Ilya Shlyakhter
Senior Bioinformatics Engineer
Cambridge, Massachusetts, United States
Summary
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Rockstar🎓
Top SchoolIlya Shlyakhter is a Senior Bioinformatics Engineer with 14 years of experience applying rigorous computer science to biological problems, blending a Ph.D. in formal verification with deep expertise in genome assembly, structural variant genotyping, and population genetics. He has built production-ready computational tools and infrastructure at the Broad Institute, Merck, Quest Diagnostics, and now GeneDx, reliably moving methods from research prototypes into scalable pipelines. His work spans low-level automation—contributing build and release improvements to the widely used bioconda ecosystem—to high-level modeling of mutation spread and selection, reflecting comfort across software engineering and computational biology. Known for translating formal-methods thinking into robust bioinformatics software, he brings a systems-oriented, reproducibility-first approach to solving complex genomics problems.
14 years of coding experience
4 years of employment as a software developer
Ph.D. Computer Science, Ph.D. Computer Science at Massachusetts Institute of TechnologyGraduate Certificate Bioinformatics, Graduate Certificate Bioinformatics at Stanford University
Stackoverflow
11reputation
131reached
0answers
2questions
Github Skills (16)
bioinformatics10
conda10
bash10
package-management10
build-automation10
git9
c-language6
configurations6
c-preprocessor6
linker6
cprogramming-language6
git-worktree6
conditional-compilation6
python5
java5
Programming languages (23)
Github contributions (5)
bioconda/bioconda-recipes
Aug 2016 - Nov 2022
Conda recipes for the bioconda channel.
Role in this project:
Automation Engineer / Build & Release Engineer
Automation Engineer / Build & Release EngineerContributions:1 review, 83 commits, 166 PRs in 6 years 3 months
Contributions summary:Ilya primarily contributed to the build and release processes of various bioinformatics tools within the bioconda ecosystem. Their commits involved updating build scripts, fixing dependencies, and integrating new versions of packages like CLARK, genometools, SPAdes, KMC, BBMap, novoalign, and others. The changes often addressed compatibility issues, corrected file paths, and enhanced the automation of software installation and testing within the conda environment. The user has also contributed to the support of JNI.
biocondacondabioinformaticspackage-management
broadinstitute/cms2-work
Jul 2020 - Jan 2025
Gather in one place various repos and files related to CMS2.0 work.
Contributions:294 pushes, 1511 branches, 1 tag in 4 years 7 months
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