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 April, 2018

  Number of cumulative papers as of April, 2018

• 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): doi: 10.1371/journal.pone.0188051
  • 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

    • 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): doi: 10.1186/s12951-017-0312-3
    • 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
    • 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): doi: 10.3389/fpls.2017.01606
    • 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): doi: 10.3389/fpls.2017.01393
    • 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): doi: 10.1186/s12864-017-3992-z
    • 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): doi: 10.1038/s41598-017-06511-6
    • 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
    • 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): doi: 10.1186/s40364-017-0104-9
    • Cystatin D (CST5): An ultra-early inflammatory biomarker of traumatic brain injury
      Scientific Reports (2017): doi: 10.1038/s41598-017-04722-5
    • 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
    • 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): doi:10.1007/s00393-016-0169-0
    • 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
      Lorthongpanich, C., Doris, T.P., Limviphuvadh, V., Knowles, B.B., Solter, D. Development (2012): 3,722–31
    • Porcn-dependent Wnt signaling is not required prior to mouse gastrulation
      Biechele, S., Cockburn, K., Lanner, F., Cox, B.J., Rossant, L. Development (2013): 2,961–71
    • Sperm-borne miRNAs and endo-siRNAs are important for fertilization and preimplantation embryonic development
      Yuan, S., Schuster, A., Tang, C. et al. Development (2016): 635–47
    • Targeted ablation of periostin-expressing activated fibroblasts prevents adverse cardiac remodeling in mice
      Kaur, H., Takefuji, M., Ngai, C.Y. et al. Circulation Research (2016): 1,906–17
    • Role played by the SP4 gene in schizophrenia and major depressive disorder in the Han Chinese population
      Chen, J., He, K., Wang, Q. et al. British Journal of Psychiatry (2016): 441–5
    • Integration of liver gene co-expression networks and eGWAs analyses highlighted candidate regulators implicated in lipid metabolism in pigs
      Ballester, M., Ramayo-Caldas, Y., Revilla, M. et al. Scientific Reports (2017): 46,539
    • 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
    • p53 Pulses Diversify Target Gene Expression Dynamics in an mRNA Half-Life-Dependent Manner and Delineate Co-regulated Target Gene Subnetworks
      Porter, J.R., Fisher, B.E., Batchelor, E. Cell Systems (2016): 272–282
    • 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
    • Variable Activation of the DNA Damage Response Pathways in Patients Undergoing SPECT Myocardial Perfusion Imaging
      Lee, W.H., Nguyen, P., Hu, S. et al. Circulation: Cardiovascular Imaging (2015): e002851
    • Successful validation of genomic biomarkers for human immunotoxicity in Jurkat T cells in vitro
      Schmeits, P.C., Shao, J., van der Krieken, D.A. et al. Journal of Applied Toxicology (2015): 831–41
    • Development of a multitissue microfluidic array for assessing changes in gene expression associated with channel catfish appetite, growth, metabolism, and intestinal health
      Schroeter, J.C., Peterson, B.C., Small, B.C. Aquaculture (2016): 213–21
    • Next-Generation Sequencing-Assisted DNA-Based Digital PCR for a Personalized Approach to the Detection and Quantification of Residual Disease in Chronic Myeloid Leukemia Patients
      Alikian, M., Ellery, P., Forbes, M. et al. The Journal of Molecular Diagnostics (2016): 176–89
    • Provision of Amniotic Fluid During Parenteral Nutrition Increases Weight Gain With Limited Effects on Gut Structure, Function, Immunity, and Microbiology in Newborn Preterm Pigs
      Østergaard, M.V., Shen, R.L., Støy, A.C.F. et al. Journal of Parenteral and Enteral Nutrition (2016): 552–66
    • Changes in Transcriptome-Wide Gene Expression of Anterior Cruciate Ligament Tears Based on Time From Injury
      Brophy, R.H., Tycksen, E.D., Sandell, L.J. et al. American Journal of Sports Medicine (2016): 2,064–75
    • Single-cell RNA-Seq resolves cellular complexity in sensory organs from the neonatal inner ear
      Burns, J.C., Kelly, M.C., Hoa, M. et al. Nature Communications (2015): 8,557
    • Transcriptome analysis reveals potential mechanisms underlying differential heart development in fast- and slow-growing broilers under heat stress
      Zhang, J., Schmidt, C.J., Lamont, S.J. BMC Genomics (2017): 295
    • Dietary and genetic influences on hemostasis in a Yup’ik Alaska Native population
      Au, N.T., Reyes, M., Boyer, B.B. et al. PLoS One (2017): e0173616
    • Claudin expression in the rat endolymphatic duct and sac - first insights into regulation of the paracellular barrier by vasopressin
      Runggaldier, D., Pradas, L.G., Neckel, P.H. et al. Scientific Reports (2017): 45,482
    • Insights into psychosis risk from leukocyte microRNA expression
      Jeffries, C.D., Perkins, D.O., Chandler, S.D. et al. Translational Psychiatry (2016): e981
    • 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
    • Expression patterns of cardiac aging in Drosophila
      Cannon, L., Zambon, A.C., Cammarato, A. et al. Aging Cell (2017): 82-92
    • Signs of ongoing inflammation in female patients with chronic widespread pain
      Gerdle, B., Ghafouri, B., Ghafouri, N. et al. Medicine (2017): e6130
    • Unique genetic responses revealed in RNA-seq of the spleen of chickens stimulated with lipopolysaccharide and short-term heat
      Van Goor, A., Ashwell, C.M., Persia, M.E. et al. PLoS One (2017): e0171414
    • 25-hydroxyvitamin D3 and 1,25-dihydroxyvitamin D3 exert distinct effects on human skeletal muscle function and gene expression
      Hassan-Smith, Z.K., Jenkinson, C., Smith, D.J. et. al PLoS One (2017): e0170665
    • Relationship between salivary/pancreatic amylase and body mass index: a systems biology approach
      Bonnefond, A., Yengo, L., Dechaume, A. et al. BMC Medicine (2017): 37
    • Genetic determinants of clinical heterogeneity of the coronary artery disease in the population of Hyderabad, India
      Pranavchand, R., Kumar, A.S., Reddy, B.M. Human Genomics (2017): 3
    • GENOME-WIDE ANALYSIS REVEALS DIFFERENTIAL METHYLATION REGIONS IN THE NUCLEUS ACCUMBENS OF RHESUS MACAQUES AFTER LONG-TERM ALCOHOL USE
      Cervera-Juanes, R., Wilhem, L., Park, B., et al. Alcohol and Alcoholism (2015): i38
    • The type I IFN signature as a biomarker of preclinical rheumatoid arthritis
      Lübbers, J., Brink, M., van de Stadt, L.A., et al. Annals of the Rheumatic Diseases (2013): 776–80
    • Pretreatment synovial transcriptional profile is associated with early and late clinical response in rheumatoid arthritis patients treated with rituximab
      Hogan, V.E., Holweg, C.T.J., Choy, D.F., et al. Annals of the Rheumatic Diseases (2012): 1,888–94
    • Genes expressed in blood link osteoarthritis with apoptotic pathways
      Ramos, Y.F.M., Bos, S.D., Lakenberg, N., et al. Annals of the Rheumatic Diseases (2014): 1,844–53
    • Glucocorticoid-induced leucine zipper (GILZ) inhibits B cell activation in systemic lupus erythematosus
      Jones, S.A., Toh, A.E.J., Odobasic, D., et al. Annals of the Rheumatic Diseases (2016): 739–47
    • Twelve hours of heat stress induces inflammatory signaling in porcine skeletal muscle
      Ganesan, S., Reynolds, C., Hollinger, K., et al. American Journal of Physiology - Regulatory, Integrative and Comparative Physiology (2016): 1,288–96
    • Obesity and intestinal epithelial deletion of the insulin receptor, but not the IGF 1 receptor, affect radiation-induced apoptosis in colon
      Santoro, M.A., Blue, R.E., Andres, S.F., et al. American Journal of Physiology - Gastrointestinal and Liver Physiology (2015): G578–89
    • Ischemic pre- and postconditioning has pronounced effects on gene expression profiles in the rat liver after ischemia/reperfusion
      Knudsen, A.R., Kannerup, A.S., Dich, R., et al. American Journal of Physiology - Gastrointestinal and Liver Physiology (2012): G482–9
    • Differential effects of macronutrient content in 2 energy-restricted diets on cardiovascular risk factors and adipose tissue cell size in moderately obese individuals: a randomized controlled trial
      Rizkalla, S.W., Prifti, E., Cotillard, A., et al. American Journal of Clinical Nutrition (2012): 49–63
    • Dairy proteins, dairy lipids, and postprandial lipemia in persons with abdominal obesity (DairyHealth): a 12-wk, randomized, parallel-controlled, double-blinded, diet intervention study.
