Bharat Mishra

Academic Interests:

My academic interests are focused on bioinformatics, systems biology, network analysis, and biological data science. In my current role, I will contribute to the university research by providing bioinformatics consultations, analysis support, engaging in collaborative projects, and training individuals in biological data science through Genomics and Bioinformatics Core Facility (GBCF). I will provide bioinformatics services in high-throughput sequencing analysis at tissue (RNA-Seq), single-cell transcriptomics (scRNA-Seq), spatial transcriptomics (ST), and others to delineate the factors underlying cellular functions at unprecedented level of resolution. I follow FAIR data analysis and reporting practices including version control, containerization, open-source computational tools usages, and HPC computation clusters.

My research passion is in computational systems biology approaches to understand the genetic architectural changes during stress. Biological systems operate under intricate networks of molecular interactions, encompassing hundreds to thousands of biomolecules engaged in complex relationships. The unraveling of emerging responses during a stress or disease is very time and resource exhaustive. To address these challenges, computational systems biology, machine learning, and network-centric approaches proven effective in identifying biomarkers and immune cell patterns in aging, host-pathogen interactions, auto-immune disorders, and cancer at tissue levels. The central goal of my research is to establish computational and quantitative frameworks to untangle the biomolecular interactions at unprecedented level of resolution.

Biography:

• Assistant Professor of the Practice, Bioinformatics, Department of Biological Sciences, Notre Dame, IN, 2025 – present
• Computational Biologist, The University of Alabama at Birmingham (UAB), Birmingham, AL, 2024-2024
• Bioinformatician III, UAB, Birmingham, AL, 2022 – 2024
• Junior Research Fellow in Bioinformatics, ICAR-NBPGR, New Delhi, India, 2015 – 2016

Education:

• Ph.D, Biology, University of Alabama at Birmingham, AL. 2022
• M.Tech, Bioinformatics, Indian Institute of Information Technology, Allahabad, India. 2015
• B.Tech, Bioinformatics, SRM University, Chennai, India. 2012

Selected Professional Activities:

• Editorial Board Member: Frontiers in Molecular Biosciences, Scientific Reports
• Reviewer: Frontiers in Bioinformatics, Frontiers in Plant Sciences, IJMS, and Frontiers in Molecular Biosciences ISCB Fellow, 2022
• IS-MPMI Fellow, 2019 -2020
• Phi Sigma, Full Member, 2019

Recent Papers:

• Bharat Mishra, […], Shahid Mukhtar. Integrative systems biology framework discovers common gene regulatory signatures in mechanistically distinct inflammatory skin diseases. npj Systems Biology and Application. (2025)
• Mahendra Kashyap†, Bharat Mishra†, […], Mohammad Athar, Shahid Mukhtar, and Chander Raman et al., CD2 expressing innate lymphoid and T cells are critical effectors of immunopathogenesis in hidradenitis suppurativa. PNAS. (2024) (†: shared first authors) (US Patent filed for this study)
• Justin M. Watkins, […], Bharat Mishra, Alan M. Jones et al. Phosphorylation dynamics in a flg22-induced, heterotrimeric G-protein dependent signaling network in Arabidopsis thaliana reveals a candidate PP2A phosphatase involved in AtRGS1 trafficking. Molecular & Cellular Proteomics. (2023)
• Nilesh Kumar, Bharat Mishra, and M. Shahid Mukhtar. A pipeline of integrating transcriptome and interactome to elucidate central nodes in host-pathogen interactions. STAR Protocols. (2022).
• Bharat Mishra, et al. A rice protein interaction network reveals high centrality nodes and candidate pathogen effector targets. Computational and Structural Biotechnology Journal. (2022).
• Bharat Mishra, Mohammad Athar, and Shahid Mukhtar. Transcriptional circuitry atlas of genetic diverse unstimulated murine and human macrophages define disparity in population-wide innate immunity. Scientific Reports (2021).
• Nilesh Kumar†, Bharat Mishra†, […], Shahid Mukhtar. Integrative Network Biology Framework Elucidates Molecular Mechanisms of SARS-CoV- 2 Pathogenesis. iScience (2020). (†: shared first authors)
• Bharat Mishra, Nilesh Kumar, and M. Shahid Mukhtar. Systems Biology and Machine Learning in Plant–Pathogen Interactions. MPMI (2019).
• Bharat Mishra, et al. Global temporal dynamic landscape of pathogen-mediated subversion of Arabidopsis innate immunity. Scientific Reports (2017).

Research Specialties:

Plant Bioinformatics
Functional genomics and Systems Biology
Transcriptomics
Reproducible Research and Data Analysis
Software Carpentry
Next Generation Sequencing Data Analysis