Transcriptome

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  Subject Areas on Research

  • A Beautiful Day in the Neighborhood: Application of Single-Cell Transcriptomics to Unravel Liver Cell Heterogeneity in Diseased Human Livers. 
  • A Fibrosis-Independent Hepatic Transcriptomic Signature Identifies Drivers of Disease Progression in Primary Sclerosing Cholangitis. 
  • A Human Adult Stem Cell Signature Marks Aggressive Variants across Epithelial Cancers. 
  • A Transcriptome-Wide Association Study Among 97,898 Women to Identify Candidate Susceptibility Genes for Epithelial Ovarian Cancer Risk. 
  • A coding and non-coding transcriptomic perspective on the genomics of human metabolic disease. 
  • A comparative transcriptomic analysis of astrocytes differentiation from human neural progenitor cells. 
  • A computational analysis of antisense off-targets in prokaryotic organisms. 
  • A draft genome sequence of the elusive giant squid, Architeuthis dux. 
  • 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 functional genomics predictive network model identifies regulators of inflammatory bowel disease. 
  • A gene regulatory network for root epidermis cell differentiation in Arabidopsis. 
  • A glomerular transcriptomic landscape of apolipoprotein L1 in Black patients with focal segmental glomerulosclerosis. 
  • A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck). 
  • A host transcriptional signature for presymptomatic detection of infection in humans exposed to influenza H1N1 or H3N2. 
  • A human-based multi-gene signature enables quantitative drug repurposing for metabolic disease. 
  • A meta-analysis of gene expression signatures of blood pressure and hypertension. 
  • A metabolic signature of colon cancer initiating cells. 
  • A microRNA signature profile in EBV+ diffuse large B-cell lymphoma of the elderly. 
  • A multimodal cell census and atlas of the mammalian primary motor cortex. 
  • 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 reference tissue atlas for the human kidney. 
  • 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 single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants. 
  • A statistical framework for cross-tissue transcriptome-wide association analysis. 
  • A survey of plant and algal genomes and transcriptomes reveals new insights into the evolution and function of the cellulose synthase superfamily. 
  • A timecourse analysis of systemic and gonadal effects of temperature on sexual development of the red-eared slider turtle Trachemys scripta elegans. 
  • A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex. 
  • 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. 
  • APOL1-G0 protects podocytes in a mouse model of HIV-associated nephropathy. 
  • ATM Paradoxically Promotes Oncogenic Transformation via Transcriptional Reprogramming. 
  • Absence of S100A4 in the mouse lens induces an aberrant retina-specific differentiation program and cataract. 
  • Activation of a nerve injury transcriptional signature in airway-innervating sensory neurons after lipopolysaccharide-induced lung inflammation. 
  • 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- and sex-dependent changes in levels of circulating brain-enriched microRNAs during normal aging. 
  • 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 age-independent gene signature for monitoring acute rejection in kidney transplantation. 
  • An eQTL Landscape of Kidney Tissue in Human Nephrotic Syndrome. 
  • An embryonic system to assess direct and indirect Wnt transcriptional targets. 
  • An integrative genomics approach identifies novel pathways that influence candidaemia susceptibility. 
  • An integrative model of pathway convergence in genetically heterogeneous blast crisis chronic myeloid leukemia. 
  • An intrinsic oscillator drives the blood stage cycle of the malaria parasite Plasmodium falciparum. 
  • Analyses of transcriptome sequences reveal multiple ancient large-scale duplication events in the ancestor of Sphagnopsida (Bryophyta). 
  • 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. 
  • Assessing the co-variability of DNA methylation across peripheral cells and tissues: Implications for the interpretation of findings in epigenetic epidemiology. 
  • Association between early promoter-specific DNA methylation changes and outcome in older acute myeloid leukemia patients. 
  • Avian Binocularity and Adaptation to Nocturnal Environments: Genomic Insights from a Highly Derived Visual Phenotype. 
  • Biologic effects of platelet-derived growth factor receptor α blockade in uterine cancer. 
  • Biomarkers of cavernous angioma with symptomatic hemorrhage. 
  • Blood monocyte transcriptome and epigenome analyses reveal loci associated with human atherosclerosis. 
  • Blood transcriptomes reveal novel parasitic zoonoses circulating in Madagascar's lemurs. 
  • Borderline Estrogen Receptor-Positive Breast Cancers in Black and White Women. 
  • Branching process deconvolution algorithm reveals a detailed cell-cycle transcription program. 
