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Single-Cell Glia and Neuron Gene Expression in the Central Amygdala in Opioid Withdrawal Suggests Inflammation With Correlated Gut Dysbiosis.

O'Sullivan SJ, Malahias E, Park J, Srivastava A, Reyes BAS, Gorky J, Vadigepalli R, Van Bockstaele EJ, Schwaber JS.

Front Neurosci. 2019 Jul 3;13:665. doi: 10.3389/fnins.2019.00665. eCollection 2019.


Modeling the Dynamics of Human Liver Failure Post Liver Resection.

Verma BK, Subramaniam P, Vadigepalli R.

Processes (Basel). 2018 Aug;6(8). pii: 115. doi: 10.3390/pr6080115. Epub 2018 Aug 4.


Causality Analysis and Cell Network Modeling of Spatial Calcium Signaling Patterns in Liver Lobules.

Verma A, Antony AN, Ogunnaike BA, Hoek JB, Vadigepalli R.

Front Physiol. 2018 Oct 4;9:1377. doi: 10.3389/fphys.2018.01377. eCollection 2018.


Cellular network modeling and single cell gene expression analysis reveals novel hepatic stellate cell phenotypes controlling liver regeneration dynamics.

Cook D, Achanta S, Hoek JB, Ogunnaike BA, Vadigepalli R.

BMC Syst Biol. 2018 Oct 3;12(1):86. doi: 10.1186/s12918-018-0605-7.


Single-Cell Gene Expression Analysis Identifies Chronic Alcohol-Mediated Shift in Hepatocyte Molecular States After Partial Hepatectomy.

Achanta S, Verma A, Srivastava A, Nilakantan H, Hoek JB, Vadigepalli R.

Gene Expr. 2019 Apr 18;19(2):97-119. doi: 10.3727/105221618X15361728786767. Epub 2018 Sep 6.


Credibility, Replicability, and Reproducibility in Simulation for Biomedicine and Clinical Applications in Neuroscience.

Mulugeta L, Drach A, Erdemir A, Hunt CA, Horner M, Ku JP, Myers JG Jr, Vadigepalli R, Lytton WW.

Front Neuroinform. 2018 Apr 16;12:18. doi: 10.3389/fninf.2018.00018. eCollection 2018. Review.


SPSNet: subpopulation-sensitive network-based analysis of heterogeneous gene expression data.

Belorkar A, Vadigepalli R, Wong L.

BMC Syst Biol. 2018 Mar 19;12(Suppl 2):28. doi: 10.1186/s12918-018-0538-1.


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?

Vadigepalli R, Hoek JB.

Alcohol Clin Exp Res. 2018 May;42(5):845-848. doi: 10.1111/acer.13630. Epub 2018 Apr 6. No abstract available.


Novel Influences of IL-10 on CNS Inflammation Revealed by Integrated Analyses of Cytokine Networks and Microglial Morphology.

Anderson WD, Greenhalgh AD, Takwale A, David S, Vadigepalli R.

Front Cell Neurosci. 2017 Aug 14;11:233. doi: 10.3389/fncel.2017.00233. eCollection 2017.


A data-driven modeling approach to identify disease-specific multi-organ networks driving physiological dysregulation.

Anderson WD, DeCicco D, Schwaber JS, Vadigepalli R.

PLoS Comput Biol. 2017 Jul 21;13(7):e1005627. doi: 10.1371/journal.pcbi.1005627. eCollection 2017 Jul.


Single-Cell Transcriptional Analysis Reveals Novel Neuronal Phenotypes and Interaction Networks Involved in the Central Circadian Clock.

Park J, Zhu H, O'Sullivan S, Ogunnaike BA, Weaver DR, Schwaber JS, Vadigepalli R.

Front Neurosci. 2016 Oct 25;10:481. eCollection 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.

Kuttippurathu L, Patra B, Cook D, Hoek JB, Vadigepalli R.

