Transcriptome

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  Subject Areas on Research

  • A Potential Contributory Role for Ciliary Dysfunction in the 16p11.2 600 kb BP4-BP5 Pathology. 
  • A Transcriptional Signature Identifies LKB1 Functional Status as a Novel Determinant of MEK Sensitivity in Lung Adenocarcinoma. 
  • A computational analysis of antisense off-targets in prokaryotic organisms. 
  • A diagnostic algorithm combining clinical and molecular data distinguishes Kawasaki disease from other febrile illnesses. 
  • A five-gene hedgehog signature developed as a patient preselection tool for hedgehog inhibitor therapy in medulloblastoma. 
  • A formalin-fixed paraffin-embedded (FFPE)-based prognostic signature to predict metastasis in clinically low risk stage I/II microsatellite stable colorectal cancer. 
  • A gene regulatory network for root epidermis cell differentiation in Arabidopsis. 
  • A host transcriptional signature for presymptomatic detection of infection in humans exposed to influenza H1N1 or H3N2. 
  • A meta-analysis of gene expression signatures of blood pressure and hypertension. 
  • A metabolic signature of colon cancer initiating cells. 
  • A novel diagnostic approach may reduce inappropriate antibiotic use for acute respiratory infections. 
  • A phylotranscriptomic analysis of gene family expansion and evolution in the largest order of pleurocarpous mosses (Hypnales, Bryophyta). 
  • A potentially abundant junctional RNA motif stabilized by m6A and Mg2. 
  • A seven-gene signature can predict distant recurrence in patients with triple-negative breast cancers who receive adjuvant chemotherapy following surgery. 
  • A signature of epithelial-mesenchymal plasticity and stromal activation in primary tumor modulates late recurrence in breast cancer independent of disease subtype. 
  • A timecourse analysis of systemic and gonadal effects of temperature on sexual development of the red-eared slider turtle Trachemys scripta elegans. 
  • A translatable predictor of human radiation exposure. 
  • A whole blood gene expression-based signature for smoking status. 
  • A whole-genome analysis of premature termination codons. 
  • ACTL6A Is Co-Amplified with p63 in Squamous Cell Carcinoma to Drive YAP Activation, Regenerative Proliferation, and Poor Prognosis. 
  • ADAR-Mediated RNA Editing Predicts Progression and Prognosis of Gastric Cancer. 
  • AHR2-Mediated transcriptomic responses underlying the synergistic cardiac developmental toxicity of PAHs. 
  • ALS-associated mutation FUS-R521C causes DNA damage and RNA splicing defects. 
  • Activation of the mTOR Pathway by Oxaliplatin in the Treatment of Colorectal Cancer Liver Metastasis. 
  • Adaptive Activation of a Stress Response Pathway Improves Learning and Memory Through Gs and β-Arrestin-1-Regulated Lactate Metabolism. 
  • Adjuvant-dependent innate and adaptive immune signatures of risk of SIVmac251 acquisition. 
  • Adult high-grade B-cell lymphoma with Burkitt lymphoma signature: genomic features and potential therapeutic targets. 
  • Age-dependent hepatic lymphoid organization directs successful immunity to hepatitis B. 
  • Allelic Imbalance Is a Prevalent and Tissue-Specific Feature of the Mouse Transcriptome. 
  • Alpha satellite DNA biology: finding function in the recesses of the genome. 
  • Alterations of a Cellular Cholesterol Metabolism Network Are a Molecular Feature of Obesity-Related Type 2 Diabetes and Cardiovascular Disease. 
  • Alveolar rhabdomyosarcoma-associated PAX3-FOXO1 promotes tumorigenesis via Hippo pathway suppression. 
  • An Eighteen-Gene Classifier Predicts Locoregional Recurrence in Post-Mastectomy Breast Cancer Patients. 
  • An age- and sex-specific gene expression score is associated with revascularization and coronary artery disease: Insights from the Prospective Multicenter Imaging Study for Evaluation of Chest Pain (PROMISE) trial. 
  • An integrative genomics approach identifies novel pathways that influence candidaemia susceptibility. 
  • Analyses of transcriptome sequences reveal multiple ancient large-scale duplication events in the ancestor of Sphagnopsida (Bryophyta). 
  • Analysis of blood-based gene expression signature in first-episode psychosis. 
  • Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation. 
  • Anchoring ethinylestradiol induced gene expression changes with testicular morphology and reproductive function in the medaka. 
  • Angiotensin receptor signaling and prostate tumor growth in mice. 
  • Assessment of gene expression in peripheral blood using RNAseq before and after weight restoration in anorexia nervosa. 
