Gene Regulatory Networks

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  Subject Areas on Research

  • "Good enough solutions" and the genetics of complex diseases. 
  • A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers. 
  • A Functionally Conserved Gene Regulatory Network Module Governing Olfactory Neuron Diversity. 
  • A GWAS Study on Liver Function Test Using eMERGE Network Participants. 
  • A Systems Approach Dissociates Fructose-Induced Liver Triglyceride from Hypertriglyceridemia and Hyperinsulinemia in Male Mice. 
  • A brave new synthetic world. A report of the first meeting on 'Frontiers in Synthetic Biology', Boston, USA, 1-2 December 2008. 
  • A densely interconnected genome-wide network of microRNAs and oncogenic pathways revealed using gene expression signatures. 
  • A different life? 
  • A functional genomics predictive network model identifies regulators of inflammatory bowel disease. 
  • A gene regulatory network for root epidermis cell differentiation in Arabidopsis. 
  • A genomic approach to identify regulatory nodes in the transcriptional network of systemic acquired resistance in plants. 
  • A map of human cancer signaling. 
  • A plant genetic network for preventing dysbiosis in the phyllosphere. 
  • A predictive model for transcriptional control of physiology in a free living cell. 
  • A regulatory hierarchy controls the dynamic transcriptional response to extreme oxidative stress in archaea. 
  • A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability. 
  • A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants. 
  • A stele-enriched gene regulatory network in the Arabidopsis root. 
  • A synthetic biology approach to understanding cellular information processing. 
  • A synthetic mechanogenetic gene circuit for autonomous drug delivery in engineered tissues. 
  • A transcription network of interlocking positive feedback loops maintains intracellular iron balance in archaea. 
  • A validated regulatory network for Th17 cell specification. 
  • A20 modulates lipid metabolism and energy production to promote liver regeneration. 
  • ATM regulates a DNA damage response posttranscriptional RNA operon in lymphocytes. 
  • Adaptive evolution: evaluating empirical support for theoretical predictions. 
  • Addressing biological uncertainties in engineering gene circuits. 
  • Alzheimer's Risk Factors Age, APOE Genotype, and Sex Drive Distinct Molecular Pathways. 
  • An Optogenetic Method to Study Signal Transduction in Intestinal Stem Cell Homeostasis. 
  • An integration of complementary strategies for gene-expression analysis to reveal novel therapeutic opportunities for breast cancer. 
  • An integrative approach to characterize disease-specific pathways and their coordination: a case study in cancer. 
  • An introduction to small non-coding RNAs: miRNA and snoRNA. 
  • Arabidopsis thaliana as a model organism in systems biology. 
  • Architecture of the human regulatory network derived from ENCODE data. 
  • Associations between RNA splicing regulatory variants of stemness-related genes and racial disparities in susceptibility to prostate cancer. 
  • Autism genome-wide copy number variation reveals ubiquitin and neuronal genes. 
  • Bisphenol A exposure alters developmental gene expression in the fetal rhesus macaque uterus. 
  • Block-diagonal discriminant analysis and its bias-corrected rules. 
  • Brassinosteroid gene regulatory networks at cellular resolution in the Arabidopsis root. 
  • Caenorhabditis elegans as an emerging model system in environmental epigenetics. 
  • Cancer systems biology: exploring cancer-associated genes on cellular networks. 
  • Cancer's insatiable appetite. 
  • Causal structure of oscillations in gene regulatory networks: Boolean analysis of ordinary differential equation attractors. 
  • Cell type-specific transcriptional profiling: implications for metabolite profiling. 
  • Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal. 
  • Checkpoints couple transcription network oscillator dynamics to cell-cycle progression. 
  • Chromatin architecture reorganization during stem cell differentiation. 
  • Coding and noncoding variants in EBF3 are involved in HADDS and simplex autism. 
  • 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 Molecular Analysis of Gastrointestinal Adenocarcinomas. 
  • Comparative genomics of mammalian hibernators using gene networks. 
  • Comprehensive functional genomic resource and integrative model for the human brain. 
  • Comprehensive genomic meta-analysis identifies intra-tumoural stroma as a predictor of survival in patients with gastric cancer. 