      Bohl, M., Bjørnshave, A., Rasmussen, K.V., et al. The American Journal of Clinical Nutrition (2015): 870–8
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    • Discordant Expression of Circulating microRNA from Cellular and Extracellular Sources
      Shah, R., Tanriverdi, K., Levy, D., Larson, M., Gerstein, M., Mick, E., Rozowsky, J., Kitchen, R., Murthy, V., Mikalev, E., Freedman, J.E. PLoS One (2016): e0153691
    • 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., Rösch, S., Waltenberger, J., Sechtem, U., Schwab, M., Schaeffeler, E., Yilmaz, A. Journal of Cardiovascular Magnetic Resonance (2016): 25
    • 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., Liang, H., McAulley, A.K., Hewitt, A.W., Thomas, H.E., Loudovaris, T., Kay, T.W.H., Jenkins, A., Hardikara, A.A. Scientific Reports (2015): 10,375
    • 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., Pelloux, V., Rouault, C., Allouche, R., Laromiguière, M., Kong, L., Darakhshan, F., Massiera, F., Clement, K. The American Journal of Clinical Nutrition (2012): 49–63
    • 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., Fairbridge, N.A., Rasmussen, J., Man, J.H.Y., Bujold, M., Juriloff, D., King-Jones, K., McDermid, H.E. Physiological Genomics (2011): 35–46
    • Further Improvement in Quanitfying Male Fetal DNA in Maternal Plasma
      Jin, S., Lin, X.M., Law, H., Kwek, K.Y.C., Yeo, G.S.H., Ding, C. Clinical Chemistry (2012): 465–8
    • Age-related behaviors have distinct transcriptional profiles in Caenorhabditis elegans
      Golden, T.R., Hubbard, A., Dando, C., Herren, M.A., Melov, S. Aging Cell (2008): 850–65
    • 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., de Vera, V., Gularte, R., Islas-Trejo, A., Wen, P., Horvath, S., Lucero, M., Lusis, A.J., Medrano, J.F. Physiological Genomics (2009): 294–302
    • Reduced Adiposed Tissue Inflammation Represents an Intermediate Cardiometabolic Phenotype in Obesity
      Farb, M.G., Bigornia, S., Mott, M., Tanriverdi, K., Morin, K.M., Freedman, J.E., Joseph, L., Hess, D.T., Apovian, C.M., Vita, J.A., Gokce, N. Journal of the American College of Cardiology (2011): 232–7
    • A genome-wide association study identifies two new risk loci for Graves' disease
      Chu, X., Pan, C.M., Zhao, S.X., Liang, J., Gao, G.Q., Zhang, X.M., Yuan, G.Y., Li, C.G., Xue, L.Q., Shen, M., Liu, W., Xie, F., Yang, S.Y., Wang, H.F., Shi, J.Y., Sun, W.W., Du, W.H., Zuo, C.L., Shi, J.X., Liu, B.L., Guo, C.C., Zhan, M., Gu, Z.H., Zhang, X.N., Sun, F., Wang, Z.Q., Song, Z.Y., Zou, C.Y., Sun, W.H., Guo, T., Cao, H.M., Ma, J.H., Han, B., Li, P., Jiang, H., Huang, Q.H., Liang, L., Liu, L.B., Chen, G., Su, Q., Peng, Y.D., Zhao, J.J., Ning, G., Chen, Z., Chen, J.L., Chen, S.J., Wei Huang, W., Huai-Dong Song, H.D. Nature Genetics (2011): 897–901
    • A Plasmablast Biomarker for Nonreponse to Antibody Therapy to CD20 in Rheumatoid Arthritis
      Owczarczyk, K., Lal, P., Abbas, A.R., Wolslegel, K., Holweg, C., Dummer, W., Kelman, A., Brunetta, P., Lewin-Koh, N., Sorani, M., Leong, D., Fielder, P., Yocum, D., Ho, C., Ortmann, W., Townsend, M.J., Behrens, T.W. Science Translational Medicine (2011): 101ra92
    • Arteriolar Function in Visceral Adipose Tissue Is Impaired in Human Obesity
      Farb, M.G., Ganley-Leal, L., Mott, M., Liang, Y., Ercan, B., Widlansky, M.E., Bigornia, S.J., Fiscale, A.J., Apovian, C.M., Carmine, B., Hess, D.T., Vita, J.A., Gokce, N. Arteriosclerosis, Thrombosis, and Vascular Biology (2011): 467–73
    • Cell-Free DNA in Maternal Plasma: Has the Size-Distribution Puzzle Been Solved?
      Hahn, S., Zimmermann, B.G. Clinical Chemistry (2010): 1210–1
    • Evaluation of Nanofluidics Technology for High-Throughput SNP Genotyping in a Clinical Setting
      Chan, M., Chan, M.W., Loh, T.W., Law, H.Y., Yoon, C.S., Than, S.S., Chua, J.M., Wong, C.Y., Yong, W.S., Yap, Y.S., Ho, G.H., Ang, P., Lee, A.S.G. Journal of Molecular Diagnostics (2011): 305–12
    • 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., Luo, R., Murtha, M.T., Moreno-De-Luca, D., Chu, S.H., Moreau, M.P., Gupta, A.R., Thomson, S.A., Mason, C.E., Bilguvar, K., Celestino-Soper, P.B.S., Murim Choi, M., Crawford, E.L., Davis, L., Wright, N.R.D., Dhodapkar, R.M., DiCola, M., DiLullo, N.M., Fernandez, T.V., Fielding-Singh, V., Fishman, D.O., Frahm, S., Garagaloyan, R., Goh, G.S., Kammela, S., Klei, L., Lowe, J.K., Lund, S.C., McGrew, A.D., Meyer, K.A., Moffat, W.J., Murdoch, J.D., O'Roak, B.J., Ober, G.T., Pottenger, R.S., Raubeson, M.J., Song, Y., Wang, Q., Yaspan, B.L., Yu, T.W., Yurkiewicz, I.R., Beaudet, A.L., Cantor, R.M., Curland, M., Grice, D.E., Günel, M., Lifton, R.P., Mane, S.M., Martin, D.M., Shaw, C.A., Sheldon, M., Tischfield, J.A., Walsh, C.A., Morrow, E.M., Ledbetter, D.H., Fombonne, E., Lord, C., Martin, C.L., Brooks, A.I., Sutcliffe, J.S., Cook Jr., E.H., Geschwind, D., Roeder, K., Devlin, B., State, M.W. Neuron (2011): 863–85
    • 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., Ulger, M., Serin, M.S., Sezgin, O., Altintas, E., Tiftik, E.N. Molecular Biology Reports (2014): 4513–9
    • Huntington's disease biomarker progression profile identified by transcriptome sequencing in peripheral blood
      Mastrokolias, A., Ariyurek, Y., Goeman, J.J., van Duijn, E., Roos, R.A., van der Mast, R.C., van Ommen, G.B., den Dunnen, J.T., 't Hoen. P.A., van Roon-Mom, W.M. European Journal of Human Genetics (2015): 1349–56

  • 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

    • 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
    • Characterization of CD8+ T Cell Differentiation following SIVΔnef Vaccination by Transcription Factor Expression Profiling
      Billingsley, J.M., Rajakumar, P.A., Connole, M.A., Salisch, N.C., Adnan, S., Kuzmichev, Y.V., Hong, H.S., Reeves, R.K., Kang, H.J., Li, W., Li, Q., Haase, A.T., Johnson, R.P. PLoS Pathogens (2015): e1004740
    • A genetic basis for the variation in the vulnerability of cancer to DNA damage
      Yard, B.D., Adams, D.J., Chie, E.K., Tamayo, P., Battaglia, J.S., Gopal, P., Rogacki, K., Pearson, B.E., Phillips, J., Raymond, D.P., Pennell, N.A., Almeida, F., Cheah, J.H., Clemons, P.A., Shamji, A., Peacock, C.D., Schreiber, S.L., Hammerman, P.S., Abazeed, M.E. Nature Communications (2016): 11,428
    • Human Biosample Authentication Using the High-Throughput, Cost-Effective SNPtrace™ System
      Liang-Chu, M.M.Y., Yu, M., Haverty, P.M., Koeman, J., Ziegle, J., Lee, M., Bourgon, R., Neve, R.M. PLoS One (2015): e0116218

  • 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

  • I/O

    • 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
    • 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): doi: 10.1371/journal.pone.0188051
    • 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

    • 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
    • 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): doi:10.1186/s13059-016-0957-5
    • 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
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      Sudan, B., Wacker, M.A., Wilson, M.E., Graff, J.W. Frontiers in Immunology (2015): 253
    • 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

    • 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
    • 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): 1,349–56
    • 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
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      Kerbiriou, P.J., Maliepaard, C.A., Stomph, T.J., et al. Frontiers in Plant Science (2016): 343
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    • 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
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    • 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
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      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
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    • 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
