Heng Li
Associate Professor
Boston, Massachusetts, United States
Summary
🤩
Rockstar🎓
Top SchoolHeng Li is an associate professor and computational biologist with 17 years of experience building and maintaining core bioinformatics tools used by the genomics community. Based in Boston, he bridges academic research at Harvard and Dana-Farber with hands-on systems work—contributing significant bug fixes and feature improvements to foundational C projects like samtools, htslib, bwa-mem2 and seqtk. His expertise spans low-level format parsing, performance-sensitive alignment algorithms, and reproducible package management (notably via Bioconda), reflecting both deep algorithmic training (PhD in theoretical biophysics) and production-grade engineering. Less obvious: he routinely navigates the intersection of research and infrastructure, improving stability and usability of tools that underpin large-scale sequencing pipelines.
17 years of coding experience
13 years of employment as a software developer
PhD, Theoretical biophysics, PhD, Theoretical biophysics at The Institute of Theoretical Physics, Chinese Academy of ScienceBachelor, Physics, Bachelor, Physics at Nanjing University
Chinese, English
Github Skills (39)
algorithm10
c-language10
package-management10
bam10
conda10
bash10
c-programming10
sequence-alignment10
c1110
data-structure10
vcf-files10
c1710
automatic-differentiation10
low-level-programming10
neural-network10
Programming languages (19)
Github contributions (5)
attractivechaos/klib
Mar 2012 - Sep 2018
A standalone and lightweight C library
Role in this project:
Back-end Developer
Back-end DeveloperContributions:234 commits, 7 PRs, 59 pushes in 6 years 7 months
Contributions summary:Heng primarily contributed to the core functionality of the C library `klib`, which is focused on lightweight C data structures and algorithms. The user fixed bugs in the `ksw.c` file, and added new APIs. These changes involved optimizing algorithms and data structures, such as those used in sequence alignment or similar operations.
hashtablec-librarystandalonedata-structuresbengali
attractivechaos/kann
Oct 2016 - Jan 2018
A lightweight C library for artificial neural networks
Role in this project:Back-end Developer
Back-end DeveloperContributions:512 commits, 29 pushes, 1 branch in 1 year 2 months
Contributions summary:Heng's contributions center on the implementation of auto-differentiation features within the C library for artificial neural networks. They implemented and debugged functionality related to tree linearization and added operators like subtraction, element-wise multiplication, mean square error, and several activation functions. Moreover, the user made code refactoring to streamline internal operations.
c-librarydeep-learningneural-networksmachine-learningartificial
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