GitHub & Open Source

My public repositories, plus a few projects I’m actively building. Full profile at github.com/shraddhapuntambekar.

Most of my pharma R&D and pipeline-engineering work lives inside client engagements under NDA and isn’t public. The repos below are primarily companion code to published research, teaching material, and analysis utilities — with industry-relevant artifacts being added (see Currently Building).

Featured Projects

Boolean-Modeling-Biology-MSc-2026

Course material I authored for the Systems Biology module of the M.Sc. Bioinformatics program at Savitribai Phule Pune University (March 2026). Covers Boolean network reconstruction, dynamic simulation, attractor and steady-state analysis, and sensitivity analysis — with hands-on exercises and example notebooks.

Topics: Boolean modeling · gene regulatory networks · systems biology pedagogy Audience: M.Sc. Bioinformatics students

learning_conservation_analysis_using_phylop

Companion code to my first-author Scientific Reports (2020) paper on cichlid speciation. Implements phyloP-based evolutionary rate analysis to identify accelerated regions in the cichlid genome.

Topics: Comparative genomics · evolutionary rate analysis · phyloP Linked publication: Puntambekar et al., Scientific Reports (2020)

Mathematical-model-for-sumoylation

Companion code to my first-author Journal of Biological Chemistry (2016) paper. Contains the ODE-based mathematical model of the sumoylation post-translational modification system, including model files, parameter sets, and scripts for steady-state and sensitivity analyses.

Topics: ODE modeling · sumoylation · MATLAB Linked publication: Puntambekar et al., JBC (2016)

Other Repositories

• bulk-RNAseq-analysis — Shell scripts and analysis notes for bulk RNA-seq workflows (in progress; documentation being expanded).
• mapping_conservation_scores — Utility scripts to map phyloP / phastCons conservation scores onto user-defined regions of interest.
• GATA3_analysis — Analysis scripts for ChIP-seq, ATAC-seq, and RNA-seq work supporting the BBRC (2026) GATA3 paper.
• shraddhapuntambekar.github.io — Source for this website (built on the academicpages Jekyll template).

Currently Building

Repositories currently in development:

• End-to-end Nextflow pipeline for omics analysis. A Nextflow + Docker + CI/CD template scaffold for omics pipelines, demonstrating production-grade pipeline authoring, containerization, and continuous integration end-to-end. (My production Nextflow work to date lives inside client engagements under NDA.)
• Plain-English bioinformatics analysis platform. A UI tool with a natural-language prompt — type a request like “run differential expression on this RNA-seq dataset” and the platform invokes the underlying Nextflow pipeline in the background. Combines the Nextflow work above with LLM-driven orchestration.
• End-to-end ChIP-seq shell pipeline. A reference implementation of a full ChIP-seq analysis workflow in shell — QC, alignment, peak calling, motif analysis, and visualization.
• End-to-end RNA-seq shell pipeline. A reference implementation of a full bulk RNA-seq workflow in shell — QC, alignment, quantification, and differential expression.

If any of these align with what you’re hiring for or building, get in touch.