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    • Developing single nucleotide polymorphism markers for the identification of pineapple (Ananas comosus) germplasm
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    • 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
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    • Controlling rice bacterial blight in Africa: needs and prospects
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    • Construction of a radiation hybrid panel and the first yellowtail (Seriola quinqueradiata) radiation hybrid map using a nanofluidic dynamic array
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  • Method Development

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    • 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
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    • 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
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    • Multiplexed locus-specific analysis of DNA methylation in single cells
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    • Validation of high-throughput single cell analysis methodology
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    • Quantitative single cell gene expression profiling in the avian embryo
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    • A superior strategy for single-cell mutational screening via multiplex-targeted QPCR using the BioMark HD microfluidic platform
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    • Proximity assays for sensitive quantification of proteins
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    • Cryopreservation and recovery of human endometrial epithelial cells with high viability, purity, and functional fidelity
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    • Digital polymerase chain reaction for characterisation of DNA reference materials
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    • Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape
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    • 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
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    • 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
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    • Multiplex Quantitative Measurement of mRNAs from Fixed Tissue Microarray Sections
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    • 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
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    • 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
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    • LEMming: A Linear Error Model to Normalize Parallel Quantitative Real-Time PCR (qPCR) Data as an Alternative to Reference Gene Based Methods
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    • High throughput nano-liter RT-qPCR to classify soil contamination using a soil arthropod
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      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
      Bryant, J.A., Aylward, F.O., Eppley, J.M. et al. The ISME Journal (2016): 1,308–22
    • Determining the optimal number of individual samples to pool for quantification of average herd levels of antimicrobial resistance genes in Danish pig herds using high-throughput qPCR
      Clasen, J., Mellerup, A., Olsen, J.E. et al. Veterinary Microbiology (2016): 46–51
    • A high-throughput open-array qPCR gene panel to identify, virulotype, and subtype O157 and non-O157 enterohemorrhagic Escherichia coli
      Gonzales, T.K., Kulow, M., Park, D.J. et al. Molecular and Cellular Probes (2011): 222–30
    • Significant differences in fecal microbiota are associated with various stages of glucose tolerance in African American male veterans
      Ciubotaru, I., Green, S.J., Kukreja, S., Barengolts, E. Translational Research (2015): 401–11
    • A comparative study of digital RT-PCR and RT-qPCR for quantification of Hepatitis A virus and Norovirus in lettuce and water samples
      Coudray-Meunier, C., Fraisse, A., Martin-Latil, S. et al. International Journal of Food Microbiology (2015): 17–26
    • Quantification of Hepatitis E Virus in Naturally-Contaminated Pig Liver Products
      Martin-Latil, S., Hennechart-Collette, C., Delannoy, S. et al. Frontiers in Microbiology (2016): 1,183
    • Development of an objective gene expression panel as an alternative to self-reported symptom scores in human influenza challenge trials
      Muller, J., Parizotto, E., Antrobus, R. et al. Journal of Translational Medicine (2017): 134
    • Shiga toxin-producing Escherichia coli strains isolated from dairy products — Genetic diversity and virulence gene profiles
      Douëllou, T., Delannoy, S., Ganet, S. et al. International Journal of Food Microbiology (2016): 52–62
    • Lipidomic Profiling of Influenza Infection Identifies Mediators that Induce and Resolve Inflammation
      Tam, V.C., Quehenberger, O., Oshansky, C.M. et al. Cell (2013): 213–27
    • Molecular signatures at imminent death: Hemocyte gene expression profiling of shrimp succumbing to viral and fungal infections
      Goncalves, P., Guertler, C., Bachère, E. et al. Developmental and Comparative Immunology (2014): 294–301
    • Molecular quantification of environmental DNA using microfluidics and digital PCR
      Hoshino, T., Inagaki, F. Systematic and Applied Microbiology (2012): 390–5
    • Estimated copy number of Bacillus anthracis plasmids pXO1 and pXO2 using digital PCR
      Straub, T., Baird, C., Bartholomew, R.A. et al. Journal of Microbiological Methods (2013): 9–10
    • Differential regulation of type III secretion and virulence genes in Bordetella pertussis and Bordetella bronchiseptica by a secreted anti-σ factor
      Ahuja, U., Shokeen, B., Cheng, N. et al. Proceedings of the National Academy of Sciences (2016): 2,341–8
    • Genetic susceptibility to S. aureus mastitis in sheep: differential expression of mammary epithelial cells in response to live bacteria or supernatant
      Bonnefont, C.M., Rainard, P., Cunha, P. et al. Physiological Genomics (2012): 403–16
    • Variable tellurite resistance profiles of clinically-relevant Shiga toxin-producing Escherichia coli (STEC) influence their recovery from foodstuffs
      Kerangart, S., Douëllou, T., Delannoy, S. et al. Food Microbiology (2016): 32–42
    • Enhanced Influenza Virus-Like Particle Vaccination with a Structurally Optimized RIG-I Agonist as Adjuvant
      Beljanski, V., Chiang, C., Kirchenbaum, G.A. et al. Journal of Virology (2015): 10,612–24
    • The use of digital PCR to improve the application of quantitative molecular diagnostic methods for tuberculosis
      Devonshire, A.S., O'Sullivan, D.M., Honeyborne, I. et al. BMC Infectious Diseases (2016): 366
    • Analytical Performance of Multiplexed Screening Test for 10 Antibiotic Resistance Genes from Perianal Swab Samples
      Walker, G.T., Rockweiler, T.J., Kersey, R.K. et al. Clinical Chemistry (2016): 353–9
    • Hepatic deficiency of the pioneer transcription factor FoxA restricts hepatitis B virus biosynthesis by the developmental regulation of viral DNA methylation
      McFadden, V.C., Shalaby, R.E., Iram, S. et al. PLoS Pathogens (2017): e1006239
    • Mechanism for microbial population collapse in a fluctuating resource environment
      Turkarslan, S., Raman, A.V., Thompson, A.W. et al. Molecular Systems Biology (2017): 919
    • A high-throughput qPCR system for simultaneous quantitative detection of dairy Lactococcus lactis and Leuconostoc bacteriophages
      Muhammed, M.K., Krych, L., Nielsen, D.S. et al. PLoS One (2017): e0174223
    • T-bet+ B cells are induced by human viral infections and dominate the HIV gp140 response
      Knox, J.J., Buggert, M., Kardava, L. et al. JCI Insight (2017): doi: 10.1172/jci.insight.92943
    • Borrelia Diversity and Co-infection with Other Tick Borne Pathogens in Ticks
