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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.
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.
Closed-loop modeling of central and intrinsic cardiac nervous system circuits underlying cardiovascular control
Conditional expression of endorepellin in the tumor vasculature attenuates breast cancer growth, angiogenesis and hyaluronan deposition
Elucidating the Mechanisms of Dynamic and Robust Control of the Liver Homeostatic Renewal Process: Cell Network Modeling and Analysis
Unpacking the multimodal, multi-scale data of the fast and slow lanes of the cardiac vagus through computational modelling
Longitudinal ultrasound imaging and network modeling in rats reveal sex-dependent suppression of liver regeneration after resection in alcoholic liver disease
Genome-Scale Metabolic Modeling Reveals Sequential Dysregulation of Glutathione Metabolism in Livers from Patients with Alcoholic Hepatitis
Investigating Drivers of Antireward in Addiction Behavior with Anatomically Specific Single-Cell Gene Expression Methods
Dysregulation of miR-21-associated miRNA regulatory networks by chronic ethanol consumption impairs liver regeneration
A Spatial Model of Hepatic Calcium Signaling and Glucose Metabolism Under Autonomic Control Reveals Functional Consequences of Varying Liver Innervation Patterns Across Species
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
Retinoic Acid Fluctuation Activates an Uneven, Direction-Dependent Network-Wide Robustness Response in Early Embryogenesis
Analyzing the relationships between city opioid deaths and socioeconomic factors
3D single cell scale anatomical map of sex-dependent variability of the rat intrinsic cardiac nervous system
A single cell transcriptomics map of paracrine networks in the intrinsic cardiac nervous system
Mapping the little brain at the heart by an interdisciplinary systems biology team
Innervation and Neuronal Control of the Mammalian Sinoatrial Node a Comprehensive Atlas
Integrated Multiomics Reveals Glucose Use Reprogramming and Identifies a Novel Hexokinase in Alcoholic Hepatitis
Input-output signal processing plasticity of vagal motor neurons in response to cardiac ischemic injury
Hepatic lipocalin 2 promotes liver fibrosis and portal hypertension
Credible practice of modeling and simulation in healthcare: Ten rules from a multidisciplinary perspective
A Comprehensive Integrated Anatomical and Molecular Atlas of Rat Intrinsic Cardiac Nervous System
Investigating the Effects of Brainstem Neuronal Adaptation on Cardiovascular Homeostasis
Diurnal Patterns of Gene Expression in the Dorsal Vagal Complex and the Central Nucleus of the Amygdala – Non-rhythm-generating Brain Regions
Combining laser capture microdissection and microfluidic qpcr to analyze transcriptional profiles of single cells: A systems biology approach to opioid dependence
Inflammation-associated suppression of metabolic gene networks in acute and chronic liver disease