Physiol Genomics. 2017 Jan 1;49(1):11-26. doi: 10.1152/physiolgenomics.00097.2016. Epub 2016 Nov 4.


Inhibition of miR-21 rescues liver regeneration after partial hepatectomy in ethanol-fed rats.

Juskeviciute E, Dippold RP, Antony AN, Swarup A, Vadigepalli R, Hoek JB.

Am J Physiol Gastrointest Liver Physiol. 2016 Nov 1;311(5):G794-G806. doi: 10.1152/ajpgi.00292.2016. Epub 2016 Sep 15.


Integrated live imaging and molecular profiling of embryoid bodies reveals a synchronized progression of early differentiation.

Boxman J, Sagy N, Achanta S, Vadigepalli R, Nachman I.

Sci Rep. 2016 Aug 17;6:31623. doi: 10.1038/srep31623.


Systemic leukotriene B4 receptor antagonism lowers arterial blood pressure and improves autonomic function in the spontaneously hypertensive rat.

Marvar PJ, Hendy EB, Cruise TD, Walas D, DeCicco D, Vadigepalli R, Schwaber JS, Waki H, Murphy D, Paton JF.

J Physiol. 2016 Oct 15;594(20):5975-5989. doi: 10.1113/JP272065. Epub 2016 Jul 8.


Computational Modeling of Spatiotemporal Ca(2+) Signal Propagation Along Hepatocyte Cords.

Verma A, Makadia H, Hoek JB, Ogunnaike BA, Vadigepalli R.

IEEE Trans Biomed Eng. 2016 Oct;63(10):2047-55. doi: 10.1109/TBME.2016.2550045. Epub 2016 Apr 4.


HuR Contributes to TRAIL Resistance by Restricting Death Receptor 4 Expression in Pancreatic Cancer Cells.

Romeo C, Weber MC, Zarei M, DeCicco D, Chand SN, Lobo AD, Winter JM, Sawicki JA, Sachs JN, Meisner-Kober N, Yeo CJ, Vadigepalli R, Tykocinski ML, Brody JR.

Mol Cancer Res. 2016 Jul;14(7):599-611. doi: 10.1158/1541-7786.MCR-15-0448. Epub 2016 Apr 6.


Modeling cytokine regulatory network dynamics driving neuroinflammation in central nervous system disorders.

Anderson WD, Vadigepalli R.

Drug Discov Today Dis Models. 2016 Spring;19:59-67. doi: 10.1016/j.ddmod.2017.01.003. Epub 2017 Apr 10.


A novel comparative pattern analysis approach identifies chronic alcohol mediated dysregulation of transcriptomic dynamics during liver regeneration.

Kuttippurathu L, Juskeviciute E, Dippold RP, Hoek JB, Vadigepalli R.

BMC Genomics. 2016 Mar 25;17:260. doi: 10.1186/s12864-016-2492-x.


Erratum to: Molecular variability elicits a tunable switch with discrete neuromodulatory response phenotypes.

Anderson WD, Makadia HK, Vadigepalli R.

J Comput Neurosci. 2016 Feb;40(1):83. doi: 10.1007/s10827-015-0589-x. No abstract available.


Molecular variability elicits a tunable switch with discrete neuromodulatory response phenotypes.

Anderson WD, Makadia HK, Vadigepalli R.

J Comput Neurosci. 2016 Feb;40(1):65-82. doi: 10.1007/s10827-015-0584-2. Epub 2015 Dec 1. Erratum in: J Comput Neurosci. 2016 Feb;40(1):83.


Systems analysis of non-parenchymal cell modulation of liver repair across multiple regeneration modes.

Cook D, Ogunnaike BA, Vadigepalli R.

BMC Syst Biol. 2015 Oct 22;9:71. doi: 10.1186/s12918-015-0220-9.


Intracellular Information Processing through Encoding and Decoding of Dynamic Signaling Features.

Makadia HK, Schwaber JS, Vadigepalli R.

PLoS Comput Biol. 2015 Oct 22;11(10):e1004563. doi: 10.1371/journal.pcbi.1004563. eCollection 2015 Oct.