      Raileanu, C., Moutailler, S., Pavel, I. et al. Frontiers in Cellular and Infection Microbiology (2017): 36
    • Transcriptomic Study of the Soybean-Fusarium virguliforme Interaction Revealed a Novel Ankyrin-Repeat Containing Defense Gene, Expression of Whose during Infection Led to Enhanced Resistance to the Fungal Pathogen in Transgenic Soybean Plants
      Ngaki, M.N., Wang, B., Sahu, B.B. et al. PLoS One (2016): e0163106
    • Lipid Droplet Formation, Their Localization and Dynamics during Leishmania major Macrophage Infection
      Rabhi, S., Rabhi, I., Trentin, B. et al. PLoS One (2016): e0148640
    • Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB)
      Pamp, S.J., Harrington, E.D., Quake, S.R. et al. Genome Research (2012): 1,107-19
    • AMMI Canada – CACMID Annual Conference
      Canadian Journal of Infectious Diseases and Medical Microbiology (2014): e20
    • Opposing Roles of Membrane and Soluble Forms the Receptor for Advanced Glycation End Products in Primary Respiratory Syncytial Virus Infection
      Miller, A.L., Sims, G.P., Brewah, Y.A. et al. The Journal of Infectious Diseases (2012): 1,311-20
    • Cooperativity of HIV-Specific Cytolytic CD4 T Cells and CD8 T Cells in Control of HIV Viremia
      Johnson, S., Eller, M., Maloveste, S.M. et al. Journal of Virology (2015): 7,494-505
    • Association of Thymidylate Synthase Gene Polymorphisms with Stavudine Triphosphate Intracellular Levels and Lipodystrophy
      Domingo, P., Cabeza, M.C., Pruvost, A. et al. Antimicrobial Agents and Chemotherapy (2011): 1,428–35
    • Tripartite species interaction: eukaryotic hosts suffer more from phage susceptible than from phage resistant bacteria
      Wendling, C.C., Piecyk, A., Refardt, D. et al. BMC Evolutionary Biology (2017): 98
    • BCG vaccination induces HIV target cell activation in HIV-exposed infants in a randomized trial
      Gaspar, M.A., Hesseling, A.C., Mohar, I. et al. JCI Insight (2017): e91963
    • Heart and skeletal muscle inflammation (HSMI) disease diagnosed on a British Columbia salmon farm through a longitudinal farm study
      Di Cicco, E., Ferguson, H.W., Schulze, A.D. et al. PLoS One (2017): e171471
    • The Escherichia coli Serogroup O1 and O2 Lipopolysaccharides Are Encoded by Multiple O-antigen Gene Clusters
      Delannoy, S., Beutin, L., Mariani-Kurkdjian, P. et al. Frontiers in Cellular and Infection Microbiology (2017): 30
    • Molecular Profiling of Shiga Toxin-Producing Escherichia coli and Enteropathogenic E. coli Strains Isolated from French Coastal Environments
      Balière, C., Rincé, A., Delannoy, S., Fach, P., Gourmelon, M. Applied and Environmental Microbiology (2016): 3,913–27
    • The genome of cultivated sweet potato contains Agrobacterium T-DNAs with expressed genes: An example of a naturally transgenic food crop
      Kyndt, T., Quispe, D., Zhai, H., et al. Proceedings of the National Academy of Sciences of the United States of America (2015): 5,844–9
    • IscR Regulates Synthesis of Colonization Factor Antigen I Fimbriae in Response to Iron Starvation in Enterotoxigenic Escherichia coli
      Haines, S., Arnaud-Barbe, N., Poncet, D., et al. Journal of Bacteriology (2015): 2,896–907
    • Human Dendritic Cell Response Signatures Distinguish 1918, Pandemic, and Seasonal H1N1 Influenza Viruses
      Hartmann, B.M., Thakar, J., Albrecht, R.A., et al. Journal of Virology (2015): 10,190–205
    • Ticks and Tick-borne diseases in Ireland
      Zintl, A., Moutailler, S., Stuart, P. et al. Irish Veterinary Journal (2017): 4
    • Development of a High Resolution Virulence Allelic Profiling (HReVAP) Approach Based on the Accessory Genome of Escherichia coli to Characterize Shiga-Toxin Producing E. coli (STEC)
      Michelacci, V., Orsini, M., Knijn, A., et al. Frontiers in Microbiology (2016): 202
    • Co-infection of Ticks: The Rule Rather Than the Exception
      Moutailler, S., Moro, C.V., Vaumourin, E., et al. PLoS Neglected Tropical Diseases (2016): e0004539
    • Ablating the aryl hydrocarbon receptor (AhR) in CD11c+ cells perturbs intestinal epithelium development and intestinal immunity
      Chng, S.H., Kundu, P., Dominguez-Brauer, C., et al. Scientific Reports (2016): 23,820
    • Early T Cell Recognition of B Cells following Epstein-Barr Virus Infection: Identifying Potential Targets for Prophylactic Vaccination
      Brooks, J.M., Long, H.M., Tierney, R.J., et al. PLoS Pathogens (2016): e1005549
    • Viral diagnostics in the era of digital PCR
      Sedlak, R.H., Jerome, K.R. Diagnostic Microbiology and Infectious Disease (2013): 1–4
    • Ultrasensitive Detection of Drug-Resistant Pandemic 2009 (H1N1) Influenza A Virus by Rare-Variant-Sensitive High-Resolution Melting-Curve Analysis
      Chen, N., Pinsky, B.A., Lee, B.P., et al. Clinical Microbiology (2011): 2,602–9
    • Transcriptomic Signature of Leishmania Infected Mice Macrophages: A Metabolic Point of View
      Rabhi, I., Rabhi, S., Ben-Othman, R., et al. PLoS Neglected Tropical Diseases (2012): e1763
    • Transcriptomic analysis of the interaction between Helianthus annuus and its obligate parasite Plasmopara halstedii shows single nucleotide polymorphisms in CRN sequences
      As-sadi, F., Carrere, S., Gascuel, Q., et al. BMC Genomics (2011): 498
    • The Epstein-Barr Virus BamHI C Promoter Is Not Essential for B Cell Immortalization In Vitro, but It Greatly Enhances B Cell Growth Transformation
      Tierney, R.J., Nagra, J., Rowe, M., et al. Journal of Virology (2015): 2,483–93
    • The effect of high-fat diet on the composition of the gut microbiota in cloned and non-cloned pigs of lean and obese phenotype
      Pedersen, R., Andersen, A.D., Hermann-Bank, M.L., et al. Gut Microbes (2013): 371–81
    • Specific Inflammatory Stimuli Lead to Distinct Platelet Responses in Mice and Humans
      Beaulieu, L.M., Clancy, L., Tanriverdi, K., et al. PLoS One (2015): e0131688
    • Simultaneous Quantification of Multiple Food- and Waterborne Pathogens by Use of Microfluidic Quantitative PCR
      Ishii, S., Segawa, T., Okabe, S. Applied and Environmental Microbiology (2013): 2,891–98
    • Relationship between Plasmodium falciparum malaria prevalence, genetic diversity and endemic Burkitt lymphoma in Malawi
      Johnston, W.T., Mutalima, N., Sun, D., et al. Scientific Reports (2014): 3,741
    • Pre-miR-146a (rs2910164 G>C) Single Nucleotide Polymorphism Is Genetically and Functionally Associated with Leprosy
      Cezar-de-Mello, P.F.T., Toledo-Pinto, T.G., Marques, C.S., et al. PLoS Neglected Tropical Diseases (2014): e3099
    • Pig α1-Acid Glycoprotein: Characterization and First Description in Any Species as a Negative Acute Phase Protein
      Heegaard, P.M.H., Miller, I., Sorensen, N.S., et al. PLoS One (2013): e68110
    • Pattern and synchrony of gene expression among sympatric marine microbial populations
      Ottesen, E.A., Young, C.R., Eppley, J.M., et al. Proceedings of the National Academy of Sciences of the United States of America (2013): E488–97
    • Pathogen-associated molecular pattern-triggered immunity and resistance to the root pathogen Phytophthora parasitica in Arabidopsis
      Larroque, M., Belmas, E., Martinez, T., et al. Journal of Experimental Botany (2013): 3,615–25
    • Natural Blood Feeding and Temperature Shift Modulate the Global Transcriptional Profile of Rickettsia rickettsii Infecting Its Tick Vector
      Galletti, M.F.B.M., Fujita, A., Nishiyama Jr., M.Y., et al. PLoS One (2013): e77388
    • Multiple detection of pathogens in ticks: development of a high throughput real time PCR chip used as a new epidemiologic investigative tool
      Michelet, L., Delannoy, S., Devillers, E., et al. Parasites and Vectors (2014): O12
    • Molecular identification in monophasic and nonmotile variants of Salmonella enterica serovar Typhimurium
      Bugarel, M., Vignaud, M.L., Moury, F., et al. MicrobiologyOpen (2012): 481–9
    • Molecular and Phenotypic Characterization of Escherichia coli O26:H8 among Diarrheagenic E. coli O26 Strains Isolated in Brazil
