y., Kalisky, T., Lee, J.J., Dalerba, P., Scheeren, F., Lobo, N., Kulkarni, S., Sim, S., Qian, D., Beachy, P.A., Pasricha, P.J., Quake, S.R., Clarke, M.F. Gastroenterology (2012): 1195–205
    • Intergrative Genome-wide Analysis Reveals Cooperative Regulation of Alternative Splicing by hnRNP Proteins
      Huelga, S.C., Vu, A.Q., Arnold, J.D., Liang, T.Y., Liu, P.P., Yan, B.Y., Donohue, J.P., Shiue, L., Hoon, S., Brenner, S., Ares, M. Jr, Yeo., G.W. Cell (2012): 167–78
    • Absolute quantitative detection of ABL tyrosine kinase domain point mutations in chronic myeloid leukemia using a novel nanofluidic platform and mutation-specific PCR
      Oehler, V.G., Qin, J., Ramakrishnan, R., Facer, G., Ananthnarayan, S., Cummings, C., Deininger, M., Shah, N., McCormick, F., Willis, S., Daridon, A., Unger, M., Radich, J.P. Leukemia (2008): 396–9
    • Microfluidics digital PCR reveals a higher than expected fraction of fetal DNA in maternal plasma
      Lun, F.M., Chiu, R.W., Chan, K.C., Leung, T.Y., Lau, T.K., Lo, Y.M. Clinical Chemistry (2008): 1664–72
    • Circulating tumor cells are transcriptionally similar to the primary tumor in a murine prostate model
      Helzer, K.T., Barnes, H.E., Day, L., Harvey, J., Billings, P.R., Forsyth, A. Cancer Research (2009): 7860–6
    • Quantifying EGFR Alterations in the Lung Cancer Genome with Nanofluidic Digital PCR Arrays
      Wang, J., Ramakrishnan, R., Tang, Z., Fan, W., Kluge, A., Dowlati , A., Jones, R.C., Ma, P.C. Clinical Chemistry (2010): 623–32
    • Modeling interactions between leukemia-specific chromosomal changes, somatic mutations, and gene expression patterns during progression of core-binding factore leukemias
      Jones, D., Yao, H., Romans, A., Dando, C., Pierce, S., Borthakur, G., Hamilton, A., Bueso-Ramos, C., Ravandi, F., Garcia-Manero, G., Kantarjian, H. Genes, Chromosomes and Cancer (2010): 182–91
    • Genetic polymorphism of IGF-I predicts recurrence in patients with gastric cancer who have undergone curative gastrectomy
      Shitara, K., Ito, S., Misawa, K., Ito, Y., Ito, H., Hosono, S., Watanabe, M., Tajima, K., Tanaka, H., Muro, K., Matsuo, K. Annals of Oncology (2011): 659–64
    • Microfluidic based multiplex qRT-PCR identifies diagnostic microRNA signatures in sera of prostate cancer patients
      Moltzahn, F., Olshen, A.B., Baehner, L., Peek, A.S., Fong, L., Stöppler, H.J., Simko, J., Hilton, J.F., Carroll, P.R., Blelloch, R. Cancer Research (2011): 550–60
    • Correlation of FCGR3A and EGFR germline polymorphisms with the efficacy of cetuximab in KRAS wild-type metastatic colorectal cancer
      Pander, J., Gelderblom, H., Antonini, N.F., Tol, J., van Krieken, J.H.J.M., van der Straaten, T., Punt, C.J.A., Guchelaar, H.J. European Journal of Cancer (2010): 1829–34
    • Immunoglobulin G fragment C receptor polymorphisms and KRAS mutations: are they useful biomarkers of clinical outcome in advanced colorectal cancer treated with anti-EGFR-based therapy?
      Paez. D., Paré, L., Espinosa, I., Salazar, J., del Rio, E., Barnadas, A., Marcuello. E., Baiget, M. Cancer Science 2048–53
    • The Role of KRAS rs61764370 in Invasive Epithelial Ovarian Cancer: Implications for Clinical Testing
      Pharoah, P.D.P, Palmieri, R.T., Ramus, S.J. et al. Clinical Cancer Research (2011): 3742–50
    • Sensitive quantitation of minimal residual disease in chronic myleoid leukemia using nanofluisidc digitial polymerase chain reaction assay
      Goh, H.G., Lin, M., Fukushima, T., Saglio, G., Kim, D., Choi, S.Y., Kim, S.H., Lee, J., Lee, Y.S., Oh, S.M., Kim, D.W. Leukemia & Lymphoma (2011): 896–904
    • Identification of molecular pathways involved in oxaliplatin-associated sinsoidal dilation
      Agostini, J., Benoist, S., Seman, M., Julié, C., Imbeaud, S., Letourneur, F., Cagnard, N., Rougier, P., Brouquet, A., Zucman-Rossi, J., Laurent-Puig, P. Journal of Hepatology (2011): 869–76
    • Multiparameter analyses of three-dimensionally cultured tumor spheroids based on respiratory activity and comprehensive gene expression profiles
      Zhou, Y., Arai, T., Horiguchi, Y., Ino, K., Matsue, T., Shiku, H. Analytical Biochemistry (2013): 187–93
    • Diffuse large B-cell lymphoma: sub-classification by massive parallel quantitative RT-PCR
      Xue, X., Zeng, N., Gao, Z., Du, M.Q. Laboratory Investigation (2014): 113–20
    • ERCC1 and CYP1B1 polymorphisms as predictors of response to neoadjuvant chemotherapy in estrogen positive breast tumors
      Dumont, A., Pannier, D., Ducoulombier, A., Tresch, E., Chen, J., Kramar, A., Révillion, F., Peyrat, J.P., Bonneterre, J. Springerplus (2015): 327
    • Nanofluidic Digital PCR for KRAS Mutation Detection and Quantification in Gastrointestinal Cancer
