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Heng Li

@lh3lh3.bsky.social

Associate Professor DFCI & HMS

74 Posts1268 Follower120 Folgt
Luca Pinello@lucapinello.bsky.social · 3w ago

1/ I'm excited to share that we're launching NECB 2026, the inaugural New England Computational Biology Symposium. Oct 1-2 at Microsoft Research New England, Cambridge. Two days of keynotes,talks, and posters to bring our community together across institutions.Space is limited. newenglandcompbio.org

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Jeffrey Ross-Ibarra@jrossibarra.bsky.social · 4w ago

Just added a couple more job apps (thanks Rachel and Arun!) but if you've gotten a job in industry, academia (R1, PUI, whatever!) in the last 5 years or so, please consider submitting your job app materials to help other folks! github.com/RILAB/statem...

GitHub - RILAB/statements: Successful Job Applications and Grants

Successful Job Applications and Grants. Contribute to RILAB/statements development by creating an account on GitHub.

github.com

Andrew Carroll@acarroll.bsky.social · last mo.

How good is MiniBWA, the successor to BWA? To test it, I ran MiniBWA on sequencing from 76 different species, comparing mapping speed, rate and accuracy with BWA MEM. In short, it's really good. If you map short reads, it's well worth your time. andrewcarroll.github.io/2026/06/30/t...

The Best of Both Worlds - Assessing MiniBWA

Recently, Heng Li released MiniBWA (GitHub) alongside a paper by Heng Li and Nils Homer describing the method (paper). MiniBWA builds on the approaches in Minimap2 (also by Heng Li), but falls back on...

andrewcarroll.github.io

Fulcrum Genomics@fulcrumgenomics.com · last mo.

New on the Fulcrum blog: minibwa, a faster mapper from @lh3lh3.bsky.social and our @nilshomer.com Its speed is great, yes, but more interesting is the decision to revisit BWA-MEM as infrastructure – keep what still works, change what limits performance, then test downstream impact. shorturl.at/xxqeI

Minibwa: alignment is never solved

Heng Li and Nils Homer revisit BWA-MEM with a faster mapper for short reads, accurate long reads, and bisulfite sequencing data.

blog.fulcrumgenomics.com

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Heng Li@lh3lh3.bsky.social · last mo.

minibwa v0.3 released with a few minor bug fixes and two missing bwa-mem features (XA tag for secondary hits and option -H to inject header lines). Also added the "mem" subcommand to mimic "bwa mem" CLI to some extent. github.com/lh3/minibwa/...

Release Minibwa-0.3 (r391) · lh3/minibwa

Notable changes: New feature: added the mem subcommand to mimic the bwa-mem command-line interface (CLI). Most input/output options and commonly used options are retained; unsupported or incompat...

github.com

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Heng Li@lh3lh3.bsky.social · 2mo ago

Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357

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Jim Shaw@jimshaw.bsky.social · 2mo ago

Our method, savont, for generating amplicon sequence variants (ASVs) for long-read amplicons is now on bioRxiv. Work with @lh3lh3.bsky.social and help from @mkddueholm.bsky.social and team (Marie Riisgaard-Jensen, @kirk3gaard.bsky.social, Kasper Skytte Andersen) github.com/bluenote-157... 1/6

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 2mo ago

Sensitive long-read amplicon sequence variant recovery with savont https://www.biorxiv.org/content/10.64898/2026.05.26.727271v1

Jim Shaw@jimshaw.bsky.social · 2mo ago

Excited to speak at ASM Microbe 2026 in the Oxford Nanopore session about new tools for long-read metagenomics + 16S sequencing. If you're attending ASM Microbe June 4-7 in D.C. and want to chat, let me know!

Oxford Nanopore@nanoporetech.com · 2mo ago

Join Jim Shaw at #ASMicrobe to uncover how to unlock high-resolution, strain-level microbiome insights. Learn how this is could be crucial to helping deliver more precise diagnostics and treatment in the future. https://bit.ly/4v4XuKE

Molly Schumer@mollyschumer.bsky.social · 4mo ago

Please share widely! We will imminently be posting a technician position in our lab group since @rheasood.bsky.social is off to grad school 🙌! If you know of anyone excited about molecular biology, evolution, and functional genomics please have them reach out (schumer at stanford). Start date ~June

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Heng Li@lh3lh3.bsky.social · 4mo ago

LongcallR for competitive SNP calling and haplotype phasing, and simplified allele-specific analysis with long RNA-seq reads. Found ~100 junctions affected by SNPs per sample with most junctions novel. Developed by Neng Huang. Published in @natmethods.nature.com. Read at rdcu.be/faKhL

SNP calling, haplotype phasing and allele-specific analysis with long RNA-seq reads

Nature Methods - In this study, long-read RNA sequencing achieves accurate single-nucleotide polymorphism calling, haplotype phasing and allele-specific expression analysis.

rdcu.be

Jim Shaw@jimshaw.bsky.social · 5mo ago

Myloasm, our long-read metagenome assembler, is now published! w/ @mgmarin.bsky.social and @lh3lh3.bsky.social Very rewarding after > a year of development and countless hours thinking about assembly. Thanks to beta testers, Li lab, and reviewers who gave very helpful feedback. rdcu.be/famFj

High-resolution metagenome assembly for modern long reads with myloasm

Nature Biotechnology - A long-read metagenome assembly method recovers circular and complete genomes better than existing tools.

rdcu.be

Nature Biotechnology@natbiotech.nature.com · 5mo ago

High-resolution metagenome assembly for modern long reads with myloasm - @lh3lh3.bsky.social @jimshaw.bsky.social @danafarber.bsky.social @harvardmed.bsky.social go.nature.com/3PBEwvR

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Heng Li@lh3lh3.bsky.social · 5mo ago

Long reads carry multiple small vars and SVs and their phasing. LongcallD is the only caller that tightly integrates germline/mosaic small/structural vars/MEIs and their phasing in a single C program. One command line to get competitive small variant calls and better SVs. Led by Yan Gao.

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bioRxiv Genomics@biorxiv-genomic.bsky.social · 5mo ago

LongcallD: joint calling and phasing of small, structural and mosaic variants from long reads https://www.biorxiv.org/content/10.64898/2026.03.20.713111v1