Sudin Bhattacharya, PhD

Associate Professor
Biomedical Engineering, Pharmacology & Toxicology

Bio

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.

Colleges

• College of Veterinary Medicine
• College of Engineering

Associations

• Institute for Quantitative Health Science and Engineering, Center for Research on Ingredient Safety, Institute for Integrative Toxicology

Programs

• Integrated Pharmacological Sciences Training Program
• Environmental & Integrative Toxicological Sciences Training Program
• Doctor of Philosophy in Pharmacology and Toxicology

Education

• PhD, Mechanical Engineering, University of Michigan (1999-08-01—2006-05-30)
• MS, Mechanical Engineering, University of Kentucky (1997-08-01—1999-05-30)

Education

• QQQ 1PhD, 2Mechanical Engineering, 3University of Michigan 4Mechanical Engineering (1999-08-01—2006-05-30)
• QQQ 1MS, 2Mechanical Engineering, 3University of Kentucky 4Mechanical Engineering (1997-08-01—1999-05-30)

Funding

• A Multi-scale Dose-response Model of AHR Toxicity Pathway Activation in the Human Liver, Environmental Protection Agency (2011-06-01—2015-05-30)
• Perivascular Adipose Tissue (PVAT) as a Central Integrator of Vascular Health, National Heart Lung and Blood Institute (2021-12-22—2026-11-30)
• Integrative transcriptional and epigenomic modeling of xenobiotic-activated gene regulatory networks, National Institute of Environmental Health Sciences (2020-07-03—2025-06-30)

Works

• Protocol for predicting single- and multiple-dose-dependent gene expression using deep generative learning. STAR Protocols (2025)
• PVAT-conditioned media from Dahl S rats on high fat diet promotes inflammatory cytokine secretion by activated T cells prior to the development of hypertension. PLOS ONE (2024-10-03)
• 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 (2024-05-01)
• A multiscale model of the mammalian liver circadian clock supports synchronization of autonomous oscillations by intercellular communication. (2024-02-20)
• Perivascular Adipose Tissue Remodels Only after Elevation of Blood Pressure in the Dahl SS Rat Fed a High-Fat Diet. Journal of vascular research (2023-12-19)
• A patterned human primitive heart organoid model generated by pluripotent stem cell self-organization. Nature Communications (2023-12-12)
• Interpretable predictive models of genome-wide aryl hydrocarbon receptor-DNA binding reveal tissue-specific binding determinants. Toxicological Sciences (2023-11-28)
• A Cell Atlas of Thoracic Aortic Perivascular Adipose Tissue: a focus on mechanotransducers. (2023-10-09)
• 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 (2023-05-12)
• Single-cell transcriptomics shows dose-dependent disruption of hepatic zonation by TCDD in mice. Toxicological Sciences (2023-01-31)
• Dose-dependent disruption of hepatic zonation by 2,3,7,8-tetrachlorodibenzo-p-dioxin in mice: integration of single-nuclei RNA sequencing and spatial transcriptomics. (2022-06-17)
• Benchmarking of a Bayesian single cell RNAseq differential gene expression test for dose–response study designs. Nucleic Acids Research (2022-05-06)
• 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)
• Benchmarking of a Bayesian single cell RNAseq differential gene expression test for dose-response study designs. (2021-09-10)
• Bioengineering of Genetically Encoded Gene Promoter Repressed by the Flavonoid Apigenin for Constructing Intracellular Sensor for Molecular Events. Biosensors (2021-04-28)
• Bioengineering of genetically encoded gene promoter repressed by flavonoids for constructing intracellular sensor for molecular events. (2021-02-18)
• Blood pressure changes PVAT function and transcriptome: use of the mid-thoracic aorta coarcted rat. American Journal of Physiology-Heart and Circulatory Physiology (2020-12-01)
• Application of single nuclei RNA sequencing to assess the hepatic effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin. (2020-04-08)
• 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 (2020-01-14)
• The role of cellular contact and TGF-beta signaling in the activation of the epithelial mesenchymal transition (EMT). Cell Adhesion & Migration (2019-01-01)
• 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 21^st 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)

Employment

• ZZ1Associate Professor , ZZ2Michigan State University ZZ3East Lansing ZZ$https://ror.org/05hs6h993 (2023-08-01)
• ZZ1Assistant Professor, ZZ2Michigan State University ZZ3East Lansing ZZ$3078 (2017-01-15—2023-07-30)
• ZZ1Assistant Professor, ZZ2Michigan State University ZZ3East Lansing ZZ$3078 (2015-10-15—2017-01-14)
• ZZ1Research Investigator, ZZ2The Hamner Institutes for Health Sciences ZZ3Durham ZZ$grid.281043.c (2009-03-01—2015-10-01)