Rajanikanth Vadigepalli

Rajanikanth Vadigepalli

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Rajanikanth Vadigepalli

Rajanikanth Vadigepalli

Publications by authors named "Rajanikanth Vadigepalli"

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

Front Neurosci 2019 3;13:665. Epub 2019 Jul 3.

Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, United States.

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http://dx.doi.org/10.3389/fnins.2019.00665DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6619439PMC
July 2019

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

Gene Expr 2019 04 6;19(2):97-119. Epub 2018 Sep 6.

Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA.

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http://www.ingentaconnect.com/content/10.3727/105221618X1536
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http://dx.doi.org/10.3727/105221618X15361728786767DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6466177PMC
April 2019

Model-based virtual patient analysis of human liver regeneration predicts critical perioperative factors controlling the dynamic mode of response to resection.

BMC Syst Biol 2019 01 16;13(1). Epub 2019 Jan 16.

Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA.

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https://bmcsystbiol.biomedcentral.com/articles/10.1186/s1291
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http://dx.doi.org/10.1186/s12918-019-0678-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6335689PMC
January 2019

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

Front Physiol 2018 4;9:1377. Epub 2018 Oct 4.

Department of Pathology, Anatomy and Cell Biology, Daniel Baugh Institute for Functional Genomics and Computational Biology, Thomas Jefferson University, Philadelphia, PA, United States.

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http://dx.doi.org/10.3389/fphys.2018.01377DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6180170PMC
October 2018

Modeling the Dynamics of Human Liver Failure Post Liver Resection.

Processes (Basel) 2018 Aug 4;6(8). Epub 2018 Aug 4.

Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.

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http://www.mdpi.com/2227-9717/6/8/115
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http://dx.doi.org/10.3390/pr6080115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6534166PMC
August 2018

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?

Alcohol Clin Exp Res 2018 05 6;42(5):845-848. Epub 2018 Apr 6.

Department of Pathology, Anatomy & Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania.

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http://dx.doi.org/10.1111/acer.13630DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5915906PMC
May 2018

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

Front Neuroinform 2018 16;12:18. Epub 2018 Apr 16.

Department of Neurology, SUNY Downstate Medical Center, The State University of New York, New York, NY, United States.

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http://dx.doi.org/10.3389/fninf.2018.00018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5911506PMC
April 2018

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

BMC Syst Biol 2018 03 19;12(Suppl 2):28. Epub 2018 Mar 19.

School of Computing, National University of Singapore, 13 Computing Drive, Singapore, 117417, Singapore.

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http://dx.doi.org/10.1186/s12918-018-0538-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5861489PMC
March 2018

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

Front Cell Neurosci 2017 14;11:233. Epub 2017 Aug 14.

Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson UniversityPhiladelphia, PA, United States.

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http://dx.doi.org/10.3389/fncel.2017.00233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5557777PMC
August 2017

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

PLoS Comput Biol 2017 Jul 21;13(7):e1005627. Epub 2017 Jul 21.

Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA.

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http://dx.doi.org/10.1371/journal.pcbi.1005627DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5521738PMC
July 2017

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

Drug Discov Today Dis Models 2016 10;19:59-67. Epub 2017 Apr 10.

Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology, Anatomy and Cell Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA.

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http://dx.doi.org/10.1016/j.ddmod.2017.01.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5609716PMC
April 2017

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.

Physiol Genomics 2017 01 4;49(1):11-26. Epub 2016 Nov 4.

Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania;

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http://www.physiology.org/doi/10.1152/physiolgenomics.00097.
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http://dx.doi.org/10.1152/physiolgenomics.00097.2016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5283919PMC
January 2017

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

Am J Physiol Gastrointest Liver Physiol 2016 11 15;311(5):G794-G806. Epub 2016 Sep 15.

Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania

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http://dx.doi.org/10.1152/ajpgi.00292.2016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5130549PMC
November 2016

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

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

Department of Pathology, Anatomy and Cell Biology, Daniel Baugh Institute for Functional Genomics and Computational Biology, Sidney Kimmel Medical College, Thomas Jefferson UniversityPhiladelphia, PA, USA; Department of Chemical and Biomolecular Engineering, University of DelawareNewark, NJ, USA.