  • Connecting genetic risk to disease end points through the human blood plasma proteome. 
  • Connecting virulence pathways to cell-cycle progression in the fungal pathogen Cryptococcus neoformans. 
  • Consensus Coexpression Network Analysis Identifies Key Regulators of Flower and Fruit Development in Wild Strawberry. 
  • Conservation of dynamic characteristics of transcriptional regulatory elements in periodic biological processes. 
  • Construction of a global pain systems network highlights phospholipid signaling as a regulator of heat nociception. 
  • Contribution of plasma cells and B cells to hidradenitis suppurativa pathogenesis. 
  • Control of Arabidopsis root development. 
  • Convergence of genes and cellular pathways dysregulated in autism spectrum disorders. 
  • Core and region-enriched networks of behaviorally regulated genes and the singing genome. 
  • Coupling spatial segregation with synthetic circuits to control bacterial survival. 
  • Cross-species DNA copy number analyses identifies multiple 1q21-q23 subtype-specific driver genes for breast cancer. 
  • Crosstalk in competing endogenous RNA networks reveals new circular RNAs involved in the pathogenesis of early HIV infection. 
  • DNA mismatch repair is required for the host innate response and controls cellular fate after influenza virus infection. 
  • De novo mutations in synaptic transmission genes including DNM1 cause epileptic encephalopathies. 
  • Decline in biological resilience as key manifestation of aging: Potential mechanisms and role in health and longevity. 
  • Decoding biological principles using gene circuits. 
  • Decoding the Long Noncoding RNA During Cardiac Maturation: A Roadmap for Functional Discovery. 
  • Deployment of a retinal determination gene network drives directed cell migration in the sea urchin embryo. 
  • Development of a larval nervous system in the sea urchin. 
  • 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. 
  • Dissection of genetic pathways in C. elegans. 
  • Distinct COPD subtypes in former smokers revealed by gene network perturbation analysis. 
  • Divergence in problem-solving skills is associated with differential expression of glutamate receptors in wild finches. 
  • Dynamic zebrafish interactome reveals transcriptional mechanisms of dioxin toxicity. 
  • Early complement genes are associated with visual system degeneration in multiple sclerosis. 
  • Effects of Space Flight on Mouse Liver versus Kidney: Gene Pathway Analyses. 
  • Elucidation of the calcineurin-Crz1 stress response transcriptional network in the human fungal pathogen Cryptococcus neoformans. 
  • Engineered cell-cell communication and its applications. 
  • Engineering microbial systems to explore ecological and evolutionary dynamics. 
  • Enhanced MyoD-induced transdifferentiation to a myogenic lineage by fusion to a potent transactivation domain. 
  • Eric H. Davidson (1937–2015). 
  • Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution. 
  • Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors. 
  • Evolution, interactions, and biological networks. 
  • Evolutionary Changes in the Chromatin Landscape Contribute to Reorganization of a Developmental Gene Network During Rapid Life History Evolution in Sea Urchins. 
  • Evolutionary crossroads in developmental biology: sea urchins. 
  • Experimental guidance for discovering genetic networks through hypothesis reduction on time series. 
  • Failure of terminal erythroid differentiation in EKLF-deficient mice is associated with cell cycle perturbation and reduced expression of E2F2. 
  • Fine time course expression analysis identifies cascades of activation and repression and maps a putative regulator of mammalian sex determination. 
  • From genotype to phenotype: systems biology meets natural variation. 
  • GTL1 and DF1 regulate root hair growth through transcriptional repression of ROOT HAIR DEFECTIVE 6-LIKE 4 in Arabidopsis. 
  • Gene Expression Profiling of Bronchoalveolar Lavage Cells During Aspergillus Colonization of the Lung Allograft. 
  • Gene Network Polymorphism Illuminates Loss and Retention of Novel RNAi Silencing Components in the Cryptococcus Pathogenic Species Complex. 
  • Gene expression profiles linked to AT1 angiotensin receptors in the kidney. 
  • Gene expression signatures that predict radiation exposure in mice and humans. 
  • Gene regulatory programmes of tissue regeneration. 
  • Gene-environment regulatory circuits of right ventricular pathology in tetralogy of fallot. 
  • Genes and networks regulating root anatomy and architecture. 
