Daniel Baugh Institute for Functional Genomics and Computational Biology,
Department of Pathology,
Anatomy,
and Cell Biology,
Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy, and Cell Biology
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Single-Cell Transcriptional Analysis Reveals Novel Neuronal Phenotypes and Interaction Networks Involved in the Central Circadian Clock.
Frontiers in neuroscience , 2016 | Pubmed ID: 27826225
PAINT: a promoter analysis and interaction network generation tool for gene regulatory network identification.
Omics : a journal of integrative biology , 2003 | Pubmed ID: 14583114
Erythroid-induced commitment of K562 cells results in clusters of differentially expressed genes enriched for specific transcription regulatory elements.
Physiological genomics Sep, 2004 | Pubmed ID: 15252187
Chronic alcohol exposure alters transcription broadly in a key integrative brain nucleus for homeostasis: the nucleus tractus solitarius.
Physiological genomics Dec, 2005 | Pubmed ID: 16189278
The inflammatory and normal transcriptome of mouse bladder detrusor and mucosa.
BMC physiology Jan, 2006 | Pubmed ID: 16420690
Systems analysis of circadian time-dependent neuronal epidermal growth factor receptor signaling.
Genome biology , 2006 | Pubmed ID: 16784547
Epidermal growth factor receptor-induced circadian-time-dependent gene regulation in suprachiasmatic nucleus.
Neuroreport Sep, 2006 | Pubmed ID: 16932154
Bladder inflammatory transcriptome in response to tachykinins: neurokinin 1 receptor-dependent genes and transcription regulatory elements.
BMC urology May, 2007 | Pubmed ID: 17519035
From promoter analysis to transcriptional regulatory network prediction using PAINT.
Methods in molecular biology (Clifton, N.J.) , 2007 | Pubmed ID: 18314577
Dynamic transcriptomic response to acute hypertension in the nucleus tractus solitarius.
American journal of physiology. Regulatory, integrative and comparative physiology Jul, 2008 | Pubmed ID: 18434436
Transcriptional regulatory network analysis during epithelial-mesenchymal transformation of retinal pigment epithelium.
Molecular vision Aug, 2008 | Pubmed ID: 18682805
Temporal and functional profile of the transcriptional regulatory network in the early regenerative response to partial hepatectomy in the rat.
BMC genomics Nov, 2008 | Pubmed ID: 18990226
Robust dynamic balance of AP-1 transcription factors in a neuronal gene regulatory network.
BMC systems biology Dec, 2010 | Pubmed ID: 21167049
Adaptive transcriptional dynamics of A2 neurons and central cardiovascular control pathways.
Experimental physiology Apr, 2012 | Pubmed ID: 22002872
Rapid temporal changes in the expression of a set of neuromodulatory genes during alcohol withdrawal in the dorsal vagal complex: molecular evidence of homeostatic disturbance.
Alcoholism, clinical and experimental research Oct, 2012 | Pubmed ID: 22486438
Temporal changes in innate immune signals in a rat model of alcohol withdrawal in emotional and cardiorespiratory homeostatic nuclei.
Journal of neuroinflammation May, 2012 | Pubmed ID: 22626265
Effects of developmental lead exposure on the hippocampal transcriptome: influences of sex, developmental period, and lead exposure level.
Toxicological sciences : an official journal of the Society of Toxicology Sep, 2012 | Pubmed ID: 22641619
Integrative gene regulatory network analysis reveals light-induced regional gene expression phase shift programs in the mouse suprachiasmatic nucleus.
PloS one , 2012 | Pubmed ID: 22662235
Chronic ethanol feeding enhances miR-21 induction during liver regeneration while inhibiting proliferation in rats.
American journal of physiology. Gastrointestinal and liver physiology Sep, 2012 | Pubmed ID: 22790595
Chronic ethanol feeding alters miRNA expression dynamics during liver regeneration.
Alcoholism, clinical and experimental research Jan, 2013 | Pubmed ID: 22823254
Coordinated dynamic gene expression changes in the central nucleus of the amygdala during alcohol withdrawal.
Alcoholism, clinical and experimental research Jan, 2013 | Pubmed ID: 22827539
Decorin protein core affects the global gene expression profile of the tumor microenvironment in a triple-negative orthotopic breast carcinoma xenograft model.
PloS one , 2012 | Pubmed ID: 23029096
MicroRNA profiling in lung cancer reveals new molecular markers for diagnosis.
Acta cytologica , 2012 | Pubmed ID: 23207443
Ethanol alters the balance of Sox2, Oct4, and Nanog expression in distinct subpopulations during differentiation of embryonic stem cells.
Stem cells and development Aug, 2013 | Pubmed ID: 23470161
Ethanol diverts early neuronal differentiation trajectory of embryonic stem cells by disrupting the balance of lineage specifiers.