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http://dx.doi.org/10.3389/fnins.2016.00481DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5079116PMC
October 2016

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

Mol Cancer Res 2016 07 6;14(7):599-611. Epub 2016 Apr 6.

Division of Surgical Research, Department of Surgery, Jefferson Pancreas, Biliary, and Related Cancer Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania.

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http://dx.doi.org/10.1158/1541-7786.MCR-15-0448DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5312260PMC
July 2016

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

PLoS One 2015 9;10(10):e0140236. Epub 2015 Oct 9.

Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America; MitoCare Center for Mitochondrial Research, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0140236PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4599916PMC
June 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.

Mol Biosyst 2016 Mar;12(3):1037-56

Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA. and Mitocare Center for Mitochondrial Research, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.

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http://xlink.rsc.org/?DOI=C5MB00740B
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http://dx.doi.org/10.1039/c5mb00740bDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4891188PMC
March 2016

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

BMC Genomics 2016 Mar 25;17:260. Epub 2016 Mar 25.

Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA.

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http://dx.doi.org/10.1186/s12864-016-2492-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4807561PMC
March 2016

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

J Comput Neurosci 2016 Feb 1;40(1):65-82. Epub 2015 Dec 1.

Daniel Baugh Institute for Functional Genomics and Computational Biology, Thomas Jefferson University, 1020 Locust St, Philadelphia, PA, 19107, USA.

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http://dx.doi.org/10.1007/s10827-015-0584-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4867553PMC
February 2016

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

J Comput Neurosci 2016 Feb;40(1):83

Daniel Baugh Institute for Functional Genomics and Computational Biology, Thomas Jefferson University, 1020 Locust St, Philadelphia, PA, 19107, USA.

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http://dx.doi.org/10.1007/s10827-015-0589-xDOI Listing
February 2016

Computational modeling of cytokine signaling in microglia.

Mol Biosyst 2015 Dec;11(12):3332-46

Daniel Baugh Institute for Functional Genomics and Computational Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA. and Graduate Program in Neuroscience, Jefferson College of Biomedical Sciences, Thomas Jefferson University, Philadelphia, PA, USA.

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http://dx.doi.org/10.1039/c5mb00488hDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5520540PMC
December 2015

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

PLoS Comput Biol 2015 Oct 22;11(10):e1004563. Epub 2015 Oct 22.

Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America.

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https://dx.plos.org/10.1371/journal.pcbi.1004563
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http://dx.doi.org/10.1371/journal.pcbi.1004563DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4619640PMC
October 2015

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

BMC Syst Biol 2015 Oct 22;9:71. Epub 2015 Oct 22.

Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA.

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http://dx.doi.org/10.1186/s12918-015-0220-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4618752PMC
October 2015

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

Physiol Genomics 2015 Sep 30;47(9):388-99. Epub 2015 Jun 30.

Department of Pathology, Anatomy and Cell Biology, Daniel Baugh Institute for Functional Genomics/Computational Biology, Thomas Jefferson University, Philadelphia, Pennsylvania

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http://dx.doi.org/10.1152/physiolgenomics.00047.2015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4556940PMC
September 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.

Front Physiol 2015 7;6:189. Epub 2015 Jul 7.

Department of Pathology, Anatomy and Cell Biology, Daniel Baugh Institute for Functional Genomics/Computational Biology, Thomas Jefferson University Philadelphia, PA, USA ; Department of Chemical and Biomolecular Engineering, University of Delaware Newark, DE, USA.

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http://dx.doi.org/10.3389/fphys.2015.00189DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4493398PMC
July 2015

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

Prog Biophys Mol Biol 2015 Jan 27;117(1):87-98. Epub 2014 Nov 27.

Department of Chemical and Biochemical Engineering, University of Delaware, Newark, DE 19716, USA; Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA. Electronic address:

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http://dx.doi.org/10.1016/j.pbiomolbio.2014.11.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4366310PMC
January 2015

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

Biophys J 2015 Jan;108(1):211-23

Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania; Graduate Program in Neuroscience, Thomas Jefferson University, Philadelphia, Pennsylvania. Electronic address:

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http://researchrepository.ucd.ie/bitstream/handle/10197/6649
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http://linkinghub.elsevier.com/retrieve/pii/S000634951403061
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http://dx.doi.org/10.1016/j.bpj.2014.11.1851DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286605PMC
January 2015

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

J Physiol 2015 Jan;593(2):365-83

MitoCare Center for Mitochondrial Research, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA.