  • Brassinosteroid, gibberellin, and phytochrome signalling pathways impinge on a common transcription module in Arabidopsis 
  • Bridging the gaps: using an NHP model to predict single dose radiation absorption in humans. 
  • CD30 expression defines a novel subgroup of diffuse large B-cell lymphoma with favorable prognosis and distinct gene expression signature: a report from the International DLBCL Rituximab-CHOP Consortium Program Study. 
  • 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. 
  • Causal network inference from gene transcriptional time-series response to glucocorticoids. 
  • Cell type- and species-specific host responses to Toxoplasma gondii and its near relatives. 
  • 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. 
  • Childhood cerebellar tumours mirror conserved fetal transcriptional programs. 
  • Citrullination of histone H3 drives IL-6 production by bone marrow mesenchymal stem cells in MGUS and multiple myeloma. 
  • Clinical features, tumor biology, and prognosis associated with MYC rearrangement and Myc overexpression in diffuse large B-cell lymphoma patients treated with rituximab-CHOP. 
  • Clinical-pathological correlations of BAV and the attendant thoracic aortopathies. Part 2: Pluridisciplinary perspective on their genetic and molecular origins. 
  • Clinicopathological Features of Triple-Negative Breast Cancer Epigenetic Subtypes. 
  • Collagen type-V is a danger signal associated with primary graft dysfunction in lung transplantation. 
  • 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 RNA sequencing reveals substantial genetic variation in endangered primates. 
  • Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi. 
  • Comparative cellular analysis of motor cortex in human, marmoset and mouse. 
  • Comparative integrated molecular analysis of intraocular medulloepitheliomas and central nervous system embryonal tumors with multilayered rosettes confirms that they are distinct nosologic entities. 
  • Comparative transcriptomics of fungal endophytes in co-culture with their moss host Dicranum scoparium reveals fungal trophic lability and moss unchanged to slightly increased growth rates. 
  • Comparing reference-based RNA-Seq mapping methods for non-human primate data. 
  • Comparison of Human Tissue Microarray to Human Pericyte Transcriptome Yields Novel Perivascular Cell Markers. 
  • 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. 
  • Computational Analysis of Targeting SARS-CoV-2, Viral Entry Proteins ACE2 and TMPRSS2, and Interferon Genes by Host MicroRNAs. 
  • Constitutively active ESR1 mutations in gynecologic malignancies and clinical response to estrogen-receptor directed therapies. 
  • Contribution of plasma cells and B cells to hidradenitis suppurativa pathogenesis. 
  • Convergent transcriptional specializations in the brains of humans and song-learning birds. 
  • Copper Availability Influences the Transcriptomic Response of Candida albicans to Fluconazole Stress. 
  • Copy number variation is associated with gene expression change in archaea. 
  • 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. 
  • Cryptococcus neoformans Chitin Synthase 3 Plays a Critical Role in Dampening Host Inflammatory Responses. 
  • Cryptococcus neoformans resists to drastic conditions by switching to viable but non-culturable cell phenotype. 
  • DART-seq: an antibody-free method for global m6A detection. 
  • DO-RIP-seq to quantify RNA binding sites transcriptome-wide. 
  • Data-driven asthma endotypes defined from blood biomarker and gene expression data. 
  • De Novo SOX6 Variants Cause a Neurodevelopmental Syndrome Associated with ADHD, Craniosynostosis, and Osteochondromas. 
  • De novo transcriptomics reveal distinct phototransduction signaling components in the retina and skin of a color-changing vertebrate, the hogfish (Lachnolaimus maximus). 
  • Deep-RACE: Comprehensive Search for Novel ncRNAs Associated to a Specific Locus. 
  • Deletion of the glucagon receptor gene before and after experimental diabetes reveals differential protection from hyperglycemia. 
  • Desensitization and Incomplete Recovery of Hepatic Target Genes After Chronic Thyroid Hormone Treatment and Withdrawal in Male Adult Mice. 
  • Detection of differentially abundant cell subpopulations in scRNA-seq data. 
  • Determining clinical course of diffuse large B-cell lymphoma using targeted transcriptome and machine learning algorithms. 
  • Development and Validation of the Gene Expression Predictor of High-grade Serous Ovarian Carcinoma Molecular SubTYPE (PrOTYPE). 
  • Development of an objective gene expression panel as an alternative to self-reported symptom scores in human influenza challenge trials. 
  • Developmental single-cell transcriptomics in the Lytechinus variegatus sea urchin embryo. 