  • Association between early promoter-specific DNA methylation changes and outcome in older acute myeloid leukemia patients. 
  • Biologic effects of platelet-derived growth factor receptor α blockade in uterine cancer. 
  • Biological pathway selection through Bayesian integrative modeling. 
  • Blood transcriptomes reveal novel parasitic zoonoses circulating in Madagascar's lemurs. 
  • Branching process deconvolution algorithm reveals a detailed cell-cycle transcription program. 
  • Brassinosteroid, gibberellin and phytochrome impinge on a common transcription module in Arabidopsis. 
  • CD4 T follicular helper cell dynamics during SIV infection. 
  • Caenorhabditis elegans as an emerging model system in environmental epigenetics. 
  • Catabolic Defect of Branched-Chain Amino Acids Promotes Heart Failure. 
  • Challenges in elucidating the genetics of diabetic retinopathy. 
  • Chemotherapy Induces Programmed Cell Death-Ligand 1 Overexpression via the Nuclear Factor-κB to Foster an Immunosuppressive Tumor Microenvironment in Ovarian Cancer. 
  • Citrullination of histone H3 drives IL-6 production by bone marrow mesenchymal stem cells in MGUS and multiple myeloma. 
  • Comparative Developmental Transcriptomics Reveals Rewiring of a Highly Conserved Gene Regulatory Network during a Major Life History Switch in the Sea Urchin Genus Heliocidaris. 
  • Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi. 
  • Comparative integrated molecular analysis of intraocular medulloepitheliomas and central nervous system embryonal tumors with multilayered rosettes confirms that they are distinct nosologic entities. 
  • Comparing reference-based RNA-Seq mapping methods for non-human primate data. 
  • Comparison of immunogenicity, efficacy and transcriptome changes of inactivated rabies virus vaccine with different adjuvants. 
  • Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer. 
  • Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons. 
  • Comprehensive functional genomic resource and integrative model for the human brain. 
  • Comprehensive profiling of amino acid response uncovers unique methionine-deprived response dependent on intact creatine biosynthesis. 
  • Convergent transcriptional specializations in the brains of humans and song-learning birds. 
  • Core and region-enriched networks of behaviorally regulated genes and the singing genome. 
  • Cost-effectiveness of the 21-gene recurrence score assay in the context of multifactorial decision making to guide chemotherapy for early-stage breast cancer. 
  • DO-RIP-seq to quantify RNA binding sites transcriptome-wide. 
  • Data-driven asthma endotypes defined from blood biomarker and gene expression data. 
  • Desensitization and Incomplete Recovery of Hepatic Target Genes After Chronic Thyroid Hormone Treatment and Withdrawal in Male Adult Mice. 
  • Development of an objective gene expression panel as an alternative to self-reported symptom scores in human influenza challenge trials. 
  • Differential expression of the nuclear-encoded mitochondrial transcriptome in pediatric septic shock. 
  • Differential pulmonary transcriptomic profiles in murine lungs infected with low and highly virulent influenza H3N2 viruses reveal dysregulation of TREM1 signaling, cytokines, and chemokines. 
  • Differentially Expressed miRNAs in Hepatocellular Carcinoma Target Genes in the Genetic Information Processing and Metabolism Pathways. 
  • Differentially expressed microRNAs and affected biological pathways revealed by modulated modularity clustering (MMC) analysis of human preeclamptic and IUGR placentas. 
  • Divergent effects of glucose and fructose on hepatic lipogenesis and insulin signaling. 
  • Dynamic mRNA Transport and Local Translation in Radial Glial Progenitors of the Developing Brain. 
  • EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms. 
  • Effect of Human Genetic Variability on Gene Expression in Dorsal Root Ganglia and Association with Pain Phenotypes. 
  • Effects of Pubertal Exposure to Dietary Soy on Estrogen Receptor Activity in the Breast of Cynomolgus Macaques. 
  • Efficient purging of deleterious mutations in plants with haploid selfing. 
  • Epitranscriptomic Enhancement of Influenza A Virus Gene Expression and Replication. 
  • Evaluating whole transcriptome amplification for gene profiling experiments using RNA-Seq. 
  • Evaluation of microRNA expression in patient bone marrow aspirate slides. 
  • Evidence for type II cells as cells of origin of K-Ras-induced distal lung adenocarcinoma. 
  • Evolutionary Divergence of Gene and Protein Expression in the Brains of Humans and Chimpanzees. 
  • Exome sequencing identifies highly recurrent MED12 somatic mutations in breast fibroadenoma. 
  • Expression profiling of in vivo ductal carcinoma in situ progression models identified B cell lymphoma-9 as a molecular driver of breast cancer invasion. 
