Rajanikanth Vadigepalli

Daniel Baugh Institute for Functional Genomics and Computational Biology, Thomas Jefferson University

Affiliated withThomas Jefferson University

Research Area

Biography

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JoVE Journal Publications

ArticleTotal : 2	Year
Publication title Cited by 9	2020
Publication title Cited by 1	2022

Other Publications

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