Muhammad Shamim
Clinical Pathology Resident
Cambridge, Massachusetts, United States
Summary
👤
Senior🎓
Top SchoolMuhammad Shamim is a clinical pathology resident and MD/PhD trained physician-scientist with 11 years of experience at the intersection of genomics, bioinformatics, and clinical medicine. He brings deep technical chops from a Computer Science/Applied Math background and hands-on bioinformatics work in the Aiden Lab, where he contributed scripting and workflow automation to the widely used juicer Hi-C analysis pipeline. A Paul & Daisy Soros Fellow and former Donald A. Elliott Scholar, he combines rigorous research training from Rice and Baylor with practical DevOps and high-performance computing experience (UGER/SLURM). Based in Cambridge, MA, he has a track record of translating complex computational methods into reproducible tools for pathology and genomics.
11 years of coding experience
5 years of employment as a software developer
Doctor of Philosophy - PhD Bioengineering, Doctor of Philosophy - PhD Bioengineering at Rice UniversityMD/PhD Medical Scientist Training Program, MD/PhD Medical Scientist Training Program at Baylor College of MedicineHigh School, High School at The Science Academy of South Texas
English, urdu/hindi, Spanish, Arabic
Github Skills (15)
bioinformatics10
bash10
devops10
slurm9
automation9
automations9
genomics8
python8
data-pipeline8
data-pipelines8
ng7
scripting7
script7
sh7
shell7
Programming languages (14)
Github contributions (5)
aidenlab/juicer
Dec 2015 - Jul 2022
A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
Role in this project:
Back-end & DevOps Engineer
Back-end & DevOps EngineerContributions:1 review, 52 commits, 23 PRs in 6 years 7 months
Contributions summary:Muhammad contributed significantly to the `juicer` repository, focusing on scripting and automation tasks. They developed and updated bash scripts for managing and processing Hi-C data, specifically related to the mega-map pipeline. The contributions also involved modifying scripts for job submission and optimizing the workflow within the UGER and SLURM environments.
analyzingone-clickpipeline-framework3d-genomeresolution
sa501428/RobustConcurrentKMeans
Aug 2021 - Nov 2022
Robust implementation of Concurrent KMeans to handle missing values
Contributions:4 releases, 2 PRs, 13 pushes in 1 year 2 months
missing-valuesmissingkmeanshandleconcurrent
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