Saket Choudhary
Assistant Professor at Indian Institute of Technology, Bombay
Mumbai, Maharashtra, India
Summary
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Rockstar🎓
Top SchoolSaket Choudhary is an assistant professor and computational biologist with 14 years of experience building methods to decode translation regulation and applying mathematical and computational statistics to genomics. He completed a PhD in Computational Biology and dual MS degrees in Computer Science and Statistics at USC, followed by a postdoc at the New York Genome Center, and now leads research at IIT Bombay. Saket blends academic rigor with hands-on engineering—his open-source contributions span Biopython (CLI wrappers for BWA and testing/docs improvements) and integration work for Seurat’s FIt-SNE support, reflecting deep familiarity with bioinformatics tooling and reproducible analysis. He has also tackled build and release challenges as an automation engineer for Linuxbrew, demonstrating cross-platform packaging and DevOps skills. Based in Mumbai, he brings a rare mix of theoretical statistics, practical software engineering, and domain expertise in single-cell and translation biology. Colleagues appreciate that he moves fluidly between producing publishable methods and shipping robust, usable code for the community.
14 years of coding experience
4 years of employment as a software developer
Graduate Certificate in Public Policy, Graduate Certificate in Public Policy at The Takshashila InstitutionDoctor of Philosophy - PhD Computational Biology, Doctor of Philosophy - PhD Computational Biology at University of Southern CaliforniaIndian Institute of Technology BombayAtomic Energy Junior College - IndiaAtomic Energy Central School
Stackoverflow
624reputation
94kreached
11answers
17questions
Github Skills (27)
python10
dimensionality-reduction10
scripting10
package-management10
r10
command-line-interface10
biopython10
sequence-alignment10
script10
build-automation10
command-line10
bioinformatics10
sh10
shell10
cli10
Programming languages (15)
Github contributions (5)
satijalab/seurat
Jul 2020 - Nov 2022
R toolkit for single cell genomics
Role in this project:
Back-end Developer
Back-end DeveloperContributions:2 releases, 1 review, 134 commits in 2 years 4 months
Contributions summary:Saket contributed significantly to the FIt-SNE integration within the Seurat package, adding support for FIt-SNE versions 1.2+. The commits demonstrate modifications to the dimensional reduction functions, including the addition of new parameters and checks for different FIt-SNE versions. Furthermore, the user updated the code to handle various initialization methods for FIt-SNE, reflecting a deep understanding of the underlying algorithm and its integration within the Seurat framework.
single-cell-genomicscranhuman-cell-atlasgenomicsbioinformatics
biopython/biopython
Mar 2013 - Nov 2017
Official git repository for Biopython (originally converted from CVS)
Role in this project:Back-end Developer & DevOps Engineer
Back-end Developer & DevOps EngineerContributions:8 commits, 6 PRs, 26 comments in 4 years 8 months
Contributions summary:Saket contributed to the Biopython project by developing command-line wrappers for bioinformatics tools, particularly focusing on the BWA aligner. They implemented and modified Python code to interact with external tools and improve the usability of the library. Additionally, the user made changes to test files, cleaning up after running tests and improving the testing infrastructure. Furthermore, the user's contributions include improvements to the documentation and general formatting of the codebase.
git-repositoryphylogeneticspythondnagenomics
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