Research profile
Computational systems biologist developing mechanistic models and scientific software for signalling dynamics, multi-omics and drug response. My work links biological questions to mathematical representations, numerical inference and reproducible computational outputs.
Education
- Master of Science, Bioinformatics — Freie Universität Berlin, Germany, 2025
Thesis: Mathematical Optimization of Signalling Networks in Triple Negative Breast Cancer Cell Lines. Archived thesis - Bachelor of Technology, Bioinformatics — Jaypee University of Information Technology, India, 2017
Thesis: Identification of Potent Biomarkers for Prostate Cancer Through AR, MAPK, and mTOR Signalling Pathway Mining. Project repository
Research experience
- Research Intern — Institute for Biology, Humboldt-Universität zu Berlin (Jan–Feb 2025)
Developed a physiologically based pharmacokinetic model for tirzepatide using curated clinical data and parameter optimization. Public model repository - Master’s Thesis Student — Theoretical Biophysics, Humboldt-Universität zu Berlin (May 2024–Jan 2025)
Developed an optimization framework for reconstructing triple-negative breast-cancer phosphorylation networks from LC–MS and kinase–substrate data using differential evolution and sequential least-squares programming. PhosKinTime - Bachelor’s Thesis Student — JUIT, India (Feb 2016–Mar 2017)
Implemented a gene-expression and pathway-analysis workflow for prostate-cancer biomarker discovery. Project repository - Project Researcher — JUIT, India (Aug 2015–Mar 2016)
Developed a molecular-docking workflow to screen approved compounds against the dopamine D3 receptor and analysed predicted molecular interactions. Poster materials
Selected outputs
- Mishra, A. & König, M. Physiologically Based Pharmacokinetic Model of Tirzepatide. Zenodo, 2025. DOI
- Asati, N., Mishra, A., Shukla, A., & Singh, T. Gene Expression Studies to Identify Significant Genes in AR, MTOR, MAPK Pathways and their Overlapping Regulatory Role in Prostate Cancer. Journal of Integrative Bioinformatics 16(3), 2019. DOI
- See Publications & Outputs and the curated Software portfolio for resource-level links.
Technical competencies
Mathematical & mechanistic modelling
ODE and PDE systems · dynamical systems · PBPK · parameter estimation · sensitivity analysis · network models
Statistical inference & optimization
Constrained and nonlinear optimization · Bayesian inference · uncertainty analysis · likelihood-based modelling
Scientific computing
Python · JAX · NumPy/SciPy · C++ · parallel computing · numerical model implementation
Bioinformatics
Phosphoproteomics · time-course molecular data · sequence analysis · pathway and network analysis · genomic workflows
Reproducible computing
Nextflow · containers · GitHub Actions · testing · packaging · documentation · SBML/PEtab
Open science & community
- Administrator, BioBaes (since 2020) — community initiative for bioinformatics learning, mentoring and open knowledge.
- Member, International Society for Computational Biology — one-year membership.
Awards & honours
- Third prize, poster presentation, NSCSB 2016, JUIT India.
- GATE qualified, All India Rank 681 (2018).