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http://doi.wiley.com/10.1113/jphysiol.2014.284109
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http://dx.doi.org/10.1113/jphysiol.2014.284109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4303383PMC
January 2015

Inputs drive cell phenotype variability.

Genome Res 2014 Jun 26;24(6):930-41. Epub 2014 Mar 26.

Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Jefferson Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA; Department of Chemical and Biochemical Engineering, University of Delaware, Newark, Delaware 19716, USA;

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http://dx.doi.org/10.1101/gr.161802.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4032857PMC
June 2014

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

PLoS One 2013 28;8(5):e63794. Epub 2013 May 28.

Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0063794PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3665827PMC
January 2014

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

Stem Cells Dev 2013 Aug 9;22(15):2196-210. Epub 2013 Apr 9.

Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Jefferson Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA.

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https://www.liebertpub.com/doi/10.1089/scd.2012.0513
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http://dx.doi.org/10.1089/scd.2012.0513DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715797PMC
August 2013

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

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

Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA.

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http://dx.doi.org/10.1159/000343473DOI Listing
February 2013

Chronic ethanol feeding alters miRNA expression dynamics during liver regeneration.

Alcohol Clin Exp Res 2013 Jan 23;37 Suppl 1:E59-69. Epub 2012 Jul 23.

Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA.

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http://doi.wiley.com/10.1111/j.1530-0277.2012.01852.x
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http://dx.doi.org/10.1111/j.1530-0277.2012.01852.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3482264PMC
January 2013

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

Alcohol Clin Exp Res 2013 Jan 24;37 Suppl 1:E88-100. Epub 2012 Jul 24.

Department of Pathology, Anatomy and Cell Biology (KF, MMS, RV, GEG, JBH, JSS), Daniel Baugh Institute for Functional Genomics and Computational Biology, Thomas Jefferson University, Philadelphia, Pennsylvania; Department of Chemical Engineering (MMS), Rowan University, Glassboro, New Jersey; Department of Chemical Engineering (MMS, BAO), University of Delaware, Newark, Delaware.

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http://doi.wiley.com/10.1111/j.1530-0277.2012.01910.x
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http://dx.doi.org/10.1111/j.1530-0277.2012.01910.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4408903PMC
January 2013

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.

Alcohol Clin Exp Res 2012 Oct 6;36(10):1688-700. Epub 2012 Apr 6.

Department of Pathology, Anatomy and Cell Biology, Daniel Baugh Institute for Functional Genomics and Computational Biology, Thomas Jefferson University Philadelphia, Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1111/j.1530-0277.2012.01791.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4419739PMC
October 2012

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

Toxicol Sci 2012 Sep 28;129(1):108-25. Epub 2012 May 28.

Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA.

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http://dx.doi.org/10.1093/toxsci/kfs189DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3499078PMC
September 2012

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

Am J Physiol Gastrointest Liver Physiol 2012 Sep 12;303(6):G733-43. Epub 2012 Jul 12.

Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA.

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http://www.physiology.org/doi/10.1152/ajpgi.00019.2012
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http://dx.doi.org/10.1152/ajpgi.00019.2012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3468539PMC
September 2012

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

J Neuroinflammation 2012 May 24;9:97. Epub 2012 May 24.

Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA.

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http://dx.doi.org/10.1186/1742-2094-9-97DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3411448PMC
May 2012

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

Exp Physiol 2012 Apr 14;97(4):462-8. Epub 2011 Oct 14.

Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1113/expphysiol.2011.059790DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4414336PMC
April 2012

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

BMC Syst Biol 2010 Dec 17;4:171. Epub 2010 Dec 17.

Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University Philadelphia, PA 19107, USA.

