Sudin Bhattacharya , PhD
Biography
Dr. Sudin Bhattacharya (he/him/his) is an Associate Professor in the departments of Biomedical Engineering and Pharmacology & Toxicology. He leads a lab that conducts research at the interface of computation and biology, using quantitative tools to study the signaling and transcriptional networks that regulate cell fate and its perturbation by environmental pollutants. Dr. Bhattacharya joined MSU as an assistant professor in November 2015. Originally from Kolkata, India, he completed his undergraduate degree at Jadavpur University in India, his master’s degree at the University of Kentucky, and his Ph.D. at the University of Michigan, all in mechanical engineering. He completed his postdoc in computational biology at The Hamner Institutes in Research Triangle Park, North Carolina.
Education
PhD, Mechanical Engineering, University of Michigan, 1999
MS, Mechanical Engineering, University of Kentucky, 1997
Employment
Associate Professor , Michigan State University, East Lansing, 2023 - Present
Assistant Professor, Michigan State University, East Lansing, 2017 - 2023
Assistant Professor, Michigan State University, East Lansing, 2015 - 2017
Research Investigator, The Hamner Institutes for Health Sciences, Durham, 2009 - 2015
Publications
Protocol for predicting single- and multiple-dose-dependent gene expression using deep generative learning STAR Protocols (2025)
Unique challenges and best practices for single cell transcriptomic analysis in toxicology Current Opinion in Toxicology (2024)
A cell atlas of thoracic aortic perivascular adipose tissue: a focus on mechanotransducers American Journal of Physiology-Heart and Circulatory Physiology (2024)
Perivascular Adipose Tissue Remodels Only after Elevation of Blood Pressure in the Dahl SS Rat Fed a High-Fat Diet. Journal of vascular research (2023)
A patterned human primitive heart organoid model generated by pluripotent stem cell self-organization Nature Communications (2023)
Interpretable predictive models of genome-wide aryl hydrocarbon receptor-DNA binding reveal tissue-specific binding determinants Toxicological Sciences (2023)
Generative modeling of single-cell gene expression for dose-dependent chemical perturbations Patterns (2023)
Prediction of mammalian tissue-specific CLOCK–BMAL1 binding to E-box DNA motifs Scientific Reports (2023)
Single-cell transcriptomics shows dose-dependent disruption of hepatic zonation by TCDD in mice Toxicological Sciences (2023)
Benchmarking of a Bayesian single cell RNAseq differential gene expression test for dose–response study designs Nucleic Acids Research (2022)
A Negative Feedback Loop and Transcription Factor Cooperation Regulate Zonal Gene Induction by 2, 3, 7, 8‐Tetrachlorodibenzo‐p‐Dioxin in the Mouse Liver Hepatology Communications (2022)
Bioengineering of Genetically Encoded Gene Promoter Repressed by the Flavonoid Apigenin for Constructing Intracellular Sensor for Molecular Events Biosensors (2021)
Blood pressure changes PVAT function and transcriptome: use of the mid-thoracic aorta coarcted rat American Journal of Physiology-Heart and Circulatory Physiology (2020)
Identifying qualitative differences in PPARα signaling networks in human and rat hepatocytes and their significance for next generation chemical risk assessment methods Toxicology in Vitro (2020)
Gene co-regulation and co-expression in the aryl hydrocarbon receptor-mediated transcriptional regulatory network in the mouse liver Archives of Toxicology (2020)
The role of cellular contact and TGF-beta signaling in the activation of the epithelial mesenchymal transition (EMT) Cell Adhesion & Migration (2019)
A Theoretical Model of the Wnt Signaling Pathway in the Epithelial Mesenchymal Transition Theoretical Biology and Medical Modelling (2017)
Aryl hydrocarbon receptor activation suppresses EBF1 and PAX5 and impairs human B Lymphopoiesis Journal of Immunology (2017)
Identification of a unique gene expression signature in mercury and 2,3,7,8-tetrachlorodibenzo-p-dioxin co-exposed cells Toxicology Research (2017)
Adaptive posttranslational control in cellular stress response pathways and its relationship to toxicity testing and safety assessment Toxicological Sciences (2015)
Molecular signaling network motifs provide a mechanistic basis for cellular threshold responses Environmental Health Perspectives (2015)
A map of the PPARα transcription regulatory network for primary human hepatocytes Chemico-Biological Interactions (2014)
All-or-none suppression of B cell terminal differentiation by environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin Toxicology and Applied Pharmacology (2013)
Recent advances in 2D and 3D in vitro systems using primary hepatocytes, alternative hepatocyte sources and non-parenchymal liver cells and their use in investigating mechanisms of hepatotoxicity, cell signaling and ADME Archives of Toxicology (2013)
Toxicogenomics for transcription factor-governed molecular pathways: Moving on to roles beyond classification and prediction Archives of Toxicology (2013)
Ultrasensitive response motifs: Basic amplifiers in molecular signalling networks Open Biology (2013)
Modeling drug- and chemical-induced hepatotoxicity with systems biology approaches Frontiers in Physiology (2012)
A deterministic map of Waddington's epigenetic landscape for cell fate specification BMC Systems Biology (2011)
Role of Core Biological Motifs in Dose-Response Modeling: An Example with Switchlike Circuits Systems Bio in Drug Discovery (2011)
Toxicity testing in the 21st century: Defining new risk assessment approaches based on perturbation of intracellular toxicity pathways PLoS ONE (2011)
A bistable switch underlying B-cell differentiation and its disruption by the environmental contaminant 2,3,7,8-Tetrachlorodibenzo-p-dioxin Toxicological Sciences (2010)
Bistable Signaling Motifs and Cell Fate Decisions Quantitative Modeling in Toxicology (2010)
Computational systems biology and dose-response modeling in relation to new directions in toxicity testing Journal of Toxicology and Environmental Health - Part B: Critical Reviews (2010)
Gene and Protein Expression - Modeling Nested Motifs in Cellular and Tissue Response Networks Quantitative Modeling in Toxicology (2010)
Stochastic modeling of b lymphocyte terminal differentiation and its suppression by dioxin BMC Systems Biology (2010)
Ultrasensitive Response Motifs in Biochemical Networks Quantitative Modeling in Toxicology (2010)
Computational Systems Biology Modeling of Dosimetry and Cellular Response Pathways Drug Efficacy, Safety, and Biologics Discovery: Emerging Technologies and Tools (2008)
Molecular dynamics simulation study of growth regimes during polycondensation of silicic acid: From silica nanoparticles to porous gels Journal of Physical Chemistry C (2008)
Fractal dimensions of silica gels generated using reactive molecular dynamics simulations Journal of Chemical Physics (2005)