      Azuara, D., Ginesta, M.M., Gausachs, M., Rodriguez-Moranta, F., Fabregat, J., Busquets, J., Pelaez, N., Boadas, J., Galter, S., Moreno, V., Costa, J., Javier de Oca, J., Capellá, G. Clinical Chemistry (2012):
    • A validated miRNA profile predicts response to therapy in esophageal adenocarcinoma
      Skinner, H.D., Lee, J.H., Bhutani, M.S., Weston, B., Hofstetter, W., Komaki, R., Shiozaki, H., Wadhwa, R., Sudo, K., Elimova, E., Song, S., Ye, Y., Huang, M., Ajani, J., Wu, X. Cancer (2014):

  • Parentage ID

    • Broodstock History Strongly Influences Natural Spawning Success in Hatchery Steelhead (Oncorhynchus mykiss)
      Ford, M.J., Murdoch, A.R., Hughes, M.S. et al. PLoS One e0164801
    • Development and validation of a SNP panel for parentage assignment in rainbow trout
      Liu, S., Palti, Y., Gao, G., Rexroad III, C.E. Aquaculture (2016): 178–82
    • Stock composition and ocean spatial distribution inference from California recreational Chinook salmon fisheries using genetic stock identification
      Satterthwaite, W.H., Ciancio, J., Crandall, E. et al. Fisheries Research (2015): 166–78
    • Genetic heterogeneity and local adaptation of Asian seabass across Indonesian Archipelago revealed with gene-associated SNP markers
      Wang, A., Wan, Z.Y., Lim, H.S., Yue, G.H. Fisheries Research (2015): 205–11
    • Migrating adult steelhead utilize a thermal refuge during summer periods with high water temperatures
      Hess, M.A., Hess, J.E., Matala, A.P. et al. ICES Journal of Marine Science (2016): 2,616–24
    • What goes up does not come down: the stock composition and demographic characteristics of upstream migrating steelhead differ from post-spawn emigrating kelts
      Matala, A.P., Hatch, D.R., Everett, S. et al. ICES Journal of Marine Science (2016): 2,595–605
    • The Ghost of Outcrossing Past in Downy Brome, an Inbreeding Annual Grass
      Meyer, S.E., Ghimire, S., Decker, S., Merrill K.R., Coleman, C.E. Journal of Heredity (2013): 476–90
    • Shifting Thresholds: Rapid Evolution of Migratory Life Histories in Steelhead/Rainbow Trout, Oncorhynchus mykiss
      Phillis, C.C., Moore, J.W., Buoro, M. et al. Journal of Heredity (2016): 51–60
    • Estimating population size using single‐nucleotide polymorphism‐based pedigree data
      Spitzer, R., Norman, A.J., Schneider, M., Spong, G. Ecology and Evolution (2016): 3,174–84
    • Mitochondrial DNA and the Y chromosome suggest the settlement of Madagascar by Indonesian sea nomad populations
      Kusuma, P., Cox, M.P., Pierron, D., et al. BMC Genomics (2015): 191
    • Imprinting control regions (ICRs) are marked by mono-allelic bivalent chromatin when transcriptionally inactive
      Maupetit-Méhouas, S., Montibus, B., Nury, D., et al. Nucleic Acids Research (2016): 621–35
    • A single-nucleotide polymorphism-based approach for rapid and cost-effective genetic wolf monitoring in Europe based on noninvasively collected samples
      Kraus, R.H., vonHoldt, B., Cocchiararo, B. et al. Molecular Ecology Resources (2015): 295–305
    • Comparison of single nucleotide polymorphisms and microsatellites in non-invasive genetic monitoring of a wolf population
      Fabbri, E., Caniglia, R., Mucci, N., Randi, E. Archives of Biological Sciences (2011): 321–35
    • A SNP chip to detect introgression in wildcats allows accurate genotyping of single hairs
      Nussberger, B., Wandeler, P., Camenisch, G. European Journal of Wildlife Research (2014): 405–10
    • Using Next-Generation Sequencing to Assist a Conservation Hatchery: a Single-Nucleotide Polymorphism Panel for the Genetic Management of Endangered Delta Smelt
      Lew, R.M., Finger, A.J., Baerwald, M.R. et al. Transactions of the American Fisheries Society (2015): 767–79
    • Kinship analyses identify fish dispersal events on a temperate coastline
      Schunter, C., Pascual, M., Garza, J.C., et al. Proceedings of the Royal Society B: Biological Sciences (2014): doi: 10.1098/rspb.2014.0556
    • Patterns of hybridization among cutthroat trout and rainbow trout in northern Rocky Mountain streams
      McKelvey, K.S., Young, M.K., Wilcox, T.M., et al. Ecology and Evolution (2016): 688–706
    • Assessing patterns of hybridization between North Atlantic eels using diagnostic single-nucleotide polymorphisms
      Pujolar, J.M., Jacobsen, M.W., Als, T.D., Frydenberg, J., Magnussen, E., Jónsson, B., Jiang, X., Cheng, L., Bekkevold, D., Maes, G.E., Bernatchez, L., Hansen, M.M. Heredity (2014): 627–37
    • Novel heterozygous Bbeta (c.1311T>A) mutation (Fibrinogen St Kilda) associated with recurrent pregnancy loss
      Aung, N.N., Kennedy, H., Faed, J.M., Brennan S.O. Pathology (2015): 583–585
    • A validation of parentage-based tagging using hatchery steelhead in the Snake River basin
