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bibymaths/README.md

Abhinav Mishra

Bioinformatician · computational systems biologist · mathematical modeller · research software developer

I work across bioinformatics, systems biology and quantitative modelling, from classical omics analysis and biological data integration to mechanistic models of signalling, pharmacology and drug response.

My work combines multi-omics analysis, mathematical modelling, optimization, Bayesian inference and reproducible scientific computing to turn biological questions into quantitative, testable workflows and models.

Research · Software · Publications · CV

Elsewhere

Website · ORCID · LinkedIn · Email

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  1. fastdpplot fastdpplot Public

    Rust-accelerated dot plot renderer for bioinformatics data, available as a Python library, CLI, and desktop GUI.

    Python

  2. bio-sea-pearl bio-sea-pearl Public

    A hybrid Python + Perl toolkit for sequence alignment, Markov modeling, FM-index search, and sequence analysis with a unified CLI, REST API, and Docker support.

    Python

  3. phoskintime phoskintime Public

    A Network Dynamics Toolkit for Phosphorylation Cascades

    Python

  4. pynetworkin pynetworkin Public

    A modernised Python 3 port of the original NetworKIN 3.0 tool (Linding, Jensen, Horn & Kim, 2005–2013), extended to support STRING v12 protein interaction data

    Python

  5. KinOpt KinOpt Public

    Optimization-based estimation of cumulative kinase effects on substrate phosphorylation, including the effects of kinase autophosphorylation on its own activity.

    Jupyter Notebook

  6. CETSAx CETSAx Public

    CETSA-MS modelling toolkit for dose–response analysis, binder classification, Bayesian inference, ML curve typing, and proteome-wide stability networks.

    Python