      Piazza, R.M.F., Delannoy, S., Fach, P., et al. Applied and Environmental Microbiology (2013): 6,847–54
    • Microfluidic Quantitative PCR for Simultaneous Quantification of Multiple Viruses in Environmental Water Samples
      Ishii, S., Kitamura, G., Segawa, T., et al. Applied and Environmental Microbiology (2014): 7,505–11
    • Reduced Innate Immune Response to a Staphylococcus aureus Small Colony Variant Compared to Its Wild-Type Parent Strain
      Ou, J.J.J., Drilling, A.J., Cooksley, C. et al. Frontiers in Cellular and Infection Microbiology (2017): 187
    • High-throughput screening of tick-borne pathogens in Europe
      Michelet, L., Delannoy, S., Devillers, E., et al. Frontiers in Cellular and Infection Microbiology (2014): 103
    • Genome-Wide Expression Profiling Identifies Type 1 Interferon Response Pathways in Active Tuberculosis
      Ottenhoff, T.H.M., Dass, R.H., Yang, N., et al. PLoS One (2012): e45839
    • Genome Wide Expression Profiling Reveals Suppression of Host Defence Responses during Colonisation by Neisseria meningitides but not N. lactamica
      Wong, H.E.E., Li, M.S., Kroll, J.S., et al. PLoS One (2011): e26130
    • Genetic Diversity and Virulence Potential of Shiga Toxin-Producing Escherichia coli O113:H21 Strains Isolated from Clinical, Environmental, and Food Sources
      Feng, P.C.H., Delannoy, S., Lacher, D.W., et al. Applied and Environmental Microbiology (2014): 4,757–63
    • Gene Expression Profiling Specifies Chemokine, Mitochondrial and Lipid Metabolism Signatures in Leprosy
      Guerreiro, L.T.A., Robottom-Ferreira, A.B., Ribeiro-Alves, M., et al. PLoS One (2013): e64748
    • Field Monitoring of Avian Influenza Viruses: Whole-Genome Sequencing and Tracking of Neuraminidase Evolution Using 454 Pyrosequencing
      Croville, G., Soubies, S.M., Barbieri, J., et al. Journal of Clinical Microbiology (2012): 2,881–7
    • Differential Transcriptomic Response in the Spleen and Head Kidney Following Vaccination and Infection of Asian Seabass with Streptococcus iniae
      Jiang, J., Miyata, M., Chan, C., et al. PLoS One (2014): e99128
    • Differential Host Response, Rather Than Early Viral Replication Efficiency, Correlates with Pathogenicity Caused by Influenza Viruses
      Askovich, P.S., Sanders, C.J., Rosenberger, C.M., et al. PLoS One (2013): e74863
    • MtNF-YA1, A Central Transcriptional Regulator of Symbiotic Nodule Development, Is Also a Determinant of Medicago truncatula Susceptibility toward a Root Pathogen
      Rey, T., Laporte, P., Bonhomme, M. et al. Frontiers in Plant Science (2016): 1,837
    • Transcription Profiling of Malaria-Naïve and Semi-immune Colombian Volunteers in a Plasmodium vivax Sporozoite Challenge
      Rojas-Peña, M.L., Vallejo, A., Herrera, S. et al. PLoS Neglected Tropical Diseases (2015): e0003978
    • Discovery and Validation of Prognostic Biomarker Models to Guide Triage among Adult Dengue Patients at Early Infection
      Pang, J., Lindblom, A., Tolfvenstam, T. et al. PLoS One (2016): e0155993
    • Virulence genes of Rickettsia rickettsii are differentially modulated by either temperature upshift or blood-feeding in tick midgut and salivary glands
      Galletti, M.F.B.M., Fujita, A., Rosa, R.D. et al. Parasites and Vectors (2016): 331
    • Concurrent host-pathogen gene expression in the lungs of pigs challenged with Actinobacillus pleuropneumoniae
      Brogaard, L., Klitgaard, K., Heegaard, P.M.H. et al. BMC Genomics (2015): 417
    • Identification by Random Mutagenesis of Functional Domains in KREPB5 That Differentially Affect RNA Editing between Life Cycle Stages of Trypanosoma brucei
      McDermott, S.M., Carnes, J., Stuart, K. Molecular and Cellular Biology (2015): 3,945–61
    • Complement component 5 contributes to poor disease outcome in humans and mice with pneumococcal meningitis
      Woehrl, B., Brouwer, M.C., Murr, C. et al. Journal of Clinical Investigation (2011): 3,943–53
    • Virus-specific CD4+ memory phenotype T cells are abundant in unexposed adults
      Su, L.F., Kidd, B.A., Han, A., Kotzin, J.J., Davis, M.M. Immunity (2013): 373–83
    • Screen of whole blood responses to flagellin identifies TLR5 variation associated with outcome in melioidosis
      Chantratita, N., Tandhavanant, S., Myers, N.D., Chierakul, W., Robertson, J.D., Mahavanakul, W., Singhasivanon, P., Emond, M.J., Peacock, S.J., West, T.E. Genes and Immunity (2014): 63–71
    • Parasitism and survival rate of Diadegma fenestrale (Hymenoptera: Ichneumonidae) and DfIV gene expression patterns in two lepidopteran hosts
      Kim, J.I., Kwon, M., Lee, S.H., Kim, Y. Biochemical and Biophysical Research Communications (2015): 579–84
    • Purification and quantitation of bacteriophage M13 using desalting spin columns and digital PCR
      Reitinger, S., Petriv, O.I., Mehr, K., Hansen, C.L., Withers, S.G. Journal of Virological Methods (2012): 171-4
    • Gene expression differences underlying genotype-by-genotype specificity in a host-parasite system.
      Barribeau, S.M., Sadd, B.M., du Plessism L., Schmid-Hempel, P. Proceedings of the National Academy of Sciences (2014): 3,496–501
    • Independent, Parallel Pathways to CXCL10 Induction in HCV-Infected Hepatocytes
      Brownell, J., Wagoner, J., Lovelace, E.S., Thirstrup, D., Mohar, I., Smith, W., Giugliano, S., Li, K., Crispe, I.N., Rosen, H.R., Polyak, S.J. Journal of Hepatology (2013): 701–8
    • Genetic Diversity and Pathogenic Potential of Attaching and Effacing Escherichia coli O26:H11 Strains Recovered from Bovine Feces in the United States
      Ison, S.A., Delannoy, S., Bugarel, M., Nightingale, K.K., Webb, H.E., Renter, D.G., Nagaraja, T.G., Loneragan, G.H., Fach, P. Applied and Environmental Microbiology (2015): 3,671–8
    • Diverse Virulence Gene Content of Shiga Toxin-Producing Escherichia coli from Finishing Swine
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    • Detection and characterization of respiratory viruses causing acute respiratory illness and asthma exacerbation in children during three different seasons (2011–2014) in Mexico City
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    • Carboxymefloquine, the Major Metabolite of the Antimalarial Drug Mefloquine, Induces Drug-Metabolizing Enzyme and Transporter Expression by Activation of Pregnane X Receptor
      Piedade, R., Traub, S., Bitter, A., Nüssler, A.K., Gil, J.P., Schwab, M., Burk, O. Antimicrobial Agents and Chemotherapy (2015): 96–104
    • A certified plasmid reference material for the standardisation of BCR–ABL1 mRNA quantification by real-time quantitative PCR
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    • Unexpected patterns of Epstein–Barr virus transcription revealed by a High throughput PCR array for absolute quantification of viral mRNA
      Tierney, R.J., Shannon-Lowe, C.D., Fitzsimmons, L., Bell, A.I., Rowe, M. Virology (2014): 117–30
    • Triggering Dectin-1-Pathway Alone Is Not Sufficient to Induce Cytokine Production by Murine Macrophages
      Walachowski, S., Tabouret, G., Foucras, G. PLoS One (2016): e0148464
    • Mixture models for single-cell assays with applications to vaccine studies
      Finak, G., McDavid, A., Chattopadhyay, P., Dominguez, M., De Rosa, S., Roederer, M., Gottardo, R. Biostatistics (2014): 87–101
    • The effects of Nigella sativa (Ns), Anthemis hyalina (Ah) and Citrus sinensis (Cs) extracts on the replication of coronavirus and the expression of TRP genes family
      Ulasli, M., Gurses, S.A., Bayraktar, R., Yumrutas, O., Oztuzcu, S., Igci, M., Igci, Y.Z., Cakmak, E.A., Arslan, A. Molecular Biology Reports (2014): 1,703–11
    • Combination of RNAseq and SNP nanofluidic array reveals the center of genetic diversity of cacao pathogen Moniliophthora roreri in the upper Magdalena Valley of Colombia and its clonality
      Ali, S.S., Shao, J., Strem, M.D., Phillips-Mora, W., Zhang, D., Meinhardt, L.W., Bailey, B.A. Frontiers in Microbiology (2015): 850
