{"id":24745787,"url":"https://github.com/bibymaths/bibymaths","last_synced_at":"2026-05-05T03:34:16.722Z","repository":{"id":273112605,"uuid":"918731021","full_name":"bibymaths/bibymaths","owner":"bibymaths","description":null,"archived":false,"fork":false,"pushed_at":"2025-03-15T01:43:12.000Z","size":16,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-03-15T02:31:33.066Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"cc0-1.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/bibymaths.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2025-01-18T17:56:05.000Z","updated_at":"2025-03-15T01:43:15.000Z","dependencies_parsed_at":"2025-01-18T19:27:11.831Z","dependency_job_id":"b62c5234-6eae-4ac1-bd27-8e34c8d21562","html_url":"https://github.com/bibymaths/bibymaths","commit_stats":null,"previous_names":["bibymaths/bibymaths"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bibymaths%2Fbibymaths","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bibymaths%2Fbibymaths/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bibymaths%2Fbibymaths/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bibymaths%2Fbibymaths/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bibymaths","download_url":"https://codeload.github.com/bibymaths/bibymaths/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245037437,"owners_count":20550871,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2025-01-28T03:29:42.414Z","updated_at":"2026-05-05T03:34:16.716Z","avatar_url":"https://github.com/bibymaths.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003cdiv align=\"center\"\u003e\n\n\u003c!-- SVG Logo: stylized DNA-helix + math integral mark --\u003e\n\u003csvg width=\"72\" height=\"72\" viewBox=\"0 0 72 72\" fill=\"none\" xmlns=\"http://www.w3.org/2000/svg\" aria-label=\"Abhinav Mishra logo\"\u003e\n  \u003ccircle cx=\"36\" cy=\"36\" r=\"34\" stroke=\"#01696f\" stroke-width=\"2\"/\u003e\n  \u003c!-- Integral / stylised σ path --\u003e\n  \u003cpath d=\"M44 18 C38 18 28 22 28 36 C28 50 38 54 44 54\" stroke=\"#01696f\" stroke-width=\"2.5\" stroke-linecap=\"round\" fill=\"none\"/\u003e\n  \u003c!-- Node dots on curve --\u003e\n  \u003ccircle cx=\"28\" cy=\"28\" r=\"2.5\" fill=\"#01696f\"/\u003e\n  \u003ccircle cx=\"28\" cy=\"44\" r=\"2.5\" fill=\"#01696f\"/\u003e\n  \u003ccircle cx=\"36\" cy=\"36\" r=\"2.5\" fill=\"#4f98a3\"/\u003e\n  \u003c!-- Cross-links (helix rungs) --\u003e\n  \u003cline x1=\"28\" y1=\"28\" x2=\"44\" y2=\"24\" stroke=\"#01696f\" stroke-width=\"1.5\" stroke-linecap=\"round\" opacity=\"0.6\"/\u003e\n  \u003cline x1=\"28\" y1=\"36\" x2=\"44\" y2=\"36\" stroke=\"#01696f\" stroke-width=\"1.5\" stroke-linecap=\"round\" opacity=\"0.6\"/\u003e\n  \u003cline x1=\"28\" y1=\"44\" x2=\"44\" y2=\"48\" stroke=\"#01696f\" stroke-width=\"1.5\" stroke-linecap=\"round\" opacity=\"0.6\"/\u003e\n\u003c/svg\u003e\n\n# Abhinav Mishra\n\n**Computational Biologist · Mathematical Modeller · Open-Science Advocate**\n\n*Transforming biological complexity into computationally tractable problems*\n\n\u003cp align=\"center\"\u003e\n  \u003cimg src=\"https://komarev.com/ghpvc/?username=bibymaths\u0026label=Profile%20views\u0026color=0e75b6\u0026style=flat\" alt=\"Profile Views\" /\u003e\n\u003c/p\u003e\n\n[![LinkedIn](https://img.shields.io/badge/LinkedIn-0A66C2?style=flat-square\u0026logo=linkedin\u0026logoColor=white)](https://linkedin.com/in/bibymaths)\n[![Email](https://img.shields.io/badge/Email-EA4335?style=flat-square\u0026logo=gmail\u0026logoColor=white)](mailto:mishraabhinav36@gmail.com)\n[![Website](https://img.shields.io/badge/Portfolio-01696f?style=flat-square\u0026logo=About.me\u0026logoColor=white)](https://bibymaths.github.io)\n[![CV](https://img.shields.io/badge/CV-PDF-01696f?style=flat-square\u0026logo=adobeacrobatreader\u0026logoColor=white)](https://bibymaths.github.io/files/Abhinav_Mishra_CV_03_04_2026.pdf)\n\n\u003c/div\u003e\n\n---\n\n## About Me\n\nI 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.\n\nMy work sits at the intersection of **mathematical modelling**, **systems biology**, and **precision medicine** — where equations and algorithms translate biological noise into clinical insight.