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bibymaths/README.md

✨ Welcome to my GitHub!

I am a computational biologist and open-science advocate, motivated by mathematics and programming to transform biological complexity into computationally tractable problems. I integrate multi-omics data, build optimization-driven models that link molecular networks to drug responses, and develop open-source pipelines using high-performance computing, containerization, and workflow systems.

I hold an M.Sc. in Bioinformatics from Freie Universität Berlin (2025) and a B.Tech. in Bioinformatics from Jaypee University of Information Technology, India (2017).

Professionally, I have:

  • Built and validated an optimization framework to reconstruct phosphorylation networks in triple-negative breast cancer (TNBC) using proteomics data (DOI & Code)
  • Developed a physiologically-based pharmacokinetic (PBPK) model for drug distribution in the human body (Model)
  • Tested a pipeline for prostate cancer biomarker discovery using gene expression data and pathway analysis, leading (Publication).
  • Designed a docking workflow to screen FDA-approved drugs against the dopamine D3 receptor for potential repurposing in Schizophrenia (Poster)

I’m always glad to connect with others in bioinformatics, computational biology, and open science. Looking ahead, I aim to expand my modeling and integration methods toward precision medicine, where predictive models can guide real-world clinical decisions.

For a detailed overview of my work, visit the About and Portfolio sections of my website.

For my full CV, see the CV.


LinkedIn Email Portfolio


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  1. tirzepatide-model tirzepatide-model Public

    Forked from matthiaskoenig/tirzepatide-model

    Physiologically based pharmacokinetics (PBPK) model of tirzapetide

    HTML

  2. nf-illumina2lineage nf-illumina2lineage Public

    A Nextflow pipeline for SARS-CoV-2 genome assembly from Illumina reads.

    Nextflow

  3. SequenceAligner SequenceAligner Public

    A high-performance tool for global and local sequence alignment using Needleman-Wunsch, Smith-Waterman, and LCS algorithms, accelerated with MPI, OpenMP, and SIMD for DNA and protein sequences

    C++

  4. CasTuner CasTuner Public

    Python port of CasTuner: ODE modeling and reproducible analysis of CRISPR-based gene regulation.

    Jupyter Notebook

  5. CETSAx CETSAx Public

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

    Python

  6. pynetphorest pynetphorest Public

    Forked from gwilson9/NetworKINImplementation

    A modern Python implementation of NetPhorest for kinase–substrate prediction and phosphorylation crosstalk analysis.

    C