PloS one , 2013 | Pubmed ID: 23724002
Molecular modeling of ErbB4/HER4 kinase in the context of the HER4 signaling network helps rationalize the effects of clinically identified HER4 somatic mutations on the cell phenotype.
Biotechnology journal Dec, 2013 | Pubmed ID: 24318637
Inputs drive cell phenotype variability.
Genome research Jun, 2014 | Pubmed ID: 24671852
Identifying functional gene regulatory network phenotypes underlying single cell transcriptional variability.
Progress in biophysics and molecular biology Jan, 2015 | Pubmed ID: 25433230
Multiscale model of dynamic neuromodulation integrating neuropeptide-induced signaling pathway activity with membrane electrophysiology.
Biophysical journal Jan, 2015 | Pubmed ID: 25564868
Adiponectin fine-tuning of liver regeneration dynamics revealed through cellular network modelling.
The Journal of physiology Jan, 2015 | Pubmed ID: 25630259
MicroRNA network changes in the brain stem underlie the development of hypertension.
Physiological genomics Sep, 2015 | Pubmed ID: 26126791
A novel, dynamic pattern-based analysis of NF-κB binding during the priming phase of liver regeneration reveals switch-like functional regulation of target genes.
Frontiers in physiology , 2015 | Pubmed ID: 26217230
Computational modeling of cytokine signaling in microglia.
Molecular bioSystems Dec, 2015 | Pubmed ID: 26440115
In Vivo Zonal Variation and Liver Cell-Type Specific NF-κB Localization after Chronic Adaptation to Ethanol and following Partial Hepatectomy.
PloS one , 2015 | Pubmed ID: 26452159
Intracellular Information Processing through Encoding and Decoding of Dynamic Signaling Features.
PLoS computational biology Oct, 2015 | Pubmed ID: 26491963
Systems analysis of non-parenchymal cell modulation of liver repair across multiple regeneration modes.
BMC systems biology Oct, 2015 | Pubmed ID: 26493454
Molecular variability elicits a tunable switch with discrete neuromodulatory response phenotypes.
Journal of computational neuroscience Feb, 2016 | Pubmed ID: 26621106
Erratum to: Molecular variability elicits a tunable switch with discrete neuromodulatory response phenotypes.
Journal of computational neuroscience Feb, 2016 | Pubmed ID: 26791519
A novel comparative pattern count analysis reveals a chronic ethanol-induced dynamic shift in immediate early NF-κB genome-wide promoter binding during liver regeneration.
Molecular bioSystems Mar, 2016 | Pubmed ID: 26847025
A novel comparative pattern analysis approach identifies chronic alcohol mediated dysregulation of transcriptomic dynamics during liver regeneration.
BMC genomics Mar, 2016 | Pubmed ID: 27012785
HuR Contributes to TRAIL Resistance by Restricting Death Receptor 4 Expression in Pancreatic Cancer Cells.
Molecular cancer research : MCR 07, 2016 | Pubmed ID: 27053682
Computational Modeling of Spatiotemporal Ca(2+) Signal Propagation Along Hepatocyte Cords.
IEEE transactions on bio-medical engineering 10, 2016 | Pubmed ID: 27076052
Systemic leukotriene B receptor antagonism lowers arterial blood pressure and improves autonomic function in the spontaneously hypertensive rat.
The Journal of physiology 10, 2016 | Pubmed ID: 27230966
Integrated live imaging and molecular profiling of embryoid bodies reveals a synchronized progression of early differentiation.
Scientific reports 08, 2016 | Pubmed ID: 27530599
Inhibition of miR-21 rescues liver regeneration after partial hepatectomy in ethanol-fed rats.
American journal of physiology. Gastrointestinal and liver physiology 11, 2016 | Pubmed ID: 27634014
Pattern analysis uncovers a chronic ethanol-induced disruption of the switch-like dynamics of C/EBP-β and C/EBP-α genome-wide binding during liver regeneration.
Physiological genomics 01, 2017 | Pubmed ID: 27815535
A data-driven modeling approach to identify disease-specific multi-organ networks driving physiological dysregulation.
PLoS computational biology Jul, 2017 | Pubmed ID: 28732007
Novel Influences of IL-10 on CNS Inflammation Revealed by Integrated Analyses of Cytokine Networks and Microglial Morphology.
Frontiers in cellular neuroscience , 2017 | Pubmed ID: 28855862
Modeling cytokine regulatory network dynamics driving neuroinflammation in central nervous system disorders.
Drug discovery today. Disease models , 2016 | Pubmed ID: 28947907
Introduction to the Virtual Issue Alcohol and Epigenetic Regulation: Do the Products of Alcohol Metabolism Drive Epigenetic Control of Gene Expression in Alcohol-Related Disorders?
Alcoholism, clinical and experimental research 05, 2018 | Pubmed ID: 29532481
SPSNet: subpopulation-sensitive network-based analysis of heterogeneous gene expression data.