  • Genetic Differences in the Immediate Transcriptome Response to Stress Predict Risk-Related Brain Function and Psychiatric Disorders. 
  • Genetic Sharing with Cardiovascular Disease Risk Factors and Diabetes Reveals Novel Bone Mineral Density Loci. 
  • Genetic interaction screens identify a role for hedgehog signaling in Drosophila border cell migration. 
  • Genetic network identification using convex programming. 
  • Genetic pathway analysis reveals a major role for extracellular matrix organization in inflammatory and neuropathic pain. 
  • Genetic variants in the genes encoding rho GTPases and related regulators predict cutaneous melanoma-specific survival. 
  • Genetics of gene expression responses to temperature stress in a sea urchin gene network. 
  • Genetics of physiological dysregulation: findings from the long life family study using joint models. 
  • Genome-Wide Meta-Analyses of Breast, Ovarian, and Prostate Cancer Association Studies Identify Multiple New Susceptibility Loci Shared by at Least Two Cancer Types. 
  • Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types. 
  • Genome-wide association meta-analysis of corneal curvature identifies novel loci and shared genetic influences across axial length and refractive error. 
  • Genome-wide identification of regulatory elements in Sertoli cells. 
  • Genomic analysis reveals distinct mechanisms and functional classes of SOX10-regulated genes in melanocytes. 
  • Genomic and Transcriptomic Profiling of Combined Hepatocellular and Intrahepatic Cholangiocarcinoma Reveals Distinct Molecular Subtypes. 
  • Getting to the root of plant biology: impact of the Arabidopsis genome sequence on root research. 
  • Hacking DNA copy number for circuit engineering. 
  • Identification and Functional Validation of Reciprocal microRNA-mRNA Pairings in African American Prostate Cancer Disparities. 
  • Identification of amygdala-expressed genes associated with autism spectrum disorder. 
  • Identification of functional elements and regulatory circuits by Drosophila modENCODE. 
  • Identification of neural transcription factors required for the differentiation of three neuronal subtypes in the sea urchin embryo. 
  • Identification of novel candidate risk genes for myelomeningocele within the glucose homeostasis/oxidative stress and folate/one-carbon metabolism networks. 
  • Identifying Gene Regulatory Networks in Arabidopsis by In Silico Prediction, Yeast-1-Hybrid, and Inducible Gene Profiling Assays. 
  • Identifying gene expression from single cells to single genes. 
  • Increased miR-124-3p in microglial exosomes following traumatic brain injury inhibits neuronal inflammation and contributes to neurite outgrowth via their transfer into neurons. 
  • Induction of the unfolded protein response drives enhanced metabolism and chemoresistance in glioma cells. 
  • Inference of Gene Regulatory Network Uncovers the Linkage between Circadian Clock and Crassulacean Acid Metabolism in Kalanchoë fedtschenkoi. 
  • Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach. 
  • Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline. 
  • Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana. 
  • Integrative functional genomic analysis of human brain development and neuropsychiatric risks. 
  • Integrative genomics reveals novel molecular pathways and gene networks for coronary artery disease. 
  • Investigating Conservation of the Cell-Cycle-Regulated Transcriptional Program in the Fungal Pathogen, Cryptococcus neoformans. 
  • Joint eQTL assessment of whole blood and dura mater tissue from individuals with Chiari type I malformation. 
  • Know Me! Unraveling the Riddle of Calcific Aortic Valve Disease by Bioinformatics. 
  • LIN28B promotes the development of neuroendocrine prostate cancer. 
  • Label propagation defines signaling networks associated with recurrently mutated cancer genes. 
  • Large-Scale microRNA Expression Profiling Identifies Putative Retinal miRNA-mRNA Signaling Pathways Underlying Form-Deprivation Myopia in Mice. 
  • Large-scale association analysis identifies new risk loci for coronary artery disease. 
  • Large-scale genomic analyses link reproductive aging to hypothalamic signaling, breast cancer susceptibility and BRCA1-mediated DNA repair. 
  • Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. 
  • Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells. 
  • Linking Genes to Cardiovascular Diseases: Gene Action and Gene-Environment Interactions. 
  • Longevity-related molecular pathways are subject to midlife "switch" in humans. 