  • 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 conserved transcriptomic response to adversity related to self-rated health in the multi-ethnic study of atherosclerosis. 
  • Differentially expressed microRNAs and affected biological pathways revealed by modulated modularity clustering (MMC) analysis of human preeclamptic and IUGR placentas. 
  • Discriminating Bacterial and Viral Infection Using a Rapid Host Gene Expression Test. 
  • Dissecting the human kidney allograft transcriptome: single-cell RNA sequencing. 
  • Distinct functional programming of human fetal and adult monocytes. 
  • Divergence in problem-solving skills is associated with differential expression of glutamate receptors in wild finches. 
  • Divergent effects of glucose and fructose on hepatic lipogenesis and insulin signaling. 
  • Diverse genetic-driven immune landscapes dictate tumor progression through distinct mechanisms. 
  • Dynamic evolution of base composition: causes and consequences in avian phylogenomics. 
  • Dynamic mRNA Transport and Local Translation in Radial Glial Progenitors of the Developing Brain. 
  • Dysregulated CXCR4 expression promotes lymphoma cell survival and independently predicts disease progression in germinal center B-cell-like diffuse large B-cell lymphoma. 
  • Dysregulated transcriptional responses to SARS-CoV-2 in the periphery. 
  • Dysregulation of multiple metabolic networks related to brain transmethylation and polyamine pathways in Alzheimer disease: A targeted metabolomic and transcriptomic study. 
  • EZH2 expression is associated with inferior overall survival in mantle cell lymphoma. 
  • 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 Combined Tristetraprolin/Tumor Necrosis Factor Receptor Deficiency on the Splenic Transcriptome. 
  • Effects of Pubertal Exposure to Dietary Soy on Estrogen Receptor Activity in the Breast of Cynomolgus Macaques. 
  • Efferocytosis induces a novel SLC program to promote glucose uptake and lactate release. 
  • Efficacy and safety of next-generation tick transcriptome-derived direct thrombin inhibitors. 
  • Efficient purging of deleterious mutations in plants with haploid selfing. 
  • Electrotaxis of Glioblastoma and Medulloblastoma Spheroidal Aggregates. 
  • Emerging approaches and technologies in transplantation: the potential game changers. 
  • Enhancer selection dictates gene expression responses in remote organs during tissue regeneration. 
  • Epigenetic Signatures of Cigarette Smoking. 
  • Epigenetic and epitranscriptomic regulation of viral replication. 
  • Epigenetic dysregulation of Oxtr in Tet1-deficient mice has implications for neuropsychiatric disorders. 
  • Epitranscriptomic Addition of m5C to HIV-1 Transcripts Regulates Viral Gene Expression. 
  • Epitranscriptomic Enhancement of Influenza A Virus Gene Expression and Replication. 
  • Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution. 
  • Evaluating whole transcriptome amplification for gene profiling experiments using RNA-Seq 
  • Evaluation of NF-κB subunit expression and signaling pathway activation demonstrates that p52 expression confers better outcome in germinal center B-cell-like diffuse large B-cell lymphoma in association with CD30 and BCL2 functions. 
  • 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. 
  • Evolution of vocal learning and spoken language. 
  • 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 Profiling of Bronchoalveolar Lavage Cells During Aspergillus Colonization of the Lung Allograft. 
  • Gene Expression Profiling of Cutaneous Injured and Non-Injured Nociceptors in SNI Animal Model of Neuropathic Pain. 
  • Gene Expression of Diverse Cryptococcus Isolates during Infection of the Human Central Nervous System. 
  • Gene Expression of Haloferax volcanii on Intermediate and Abundant Sources of Fixed Nitrogen. 
  • 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 expression signatures of individual ductal carcinoma in situ lesions identify processes and biomarkers associated with progression towards invasive ductal carcinoma. 
  • Gene flow, divergent selection and resistance to introgression in two species of morning glories (Ipomoea). 
  • 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. 
  • Genetic architecture of gene expression traits across diverse populations. 
  • Genetic pathway analysis reveals a major role for extracellular matrix organization in inflammatory and neuropathic pain. 
  • Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines. 
  • Genome-scale transcriptomic insights into early-stage fruit development in woodland strawberry Fragaria vesca. 
  • Genome-wide analysis of miRNA signature in the APPswe/PS1ΔE9 mouse model of alzheimer's disease. 
  • Genome-wide expression profiles of subchondral bone in osteoarthritis. 
  • Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities. 
  • Genomic and Transcriptomic Profiling of Combined Hepatocellular and Intrahepatic Cholangiocarcinoma Reveals Distinct Molecular Subtypes. 
