Heng Li
Associate Professor
Boston, Massachusetts, United States
Summary
🤩
Rockstar🎓
Top SchoolHeng Li is an Associate Professor at Dana-Farber Cancer Institute and Harvard Medical School in Boston with 16 years of experience building foundational bioinformatics software and leading academic research. He is a core contributor to flagship open-source projects such as htslib and samtools and to performance-critical tools like bwa-mem2 and seqtk, specializing in low-level C implementations for VCF/BAM parsing, record I/O, and alignment algorithms. His contributions range from bug fixes and performance tuning to package maintenance for bioconda, keeping large-scale sequencing pipelines robust and reproducible. Trained as a physicist with a PhD in theoretical biophysics, he uniquely combines deep algorithmic and systems expertise with hands-on C engineering — even implementing auto-differentiation primitives for a lightweight neural-network C library.
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 (42)
algorithm10
c-language10
package-management10
bam10
bash10
conda10
c-programming10
sequence-alignment10
c1110
data-structure10
vcf-files10
c1710
automatic-differentiation10
low-level-programming10
neural-networks10
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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