  • LungMAP: The Molecular Atlas of Lung Development Program. 
  • Mammalian Synthetic Biology: Engineering Biological Systems. 
  • Metabolic regulation of T lymphocytes. 
  • Minimum requirements for changing and maintaining endodermis cell identity in the Arabidopsis root. 
  • Mining database for the expression and gene regulation network of JAK2 in skin cutaneous melanoma. 
  • Module-based association analysis for omics data with network structure. 
  • Molecular profiling of the developing avian telencephalon: regional timing and brain subdivision continuities. 
  • Morphogenesis in sea urchin embryos: linking cellular events to gene regulatory states. 
  • Mucor circinelloides Thrives inside the Phagosome through an Atf-Mediated Germination Pathway. 
  • Multiancestry genome-wide association study of 520,000 subjects identifies 32 loci associated with stroke and stroke subtypes. 
  • Network-assisted genetic dissection of pathogenicity and drug resistance in the opportunistic human pathogenic fungus Cryptococcus neoformans. 
  • Neurogenesis in the sea urchin embryo is initiated uniquely in three domains. 
  • Novel Regulatory Mechanisms for the SoxC Transcriptional Network Required for Visual Pathway Development. 
  • Novel loci and pathways significantly associated with longevity. 
  • Omics meet networks - using systems approaches to infer regulatory networks in plants. 
  • Open chromatin mapping identifies transcriptional networks regulating human epididymis epithelial function. 
  • Organoid Profiling Identifies Common Responders to Chemotherapy in Pancreatic Cancer. 
  • Origin of bistability underlying mammalian cell cycle entry. 
  • Oscillating gene expression determines competence for periodic Arabidopsis root branching. 
  • Pairing of competitive and topologically distinct regulatory modules enhances patterned gene expression. 
  • Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context. 
  • Prevalence of transcription promoters within archaeal operons and coding sequences. 
  • Primary tumor microRNA signature predicts recurrence and survival in patients with locally advanced esophageal adenocarcinoma. 
  • Protein-DNA binding dynamics predict transcriptional response to nutrients in archaea. 
  • Pulling the genome in opposite directions to dissect gene networks. 
  • RNA regulons: coordination of post-transcriptional events. 
  • Recent reconfiguration of an ancient developmental gene regulatory network in Heliocidaris sea urchins. 
  • Reconciling conflicting models for global control of cell-cycle transcription. 
  • Reconstructing regulatory network transitions. 
  • Regulation of Division and Differentiation of Plant Stem Cells. 
  • Regulation of γδ T Cell Effector Diversification in the Thymus. 
  • Regulatory logic and pattern formation in the early sea urchin embryo. 
  • Reliability of transcriptional cycles and the yeast cell-cycle oscillator. 
  • Repulsive expansion dynamics in colony growth and gene expression. 
  • SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data. 
  • Sea Urchin Morphogenesis. 
  • Severe tuberculosis induces unbalanced up-regulation of gene networks and overexpression of IL-22, MIP-1alpha, CCL27, IP-10, CCR4, CCR5, CXCR3, PD1, PDL2, IL-3, IFN-beta, TIM1, and TLR2 but low antigen-specific cellular responses. 
  • Sex and the circuitry: progress toward a systems-level understanding of vertebrate sex determination. 
  • Single nucleus multi-omics regulatory landscape of the murine pituitary. 
  • Social environment is associated with gene regulatory variation in the rhesus macaque immune system. 
  • Spatiotemporal analysis identifies ABF2 and ABF3 as key hubs of endodermal response to nitrate. 
  • Spatiotemporal signalling in plant development. 
  • Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53. 
  • Sperm DNA methylation altered by THC and nicotine: Vulnerability of neurodevelopmental genes with bivalent chromatin. 
  • Sub-circuits of a gene regulatory network control a developmental epithelial-mesenchymal transition. 
  • Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits. 
  • Synthetic biology looks good on paper. 
  • Synthetic biology: Division of logic labour. 
  • Systems Genetics Approach Identifies Gene Pathways and Adamts2 as Drivers of Isoproterenol-Induced Cardiac Hypertrophy and Cardiomyopathy in Mice. 