  • Genomic and phenotypic insights from an atlas of genetic effects on DNA methylation. 
  • Genomic profiling in locally advanced and inflammatory breast cancer and its link to DCE-MRI and overall survival. 
  • Genomic signatures of G-protein-coupled receptor expansions reveal functional transitions in the evolution of cephalopod signal transduction. 
  • Germline AGO2 mutations impair RNA interference and human neurological development. 
  • Global Identification of EVI1 Target Genes in Acute Myeloid Leukemia. 
  • Global gene expression and chromatin accessibility of the peripheral nervous system in animal models of persistent pain. 
  • Glucose-Induced Trophic Shift in an Endosymbiont Dinoflagellate with Physiological and Molecular Consequences. 
  • Haploinsufficiency for Core Exon Junction Complex Components Disrupts Embryonic Neurogenesis and Causes p53-Mediated Microcephaly. 
  • Hedgehog Signaling Regulates Metabolism and Polarization of Mammary Tumor-Associated Macrophages. 
  • Hemochromatosis drives acute lethal intestinal responses to hyperyersiniabactin-producing Yersinia pseudotuberculosis. 
  • 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. 
  • High-throughput intracellular biopsy of microRNAs for dissecting the temporal dynamics of cellular heterogeneity. 
  • Highly recurrent CBS epimutations in gastric cancer CpG island methylator phenotypes and inflammation. 
  • Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns 
  • Host cell transcriptome profile during wild-type and attenuated dengue virus infection. 
  • Human Lung Stem Cell-Based Alveolospheres Provide Insights into SARS-CoV-2-Mediated Interferon Responses and Pneumocyte Dysfunction. 
  • Human genetic variation in GLS2 is associated with development of complicated Staphylococcus aureus bacteremia. 
  • Hybrid error correction and de novo assembly of single-molecule sequencing reads. 
  • Identification of Long Noncoding RNAs Associated to Human Disease Susceptibility. 
  • Identification of the RNA recognition element of the RBPMS family of RNA-binding proteins and their transcriptome-wide mRNA targets. 
  • Identifying gene expression from single cells to single genes. 
  • Identifying nootropic drug targets via large-scale cognitive GWAS and transcriptomics. 
  • Identifying transcriptional profiles and evaluating prognostic biomarkers of HIV-associated diffuse large B-cell lymphoma from Malawi. 
  • Immune checkpoint modulation enhances HIV-1 antibody induction. 
  • Impact of Therapy on Genomics and Transcriptomics in High-Risk Prostate Cancer Treated with Neoadjuvant Docetaxel and Androgen Deprivation Therapy. 
  • Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline. 
  • 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. 
  • Integrated Analysis of RNA and DNA from the Phase III Trial CALGB 40601 Identifies Predictors of Response to Trastuzumab-Based Neoadjuvant Chemotherapy in HER2-Positive Breast Cancer. 
  • Integrated genomic analysis of survival outliers in glioblastoma. 
  • 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. 
  • Integrative functional genomic analysis of human brain development and neuropsychiatric risks. 
  • 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). 
  • Lacosamide improves outcome in a murine model of traumatic brain injury. 
  • Landscape of stimulation-responsive chromatin across diverse human immune cells. 
  • Large-Scale Characterization of Systemic Sclerosis Serum Protein Profile: Comparison to Peripheral Blood Cell Transcriptome and Correlations With Skin/Lung Fibrosis. 
  • Layers of regulation of cell-cycle gene expression in the budding yeast Saccharomyces cerevisiae. 
  • Long-term outdoor air pollution and DNA methylation in circulating monocytes: results from the Multi-Ethnic Study of Atherosclerosis (MESA). 
  • Longevity-related molecular pathways are subject to midlife "switch" in humans. 
  • Loss of PRDM1/BLIMP-1 function contributes to poor prognosis of activated B-cell-like diffuse large B-cell lymphoma. 
  • Loss of the tumor suppressor, Tp53, enhances the androgen receptor-mediated oncogenic transformation and tumor development in the mouse prostate. 
  • MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics. 
  • MYC/BCL2 protein coexpression contributes to the inferior survival of activated B-cell subtype of diffuse large B-cell lymphoma and demonstrates high-risk gene expression signatures: a report from The International DLBCL Rituximab-CHOP Consortium Program. 
  • Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation. 
  • Machine learning predicts stem cell transplant response in severe scleroderma. 
  • Mapping RNA Modifications Using Photo-Crosslinking-Assisted Modification Sequencing. 