  • FAS Death Receptor: A Breast Cancer Subtype-Specific Radiation Response Biomarker and Potential Therapeutic Target. 
  • Full Spectrum of LPS Activation in Alveolar Macrophages of Healthy Volunteers by Whole Transcriptomic Profiling. 
  • Gene Expression Profile of Dendritic Cell-Tumor Cell Hybrids Determined by Microarrays and Its Implications for Cancer Immunotherapy. 
  • Gene Expression Profiles Link Respiratory Viral Infection, Platelet Response to Aspirin, and Acute Myocardial Infarction. 
  • Gene expression changes in immune response pathways following oral administration of tetrabromobisphenol A (TBBPA) in female Wistar Han rats. 
  • Gene expression profile in human trabecular meshwork from patients with primary open-angle glaucoma. 
  • Gene profiling of canine B-cell lymphoma reveals germinal center and postgerminal center subtypes with different survival times, modeling human DLBCL. 
  • General olfactory sensitivity database (GOSdb): candidate genes and their genomic variations. 
  • Genetic Differences in the Immediate Transcriptome Response to Stress Predict Risk-Related Brain Function and Psychiatric Disorders. 
  • Genetic and cellular evidence of decreased inflammation associated with reduced incidence of posttraumatic arthritis in MRL/MpJ mice. 
  • Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines. 
  • Genome-wide analysis of miRNA signature in the APPswe/PS1ΔE9 mouse model of alzheimer's disease. 
  • Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities. 
  • Genomic and clinical effects associated with a relaxation response mind-body intervention in patients with irritable bowel syndrome and inflammatory bowel disease. 
  • Genomic profiling in locally advanced and inflammatory breast cancer and its link to DCE-MRI and overall survival. 
  • Global Identification of EVI1 Target Genes in Acute Myeloid Leukemia. 
  • Haploinsufficiency for Core Exon Junction Complex Components Disrupts Embryonic Neurogenesis and Causes p53-Mediated Microcephaly. 
  • Hepatic gene expression profiles differentiate presymptomatic patients with mild versus severe nonalcoholic fatty liver disease. 
  • Hierarchical regulation of mRNA partitioning between the cytoplasm and the endoplasmic reticulum of mammalian cells. 
  • Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns. 
  • Host cell transcriptome profile during wild-type and attenuated dengue virus infection. 
  • Hybrid error correction and de novo assembly of single-molecule sequencing reads. 
  • Identification of the RNA recognition element of the RBPMS family of RNA-binding proteins and their transcriptome-wide mRNA targets. 
  • Impact of Therapy on Genomics and Transcriptomics in High-Risk Prostate Cancer Treated with Neoadjuvant Docetaxel and Androgen Deprivation Therapy. 
  • Inhibition of Dipeptidyl Peptidase-4 Impairs Ventricular Function and Promotes Cardiac Fibrosis in High Fat-Fed Diabetic Mice. 
  • Insights into osteoarthritis progression revealed by analyses of both knee tibiofemoral compartments. 
  • Integrating factor analysis and a transgenic mouse model to reveal a peripheral blood predictor of breast tumors. 
  • Integrative "omic" analysis of experimental bacteremia identifies a metabolic signature that distinguishes human sepsis from systemic inflammatory response syndromes. 
  • Integrative Genomics Identifies Novel Associations with APOL1 Risk Genotypes in Black NEPTUNE Subjects. 
  • Ki67 Proliferation Index as a Tool for Chemotherapy Decisions During and After Neoadjuvant Aromatase Inhibitor Treatment of Breast Cancer: Results From the American College of Surgeons Oncology Group Z1031 Trial (Alliance). 
  • LKB1 Loss induces characteristic patterns of gene expression in human tumors associated with NRF2 activation and attenuation of PI3K-AKT. 
  • Lacosamide improves outcome in a murine model of traumatic brain injury. 
  • Long-read sequencing and de novo assembly of a Chinese genome. 
  • Long-term IL-33-producing epithelial progenitor cells in chronic obstructive lung disease. 
  • MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics. 
  • Marine diatom proteorhodopsins and their potential role in coping with low iron availability. 
  • Metabolic programming and PDHK1 control CD4+ T cell subsets and inflammation. 
  • Metabolic stress is a barrier to Epstein-Barr virus-mediated B-cell immortalization. 
  • Metatranscriptomic Study of Common and Host-Specific Patterns of Gene Expression between Pines and Their Symbiotic Ectomycorrhizal Fungi in the Genus Suillus. 
  • Metatranscriptomic analysis of ectomycorrhizal roots reveals genes associated with Piloderma-Pinus symbiosis: improved methodologies for assessing gene expression in situ. 
  • Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape. 
  • Molecular Features Underlying Neurodegeneration Identified through In Vitro Modeling of Genetically Diverse Parkinson's Disease Patients. 
  • Molecular Signature to Risk-Stratify Prostate Cancer of Intermediate Risk. 
  • Molecular alterations in skeletal muscle in rheumatoid arthritis are related to disease activity, physical inactivity, and disability. 
  • Molt-dependent transcriptomic analysis of cement proteins in the barnacle Amphibalanus amphitrite. 
  • Morphogenesis and Compartmentalization of the Intestinal Crypt. 
  • Multifunctional roles for the protein translocation machinery in RNA anchoring to the endoplasmic reticulum. 
  • Nanostring-based multigene assay to predict recurrence for gastric cancer patients after surgery. 
  • New clues to the molecular pathogenesis of Burkitt lymphoma revealed through next-generation sequencing. 
  • Notch3 pathway alterations in ovarian cancer. 
  • Nutritional control of mRNA isoform expression during developmental arrest and recovery in C. elegans. 
  • PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data. 
  • Pan-cancer transcriptomic analysis associates long non-coding RNAs with key mutational driver events. 
  • Pediatric Eosinophilic Esophagitis Symptom Scores (PEESS v2.0) identify histologic and molecular correlates of the key clinical features of disease. 
  • Peripheral androgen receptor gene suppression rescues disease in mouse models of spinal and bulbar muscular atrophy. 
  • Phosphoproteome Integration Reveals Patient-Specific Networks in Prostate Cancer. 
  • Phylotranscriptomic analysis of the origin and early diversification of land plants. 
  • Pleiotropic effects of deubiquitinating enzyme Ubp5 on growth and pathogenesis of Cryptococcus neoformans. 
  • Pleiotropic roles of the Msi1-like protein Msl1 in Cryptococcus neoformans. 
  • Prediction of autism by translation and immune/inflammation coexpressed genes in toddlers from pediatric community practices. 
  • Psychological resilience and the gene regulatory impact of posttraumatic stress in Nepali child soldiers. 
  • Qualifiers of atypia in the cytologic diagnosis of thyroid nodules are associated with different Afirma gene expression classifier results and clinical outcomes. 
  • RNA Binding Proteins Control Transdifferentiation of Hepatic Stellate Cells into Myofibroblasts. 
  • RSK3/4 mediate resistance to PI3K pathway inhibitors in breast cancer. 
  • Race-related differences in antibody responses to the inactivated influenza vaccine are linked to distinct pre-vaccination gene expression profiles in blood. 
  • Recovery from an acute infection in C. elegans requires the GATA transcription factor ELT-2. 
  • Reduced expression of brain-enriched microRNAs in glioblastomas permits targeted regulation of a cell death gene. 
  • Relationship between methylome and transcriptome in patients with nonalcoholic fatty liver disease. 
  • Rem2 is an activity-dependent negative regulator of dendritic complexity in vivo. 
  • Reply: To PMID 23913408. 
  • STAT3 Regulates Self-Renewal of Adult Muscle Satellite Cells during Injury-Induced Muscle Regeneration. 
  • Selecting cases for whom additional tests can improve prognostication. 
  • Senataxin, A Novel Helicase at the Interface of RNA Transcriptome Regulation and Neurobiology: From Normal Function to Pathological Roles in Motor Neuron Disease and Cerebellar Degeneration. 
  • Sorting multiple classes in multi-dimensional ROC analysis: parametric and nonparametric approaches. 
  • Systematic transcriptome analysis reveals elevated expression of alcohol-metabolizing genes in NAFLD livers. 
  • Systemic surfaceome profiling identifies target antigens for immune-based therapy in subtypes of advanced prostate cancer. 
  • TNF-α induces phenotypic modulation in cerebral vascular smooth muscle cells: implications for cerebral aneurysm pathology. 
  • The Cryptococcus neoformans transcriptome at the site of human meningitis. 
  • The PsychENCODE project. 
  • The draft genome of tropical fruit durian (Durio zibethinus). 
  • The dynamic epitranscriptome: N6-methyladenosine and gene expression control. 
  • The evolutionary history of ferns inferred from 25 low-copy nuclear genes. 
  • The expanding implications of polyploidy. 
  • The human olfactory transcriptome. 
  • The impact of human and mouse differences in NOS2 gene expression on the brain's redox and immune environment. 
  • The oncogenic properties of EWS/WT1 of desmoplastic small round cell tumors are unmasked by loss of p53 in murine embryonic fibroblasts. 