  • Systems approaches to identifying gene regulatory networks in plants. 
  • Systems biology approaches to defining transcription regulatory networks in halophilic archaea. 
  • Targeted Multiplex Gene Expression Profiling to Measure High-Fat Diet and Metformin Effects on Fetal Gene Expression in a Mouse Model. 
  • The ErbB2ΔEx16 splice variant is a major oncogenic driver in breast cancer that promotes a pro-metastatic tumor microenvironment. 
  • The Future is Now: Gene Expression Dynamics at Single Cell Resolution. 
  • The Local Edge Machine: inference of dynamic models of gene regulation. 
  • The Polygenic and Monogenic Basis of Blood Traits and Diseases. 
  • The RosR transcription factor is required for gene expression dynamics in response to extreme oxidative stress in a hypersaline-adapted archaeon. 
  • The association between aging-related monocyte transcriptional networks and comorbidity burden: the Multi-Ethnic Study of Atherosclerosis (MESA). 
  • The cell-cycle transcriptional network generates and transmits a pulse of transcription once each cell cycle. 
  • The control of foxN2/3 expression in sea urchin embryos and its function in the skeletogenic gene regulatory network. 
  • The genome of a songbird. 
  • The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. 
  • The impact of gene expression variation on the robustness and evolvability of a developmental gene regulatory network. 
  • The impact of the metabotropic glutamate receptor and other gene family interaction networks on autism. 
  • The right ventricular transcriptome signature in Ossabaw swine with cardiometabolic heart failure: implications for the coronary vasculature. 
  • The roles of MASPIN expression and subcellular localization in non-small cell lung cancer. 
  • The somatic genomic landscape of glioblastoma. 
  • The transcriptional landscape of Shh medulloblastoma. 
  • Therapeutic targeting of ependymoma as informed by oncogenic enhancer profiling. 
  • Topology and control of the cell-cycle-regulated transcriptional circuitry. 
  • Toward a systems analysis of the root. 
  • Toward predictive engineering of gene circuits. 
  • Transcription factors MYOCD, SRF, Mesp1 and SMARCD3 enhance the cardio-inducing effect of GATA4, TBX5, and MEF2C during direct cellular reprogramming. 
  • Transcription networks and cyclin/CDKs: the yin and yang of cell cycle oscillators. 
  • Transcription-factor-dependent enhancer transcription defines a gene regulatory network for cardiac rhythm. 
  • Transcriptional Circuit Fragility Influences HIV Proviral Fate. 
  • Transcriptional Regulation in Archaea: From Individual Genes to Global Regulatory Networks. 
  • Transcriptional network predicts viral set point during acute HIV-1 infection. 
  • Transcriptional networks in root cell fate specification. 
  • Transcriptome clarifies mechanisms of lesion genesis versus progression in models of Ccm3 cerebral cavernous malformations. 
  • Transcriptome landscape of a bacterial pathogen under plant immunity. 
  • Uncovering Gene Regulatory Networks Controlling Plant Cell Differentiation. 
  • Up-regulated expression of extracellular matrix remodeling genes in phagocytically challenged trabecular meshwork cells. 
  • Using extremal events to characterize noisy time series. 
  • Using the bioconductor GeneAnswers package to interpret gene lists. 
  • WIPI1 is a conserved mediator of right ventricular failure. 
  • WNK1 regulates uterine homeostasis and its ability to support pregnancy. 
  • Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma. 
  • Wnt-regulated lncRNA discovery enhanced by in vivo identification and CRISPRi functional validation. 
  • Wnt6 activates endoderm in the sea urchin gene regulatory network. 
  • Zac1 and the Imprinted Gene Network program juvenile NAFLD in response to maternal metabolic syndrome. 
  • Zebrafish Transcription Factor ORFeome for Gene Discovery and Regulatory Network Elucidation. 
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  Keywords of People

  • Ciofani, Maria, Associate Professor of Integrative Immunobiology, Cell Biology
  • Mitchell-Olds, Thomas, Newman Ivey White Distinguished Professor of Biology, Biology
  • Schmid, Amy K., David M. Goodner Associate Professor, Duke Science & Society
  • Wray, Gregory Allan, Professor of Biology, Evolutionary Anthropology