  • Marine diatom proteorhodopsins and their potential role in coping with low iron availability. 
  • Metabolic Network Analysis Reveals Altered Bile Acid Synthesis and Metabolism in Alzheimer's Disease. 
  • Metabolic landscape of the tumor microenvironment at single cell resolution. 
  • Metabolic programming and PDHK1 control CD4+ T cell subsets and inflammation. 
  • Metabolic stress is a barrier to Epstein-Barr virus-mediated B-cell immortalization. 
  • Metabolome-based signature of disease pathology in MS. 
  • 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. 
  • Methylomics of gene expression in human monocytes. 
  • MicroRNA miR-24-3p reduces DNA damage responses, apoptosis, and susceptibility to chronic obstructive pulmonary disease. 
  • Microarray gene expression profiles from mature gonad tissues of Atlantic bluefin tuna, Thunnus thynnus in the Gulf of Mexico. 
  • Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape. 
  • Microglial activation in an amyotrophic lateral sclerosis-like model caused by Ranbp2 loss and nucleocytoplasmic transport impairment in retinal ganglion neurons. 
  • Misexpression of ptf1a in cortical pyramidal cells in vivo promotes an inhibitory peptidergic identity. 
  • Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers. 
  • Molecular Features Underlying Neurodegeneration Identified through In Vitro Modeling of Genetically Diverse Parkinson's Disease Patients. 
  • Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma. 
  • Molecular Profiling of Human Induced Pluripotent Stem Cell-Derived Hypothalamic Neurones Provides Developmental Insights into Genetic Loci for Body Weight Regulation. 
  • 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. 
  • Molecular footprint of Medawar's mutation accumulation process in mammalian aging. 
  • Monocyte-derived transcriptome signature indicates antibody-dependent cellular phagocytosis as a potential mechanism of vaccine-induced protection against HIV-1. 
  • Morphogenesis and Compartmentalization of the Intestinal Crypt. 
  • Multi-ethnic genome-wide association study for atrial fibrillation. 
  • Multifunctional roles for the protein translocation machinery in RNA anchoring to the endoplasmic reticulum. 
  • Multiple sclerosis genomic map implicates peripheral immune cells and microglia in susceptibility. 
  • Mutation of a PER2 phosphodegron perturbs the circadian phosphoswitch. 
  • Myeloablation followed by autologous stem cell transplantation normalises systemic sclerosis molecular signatures. 
  • N6-methyladenosine alters RNA structure to regulate binding of a low-complexity protein. 
  • NCKAP1 Disruptive Variants Lead to a Neurodevelopmental Disorder with Core Features of Autism. 
  • NF-κB p50 activation associated with immune dysregulation confers poorer survival for diffuse large B-cell lymphoma patients with wild-type p53. 
  • Nanostring-based multigene assay to predict recurrence for gastric cancer patients after surgery. 
  • Neonatal Rhesus Macaques Have Distinct Immune Cell Transcriptional Profiles following HIV Envelope Immunization. 
  • Neural Crest-Like Stem Cell Transcriptome Analysis Identifies LPAR1 in Melanoma Progression and Therapy Resistance. 
  • Neuronal vulnerability and multilineage diversity in multiple sclerosis. 
  • New clues to the molecular pathogenesis of Burkitt lymphoma revealed through next-generation sequencing. 
  • Notch3 pathway alterations in ovarian cancer. 
  • Novel bioinformatic classification system for genetic signatures identification in diffuse large B-cell lymphoma. 
  • Nutritional control of mRNA isoform expression during developmental arrest and recovery in C. elegans. 
  • Obesity remodels activity and transcriptional state of a lateral hypothalamic brake on feeding. 
  • Ocean acidification induces distinct transcriptomic responses across life history stages of the sea urchin Heliocidaris erythrogramma. 
  • One thousand plant transcriptomes and the phylogenomics of green plants. 
  • Opportunities-and hard work-ahead. 
  • Osteopontin deficiency ameliorates Alport pathology by preventing tubular metabolic deficits. 
  • PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data. 
  • PAX9 regulates squamous cell differentiation and carcinogenesis in the oro-oesophageal epithelium. 
  • PI3K regulation of RAC1 is required for KRAS-induced pancreatic tumorigenesis in mice. 
  • PPM1D mutations are oncogenic drivers of de novo diffuse midline glioma formation. 
  • Pan-cancer Convergence to a Small-Cell Neuroendocrine Phenotype that Shares Susceptibilities with Hematological Malignancies. 