      Steele, C.A., Anderson, E.C., Ackerman, M.W., Hess, M.A., Campbell, N.R., Narum, S.R., Campbell, M.R. Canadian Journal of Fisheries and Aquatic Sciences (2013): 1,046–54
    • Chromosome rearrangements, recombination suppression, and limited segregation distortion in hybrids between Yellowstone cutthroat trout (Oncorhynchus clarkii bouvieri) and rainbow trout (O. mykiss)
      Ostberg, C.O., Hauser, L., Pritchard, V.L., Garza, J.C., Naish, K.A. BMC Genomics (2013): 570

  • Pharmacogenomics

    • G protein stoichiometry dictates biased agonism through distinct receptor-G protein partitioning
      Onfroy, L., Galandrin, S., Pontier, S.M. et al. Scientific Reports (2017): doi: 10.1038/s41598-017-07392-5
    • Pharmacogenetic meta-analysis of baseline risk factors, pharmacodynamic, efficacy and tolerability endpoints from two large global cardiovascular outcomes trials for darapladib
      Yeo, A., Li, L., Warren, L. et al. PLoS One (2017): doi: 10.1371/journal.pone.0182115
    • Extending and evaluating a warfarin dosing algorithim that includes CYP4F2 and pooled rare variants of CYP2C9
      Sagreiya, H., Berube, C., Wen, A., Ramakrishnan, R., Mir, A., Hamilton, A., Altman, R.B. Pharmacogenetics and Genomics (2010): 407
    • Pharmacogentic interaction analysis for the efficacy of systemic treatment in metastatic colorectal cancer
      Pander, J., Wessels, J.A.M., Gelderblom, H., van der Straaten, T., Punt, C.J.A., Guchelaar, H.-J. Annals of Oncology (2011): mdq572
    • Changes in gene expression in synovial tissue from refractory rheumatoid arthritis patients treated with rituximab
      Hogan, V., Holweg, C., Kummerfeld, S., Teng, Y.K.O., Townsend, M.T., van Laar, J.M. Annals of the Rheumatic Diseases (2011): A16

  • Population Screening

    • Single Cell Gene Expression Profiling of Skeletal Muscle-Derived Cells
      Gatto, S., Puri, P.L., Malecova, B. Methods in Molecular Biology (2017): 191-219
    • Insights on the drivers of genetic divergence in the European anchovy
      Catanese, G., Watteaux, R., Montes, I. et al. Scientific Reports (2017): 4,180
    • Atribacteria from the Subseafloor Sedimentary Biosphere Disperse to the Hydrosphere through Submarine Mud Volcanoes
      Hoshino, T., Toki, T., Ijiri, A. et al. Frontiers in Microbiology (2017): 1,135
    • Genome-Wide Association Study Reveals Four Loci for Lipid Ratios in the Korean Population and the Constitutional Subgroup
      Kim, T., Park, A.Y., Baek, Y. et al. PLoS One (2017): e0168137
    • Genetic diversity and connectivity within Mytilus spp. in the subarctic and Arctic
      Mathiesen, S.S., Thyrring, J., Hemmer-Hansen, J. et al. Evolutionary Applications (2017): 39–55
    • Ancestry and adaptive evolution of anadromous, resident, and adfluvial rainbow trout (Oncorhynchus mykiss) in the San Francisco bay area: application of adaptive genomic variation to conservation in a highly impacted landscape
      Leitwein, M., Garza, J.C., Pearse, D.E. Evolutionary Applications (2017): 56–67
    • Development of single-nucleotide polymorphism markers for Bromus tectorum (Poaceae) from a partially sequenced transcriptome
      Merrill, K.R., Coleman, C.E., Meyer, S.E. et al. Applications in Plant Sciences (2016): 1,600,068
    • Genetic variability in ABCB1, occupational pesticide exposure, and Parkinson's disease
      Narayan, S., Sinsheimer, J.S., Paul, K.C. et al. Environmental Research (2015): 98–106
    • Planktonic Euryarchaeota are a significant source of archaeal tetraether lipids in the ocean
      Lincoln, S.A., Wai, B., Eppley, J.M. et al. Proceedings of the National Academy of Sciences (2014): 9,858–63
    • Genetic population study of Y-chromosome markers in Benin and Ivory Coast ethnic groups
      Fortes-Lima, C., Brucato, N., Croze, M. et al. Forensic Science International: Genetics (2015): 232–7
    • Gene-associated markers can assign origin in a weakly structured fish, Atlantic herring
      Bekkevold, D., Helyar, S.J., Limborg, M.T. et al. ICES Journal of Marine Science (2015): 1,790–801
    • Diverse human extracellular RNAs are widely detected in human plasma
      Freedman, J.E., Gerstein, M., Mick, E. et al. Nature Communications (2016): 11,106
    • Creatine supplementation prevents the accumulation of fat in the livers of rats fed a high-fat diet
      Deminice, R., da Silva, R.P., Lamarre, S.G. et al. The Journal of Nutrition (2011): 1799–804
    • Rapid evolution of genetic and phenotypic divergence in Atlantic salmon following the colonisation of two new branches of a watercourse
      Jensen, A.J., Hansen, L.P., Johnsen, B.O. et al. Genetics Selection Evolution (2017): 22
    • Genetic Polymorphism (rs329498) in the Pellino-1 Gene as Possible Predisposal Factor for Systemic Lupus Erythematosus in a Chinese Population.