    • Advances in Molecular Serotyping and Subtyping of Escherichia coli
      Frantamico, P.M., DebRoy, C., Liu, Y., Needleman, D.S., Baranzoni, G.M., Feng, P. Frontiers in Microbiology (2016): 644
    • Polymorphisms of Pyrimidine Pathway Enzymes Encoding Genes and HLA-B*40∶01 Carriage in Stavudine-Associated Lipodystrophy in HIV-Infected Patients
      Domingo, P., Mateo, M.G., Pruvost, A., Torres, F., Salazar, J., del Mar Gutierrez, M., Cabeza, C., Domingo, J.C., Fernandez, I., Villaroya, F., Vidal, F., Baiget, M., de la Calle-Martín, O. PLoS One (2013): e67035
    • Paediatric HIV infection in the ‘omics era: defining transcriptional signatures of viral control and vaccine responses
      Cotugno, N., De Armas, L., Pallikkuth, S., Rossi, P., Palma, P., Pahwa, S. Journal of Virus Eradication (2015): 153-8
    • Digital PCR for direct quantification of viruses without DNA extraction
      Pavšič, J., Žel, J., Milavec, M. Analytical and Bioanalytical Chemistry (2015): 67–75
    • Functional Environmental Genomics of a Municipal Landfill Soil
      Roelofs, D., de Boer, M., Agamennone, V., Bouchier, P., Legler, J., van Straalen, N. Frontiers in Genetics (2012): 85
    • Differential Dermal Expression of CCL17 and CCL18 in Tuberculoid and Lepromatous Leprosy
      Berrington, W.R., Kunwar, C.B., Neupane, K., van den Eeden, S.J.F., Vary, Jr., J.C., Peterson, G.J., Wells, R.D., Geluk, A., Hagge, D.A., Hawn, T.R. PLoS Neglected Tropical Diseases (2014): e3263
    • Coxsackievirus Cloverleaf RNA Containing a 5′ Triphosphate Triggers an Antiviral Response via RIG-I Activation
      Feng, Q., Langereis, M.A., Olagnier, D., Chiang, C., van de Winkel, R., van Essen, P., Zoll, J., Hiscott, J., van Kuppeveld, F.J.M. PLoS One (2014): e95927
    • Communication between Human Dendritic Cell Subsets in Tuberculosis: Requirements for Naive CD4+ T Cell Stimulation
      Lozza, L., Farinacci, M., Bechtle, M., Stäber, M., Zedler, U., Baiocchini, A., del Nonno, F., Kaufmann, S.H.E. Frontiers in Immunology (2014): 324
    • Common TLR1 Genetic Variation Is Not Associated with Death from Melioidosis, a Common Cause of Sepsis in Rural Thailand
      Chantratita, N., Tandhavanant, S., Myers, N.D., Chierakul, W., Wuthiekanun, V., Mahavanakul, W., Limmathurotsakul, D., Peacock, S.J., West, T.E. PLoS One (2014): e83285
    • Characterisation of Gut Microbiota in Ossabaw and Göttingen Minipigs as Models of Obesity and Metabolic Syndrome
      Pedersen, R., Ingerslev, H.C., Sturek, M., Alloosh, M., Cirera, S., Christoffersen, B., Moesgaard, S.G., Larsen, N., Boye, M. PLoS One (2013): e56612
    • Cellular Oxidative Stress Response Controls the Antiviral and Apoptotic Programs in Dengue Virus-Infected Dendritic Cells
      Olagnier, D., Peri, S., Steel, C., van Montfoort, N., Chiang, C., Beljanski, V., Slifker, M., He, Z., Nichols, C.N., Lin, R., Balachandran, S., Hiscott, J. PLoS Pathogens (2014): e1004566
    • Ampicillin-Improved Glucose Tolerance in Diet-Induced Obese C57BL/6NTac Mice Is Age Dependent
      Rune, I., Hansen, C.H.F., Ellekilde, M., Nielsen, D.S., Skovgaard, K., Rolin, B.C., Lykkesfeldt, J., Josefsen, K., Tranberg, B., Kihl, P., Hansen, A.K. Journal of Diabetes Research (2013): 319,321
    • Altered expression of Arabidopsis genes in response to a multifunctional geminivirus pathogenicity protein
      Liu, L., Chung, H.Y., Lacatus, G., Baliji, S., Ruan, ,J., Sunter, G. BMC Plant Biology (2014): 302
    • A Novel High-Throughput Method for Molecular Detection of Human Pathogenic Viruses Using a Nanofluidic Real-Time PCR System
      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
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      Ottesen, E.A., Hong, J.W., Quake, S.R., Leadbetter, J.R. Science (2006): 1464–7
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      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
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      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
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      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
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    • 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
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    • 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
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    • 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
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    • Human Plasmacytoid Dendritic Cell Accumulation Amplifies Their Type 1 Interferon Production
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    • Generation of Human Striatal Neurons by MicroRNA-Dependent Direct Conversion of Fibroblasts
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    • 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

    • 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
    • "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): doi: 10.1371/journal.pone.0184451
    • 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
    • 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): doi:10.1186/s13059-015-0692-3
    • 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
      Varghese, S., Newton, R., Ross-Innes, C.S. et al. Gastroenterology (2015): 1,511–18
    • Comparison of microRNA profiles between benign and malignant salivary gland tumors in tissue, blood and saliva samples: a prospective, case-control study
      Cinpolat, O., Unal, Z.N., Ismi, O., Gorur, A., Unal, M. Brazilian Journal of Otorhinolaryngology (2017): 276–84
    • CXCL14, CXCR7 expression and CXCR4 splice variant ratio associate with survival and metastases in Ewing sarcoma patients
      Sand, L.G., Scotlandi, K., Berghuis, D. et al. European Journal of Cancer (2015): 2,624–33
    • Accurate Sample Assignment in a Multiplexed, Ultrasensitive, High-Throughput Sequencing Assay for Minimal Residual Disease
      Bartram, J., Mountjoy, E., Brooks, T. et al. The Journal of Molecular Diagnostics (2016): 494–506
    • Independent validation of genes and polymorphisms reported to be associated with radiation toxicity: a prospective analysis study
      Barnett, G.C., Coles, C.E., Elliott, R.M. et al. The Lancet Oncology (2012): 65–77
    • Associations between gastrointestinal toxicity, micro RNA and cytokine production in patients undergoing myeloablative allogeneic stem cell transplantation
      Pontoppidan, P.L., Jordan, K., Carlsen, A.L. et al. International Immunopharmacology (2015): 180–8
    • Leptin, BMI, and a Metabolic Gene Expression Signature Associated with Clinical Outcome to VEGF Inhibition in Colorectal Cancer
      Pommier, A.J., Farren, M., Patel, B. et al. Cell Metabolism (2016): 77–93
    • Integration of Public Microarray Data with Single Cell Gene Expression Profiling Facilitates Identification of Transcriptionally-Defined Subpopulations in Small Cell Lung Cancer
      Januszyk, M., Rennert, R.C., Sorkin, M. et al. Journal of Surgical Research (2014): 558–9
    • MEDI-573, alone or in combination with mammalian target of rapamycin inhibitors, targets the insulin-like growth factor pathway in sarcomas
      Zhong, H., Fazenbaker, C., Breen, S. et al. Molecular Cancer Therapeutics (2014): 2,662–73
    • Randomized Open-Label Phase II Trial of Apitolisib (GDC-0980), a Novel Inhibitor of the PI3K/Mammalian Target of Rapamycin Pathway, Versus Everolimus in Patients With Metastatic Renal Cell Carcinoma
      Powles, T., Lackner, M.R., Oudard, S. et al. Journal of Clinical Oncology (2016): 1,660–8
    • Tumor Cell Adhesion As a Risk Factor for Sentinel Lymph Node Metastasis in Primary Cutaneous Melanoma
      Meves, A., Nikolova, E., Heim, J.B. et al. Journal of Clinical Oncology (2015): 2,509–15
    • Single-cell transcriptional analysis of normal, aberrant, and malignant hematopoiesis in zebrafish
      Moore, F.E., Garcia, E.G., Lobbardi, R. et al. Journal of Experimental Medicine (2016): 979–92