  • Pan-cancer transcriptomic analysis associates long non-coding RNAs with key mutational driver events. 
  • Pathway signatures derived from on-treatment tumor specimens predict response to anti-PD1 blockade in metastatic melanoma. 
  • Patterns of transcriptional parallelism and variation in the developing olfactory system of Drosophila species. 
  • Pediatric Eosinophilic Esophagitis Symptom Scores (PEESS v2.0) identify histologic and molecular correlates of the key clinical features of disease. 
  • Peripheral blood gene expression signatures which reflect smoking and aspirin exposure are associated with cardiovascular events. 
  • Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics. 
  • Phenotypic spectrum and transcriptomic profile associated with germline variants in TRAF7. 
  • 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. 
  • Preface. 
  • Primary Bone Lymphoma Exhibits a Favorable Prognosis and Distinct Gene Expression Signatures Resembling Diffuse Large B-Cell Lymphoma Derived From Centrocytes in the Germinal Center. 
  • Primary tumor microRNA signature predicts recurrence and survival in patients with locally advanced esophageal adenocarcinoma. 
  • Prognostic and biological significance of survivin expression in patients with diffuse large B-cell lymphoma treated with rituximab-CHOP therapy. 
  • Prognostic factors, therapeutic approaches, and distinct immunobiologic features in patients with primary mediastinal large B-cell lymphoma on long-term follow-up. 
  • Prognostic gene expression signature for high-grade serous ovarian cancer. 
  • Prospective Evaluation of Clinical Outcomes Using a Multiplex Liquid Biopsy Targeting Diverse Resistance Mechanisms in Metastatic Prostate Cancer. 
  • Prostaglandin-mediated effects in early canine corpus luteum: In vivo effects on vascular and immune factors. 
  • Psychological resilience and the gene regulatory impact of posttraumatic stress in Nepali child soldiers. 
  • Pulse magnetization elicits differential gene expression in the central nervous system of the Caribbean spiny lobster, Panulirus argus. 
  • Qualifiers of atypia in the cytologic diagnosis of thyroid nodules are associated with different Afirma gene expression classifier results and clinical outcomes. 
  • Quantification of Glomerular Structural Lesions: Associations With Clinical Outcomes and Transcriptomic Profiles in Nephrotic Syndrome. 
  • RAB11FIP5-Deficient Mice Exhibit Cytokine-Related Transcriptomic Signatures. 
  • RAP2 mediates mechanoresponses of the Hippo pathway. 
  • RCA2: a scalable supervised clustering algorithm that reduces batch effects in scRNA-seq data. 
  • RIPK3 upregulation confers robust proliferation and collateral cystine-dependence on breast cancer recurrence. 
  • RNA Binding Proteins Control Transdifferentiation of Hepatic Stellate Cells into Myofibroblasts. 
  • RNA-based analyses reveal fungal communities structured by a senescence gradient in the moss Dicranum scoparium and the presence of putative multi-trophic fungi. 
  • RSK3/4 mediate resistance to PI3K pathway inhibitors in breast cancer. 
  • RUNX1 maintains the identity of the fetal ovary through an interplay with FOXL2. 
  • Race-related differences in antibody responses to the inactivated influenza vaccine are linked to distinct pre-vaccination gene expression profiles in blood. 
  • Rapid phosphoproteomic and transcriptomic changes in the rhizobia-legume symbiosis. 
  • Re-annotation of the woodland strawberry (Fragaria vesca) genome. 
  • 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. 
  • Relative contribution of clinicopathological variables, genomic markers, transcriptomic subtyping and microenvironment features for outcome prediction in stage II/III colorectal cancer. 
  • Rem2 is an activity-dependent negative regulator of dendritic complexity in vivo. 
  • Reply to L. Casadaban et al. 
  • Reply: To PMID 23913408. 
  • Ring finger protein 121 is a potent regulator of adeno-associated viral genome transcription. 
  • Risk factors, transcriptomics, and outcomes of myocardial injury following lower extremity revascularization. 
  • SIV-induced terminally differentiated adaptive NK cells in lymph nodes associated with enhanced MHC-E restricted activity. 
  • 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. 
  • Shared in planta population and transcriptomic features of nonpathogenic members of endophytic phyllosphere microbiota. 
  • Single cell transcriptomics in human osteoarthritis synovium and in silico deconvoluted bulk RNA sequencing. 
  • Single cell transcriptomics of mouse kidney transplants reveals a myeloid cell pathway for transplant rejection. 