\n\n**Education**\n- 🎓 M.Sc. Bioinformatics — Freie Universität Berlin, 2025\n- 🎓 B.Tech. Bioinformatics — Jaypee University of Information Technology, 2017\n\n---\n\n## Featured Projects\n\n### 🔬 Phosphorylation Network Reconstruction · TNBC\nBuilt and validated an **optimization framework** to reconstruct phosphorylation signalling networks in triple-negative breast cancer (TNBC) from mass-spectrometry proteomics data.  \n`Python` `Optimization` `Proteomics` `Systems Biology`  \n[![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.17290716-blue?style=flat-square)](https://doi.org/10.5281/zenodo.17290716)\n[![Code](https://img.shields.io/badge/Code-phoskintime-01696f?style=flat-square\u0026logo=github)](https://github.com/bibymaths/phoskintime)\n\n---\n\n### 💊 Physiologically-Based Pharmacokinetic (PBPK) Model\nDeveloped a mechanistic **PBPK model** for drug distribution in the human body — parameterised from tissue composition and plasma binding data.  \n`ODE Systems` `Pharmacokinetics` `Mathematical Modelling`  \n[![Model](https://img.shields.io/badge/Zenodo-14976788-blue?style=flat-square)](https://doi.org/10.5281/zenodo.14976788)\n\n---\n\n### 🧬 Prostate Cancer Biomarker Pipeline\nDesigned and tested an end-to-end bioinformatics pipeline for **prostate cancer biomarker discovery** — integrating gene expression data, differential analysis, and pathway enrichment.  \n`RNA-seq` `Bioinformatics` `Pathway Analysis`  \n[![Publication](https://img.shields.io/badge/JIB-2018--0080-green?style=flat-square)](https://doi.org/10.1515/jib-2018-0080)\n\n---\n\n### 🧠 Drug Repurposing · Dopamine D3 Receptor (Schizophrenia)\nEngineered a **molecular docking workflow** to screen FDA-approved compounds against the dopamine D3 receptor for potential repurposing in schizophrenia treatment.  \n`Molecular Docking` `Drug Repurposing` `Cheminformatics`  \n[![Poster](https://img.shields.io/badge/Poster-bibymaths.github.io-01696f?style=flat-square)](https://bibymaths.github.io/posters/#1-poster-docking-for-schizophrenia)\n\n---\n\n## Skills \u0026 Toolbox\n\n| Domain | Tools \u0026 Technologies |\n|---|---|\n| **Languages** | Python · R · Bash · MATLAB |\n| **Modelling \u0026 Optimisation** | ODE systems · Flux Balance Analysis · Constraint-based modelling · PBPK |\n| **Multi-omics** | Proteomics · Transcriptomics · scRNA-seq · Pathway enrichment |\n| **HPC \u0026 Workflow** | Snakemake · Nextflow · Singularity · SLURM |\n| **Data \u0026 Viz** | Pandas · NumPy · SciPy · Matplotlib · Seaborn · ggplot2 |\n| **Reproducibility** | Docker · Git · Zenodo · GitHub Actions |\n\n---\n\n## Research Interests\n\n```\nPrecision Medicine          →  predictive models for clinical decision support\nMathematical Pharmacology   →  PK/PD, PBPK, drug-response modelling\nNetwork Biology             →  signalling networks, phosphoproteomics, graph theory\nMulti-omics Integration     →  data fusion across genomics, proteomics, metabolomics\nOpen Science                →  FAIR data, reproducible pipelines, open-source tooling\n```\n\n---\n\n## Publications \u0026 Outputs\n\n| Year | Output | Link |\n|---|---|---|\n| 2025 | Phospho-network reconstruction framework (TNBC) | [Zenodo](https://doi.org/10.5281/zenodo.17290716) · [Code](https://github.com/bibymaths/phoskintime) |\n| 2025 | PBPK model for human drug distribution | [Zenodo](https://doi.org/10.5281/zenodo.14976788) |\n| 2018 | Prostate cancer biomarker discovery pipeline | [J. Integr. Bioinform.](https://doi.org/10.1515/jib-2018-0080) |\n\n---\n\n## Let's Connect\n\nI'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.\n\n\u003cdiv align=\"center\"\u003e\n\n[![LinkedIn](https://img.shields.io/badge/Connect_on_LinkedIn-0A66C2?style=for-the-badge\u0026logo=linkedin\u0026logoColor=white)](https://linkedin.com/in/bibymaths)\n[![Email](https://img.shields.io/badge/Send_an_Email-EA4335?style=for-the-badge\u0026logo=gmail\u0026logoColor=white)](mailto:mishraabhinav36@gmail.com)\n[![Portfolio](https://img.shields.io/badge/Visit_Portfolio-01696f?style=for-the-badge\u0026logo=About.me\u0026logoColor=white)](https://bibymaths.github.io)\n\n*\"Mathematics is the language in which biology hides its deepest secrets.\"*\n\n\u003c/div\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbibymaths%2Fbibymaths","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbibymaths%2Fbibymaths","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbibymaths%2Fbibymaths/lists"}