      Ni, J., Liu, J., Leng, R.X., Pan, H.F., Ye, D.Q. Immunological Investigations (2016): 181–90
    • Transgenerational epigenetic programming via sperm microRNA recapitulates effects of paternal stress
      Rodgers, A.B., Morgan, C.P., Leu, N.A., Bale, T.L. Proceedings of the National Academy of Sciences of the United States of America (2015): 13,699–704
    • DNMT3A mutations occur early or late in patients with myeloproliferative neoplasms and mutation order influences phenotype
      Nangalia, J., Nice, F.L., Wedge, D.C., et al. Haematologica (2015): e438–42
    • Integrated genome-wide analysis of expression quantitative trait loci aids interpretation of genomic association studies
      Joehanes, R., Zhang, X., Huan, T. et al. Genome Biology (2017): 16
    • The Relationship of Deiodinase 1 Genotype and Thyroid Function to Lifetime History of Major Depression in Three Independent Populations
      Philibert, R.A., Beach, S.R.H., Gunter, T.D., et al. American Journal of Medical Genetics (2011): 593–9
    • Rare complete knockouts in humans: population distribution and significant role in autism spectrum disorders
      Lim, E.T., Raychaudhuri, S., Sanders, S.J., et al. Neuron (2013): 235–42
    • Paternal Benzo[a]pyrene Exposure Affects Gene Expression in the Early Developing Mouse Embryo
      Brevik, A., Lindeman, B., Rusnakova, V., et al. Toxicological Studies (2012): 157–65
    • Metabolomic and Gene Expression Profiles Exhibit Modular Genetic and Dietary Structure Linking Metabolic Syndrome Phenotypes in Drosophila
      Williams, S., Dew-Budd, K., Davis, K., et al. G3: Genes|Genomes|Genetics (2015): 2,817–29
    • Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins
      Huelga, S.C., Vu, A.Q., Arnold, J.D., et al. Cell Reports (2012): 167–78
    • GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown root systems
      Rellán-Álvarez, R., Lobert, G., Lindner, H., et al. eLife (2015): e07597
    • Global Transcriptional Analysis of Dehydrated Salmonella enterica Serovar Typhimurium
      Gruzdev, N., McClelland, M., Porwollik, S., et al. Applied and Environmental Microbiology (2012): 7,866–75
    • Genome-Wide Single-Cell Analysis of Recombination Activity and de novo Mutation Rates in Human Sperm
      Wang, J., Fan, H.C., Behr, B.,Quake, S.R. Cell (2012): 402–12
    • Gene Regulatory Variation Mediates Flowering Responses to Vernalization along an Altitudinal Gradient in Arabidopsis
      Suter, L., Rüegg, M., Zemp, N., et al. Plant Physiology (2014): 1,928–42
    • Dysregulated hepatic expression of glucose transporters in chronic disease: contribution of semicarbazide-sensitive amine oxidase to hepatic glucose uptake
      Karim, S., Liaskou, E., Fear, J., et al. American Journal of Physiology - Gastrointestinal and Liver Physiology (2014): G1,180–90
    • Yeast Tolerance to Various Stresses Relies on the Trehalose-6P Synthase (Tps1) Protein, Not on Trehalose*
      Petitjean, M., Teste, M.A., François, J.M., Parrou, J.L. Journal of Biological Chemistry (2015): 16,177–90
    • A high-throughput detection method for invasive fruit fly (Diptera: Tephritidae) species based on microfluidic dynamic array
      Jiang, F., Fu, W., Clarke, A.R. et al. Molecular Ecology Resources (2016): 1,378–88
    • Liver transcriptome response to hyperthermic stress in three distinct chicken lines
      Lan, X., Hsieh, J.C.F., Schmidt, C.J. et al. BMC Genomics (2016): 955
    • Han Chinese polycystic ovary syndrome risk variants in women of European ancestry: relationship to FSH levels and glucose tolerance
      Saxena, R., Georgopoulos, N.A., Braaten, T.J. et al. Human Reproduction (2015): 1,454–9
    • Ultrahigh-Density Linkage Map for Cultivated Cucumber (Cucumis sativus L.) Using a Single-Nucleotide Polymorphism Genotyping Array
      Rubinstein, M., Katzenellenbogen, M., Eshed, R. et al. PLoS One (2015): e0124101
    • The heritability of metabolite concentrations in stored human red blood cells
      van 't Erve, T.J., Wagner, B.A., Martin, S.M. et al. Transfusion (2014): 2,055–63
    • The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color
      Motamayor, J.C., Mockaitis, K., Schmutz, J. et al. Genome Biology (2014): r53
    • The Concentration of Glutathione in Human Erythrocytes is a Heritable Trait
      van 't Erve, T.J., Wagner, B.A., Ryckman, K.K. et al. Free Radical Biology and Medicine (2013): 742–9
    • Mango (Mangifera indica L.) germplasm diversity based on single nucleotide polymorphisms derived from the transcriptome
      Sherman, A., Rubinstein, M., Eshed, R., et al. BMC Plant Biology (2015): 277
    • Genes predict long distance migration and large body size in a migratory fish, Pacific lamprey
      Hess, J.E., Caudill, C.C., Keefer, M.L., et al. Evolutionary Applications (2014): 21,192–208
    • Genetic Analysis of Trout (Oncorhynchus mykiss) in Southern California Coastal Rivers and Streams
      Jacobson, S., Marshall, J., Dalrymple, D., et al. California Department of Fish and Wildlife (2014): 675–689
    • Genetic Structure of Pacific Trout at the Extreme Southern End of Their Native Range
      Abadía-Cardoso, A., Garza, J.C., Mayden, R.L., et al. PLoS One (2015): e0141775
    • Genomic analysis of the native European Solanum species, S. dulcamara
      D'Agostino, N., Golas, T., van de Geest, H., et al. BMC Genomics (2013): 356
    • Geo-Referenced, Abundance Calibrated Ocean Distribution of Chinook Salmon (Oncorhynchus tshawytscha) Stocks across the West Coast of North America
      Bellinger, M.R., Banks, M.A., Bates, S.J., et al. PLoS One (2015): e0131276
    • Single-Nucleotide Polymorphism Markers from De-Novo Assembly of the Pomegranate Transcriptome Reveal Germplasm Genetic Diversity
      Ophir, R., Sherman, A., Rubinstein, M., et al. PLoS One (2014): e88998