BMC systems biology 03, 2018 | Pubmed ID: 29560831
Credibility, Replicability, and Reproducibility in Simulation for Biomedicine and Clinical Applications in Neuroscience.
Frontiers in neuroinformatics , 2018 | Pubmed ID: 29713272
Single-Cell Gene Expression Analysis Identifies Chronic Alcohol-Mediated Shift in Hepatocyte Molecular States After Partial Hepatectomy.
Gene expression 04, 2019 | Pubmed ID: 30189915
Cellular network modeling and single cell gene expression analysis reveals novel hepatic stellate cell phenotypes controlling liver regeneration dynamics.
BMC systems biology 10, 2018 | Pubmed ID: 30285726
Causality Analysis and Cell Network Modeling of Spatial Calcium Signaling Patterns in Liver Lobules.
Frontiers in physiology , 2018 | Pubmed ID: 30337879
Model-based virtual patient analysis of human liver regeneration predicts critical perioperative factors controlling the dynamic mode of response to resection.
BMC systems biology 01, 2019 | Pubmed ID: 30651095
Modeling the Dynamics of Human Liver Failure Post Liver Resection.
Processes (Basel, Switzerland) Aug, 2018 | Pubmed ID: 31131255
Single-Cell Glia and Neuron Gene Expression in the Central Amygdala in Opioid Withdrawal Suggests Inflammation With Correlated Gut Dysbiosis.
Frontiers in neuroscience , 2019 | Pubmed ID: 31333398
A Novel Mouse Model of Acute-on-Chronic Cholestatic Alcoholic Liver Disease: A Systems Biology Comparison With Human Alcoholic Hepatitis.
Alcoholism, clinical and experimental research Jan, 2020 | Pubmed ID: 31710124
Inflammation-associated suppression of metabolic gene networks in acute and chronic liver disease.
Archives of toxicology Jan, 2020 | Pubmed ID: 31919559
A Comprehensive Integrated Anatomical and Molecular Atlas of Rat Intrinsic Cardiac Nervous System.
iScience Jun, 2020 | Pubmed ID: 32460006
Diurnal Patterns of Gene Expression in the Dorsal Vagal Complex and the Central Nucleus of the Amygdala - Non-rhythm-generating Brain Regions.
Frontiers in neuroscience , 2020 | Pubmed ID: 32477043
Investigating the Effects of Brainstem Neuronal Adaptation on Cardiovascular Homeostasis.
Frontiers in neuroscience , 2020 | Pubmed ID: 32508573
Hepatic lipocalin 2 promotes liver fibrosis and portal hypertension.
Scientific reports 09, 2020 | Pubmed ID: 32968110
Credible practice of modeling and simulation in healthcare: ten rules from a multidisciplinary perspective.
Journal of translational medicine 09, 2020 | Pubmed ID: 32993675
Integrated Multiomics Reveals Glucose Use Reprogramming and Identifies a Novel Hexokinase in Alcoholic Hepatitis.
Gastroenterology 04, 2021 | Pubmed ID: 33309778
Innervation and Neuronal Control of the Mammalian Sinoatrial Node a Comprehensive Atlas.
Circulation research 04, 2021 | Pubmed ID: 33629877
Input-output signal processing plasticity of vagal motor neurons in response to cardiac ischemic injury.
iScience Mar, 2021 | Pubmed ID: 33665562
Mapping the little brain at the heart by an interdisciplinary systems biology team.
iScience May, 2021 | Pubmed ID: 34113808
A single cell transcriptomics map of paracrine networks in the intrinsic cardiac nervous system.
iScience Jul, 2021 | Pubmed ID: 34337356
3D single cell scale anatomical map of sex-dependent variability of the rat intrinsic cardiac nervous system.
iScience Jul, 2021 | Pubmed ID: 34355144
Analyzing the relationships between city opioid deaths and socioeconomic factors.
Journal of opioid management Sep-Oct, 2021 | Pubmed ID: 34714537
Retinoic Acid Fluctuation Activates an Uneven, Direction-Dependent Network-Wide Robustness Response in Early Embryogenesis.
Frontiers in cell and developmental biology , 2021 | Pubmed ID: 34746144
Dysregulation of miR-21-associated miRNA regulatory networks by chronic ethanol consumption impairs liver regeneration.
Physiological genomics 12, 2021 | Pubmed ID: 34796728
Single Cell Scale Neuronal and Glial Gene Expression and Putative Cell Phenotypes and Networks in the Nucleus Tractus Solitarius in an Alcohol Withdrawal Time Series.
Frontiers in systems neuroscience , 2021 | Pubmed ID: 34867221
A Spatial Model of Hepatic Calcium Signaling and Glucose Metabolism Under Autonomic Control Reveals Functional Consequences of Varying Liver Innervation Patterns Across Species.
Frontiers in physiology , 2021 | Pubmed ID: 34899380
1Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University,
2Sidney Kimmel Medical College, Thomas Jefferson University,
3Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine
SOBRE A JoVE
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