Kuttippurathu L, Juskeviciute E, Dippold RP, Hoek JB, Vadigepalli R. A novel comparative pattern analysis approach identifies chronic alcohol mediated dysregulation of transcriptomic dynamics during liver regeneration. BMC Genomics. DOI: 10.1186/s12864-016-2492-x
This paper describes a new data analysis approach named COMPACT, which is particularly suited for identifying key patterns in time series genomics data sets. The tool can be found at http://compact.jefferson.edu
Cook D, Ogunnaike BA, Vadigepalli R. (2015) Systems analysis of non-parenchymal cell modulation of liver repair across multiple regeneration modes. BMC Syst Biol. 2015 Oct 22;9:71. doi: 10.1186/s12918-015-0220-9. PubMed PMID: 26493454; PubMed Central PMCID: PMC4618752.
This paper describes a systems dynamics model of liver regeneration. Analysis of the model led to a new insight that altered non-parenchymal cell activation is sufficient to account for the deficient regeneration observed in multiple disease cases.
Anderson WD, Makadia HK, Greenhalgh AD, Schwaber JS, David S, Vadigepalli R. (2015) Computational modeling of cytokine signaling in microglia. Mol Biosyst. 2015 Oct 6. [Epub ahead of print] PubMed PMID: 26440115.
This paper describes a new model of a cytokine regulatory network in the microglia that led to an apparently counterintuitive prediction that knock out of the “anti-inflammatory” cytokine IL-10 can lead to a suppressed inflammatory response due to interaction between two kinetically imbalanced negative feedback connections. The results were validated by new experimental findings.
DeCicco D, Zhu H, Brureau A, Schwaber JS, Vadigepalli R. (2015) MicroRNA network changes in the brain stem underlie the development of hypertension. Physiol Genomics. 2015 Sep;47(9):388-99. doi: 10.1152/physiolgenomics.00047.2015. Epub 2015 Jun 30. PubMed PMID: 26126791; PubMed Central PMCID: PMC4556940. Editorial Highlight; APSselect for September 2015.
This study identified a new set of microRNAs that were upregulated in the brainstem during the onset of hypertension. These microRNAs were predicted to disinhibit neuroinflammatory processes and angiotensin II signaling, the two key processes driving the development of hypertension.
Park J, Brureau A, Kernan K, Starks A, Gulati S, Ogunnaike B, Schwaber J, Vadigepalli R. (2014) Inputs drive cell phenotype variability. Genome Res. 2014 Jun;24(6):930-41. doi: 10.1101/gr.161802.113. Epub 2014 Mar 26. PubMed PMID: 24671852; PubMed Central PMCID: PMC4032857.
This work revealed new findings that challenged the then popular paradigm that single cell gene expression variability is largely due to stochastic processes and manifests as ‘noise’. Based on measuring ~75 genes each in hundreds of single neurons, we found that the variability is highly ordered along a gradient based on inputs to individual cells, yielding a continuum of neuronal phenotypes.
- 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?
- SPSNet: Subpopulation-sensitive network-based analysis of heterogeneous gene expression data
- Novel influences of IL-10 on CNS inflammation revealed by integrated analyses of cytokine networks and microglial morphology
- A data-driven modeling approach to identify disease-specific multi-organ networks driving physiological dysregulation
- Pattern analysis uncovers a chronic ethanol-induced disruption of the switchlike dynamics of C/EBP-β and C/EBP-α genome-wide binding during liver regeneration
- Single-cell transcriptional analysis reveals novel neuronal phenotypes and interaction networks involved in the central circadian clock
- Systemic leukotriene B
4receptor antagonism lowers arterial blood pressure and improves autonomic function in the spontaneously hypertensive rat
- Computational Modeling of Spatiotemporal Ca2+Signal Propagation Along Hepatocyte Cords
- Integrated live imaging and molecular profiling of embryoid bodies reveals a synchronized progression of early differentiation
- A novel comparative pattern analysis approach identifies chronic alcohol mediated dysregulation of transcriptomic dynamics during liver regeneration
- 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
- Modeling cytokine regulatory network dynamics driving neuroinflammation in central nervous system disorders
- Erratum: Molecular variability elicits a tunable switch with discrete neuromodulatory response phenotypes (J Comput Neurosci, DOI 10.1007/s10827-015-0584-2)
- Molecular variability elicits a tunable switch with discrete neuromodulatory response phenotypes
- Inhibition of miR-21 rescues liver regeneration after partial hepatectomy in ethanol-fed rats
- HuR contributes to TRAIL resistance by restricting death receptor 4 expression in pancreatic cancer cells
- Systems analysis of non-parenchymal cell modulation of liver repair across multiple regeneration modes
- In vivo zonal variation and liver cell-type specific NF-κB localization after chronic adaptation to ethanol and following partial hepatectomy
- MicroRNA network changes in the brain stem underlie the development of hypertension
- Multiscale model of dynamic neuromodulation integrating neuropeptide-induced signaling pathway activity with membrane electrophysiology