    • Rapid parallel evolution of standing variation in a single, complex, genomic region is associated with life history in steelhead/rainbow trout
      Pearse, D.E., Miller, M.R., Abadía-Cardoso, A. Proceedings of the Royal Society B: Biological Sciences (2014): 1,783
    • Development of a Chinook Salmon Sex Identification SNP Assay Based on the Growth Hormone Pseudogene
      Von Bargen, J., Smith, C.T., Rueth, J. Journal of Fish and Wildlife Management (2015): 213–9
    • Accuracy of Assignment of Atlantic Salmon (Salmo salar L.) to Rivers and Regions in Scotland and Northeast England Based on Single Nucleotide Polymorphism (SNP) Markers
      Gilbey, J., Cauweiler, E., Coulson, M.W. et al. PLoS One (2016): e0164327
    • A Genomewide Association Study of Early Spontaneous Preterm Delivery
      Zhang, H., Baldwin, D.A., Bukowski, R.K., Parry, S., Xu, Y., Song, C., Andrews, W.W., Saade, G.R., Esplin, M.S., Sadovsky, Y., Reddy, U.M., Ilekis, J., Varner, M., Biggio Jr, J.R. Genetic Epidemiology (2015): 217–26
    • Secondary contact and changes in coastal habitat availability influence the nonequilibrium population structure of a salmonid (Oncorhynchus keta)
      Petrou, E.L., Hauser, L., Waples, R.S., Seeb, J.E., Templin, W.D., Gomez-Uchida, D., Seeb, L.W. Molecular Ecology (2013): 5,848–60
    • Antagonist Xist and Tsix co-transcription during mouse oogenesis and maternal Xist expression during pre-implantation development calls into question the nature of the maternal imprint on the X chromosome
      Deuve, J.L., Bonnet-Garnier, A., Beaujean, N., Avner, P., Morey, C. Epigenetics (2015): 931–42
    • Whole-genome molecular haplotyping of single cells
      Fan, H.C., Wang, J., Potanina, A., Quake, S.R. Nature Biotechnology (2011): 51–7
    • Population-genetic nature of copy number variations in the human genome
      Kato, M., Kawaguchi, T., Ishikawa, S., Umeda, T., Nakamichi, R., Shapero, M.H., Jones, K.W., Nakamura, Y., Aburatani, H., Tsunoda, T. Human Molecular Genetics (2010): 761-73
    • De Novo SNP Discovery in the Scandinavian Brown Bear (Ursus arctos)
      Norman, A.J., Street, N.R., Spong, G. PLoS One (2013): e81012
    • Depauperate genetic variability detected in the American and European bison using genomic techniques
      Pertoldi, C., Tokarska, M., Wójcik, J.M., Demontis, D., Loeschcke, V., Gregersen, V.R., Coltman, D., Wilson, G.A., Randi, E., Hansen, M.M., Bendixen, C. Biology Direct (2009): 48
    • A low-density SNP array for analyzing differential selection in freshwater and marine populations of threespine stickleback (Gasterosteus aculeatus)
      Ferchaud, A.L., Pedersen, S.H., Bekkevold, D., Jian, J., Niu, Y., Hansen, M.M. BMC Genomics (2014): 867
    • Low mitochondrial DNA content associates with familial longevity: the Leiden Longevity Study
      van Leeuwen, N., Beekman, M., Deelen, J., van den Akker, E.B., de Craen, A.J.M., Slagboom, P.E., 't Hart, L.M. Age (2014): 9,629
    • A Bulk Segregant Gene Expression Analysis of a Peach Population Reveals Components of the Underlying Mechanism of the Fruit Cold Response
      Pons, C., Marti, C., Forment, J., Crisosto, C.H., Dandekar, A.M., Granell, A. PLoS One (2014): e0090706
    • Coevolutionary patterning of teeth and taste buds
      Bloomquist, R.F., Parnell, N.F., Phillips, K.A., Fowler, T.E., Yu, T.Y., Sharpe, P.T., Streelman, J.T. Proceedings of the National Academy of Sciences of the United States of America (2015): E5954-62
    • Associations of genetic variations in EYA4, GRHL2 and DFNA5 with noise-induced hearing loss in Chinese population: a case- control study
      Zhang, X., Zhang, L., Yang, Z., Yang, L., Wang, X., Jiang, C., Wang, Q., Xia, Y., Chen, Y., Wu, O., Zhu, Y. Environmental Health (2015): 77
    • A highly sensitive and specific method for the screening detection of genetically modified organisms based on digital PCR without pretreatment
      Fu, W., Zhu, P., Wang, C., Huang, K., Du, Z., Tian, W., Wang, Q., Wang, H., Xu, W., Zhu, S. Scientific Reports (2015): 12,715
    • A hemocyte gene expression signature correlated with predictive capacity of oysters to survive Vibrio infections
      Rosa, R.D., de Lorgeril, J., Tailliez, P., Bruno, R., Piquemal, D., Bachère, E. BMC Genomics (2012): 252
    • SNP genotyping by the 5'-nuclease reaction: advances in high-throughput genotyping with nonmodel organisms
      Seeb, J.E., Pascal, C.E., Ramakrishnan, R., Seeb, L.W. Methods in Molecular Biology (2008): 277–92
    • Non-invasive imaging of human embryos before embryonic genomic activation predicts development to the blastocyst stage
      Wong, C.C., Loewke, K.E., Bossert, N.L., Behr, B., De Jonge, C.J., Baer, T.M., Reijo Pera, R.A. Nature Biotechnology (2010): 1115–21
    • Rheumatoid arthritis - treatment 180. Utility of Body Weight Classified Low-Dose Leflunomide in Japanese Rheumatoid Arthritis
      Nishikawa, M., Owaki, H., Fuji, T. Rheumatology (2011): iii111–iii129
    • Evaluating quantitative methods for measuring plasmid copy numbers in single cells
      Tal, S., Paulsson, J. Plasmid (2012): 167–73

  • Stem Cell

    • Differential regulation of effector and regulatory T cell function by Blimp1
      Bankoti, R., Ogawa, C., Nguyen, T. et al. Scientific Reports (2017): doi: 10.1038/s41598-017-12171-3
    • Adult human mesenchymal stem cell differentiation at the cell population and single-cell levels under alternating electric current
      Wechsler, M.E., Hermann, B.P., Bizios, R. Tissue Engineering Part C: Methods (2015): 155–64
    • Erythropoietin guides multipotent hematopoietic progenitor cells toward an erythroid fate
      Grover, A., Mancini, E., Moore, S. et al. Journal of Experimental Medicine (2014): 181–8