    • Genetic and Dietary Regulation of Glyburide Efflux by the Human Placental Breast Cancer Resistance Protein Transporter
      Bircsak, K.M., Gupta, V., Yuen, P.Y. et al. The Journal of Pharmacology and Experimental Therapeutics (2016): 103–13
    • ABCB8 mediates doxorubicin resistance in melanoma cells by protecting the mitochondrial genome
      Elliott, A.M., Al-Hajj, M.A. Molecular Cancer Research (2009): 79–87
    • Intermittent High-Dose Scheduling of AZD8835, a Novel Selective Inhibitor of PI3Kα and PI3Kδ, Demonstrates Treatment Strategies for PIK3CA-Dependent Breast Cancers
      Hudson, K., Hancox, U.J., Trigwell, C. et al. Molecular Cancer Therapeutics (2016): 877–89
    • Nanofluidic Digital PCR and Extended Genotyping of RAS and BRAF for Improved Selection of Metastatic Colorectal Cancer Patients for Anti-EGFR Therapies
      Azuara, D., Santos, C., Lopez-Doriga, A. et al. Molecular Cancer Therapeutics (2016): 1,106–12
    • Expression Profile of BCL-2, BCL-XL, and MCL-1 Predicts Pharmacological Response to the BCL-2 Selective Antagonist Venetoclax in Multiple Myeloma Models
      Punnoose, E.A., Leverson, J.D., Peale, F. et al. Molecular Cancer Therapeutics (2016): 1,132–44
    • AZD2014, an Inhibitor of mTORC1 and mTORC2, Is Highly Effective in ER+ Breast Cancer When Administered Using Intermittent or Continuous Schedules
      Guichard, S,M., Curwen, J., Bihani, T. et al. Molecular Cancer Therapeutics (2015): 2,508–18
    • AKT Antagonist AZD5363 Influences Estrogen Receptor Function in Endocrine-Resistant Breast Cancer and Synergizes with Fulvestrant (ICI182780) In Vivo
      Ribas, R., Pancholi, S., Guest, S.K. et al. Molecular Cancer Therapeutics (2015): 2,035–48
    • Defining Cancer Risk in Barrett’s Oesophagus using a 90-Gene Signature
      Varghese, S., Newton, R., Ross-Innes, C.S. et al. Gut (2013): A12
    • DGCR8 is essential for tumor progression following PTEN loss in the prostate
      Belair, C.D., Paikari, A., Moltzahn, F. et al. EMBO Reports (2015): 1,219–32
    • Gender Influences the Class III and V β-Tubulin Ability to Predict Poor Outcome in Colorectal Cancer
      Mariani, M., Zannoni, G.F., Sioletic, S. et al. Clinical Cancer Research (2012): 2,964–75
    • The Rectal Cancer microRNAome – microRNA Expression in Rectal Cancer and Matched Normal Mucosa
      Gaedcke, J., Grade, M., Camps, J. et al. Clinical Cancer Research (2012): 4,919–30
    • Functional, Genetic, and Epigenetic Aspects of Base and Nucleotide Excision Repair in Colorectal Carcinomas
      Slyskova, J., Korenkova, V., Collins, A.R. et al. Clinical Cancer Research (2012): 5,878–87
    • Phosphoinositide 3-Kinase (PI3K) Pathway Alterations Are Associated with Histologic Subtypes and Are Predictive of Sensitivity to PI3K Inhibitors in Lung Cancer Preclinical Models
      Spoerke, J.M., O'Brien, C., Huw, L. et al. Clinical Cancer Research (2012): 6,771–83
    • Identification and Analysis of In Vivo VEGF Downstream Markers Link VEGF Pathway Activity with Efficacy of Anti-VEGF Therapies
      Brauer, M.J., Zhuang, G., Schmidt, M. et al. Clinical Cancer Research (2013): 3,681–92
    • Tumor Stromal Architecture Can Define the Intrinsic Tumor Response to VEGF-Targeted Therapy
      Smith, N.R., Baker, D., Farren, M. et al. Clinical Cancer Research (2013): 6,943–56
    • Genetic Variations Associated with Postoperative Recurrence in Stage I Non–Small Cell Lung Cancer
      Yoon, K.A., Jung, M.K., Lee, D. et al. Clinical Cancer Research (2014): 3,272–9
    • Development and Validation of a Gene Profile Predicting Benefit of Postmastectomy Radiotherapy in Patients with High-Risk Breast Cancer: A Study of Gene Expression in the DBCG82bc Cohort
      Tramm, T., Mohammed, H., Myhre, S. et al. Clinical Cancer Research (2014): 5,272–80
    • Head-to-Head Comparison and Evaluation of 92 Plasma Protein Biomarkers for Early Detection of Colorectal Cancer in a True Screening Setting
      Chen H., Zucknick M., Werner S., Knebel P., Brenner H. Clinical Cancer Research (2015): 3,318–26
    • An Antibody-Drug Conjugate Directed against Lymphocyte Antigen 6 Complex, Locus E (LY6E) Provides Robust Tumor Killing in a Wide Range of Solid Tumor Malignancies
      Asundi, J., Crocker, L., Tremayne, J. et al. Clinical Cancer Research (2015): 3,252–62
    • Exome Sequencing Reveals AMER1 as a Frequently Mutated Gene in Colorectal Cancer
      Sanz-Pamplona, R., Lopez-Doriga, A., Paré-Brunet, L., Lázaro, K. et al. Clinical Cancer Research (2015): 4,709–18
    • Serum micro-rna profiles in patients with autosomal dominant polycystic kidney disease according to hypertension and renal function
      Kocyigit, I., Taheri, S., Sener, E.F. et al. BMC Nephrology (2017): 179
    • Fluorescent CXCR4 targeting peptide as alternative for antibody staining in Ewing sarcoma
      Sand, L.G.L., Buckle, T., van Leeuwen, F.W.B. et al. BMC Cancer (2017): 383
    • Gene expression study and pathway analysis of histological subtypes of intestinal metaplasia that progress to gastric cancer
      Companioni, O., Sanz-Anquela, J.M., Pardo, M.L. et al. PLoS One (2017): e0176043
    • Latent carcinogenicity of early-life exposure to dichloroacetic acid in mice
      Wood, C.E., Hester, S.D., Chorley, B.N. et al. Carcinogenesis (2015): 782–91
    • Stromal estrogen receptor-α promotes tumor growth by normalizing an increased angiogenesis
      Péqueux, C., Raymond-Letron, I., Blacher, S. et al. Cancer Research (2012): 3,010–9
    • Comparative Oncogenomics Identifies PSMB4 and SHMT2 as Potential Cancer Driver Genes
      Lee, G.Y., Haverty, P.M., Li, L. et al. Cancer Research (2014): 3,114–26
    • Cisplatin hypersensitivity of testicular germ cell tumors is determined by high constitutive Noxa levels mediated by Oct-4
      Gutekunst, M., Mueller, T., Weilbacher, A. et al. Cancer Research (2013): 1,460–9
    • Combination of protein coding and noncoding gene expression as a robust prognostic classifier in stage I lung adenocarcinoma
      Akagi, I., Okayama, H., Schetter, A.J. et al. Cancer Research (2015): 3,821–32
    • Usefulness of Nanofluidic Digital PCR Arrays to Quantify T790M Mutation in EGFR-mutant Lung Adenocarcinoma
      Isobe, K., Hata, Y., Tochigi, N. et al. Cancer Genomics and Proteomics (2015): 31–7
    • 9q31.2-rs865686 as a Susceptibility Locus for Estrogen Receptor-Positive Breast Cancer: Evidence from the Breast Cancer Association Consortium
      Warren, H., Dudbridge, F., Fletcher, O. et al. Cancer Epidemiology, Biomarkers and Prevention (2012): 1,783–91
    • CRISPR Screens Provide a Comprehensive Assessment of Cancer Vulnerabilities but Generate False-Positive Hits for Highly Amplified Genomic Regions
      Munoz, D.M., Cassiani, P.J., Li, L. et al. Cancer Discovery (2016): 900–13
    • The Potential Diagnostic Value of Serum microRNA Signature in Patients with Pancreatic Cancer
      Johansen, J.S., Calatayud, D., Albieri, V. et al. International Journal of Cancer (2016): 2,312–24
    • Minimal residual disease in breast cancer: an overview of circulating and disseminated tumour cells
      Tachtsidis, A., McInnes, L.M., Jacobsen, N. et al. Clinical and Experimental Metastatis (2016): 521–50
    • Associations between polymorphisms in folate-metabolizing genes and pancreatic cancer risk in Japanese subjects
      Nakao, H., Wakai, K., Ishii, N. et al. BMC Gastroenterology (2016): 83
    • First Selective Small Molecule Inhibitor of FGFR4 for the Treatment of Hepatocellular Carcinomas with an Activated FGFR4 Signaling Pathway
      Hagel, M., Miduturu, C., Sheets, M. et al. Cancer Discovery (2015): 424–37
    • Systematic Functional Interrogation of Rare Cancer Variants Identifies Oncogenic Alleles
      Kim, E., Ilic, N., Shrestha, Y. et al. Cancer Discovery (2016): 714–26
    • Transcriptomic Characterization of SF3B1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia
      Wang, L., Brooks, A.N., Fan, J. et al. Cancer Cell (2016): 750-63
    • The importance of analysis of long range rearrangement of BRCA1 andBRCA2 in genetic diagnosis of familial breast cancer