In Vivo Zonal Variation and Liver Cell-Type Specific NF-κB Localization after Chronic Adaptation to Ethanol and following Partial Hepatectomy.

Nilakantan H, Kuttippurathu L, Parrish A, Hoek JB, Vadigepalli R.

PLoS One. 2015 Oct 9;10(10):e0140236. doi: 10.1371/journal.pone.0140236. eCollection 2015.


Computational modeling of cytokine signaling in microglia.

Anderson WD, Makadia HK, Greenhalgh AD, Schwaber JS, David S, Vadigepalli R.

Mol Biosyst. 2015 Dec;11(12):3332-46. doi: 10.1039/c5mb00488h.


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.

Cook DJ, Patra B, Kuttippurathu L, Hoek JB, Vadigepalli R.

Front Physiol. 2015 Jul 7;6:189. doi: 10.3389/fphys.2015.00189. eCollection 2015.


MicroRNA network changes in the brain stem underlie the development of hypertension.

DeCicco D, Zhu H, Brureau A, Schwaber JS, Vadigepalli R.

Physiol Genomics. 2015 Sep;47(9):388-99. doi: 10.1152/physiolgenomics.00047.2015. Epub 2015 Jun 30.


Adiponectin fine-tuning of liver regeneration dynamics revealed through cellular network modelling.

Correnti JM, Cook D, Aksamitiene E, Swarup A, Ogunnaike B, Vadigepalli R, Hoek JB.

J Physiol. 2015 Jan 15;593(2):365-83. doi: 10.1113/jphysiol.2014.284109.


Multiscale model of dynamic neuromodulation integrating neuropeptide-induced signaling pathway activity with membrane electrophysiology.

Makadia HK, Anderson WD, Fey D, Sauter T, Schwaber JS, Vadigepalli R.

Biophys J. 2015 Jan 6;108(1):211-23. doi: 10.1016/j.bpj.2014.11.1851.


Identifying functional gene regulatory network phenotypes underlying single cell transcriptional variability.

Park J, Ogunnaike B, Schwaber J, Vadigepalli R.

Prog Biophys Mol Biol. 2015 Jan;117(1):87-98. doi: 10.1016/j.pbiomolbio.2014.11.004. Epub 2014 Nov 27.


Inputs drive cell phenotype variability.

Park J, Brureau A, Kernan K, Starks A, Gulati S, Ogunnaike B, Schwaber J, Vadigepalli R.

Genome Res. 2014 Jun;24(6):930-41. doi: 10.1101/gr.161802.113. Epub 2014 Mar 26.


Ethanol diverts early neuronal differentiation trajectory of embryonic stem cells by disrupting the balance of lineage specifiers.

Sánchez-Alvarez R, Gayen S, Vadigepalli R, Anni H.

PLoS One. 2013 May 28;8(5):e63794. doi: 10.1371/journal.pone.0063794. Print 2013.


Ethanol alters the balance of Sox2, Oct4, and Nanog expression in distinct subpopulations during differentiation of embryonic stem cells.

Ogony JW, Malahias E, Vadigepalli R, Anni H.

Stem Cells Dev. 2013 Aug 1;22(15):2196-210. doi: 10.1089/scd.2012.0513. Epub 2013 Apr 9.


MicroRNA profiling in lung cancer reveals new molecular markers for diagnosis.

Solomides CC, Evans BJ, Navenot JM, Vadigepalli R, Peiper SC, Wang ZX.

Acta Cytol. 2012;56(6):645-54. doi: 10.1159/000343473. Epub 2012 Nov 24.


Decorin protein core affects the global gene expression profile of the tumor microenvironment in a triple-negative orthotopic breast carcinoma xenograft model.

Buraschi S, Neill T, Owens RT, Iniguez LA, Purkins G, Vadigepalli R, Evans B, Schaefer L, Peiper SC, Wang ZX, Iozzo RV.