    • Human germ cell formation in xenotransplants of induced pluripotent stem cells carrying X chromosome aneuploidies
      Dominguez, A.A., Chiang, H.R., Sukhwani, M. et al. Scientific Reports (2014): 6,432
    • H2A O-GlcNAcylation at serine 40 functions genomic protection in association with acetylated H2AZ or γH2AX
      Hayakawa, K., Hirosawa, M., Tani, R. et al. Epigenetics and Chromatin (2017): doi: 10.1186/s13072-017-0157-x
    • Single-cell RNA sequencing reveals molecular and functional platelet bias of aged haematopoietic stem cells
      Grover, A., Sanjuan-Pla, A., Thongjuea, S. et al. Nature Communications (2016): 11,075
    • Direct reprogramming of human fibroblasts toward a cardiomyocyte-like state
      Fu, J.D., Stone, N.R., Liu, L. et al. Stem Cell Reports (2013): 235–47
    • Reinforcement of STAT3 activity reprogrammes human embryonic stem cells to naive-like pluripotency
      Chen, H., Aksoy, I., Gonnot, F. et al. Nature Communications (2015): 7,095
    • Deconstructing transcriptional heterogeneity in pluripotent stem cells
      Kumar, R.M., Cahan, P., Shalek, A.K. et al. Nature (2014): 56–61
    • Clonal dynamics reveal two distinct populations of basal cells in slow-turnover airway epithelium
      Watson, J.K., Rulands, S., Wilkinson, A.C. et al. Cell Reports (2015): 90–101
    • The transcription factor Mesp1 interacts with cAMP-responsive element binding protein 1 (Creb1) and coactivates Ets variant 2 (Etv2) gene expression
      Shi, X., Zirbes, K.M., Rasmussen, T.L. et al. Journal of Biological Chemistry (2015): 9,614–25
    • Alloimmune Responses of Humanized Mice to Human Pluripotent Stem Cell Therapeutics
      Kooreman, N.G., de Almeida, P.E., Stack, J.P. et al. Cell Reports (2017): 1,978-90
    • Reconstructing human pancreatic differentiation by mapping specific cell populations during development
      Raymond, C., Glaser, N., Berthault, C. et al. eLife (2017): doi: 10.7554/eLife.27564
    • Aging effects on intestinal homeostasis associated with expansion and dysfunction of intestinal epithelial stem cells
      Moorefield, E.C., Andres, S.F., Blue, R.E. et al. Aging (2017): 1,896-915
    • Reconstructing Lineage Hierarchies of Mouse Uterus Epithelial Development Using Single-Cell Analysis
      Wu, B., An, C., Li, Y. et al. Stem Cell Reports (2017): 381-96
    • Tracking the embryonic stem cell transition from ground state pluripotency
      Kalkan, T., Olova, N., Roode, M. et al. Development (2017): 1,221–34
    • Stat5 deficiency decreases transcriptional heterogeneity and supports emergence of hematopoietic sub-populations
      Wang, Z., Bunting, K.D. Oncotarget (2017): 22,477–82
    • Transcriptional Networks in Single Perivascular Cells Sorted from Human Adipose Tissue Reveal a Hierarchy of Mesenchymal Stem Cells
      Hardy, W.R., Moldovan, N.I., Livak, K.J. et al. Stem Cells (2017): 1,273–89
    • Clonal reversal of ageing-associated stem cell lineage bias via a pluripotent intermediate
      Wahlestedt, M., Erlandsson, E., Kristiansen, T. et al. Nature Communications (2017): 14,533
    • Single-Cell-Based Analysis Highlights a Surge in Cell-to-Cell Molecular Variability Preceding Irreversible Commitment in a Differentiation Process
      Richard, A., Boullu, L., Herbach, U. et al. PLoS Biology (2016): e1002585
    • Single-cell analysis reveals a nestin+ tendon stem/progenitor cell population with strong tenogenic potentiality
      Yin, Z., Hu, J.J., Yang, L. et al. Science Advances (2016): e1600874
    • Nat1 promotes translation of specific proteins that induce differentiation of mouse embryonic stem cells
      Sugiyama, H., Takahashi, K., Yamamoto, T. et al. Proceedings of the National Academy of Sciences of the United States of America (2017): 340–5
    • Human Non-Hematopoietic CD271^pos/CD140a^low/neg Bone Marrow Stroma Cells Fulfill Stringent Stem Cell Criteria in Serial Transplantations
      Ghazanfari, R., Li, H., Zacharaki, D. et al. Stem Cells and Development (2016): 1,652–8
    • Polycomb enables primitive endoderm lineage priming in embryonic stem cells
      Illingworth, R.S., Hölzenspies, J.J., Roske, F.V. et al. eLife (2016): e14926
    • mTORC1 Inhibition Corrects Neurodevelopmental and Synaptic Alterations in a Human Stem Cell Model of Tuberous Sclerosis
      Costa, V.,. Aigner, S., Vukcevic, M. et al. Cell Reports (2016): 86–95
    • A chemically defined culture medium containing Rho kinase inhibitor Y-27632 for the fabrication of stratified squamous epithelial cell grafts
      Aslanova, A., Takagi, R., Yamato, M. et al. Biochemical and Biophysical Research Communications (2015): 123–9
    • The transcription repressors Bach2 and Bach1 promote B cell development by repressing the myeloid program
      Itoh-Nakadai, A., Hikota, R., Muto, A. et al. Nature Immunology (2014): 1,171–80
    • Platelet-biased stem cells reside at the apex of the haematopoietic stem-cell hierarchy
      Sanjuan-Pla, A., Macaulay, I.C., Jensen, C.T. et al. Nature (2013): 232–6
    • Lymphomyeloid contribution of an immune-restricted progenitor emerging prior to definitive hematopoietic stem cells
      Böiers, C., Carrelha, J., Lutteropp, M. et al. Cell Stem Cell (2013): 535–48
    • Reprogramming committed murine blood cells to induced hematopoietic stem cells with defined factors
      Riddell, J., Gazit, R., Garrison, B.S. et al. Cell (2014): 549–64
    • CD41 marks the initial myelo-erythroid lineage specification in adult mouse hematopoiesis: redefinition of murine common myeloid progenitor
      Miyawaki, K., Arinobu, Y., Iwasaki, H. et al. Stem Cells (2015): 976-8–7
    • Unipotent Megakaryopoietic Pathway Bridging Hematopoietic Stem Cells and Mature Megakaryocytes
      Nishikii, H., Kanazawa, Y., Umemoto, T. et al. Stem Cells (2015): 2,196–207