  • Single cell transcriptomics of primate sensory neurons identifies cell types associated with chronic pain. 
  • Single nucleus multi-omics regulatory landscape of the murine pituitary. 
  • Single-Cell Mapping of Progressive Fetal-to-Adult Transition in Human Naive T Cells. 
  • Single-Cell-Based High-Throughput Ig and TCR Repertoire Sequencing Analysis in Rhesus Macaques. 
  • Single-cell RNA-seq reveals TOX as a key regulator of CD8+ T cell persistence in chronic infection. 
  • Single-cell RNA-seq reveals transcriptomic heterogeneity mediated by host-pathogen dynamics in lymphoblastoid cell lines. 
  • Single-cell transcriptomic analysis of the immune cell landscape in the aged mouse brain after ischemic stroke. 
  • Sorting multiple classes in multi-dimensional ROC analysis: parametric and nonparametric approaches. 
  • Spatiotemporal analysis identifies ABF2 and ABF3 as key hubs of endodermal response to nitrate. 
  • Spleen tyrosine kinase activity regulates epidermal growth factor receptor signaling pathway in ovarian cancer. 
  • Starvation causes changes in the intestinal transcriptome and microbiome that are reversed upon refeeding. 
  • Stem Cell Surface Marker Expression Defines Late Stages of Reprogramming to Pluripotency in Human Fibroblasts. 
  • Subtyping sub-Saharan esophageal squamous cell carcinoma by comprehensive molecular analysis. 
  • Sympatric speciation of spiny mice, Acomys, unfolded transcriptomically at Evolution Canyon, Israel. 
  • Systematic comparison of published host gene expression signatures for bacterial/viral discrimination. 
  • 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. 
  • T-cell transcriptomics from peripheral blood highlights differences between polymyositis and dermatomyositis patients. 
  • Temporal dynamics of Wnt-dependent transcriptome reveal an oncogenic Wnt/MYC/ribosome axis. 
  • The Arabidopsis GRAS-type SCL28 transcription factor controls the mitotic cell cycle and division plane orientation. 
  • The Cryptococcus neoformans transcriptome at the site of human meningitis. 
  • The DNA repair transcriptome in severe COPD. 
  • The Host Response to Viral Infections Reveals Common and Virus-Specific Signatures in the Peripheral Blood. 
  • The PsychENCODE project. 
  • The RNA binding protein Quaking represses splicing of the Fibronectin EDA exon and downregulates the interferon response. 
  • The RNAi Mechanism Regulates a New Exonuclease Gene Involved in the Virulence of Mucorales. 
  • The Signaling Pathways Project, an integrated 'omics knowledgebase for mammalian cellular signaling pathways. 
  • The birth of the Epitranscriptome: deciphering the function of RNA modifications. 
  • The diversity of GABAergic neurons and neural communication elements. 
  • 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 host transcriptional response to Candidemia is dominated by neutrophil activation and heme biosynthesis and supports novel diagnostic approaches. 
  • The human olfactory transcriptome. 
  • The human pain genetics database: an interview with Luda Diatchenko. 
  • 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 role of β-arrestin2-dependent signaling in thoracic aortic aneurysm formation in a murine model of Marfan syndrome. 
  • The skin transcriptome in hidradenitis suppurativa uncovers an antimicrobial and sweat gland gene signature which has distinct overlap with wounded skin. 
  • The transcriptional landscape of Shh medulloblastoma. 
  • 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. 
  • Tracing Tumor Evolution in Sarcoma Reveals Clonal Origin of Advanced Metastasis. 
  • Transcription factors MYOCD, SRF, Mesp1 and SMARCD3 enhance the cardio-inducing effect of GATA4, TBX5, and MEF2C during direct cellular reprogramming. 
  • Transcriptional and proteomic insights into the host response in fatal COVID-19 cases. 
  • Transcriptional diversity and bioenergetic shift in human breast cancer metastasis revealed by single-cell RNA sequencing. 
  • Transcriptional diversity during lineage commitment of human blood progenitors. 
  • Transcriptional profile of hippocampal dentate granule cells in four rat epilepsy models. 
  • Transcriptional profiles of JIA patient blood with subsequent poor response to methotrexate. 
  • Transcriptional profiling of olfactory system development identifies distal antenna as a regulator of subset of neuronal fates. 
  • Transcriptional programs of neoantigen-specific TIL in anti-PD-1-treated lung cancers. 
  • Transcriptome and epigenome landscape of human cortical development modeled in organoids. 