  • The phylogeny of extant starfish (Asteroidea: Echinodermata) including Xyloplax, based on comparative transcriptomics. 
  • The protein composition of the digestive fluid from the venus flytrap sheds light on prey digestion mechanisms. 
  • The role of extracellular matrix components in pin bone attachments during storage-a comparison between farmed Atlantic salmon (Salmo salar) and cod (Gadus morhua L.). 
  • The role of β-arrestin2-dependent signaling in thoracic aortic aneurysm formation in a murine model of Marfan syndrome. 
  • The transcriptional landscape of age in human peripheral blood. 
  • The transcriptomic response of rat hepatic stellate cells to endotoxin: implications for hepatic inflammation and immune regulation. 
  • Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. 
  • Tissue transcriptome-driven identification of epidermal growth factor as a chronic kidney disease biomarker. 
  • Tissue- and strain-specific effects of a genotoxic carcinogen 1,3-butadiene on chromatin and transcription. 
  • Transcription factors MYOCD, SRF, Mesp1 and SMARCD3 enhance the cardio-inducing effect of GATA4, TBX5, and MEF2C during direct cellular reprogramming. 
  • Transcriptional diversity during lineage commitment of human blood progenitors. 
  • Transcriptional profile of hippocampal dentate granule cells in four rat epilepsy models. 
  • Transcriptional profiling of olfactory system development identifies distal antenna as a regulator of subset of neuronal fates. 
  • Transcriptome and epigenome landscape of human cortical development modeled in organoids. 
  • Transcriptome changes affecting Hedgehog and cytokine signalling in the umbilical cord: implications for disease risk. 
  • Transcriptome-mining for single-copy nuclear markers in ferns. 
  • Transcriptomic Analysis of the Host Response and Innate Resilience to Enterotoxigenic Escherichia coli Infection in Humans. 
  • Transcriptomic analysis of Nodal- and BMP-associated genes during juvenile development of the sea urchin Heliocidaris erythrogramma. 
  • Transcriptomic analysis of peripheral blood mononuclear cells in rapid progressors in early HIV infection identifies a signature closely correlated with disease progression. 
  • Transcriptomic analysis of the highly derived radial body plan of a sea urchin. 
  • Unexpected role of interferon-γ in regulating neuronal connectivity and social behaviour. 
  • Unique cell-type-specific patterns of DNA methylation in the root meristem. 
  • Up-regulated expression of extracellular matrix remodeling genes in phagocytically challenged trabecular meshwork cells. 
  • Urinary-cell mRNA profile and acute cellular rejection in kidney allografts. 
  • Utilization of a Genomic Classifier for Prediction of Metastasis Following Salvage Radiation Therapy after Radical Prostatectomy. 
  • Whole blood gene expression profiles distinguish clinical phenotypes of venous thromboembolism. 
  • Whole-genome duplication and molecular evolution in Cornus L. (Cornaceae) - Insights from transcriptome sequences. 
  • miR-27b shapes the presynaptic transcriptome and influences neurotransmission by silencing the polycomb group protein Bmi1. 
  • β-Catenin-regulated myeloid cell adhesion and migration determine wound healing. 
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  Keywords of People

  • Baugh, L. Ryan, Associate Professor of Biology, Biology
  • Choi, Steven Sok, Associate Professor of Medicine, Medicine, Gastroenterology
  • Fox, Donald T, Assistant Professor of Pharmacology & Cancer Biology, Duke Science & Society
  • Hartemink, Alexander J., Professor in the Department of Computer Science, Biology
  • Hogan, Brigid L. M., George Barth Geller Professor, Cell Biology
  • Laskowitz, Daniel Todd, Professor of Neurology, Information Initiative at Duke
  • Linardic, Corinne Mary, Associate Professor of Pediatrics, Pharmacology & Cancer Biology
  • Liton, Paloma Borrajo, Associate Professor in Ophthalmology, Pathology
  • Liu, Yutao, Adjunct Assistant Professor in the Department of Medicine, Medicine, Medical Genetics
  • McClain, Micah Thomas, Associate Professor of Medicine, Medicine, Infectious Diseases
  • Meyer, Joel, Truman and Nellie Semans/Alex Brown and Sons Associate Professor of Molecular Environmental Toxicology, Duke University Energy Initiative
  • Pang, Herbert, Adjunct Assistant Professor in the Department of Biostatistics and Bioinformatics, Biostatistics & Bioinformatics
  • Shinohara, Mari L., Associate Professor of Immunology, Immunology
  • Tsalik, Ephraim, Associate Professor of Medicine, Molecular Genetics and Microbiology
  • Wray, Gregory Allan, Professor of Biology, Information Initiative at Duke