    • β2-Microglobulin is an appropriate reference gene for RT-PCR-based gene expression analysis of hematopoietic stem cells
      Matsuzaki, Y., Umemoto, T., Tanaka, Y. et al. Regenerative Therapy (2015): 91–7
    • Intestinal label-retaining cells are secretory precursors expressing Lgr5
      Buczacki, S.J., Zecchini, H.I., Nicholson, A.M. et al. Nature (2013): 65–9
    • Lgr5 expressing cells are sufficient and necessary for postnatal mammary gland organogenesis
      Plaks, V., Brenot, A., Lawson, D.A. et al. Cell Reports (2013): 70–8
    • Spontaneous reactivation of clusters of X-linked genes is associated with the plasticity of X-inactivation in mouse trophoblast stem cells
      Dubois, A., Deuve, J.L., Navarro, P. et al. Stem Cells (2014): 377–90
    • Single-cell profiling of epigenetic modifiers identifies PRDM14 as an inducer of cell fate in the mammalian embryo
      Burton, A., Muller, J., Tu, S. et al. Cell Reports (2013): 687–701
    • Induction of a human pluripotent state with distinct regulatory circuitry that resembles preimplantation epiblast
      Chan, Y.S., Göke, J., Ng, J.H. et al. Cell Stem Cell (2013): 663–75
    • Efficient endoderm induction from human pluripotent stem cells by logically directing signals controlling lineage bifurcations
      Loh, K.M., Ang, L.T., Zhang, J. et al. Cell Stem Cell (2014): 237–52
    • Determining cell division symmetry through the dissection of dividing cells using single-cell expression analysis
      Jasnos, L., Sawado, T. Nature Protocols (2014): 505–16
    • The effect of mesenchymal stromal cell sheets on the inflammatory stage of flexor tendon healing
      Shen, H., Kormpakis, I., Havlioglu, N. et al. Stem Cell Research and Therapy (2016): 144
    • A Panel of Embryonic Stem Cell Lines Reveals the Variety and Dynamic of Pluripotent States in Rabbits
      Osteil, P., Moulin, A., Santamaria, C. et al. Stem Cell Reports (2016): 383–98
    • Progenitor Cell Dysfunctions Underlie Some Diabetic Complications
      Rodrigues, M., Wong, V.W., Rennert, R.C., et al. American Journal of Pathology (2015): 2,607–18
    • Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis
      Moignard, V., Macaulay, I.C., Swiers, G. et al. Nature Cell Biology (2013): 363–72
    • Evaluating the Effect of Cell Culture on Gene Expression in Primary Tissue Samples Using Microfluidic-Based Single Cell Transcriptional Analysis
      Januszyk, M., Rennert, R.C., Sorkin, M., et al. Microarrays (2015): 540–50
    • SOX9 Maintains Reserve Stem Cells and Preserves Radioresistance in Mouse Small Intestine
      Roche, K.C., Gracz, A.D., Liu, X.F. et al Gastroenterology (2015): 1,553–63
    • Global Splicing Pattern Reversion during Somatic Cell Reprogramming
      Ohta, S., Nishida, E., Yamanaka, S., Yamamoto, T. Cell Reports (2013): 357–66
    • Hepatocyte fate upon TGF-β challenge is determined by the matrix environment
      Meyer, C., Liebe, R., Breitkopf-Heinlein, K. et al. Differentiation (2015): 105–16
    • The ACVR1 R206H mutation found in fibrodysplasia ossificans progressiva increases human induced pluripotent stem cell-derived endothelial cell formation and collagen production through BMP-mediated SMAD1/5/8 signaling
      Barruet, E., Morales, B.M., Lwin, W. et al. Stem Cell Research & Therapy (2016): 115
    • Integrated live imaging and molecular profiling of embryoid bodies reveals a synchronized progression of early differentiation
      Boxman, J., Sagy, N., Achanta, S., Vadigepalli, R., Nachmanb, I. Scientific Reports (2016): 31,623
    • High fat diet enhances stemness and tumorigenicity of intestinal progenitors
      Beyaz, S., Mana, M.D., Roper, J. et al. Nature (2016): 53–58
    • Single-Cell Transcript Profiles Reveal Multilineage Priming in Early Progenitors Derived from Lgr5+ Intestinal Stem Cells
      Kim, T.H., Saadatpour, A., Guo, G. et al. Cell Reports (2016): 2,053–60
    • Spatiotemporal Reconstruction of the Human Blastocyst by Single-Cell Gene-Expression Analysis Informs Induction of Naive Pluripotency
      Durruthy-Durruthy, J., Wossidlo, M., Pai, S. et al. Developmental Cell (2016): 100–15
    • Supplementation with small-extracellular vesicles from ovarian follicular fluid during in vitro production modulates bovine embryo development
      da Silveira, J.C., Andrade, G.M., del Collado, M. et al. PLoS One (2017): e0179451
    • Human Neuropsychiatric Disease Modeling Using Conditional Deletion Reveals Synaptic Transmission Defects Caused By Heterozygous Mutations in NRXN1
      Pak, C.H., Danko, T., Zhang, Y. et al. Cell Stem Cell (2015): 316–28
    • Cells with surface expression of CD133highCD71low are enriched for tripotent colony-forming progenitor cells in the adult murine pancreas
      Jin, L., Gao, D., Feng, T. et al. Stem Cell Research (2016): 40–53
    • Direct Induction and Functional Maturation of Forebrain GABAergic Neurons from Human Pluripotent Stem Cells
      Sun, A.X., Yuan, Q., Tan, S. et al. Cell Reports (2016): 1,942–53
    • Single-Cell Expression Analyses during Cellular Reprogramming Reveal an Early Stochastic and a Late Hierarchic Phase
      Buganim, Y., Faddah, D.A., Cheng, A.W. et al. Cell (2012): 1,209–22
    • Isolation and characterization of trophoblast-derived stem-like cells from peri-implantation porcine embryos
      Suasnavas, E.A., Heywood, S., Ward, A. et al. Animal Reproduction Science (2015): 128–141
    • Genetics, Diet, and Season Are Associated with Serum 25-Hydroxycholecalciferol Concentration in a Yup'ik Study Population from Southwestern Alaska
      Fohner, A.E., Wang, Z., Yracheta, J. et al. The Journal of Nutrition (2016): 318–25
    • Comparative long-term effects of interferon α and hydroxyurea on human hematopoietic progenitor cells