PLoS One. 2012;7(9):e45559. doi: 10.1371/journal.pone.0045559. Epub 2012 Sep 19.


Coordinated dynamic gene expression changes in the central nucleus of the amygdala during alcohol withdrawal.

Freeman K, Staehle MM, Vadigepalli R, Gonye GE, Ogunnaike BA, Hoek JB, Schwaber JS.

Alcohol Clin Exp Res. 2013 Jan;37 Suppl 1:E88-100. doi: 10.1111/j.1530-0277.2012.01910.x. Epub 2012 Jul 24.


Chronic ethanol feeding alters miRNA expression dynamics during liver regeneration.

Dippold RP, Vadigepalli R, Gonye GE, Patra B, Hoek JB.

Alcohol Clin Exp Res. 2013 Jan;37 Suppl 1:E59-69. doi: 10.1111/j.1530-0277.2012.01852.x. Epub 2012 Jul 23.


Chronic ethanol feeding enhances miR-21 induction during liver regeneration while inhibiting proliferation in rats.

Dippold RP, Vadigepalli R, Gonye GE, Hoek JB.

Am J Physiol Gastrointest Liver Physiol. 2012 Sep 15;303(6):G733-43. doi: 10.1152/ajpgi.00019.2012. Epub 2012 Jul 12.


Integrative gene regulatory network analysis reveals light-induced regional gene expression phase shift programs in the mouse suprachiasmatic nucleus.

Zhu H, Vadigepalli R, Rafferty R, Gonye GE, Weaver DR, Schwaber JS.

PLoS One. 2012;7(5):e37833. doi: 10.1371/journal.pone.0037833. Epub 2012 May 25.


Effects of developmental lead exposure on the hippocampal transcriptome: influences of sex, developmental period, and lead exposure level.

Schneider JS, Anderson DW, Talsania K, Mettil W, Vadigepalli R.

Toxicol Sci. 2012 Sep;129(1):108-25. doi: 10.1093/toxsci/kfs189. Epub 2012 May 28.


Temporal changes in innate immune signals in a rat model of alcohol withdrawal in emotional and cardiorespiratory homeostatic nuclei.

Freeman K, Brureau A, Vadigepalli R, Staehle MM, Brureau MM, Gonye GE, Hoek JB, Hooper DC, Schwaber JS.

J Neuroinflammation. 2012 May 24;9:97. doi: 10.1186/1742-2094-9-97.


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.

Freeman K, Staehle MM, Gümüş ZH, Vadigepalli R, Gonye GE, Nichols CN, Ogunnaike BA, Hoek JB, Schwaber JS.

Alcohol Clin Exp Res. 2012 Oct;36(10):1688-700. doi: 10.1111/j.1530-0277.2012.01791.x. Epub 2012 Apr 6.


Adaptive transcriptional dynamics of A2 neurons and central cardiovascular control pathways.

Vadigepalli R, Gonye GE, Paton JF, Schwaber JS.

Exp Physiol. 2012 Apr;97(4):462-8. doi: 10.1113/expphysiol.2011.059790. Epub 2011 Oct 14. Review.


Sex-based differences in gene expression in hippocampus following postnatal lead exposure.

Schneider JS, Anderson DW, Sonnenahalli H, Vadigepalli R.

Toxicol Appl Pharmacol. 2011 Oct 15;256(2):179-90. doi: 10.1016/j.taap.2011.08.008. Epub 2011 Aug 12.


Robust dynamic balance of AP-1 transcription factors in a neuronal gene regulatory network.

Miller GM, Ogunnaike BA, Schwaber JS, Vadigepalli R.

BMC Syst Biol. 2010 Dec 17;4:171. doi: 10.1186/1752-0509-4-171.


Structural properties of gene regulatory networks: definitions and connections.

Narasimhan S, Rengaswamy R, Vadigepalli R.

IEEE/ACM Trans Comput Biol Bioinform. 2009 Jan-Mar;6(1):158-70. doi: 10.1109/TCBB.2007.70231.


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