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http://link.springer.com/content/pdf/10.1186/1752-0509-4-171
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http://www.biomedcentral.com/1752-0509/4/171
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http://dx.doi.org/10.1186/1752-0509-4-171DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3019179PMC
December 2010

Structural properties of gene regulatory networks: definitions and connections.

IEEE/ACM Trans Comput Biol Bioinform 2009 Jan-Mar;6(1):158-70

Department of Chemical Engineering, IIT Madras, Chennai 600036, India.

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http://dx.doi.org/10.1109/TCBB.2007.70231DOI Listing
August 2009

Temporal and functional profile of the transcriptional regulatory network in the early regenerative response to partial hepatectomy in the rat.

BMC Genomics 2008 Nov 6;9:527. Epub 2008 Nov 6.

Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.

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http://dx.doi.org/10.1186/1471-2164-9-527DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2613928PMC
November 2008

Transcriptional regulatory network analysis during epithelial-mesenchymal transformation of retinal pigment epithelium.

Mol Vis 2008 Aug 4;14:1414-28. Epub 2008 Aug 4.

Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2493022PMC
August 2008

Dynamic transcriptomic response to acute hypertension in the nucleus tractus solitarius.

Am J Physiol Regul Integr Comp Physiol 2008 Jul 23;295(1):R15-27. Epub 2008 Apr 23.

Daniel Baugh Institute for Functional Genomics/Computational Biology, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA.

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http://dx.doi.org/10.1152/ajpregu.00152.2008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2494808PMC
July 2008

From promoter analysis to transcriptional regulatory network prediction using PAINT.

Methods Mol Biol 2007 ;408:49-68

Thomas Jefferson University, Philadelphia, PA, USA.

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http://dx.doi.org/10.1007/978-1-59745-547-3_4DOI Listing
April 2008

Systems analysis of circadian time-dependent neuronal epidermal growth factor receptor signaling.

Genome Biol 2006 ;7(6):R48

Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Thomas Jefferson University, Locust St, Philadelphia, PA 19107, USA.

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http://link.springer.com/content/pdf/10.1186/gb-2006-7-6-r48
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http://genomebiology.com/2006/7/6/R48
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http://dx.doi.org/10.1186/gb-2006-7-6-r48DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1779538PMC
October 2006

Epidermal growth factor receptor-induced circadian-time-dependent gene regulation in suprachiasmatic nucleus.

Neuroreport 2006 Sep;17(13):1437-41

Department of Pathology, Anatomy and Cell Biology, Daniel Baugh Institute for Functional Genomics and Computational Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA.

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http://dx.doi.org/10.1097/01.wnr.0000227989.15422.71DOI Listing
September 2006

The inflammatory and normal transcriptome of mouse bladder detrusor and mucosa.

BMC Physiol 2006 Jan 18;6. Epub 2006 Jan 18.

Department of Physiology, The University Oklahoma Health Sciences Center, Oklahoma City, USA.

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http://dx.doi.org/10.1186/1472-6793-6-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1382248PMC
January 2006

Chronic alcohol exposure alters transcription broadly in a key integrative brain nucleus for homeostasis: the nucleus tractus solitarius.

Physiol Genomics 2005 Dec 27;24(1):45-58. Epub 2005 Sep 27.

Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA.

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http://dx.doi.org/10.1152/physiolgenomics.00184.2005DOI Listing
December 2005

Continuous-time identification of gene expression models.

OMICS 2003 ;7(4):373-86

Department of Chemical Engineering, University of Delaware, Newark, Delaware, USA.

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http://dx.doi.org/10.1089/153623103322637689DOI Listing
October 2004

Erythroid-induced commitment of K562 cells results in clusters of differentially expressed genes enriched for specific transcription regulatory elements.

Physiol Genomics 2004 Sep 13;19(1):117-30. Epub 2004 Jul 13.

The Cardeza Foundation for Hematologic Research and Division of Hematology, Department of Medicine, Jefferson Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA.

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http://dx.doi.org/10.1152/physiolgenomics.00028.2004DOI Listing
September 2004

PAINT: a promoter analysis and interaction network generation tool for gene regulatory network identification.

OMICS 2003 ;7(3):235-52

Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA.

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http://dx.doi.org/10.1089/153623103322452378DOI Listing
May 2004