      Kwong, A., Chen, J., Shin, V.Y., et al. Cancer Genetics (2015): 448–54
    • Genomic analysis of the molecular neuropathology of tuberous sclerosis using a human stem cell model
      Grabole, N., Zhang, J.D., Aigner, S., et al. Genome Medicine (2016): 94
    • DNA Methlyation Profiling Defines Clinically Relevant Biological Subsets of Non-Small Cell Lung Cancer
      Walter, K., Holcomb, T., Januario, T. et al. Clinical Cancer Research (2012): 2,360–73
    • Microfluidic based multiplex qRT-PCR identifies diagnostic and prognostic microRNA signatures in sera of prostate cancer patients
      Moltzahn, F., Olshen, A.B., Baehner, L. et al. Cancer Research (2011): 550–60
    • Impaired fasting glucose, single-nucleotide polymorphisms, and risk for colorectal cancer in Koreans
      Jung, K.J., Kim, M.T., Jee, S.H. Epidemiology and Health (2016): e2016002
    • The Neural Crest and Cancer: A Developmental Spin on Melanoma
      Kulesa, P.M., Morrison, J.A., Bailey, C.M. Cells Tissues Organs (2015): 198
    • Synthetic Lethal Screen Identifies NF-κB as a Target for Combination Therapy with Topotecan for patients with Neuroblastoma
      Tsang, P.S., Cheuk, A.T., Chen, Q.R. et al. BMC Cancer (2012): 101
    • Multiple Functional Risk Variants in a SMAD7 Enhancer Implicate a Colorectal Cancer Risk Haplotype
      Fortini, B.K., Tring, S., Plummer, S.J. et al. PLoS One (2014): e111914
    • Intraclonal heterogeneity and distinct molecular mechanisms characterize the development of t(4;14) and t(11;14) myeloma
      Walker, B.A., Wardell, C.P., Melchor, L. et al. Blood (2012): 1,077–86
    • T-cell defect in diffuse large B-cell lymphomas involves expansion of myeloid derived suppressor cells expressing IL-10, PD-L1 and S100A12
      Azzaoui, I., Uhel, F., Rossille, D. et al. Blood (2016): 1,081–92
    • CBFβ-SMMHC creates aberrant megakaryocyte-erythroid progenitors prone to leukemia-initiation in mice
      Cai, Q., Jeannet, R., Hua, W.K. et al. Blood (2016): 1,503–15
    • Single-cell dissection of transcriptional heterogeneity in human colon tumors
      Dalerba, P., Kalisky, T., Sahoo, D. et al. Nature Biotechnology (2011): 1120–7
    • Case-control study of diabetes-related genetic variants and pancreatic cancer risk in Japan
      Kuruma, S., Egawa, N., Honda, G. et al. World Journal of Gastroenterology (2014): 17456–62
    • Inflammation Mediated Metastasis: Immune Induced Epithelial-To-Mesenchymal Transition in Inflammatory Breast Cancer Cells
      Cohen, E.N., Gao, H., Anfossi, S. et al. PLoS One (2015): e0132710
    • 5-hydroxymethylcytosine marks promoters in colon that resist DNA hypermethylation in cancer
      Uribe-Lewis, S., Stark, R., Carroll, T. et al. Genome Biology (2015): 69
    • Spatial and Temporal Heterogeneity in High-Grade Serous Ovarian Cancer: A Phylogenetic Analysis
      Schwarz, R.F., Ng, C.K., Cooke, S.L. et al. PLoS One (2015): e1001789
    • In-depth characterization of the microRNA transcriptome in a leukemia progression model
      Kuchenbauer, F., Morin, R.D., Argiropoulos, B. et al. Genome Research (2008): 1787–97
    • New regulators of Wnt/beta-catenin signaling revealed by integrative molecular screening
      Major, M.B., Roberts, B.S., Berndt, J.D. et al. Science Signaling (2008): ra12
    • Association of reactive oxygen species levels and radioresistance in cancer stem cells
      Diehn, M., Cho, R.W., Lobo, N.A. et al. Nature (2009): 780–3
    • Pharmacogenetic pathway analysis for determination of sunitinib-induced toxicity
      van Erp, N.P., Eechoute, K., van der Veldt, A.A. et al. Journal of Clinical Oncology (2009): 4406–12
    • Efficient molecular subtype classification of high-grade serous ovarian cancer
      Leong, H.S., Galletta, L., Etemadmoghadam, D., et al. Journal of Pathology (2015): 272–7
    • Cellular organization and molecular differentiation model of breast cancer-associated fibroblasts
      Busch, S., Andersson, D., Bom, E. et al. Molecular Cancer (2017): DOI 10.1186/s12943-017-0642-7
    • Association of ARID5B gene variants with acute lymphoblastic leukemia in Yemeni children
      Al-Absi, B., Noor, S.M., Saif-Ali, R. et al. Tumor Biology (2017): DOI 10.1177/1010428317697573.
    • Tissue MicroRNA profiles as diagnostic and prognostic biomarkers in patients with resectable pancreatic ductal adenocarcinoma and periampullary cancers
      Calatayud, D., Dehlendorff, C., Boisen, M.K. et al. Biomarker Research (2017): 8
    • Gene-expression Classifier in Papillary Thyroid Carcinoma: Validation and Application of a Classifier for Prognostication
      Londero, S.C., Jespersen, M.L., Krogdahl, A., et al., A Study from the Danish Thyroid Cancer Group - DATHYRCA. Anticancer Research (2016): 749–56
    • Hypoxia-regulated MicroRNAs in Gastroesophageal Cancer
      Winther, M., Alsner, J.,Sørensen, B.S., et al. Anticancer Research (2016): 721–30
    • MTUS1 and its targeting miRNAs in colorectal carcinoma: significant associations.
      Ozcan, O., Kara, M., Yumrutas, O., et al. Tumor Biology (2016): 6,637–45
    • Expression Profiling of Ribosome Biogenesis Factors Reveals Nucleolin as a Novel Potential Marker to Predict Outcome in AML Patients
      Marcel, V., Catez, F., Berger, C.M. et al. PLoS One (2017): e0170160
    • MCT4 surpasses the prognostic relevance of the ancillary protein CD147 in clear cell renal cell carcinoma
      Fisel, P., Stühler, V., Bedke, J., et al. Oncotarget (2015): 30,615–27
    • Harnessing Connectivity in a Large-Scale Small-Molecule Sensitivity Dataset
      Seashore-Ludlow, B., Rees, M.G., Cheah, J.H., et al. Cancer Discovery (2015): 1,210–23
    • Sense-antisense gene-pairs in breast cancer and associated pathological pathways
      Grinchuk, O.V., Motakis, E., Yenamandra, S.P., et al. Oncotarget (2015): 42,197–221
    • Oncovex MGM-CSF –mediated regression of contralateral (non-injected) tumors in the A20 murine lymphoma model does not involve direct viral oncolysis
      Cooke, K., Rottman, J., Zhan, J., et al. Journal for ImmunoTherapy of Cancer (2015): P336
    • Diverse in vivo effects of soluble and membrane-bound M-CSF on tumor-associated macrophages in lymphoma xenograft model
      Liao, J., Feng, W., Wang, R., et al. Oncotarget (2016): 1,354–66
    • Intratumoral heterogeneity identified at the epigenetic, genetic and transcriptional level in glioblastoma
      Parker, N.R., Hudson, A.L., Khong, P., et al. Scientific Reports (2016): 22,477
    • Dissecting Stages of Human Kidney Development and Tumorigenesis with Surface Markers Affords Simple Prospective Purification of Nephron Stem Cells
      Pode-Shakked, N., Pleniceanu, O., Gershon, R., et al. Scientific Reports (2016): 23,562
    • Variants in ELL2 influencing immunoglobulin levels associate with multiple myeloma
      Swaminathan, B., Thoreifsson, G., Jöud, M., et al. Nature Communications (2015): 7,213
    • Validation of COL11A1/procollagen 11A1 expression in TGF-β1-activated immortalised human mesenchymal cells and in stromal cells of human colon adenocarcinoma
      Galván, J.A., García-Martínez, J., Vázquez-Villa, F., et al. BMC Cancer (2014): 867
    • Transposon mutagenesis identifies genes driving hepatocellular carcinoma in a chronic hepatitis B mouse model
      Bard-Chapeau, E.A., Nguyen, A.T., Rust, A.G., et al. Nature Genetics (2014): 24–32
    • The tumor suppressor TERE1 (UBIAD1) prenyltransferase regulates the elevated cholesterol phenotype in castration resistant prostate cancer by controlling a program of ligand dependent SXR target genes
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      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

    • 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
    • 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
    • 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
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  • Other

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