      King, K.Y., Matatall, K.A., Shen, C.C. et al. Experimental Hematology (2015): 912–8
    • A dynamic niche provides Kit ligand in a stage-specific manner to the earliest thymocyte progenitors
      Buono, M., Facchini, R., Matsuoka, S. et al. Nature Cell Biology (2016): 157–67
    • Dok1 and Dok2 Proteins Regulate Cell Cycle in Hematopoietic Stem and Progenitor Cells
      Coppin, E., De Grandis, M., Pandolfi, P.P. et al. The Journal of Immunology (2016): 4,110–21
    • A Systematic Comparison of the Impact of Inflammatory Signaling on Absorption, Distribution, Metabolism, and Excretion Gene Expression and Activity in Primary Human Hepatocytes and HepaRG Cells
      Klein, M., Thomas, M., Hofmann, U. et al. Drug Metabolism and Disposition (2015): 273–83
    • Stochastic NANOG fluctuations allow mouse embryonic stem cells to explore pluripotency
      Abranches, E., Guedes, A.M., Moravec, M. et al. Development (2014): 2,770–9
    • Wnt/β-catenin and FGF signalling direct the specification and maintenance of a neuromesodermal axial progenitor in ensembles of mouse embryonic stem cells
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      Spitzer, T.L.B., Rojas, A., Zelenko, Z., Aghajanova, L., Erikson, D.W., Barragan, F., Meyer, M., Tamaresis, J.S., Hamilton, A.E., Irwin, J.C., Giudice, L.C. Biology of Reproduction (2012): 58
    • Paracrine Action of Mesenchymal Stem Cells Revealed by Single Cell Gene Profiling in Infarcted Murine Hearts
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      Guo, G., Luc, S., Marco, E., Lin, T.W., Peng, C., Kerenyi, M.A., Beyaz, S., Kim, W., Xu, J., Das, P.P., Neff, T., Zou, K., Yuan, G.C., Orkin, S.H. Cell Stem Cell (2013):
    • Lineage-specific regulation of imprinted X inactivation in extraembryonic endoderm stem cells
      Merzouk, S., Deuve, J.L., Dubois, A., Navarro, P., Avner, P., Morey, C. Epigenetics and Chromatin (2014): 11
    • Identifying Division Symmetry of Mouse Embryonic Stem Cells: Negative Impact of DNA Methyltransferases on Symmetric Self-Renewal
      Jasnos, L., Aksoy, F.B., Hersi, H.M., Wantuch, S., Sawado, T. Stem Cell Reports (2013): 360-9
    • Histone demethylase Lsd1 represses hematopoietic stem and progenitor cell signatures during blood cell maturation
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    • Generation of Human Induced Pluripotent Stem Cells Using Epigenetic Regulators Reveals a Germ Cell-Like Identity in Partially Reprogrammed Colonies
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    • Dazl functions in maintenance of pluripotency and genetic and epigenetic programs of differentiation in mouse primordial germ cells in vivo and in vitro
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    • High-throughput microfluidic single-cell RT-qPCR
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    • MicroRNA-mediated conversion of human fibrolasts to neurons
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    • Self Renewing Hematopoietic Stem Cell Is the Primary Target in Pathogenesis in Human Chronic Lymphocytic Leukemia
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    • Direct Lineage Conversion of Terminally Differentiated Hepatocytes to Function Neurons
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    • Gata3 regulates trophoblast development downstream of Tead4 and in parallel to Cdx2
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    • Cadherin-Based Adhesion Is a Potential Target for Niche Manipulation to Protect Hemtopoietic Stem Cells in Adult Bone Marrow
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    • Tracheal Basal Cells: A Facultative Progenitor Cell Pool
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    • Human Primordial Germ Cell Formation Is Diminished by Exposure to Environmental Toxicants Acting through the AHR Signaling Pathway
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    • Knockdown of N-cadherin suppresses the long-term engraftment of hemtopoietic stem cells
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    • Endothelial protein C receptor-expressing hematopoietic stem reside in the perisinusoidal niche in fetal liver
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    • Isolation and characterization of endosteal niche cell populations that regulate hematopoietic stem cells
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    • Distinguishing Human Cell Types Based on Housekeeping Gene Signatures
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    • Gene expression profiling of liver cancer stem cells by RNA-sequencing
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  • Other

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    • Comparison of Macitentan and Bosentan on Right Ventricular Remodeling in a Rat Model of Non-vasoreactive Pulmonary Hypertension
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    • Integrated Blood Barcode Chips
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    • Gene Expression Profiling Identifies Molecular Pathways Associated with Collagen VI Deficiency and Provides Novel Therapeutic Targets
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    • Design and Optimization of Coin-Shaped Microreactor Chips for PET Radiopharmaceutical Synthesis
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    • Defining the gene repertoire and spatiotemporal expression profiles of adhesion G protein-coupled receptors in zebrafish
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    • Coordinated Dynamic Gene Expression Changes in the Central Nucleus of the Amygdala During Alcohol Withdrawal
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    • Constraint and divergence of global gene expression in the mammalian embryo
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