  • Transcriptome and regulatory maps of decidua-derived stromal cells inform gene discovery in preterm birth. 
  • Transcriptome changes affecting Hedgehog and cytokine signalling in the umbilical cord: implications for disease risk. 
  • Transcriptome clarifies mechanisms of lesion genesis versus progression in models of Ccm3 cerebral cavernous malformations. 
  • Transcriptome landscape of a bacterial pathogen under plant immunity. 
  • Transcriptome regulation and chromatin occupancy by E2F3 and MYC in mice. 
  • Transcriptome, genetic editing, and microRNA divergence substantiate sympatric speciation of blind mole rat, Spalax. 
  • Transcriptome-Wide Association Study Identifies New Candidate Susceptibility Genes for Glioma. 
  • Transcriptome-Wide Association Study of Blood Cell Traits in African Ancestry and Hispanic/Latino Populations. 
  • Transcriptome-Wide Identification of 2'-O-Methylation Sites with RibOxi-Seq. 
  • 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 development to the juvenile seastar in Parvulastra exigua (Asterinidae). 
  • Transcriptomic analysis of Nodal- and BMP-associated genes during juvenile development of the sea urchin Heliocidaris erythrogramma. 
  • Transcriptomic analysis of atopic dermatitis in African Americans is characterized by Th2/Th17-centered cutaneous immune activation. 
  • 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. 
  • Transcriptomic and Proteomic Analysis of Clear Cell Foci (CCF) in the Human Non-Cirrhotic Liver Identifies Several Differentially Expressed Genes and Proteins with Functions in Cancer Cell Biology and Glycogen Metabolism. 
  • Transcriptomic changes in the nasal epithelium associated with diesel engine exhaust exposure. 
  • Transcriptomic profiles of aging in purified human immune cells. 
  • Transcriptomics Profiling of Alzheimer's Disease Reveal Neurovascular Defects, Altered Amyloid-β Homeostasis, and Deregulated Expression of Long Noncoding RNAs. 
  • Transcriptomics in the wild: Hibernation physiology in free-ranging dwarf lemurs. 
  • Transcriptomics integrated with metabolomics reveals the effect of Bisphenol F (BPF) exposure on intestinal inflammation. 
  • 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 Single-Cell Profiling Captures the Cellular Diversity of the Kidney. 
  • 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. 
  • Validation and refinement of a RUNX1 mutation-associated gene expression signature in blast crisis chronic myeloid leukemia. 
  • What Can Molecular Diagnostics Add to Locoregional Treatment Recommendations for DCIS? 
  • What causes hidradenitis suppurativa ?-15 years after. 
  • 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. 
  • Widespread activation of immunity and pro-inflammatory programs in peripheral blood leukocytes of HIV-infected patients with impaired lung gas exchange. 
  • Wood smoke particle exposure in mice reduces the severity of influenza infection. 
  • c-Maf regulates the plasticity of group 3 innate lymphoid cells by restraining the type 1 program. 
  • miR-27b shapes the presynaptic transcriptome and influences neurotransmission by silencing the polycomb group protein Bmi1. 
  • p63 expression confers significantly better survival outcomes in high-risk diffuse large B-cell lymphoma and demonstrates p53-like and p53-independent tumor suppressor function. 
  • scDART-seq reveals distinct m6A signatures and mRNA methylation heterogeneity in single cells. 
  • β-Catenin-regulated myeloid cell adhesion and migration determine wound healing. 
• 

  Keywords of People

  • Baugh, L. Ryan, Associate Professor of Biology, Biology
  • Choi, Steven Sok, Associate Professor of Medicine, Medicine, Gastroenterology
  • Fox, Donald T, Associate 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 Distinguished Professor for Research in Molecular Biology, Cell Biology
  • Laskowitz, Daniel Todd, Professor of Neurology, Duke Science & Society
  • Linardic, Corinne Mary, Associate Professor of Pediatrics, Pharmacology & Cancer Biology
  • 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, Associate Professor of Environmental Genomics in the Division of Environmental Sciences and Policy, Nicholas Institute-Energy Initiative
  • Pang, Herbert, Adjunct Assistant Professor in the Department of Biostatistics & Bioinformatics, Biostatistics & Bioinformatics
  • Shinohara, Mari L., Associate Professor of Immunology, Immunology
  • Tsalik, Ephraim, Adjunct Associate Professor in the Department of Medicine, Medicine, Infectious Diseases
  • Wray, Gregory Allan, Professor of Biology, Evolutionary Anthropology