https://github.com/bibymaths/bibymaths
https://github.com/bibymaths/bibymaths
Last synced: about 1 month ago
JSON representation
- Host: GitHub
- URL: https://github.com/bibymaths/bibymaths
- Owner: bibymaths
- License: cc0-1.0
- Created: 2025-01-18T17:56:05.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2025-03-15T01:43:12.000Z (about 1 year ago)
- Last Synced: 2025-03-15T02:31:33.066Z (about 1 year ago)
- Size: 15.6 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# Abhinav Mishra
**Computational Biologist · Mathematical Modeller · Open-Science Advocate**
*Transforming biological complexity into computationally tractable problems*
[](https://linkedin.com/in/bibymaths)
[](mailto:mishraabhinav36@gmail.com)
[](https://bibymaths.github.io)
[](https://bibymaths.github.io/files/Abhinav_Mishra_CV_03_04_2026.pdf)
---
## About Me
I integrate **multi-omics data**, build **optimization-driven models** that link molecular networks to drug responses, and develop reproducible open-source pipelines with high-performance computing, containerization, and workflow systems.
My work sits at the intersection of **mathematical modelling**, **systems biology**, and **precision medicine** — where equations and algorithms translate biological noise into clinical insight.
**Education**
- 🎓 M.Sc. Bioinformatics — Freie Universität Berlin, 2025
- 🎓 B.Tech. Bioinformatics — Jaypee University of Information Technology, 2017
---
## Featured Projects
### 🔬 Phosphorylation Network Reconstruction · TNBC
Built and validated an **optimization framework** to reconstruct phosphorylation signalling networks in triple-negative breast cancer (TNBC) from mass-spectrometry proteomics data.
`Python` `Optimization` `Proteomics` `Systems Biology`
[](https://doi.org/10.5281/zenodo.17290716)
[](https://github.com/bibymaths/phoskintime)
---
### 💊 Physiologically-Based Pharmacokinetic (PBPK) Model
Developed a mechanistic **PBPK model** for drug distribution in the human body — parameterised from tissue composition and plasma binding data.
`ODE Systems` `Pharmacokinetics` `Mathematical Modelling`
[](https://doi.org/10.5281/zenodo.14976788)
---
### 🧬 Prostate Cancer Biomarker Pipeline
Designed and tested an end-to-end bioinformatics pipeline for **prostate cancer biomarker discovery** — integrating gene expression data, differential analysis, and pathway enrichment.
`RNA-seq` `Bioinformatics` `Pathway Analysis`
[](https://doi.org/10.1515/jib-2018-0080)
---
### 🧠 Drug Repurposing · Dopamine D3 Receptor (Schizophrenia)
Engineered a **molecular docking workflow** to screen FDA-approved compounds against the dopamine D3 receptor for potential repurposing in schizophrenia treatment.
`Molecular Docking` `Drug Repurposing` `Cheminformatics`
[](https://bibymaths.github.io/posters/#1-poster-docking-for-schizophrenia)
---
## Skills & Toolbox
| Domain | Tools & Technologies |
|---|---|
| **Languages** | Python · R · Bash · MATLAB |
| **Modelling & Optimisation** | ODE systems · Flux Balance Analysis · Constraint-based modelling · PBPK |
| **Multi-omics** | Proteomics · Transcriptomics · scRNA-seq · Pathway enrichment |
| **HPC & Workflow** | Snakemake · Nextflow · Singularity · SLURM |
| **Data & Viz** | Pandas · NumPy · SciPy · Matplotlib · Seaborn · ggplot2 |
| **Reproducibility** | Docker · Git · Zenodo · GitHub Actions |
---
## Research Interests
```
Precision Medicine → predictive models for clinical decision support
Mathematical Pharmacology → PK/PD, PBPK, drug-response modelling
Network Biology → signalling networks, phosphoproteomics, graph theory
Multi-omics Integration → data fusion across genomics, proteomics, metabolomics
Open Science → FAIR data, reproducible pipelines, open-source tooling
```
---
## Publications & Outputs
| Year | Output | Link |
|---|---|---|
| 2025 | Phospho-network reconstruction framework (TNBC) | [Zenodo](https://doi.org/10.5281/zenodo.17290716) · [Code](https://github.com/bibymaths/phoskintime) |
| 2025 | PBPK model for human drug distribution | [Zenodo](https://doi.org/10.5281/zenodo.14976788) |
| 2018 | Prostate cancer biomarker discovery pipeline | [J. Integr. Bioinform.](https://doi.org/10.1515/jib-2018-0080) |
---
## Let's Connect
I'm always glad to collaborate on bioinformatics, computational biology, or open-science projects. Looking ahead, I aim to expand my modelling and integration methods toward **precision medicine**, where predictive models can guide real-world clinical decisions.
[](https://linkedin.com/in/bibymaths)
[](mailto:mishraabhinav36@gmail.com)
[](https://bibymaths.github.io)
*"Mathematics is the language in which biology hides its deepest secrets."*