Friday was my last day at NHGRI. After 10 wonderful years, my lab is headed to Johns Hopkins University
genomeinformatics.github.io/movingday/

Blog post on "The AI Rewrite Dilemma": lh3.github.io/2026/04/17/t...

For decades, molecular biology and human genetics have been built around measurements of average gene expression. That was partly conceptual, but also technological: for a long time, the mean was the quantity we could measure most reliably. Our new preprint argues that this framework is incomplete.

Welcome to RustQC Fast quality control tools for sequencing data, written in Rust.

Super excited to be launching two things today: #RustQC 🦀🧬 and rewrites.bio 🚀

I used AI to rewrite 15 RNA-seq QC tools into a single Rust binary (I've never written any Rust). It ended up being over 60x faster. Here's the story 🧵

seqeralabs.github.io/RustQC/

More acrocentric investigations, this one led by @arhie.bsky.social 🕵🏻‍♀️ “Biobank-scale genotyping of Robertsonian translocations reveals hidden structural variation on the human acrocentric chromosomes” 🧵[1/8]
📄 www.biorxiv.org/content/10.6...

Delighted to share our latest preprint: Julie Zhu identifies a surprising reason why the genetic architecture of brain-related traits is so different than other traits. Check it out!

AI is starting to look like pseudoscience Not all of it, but some scientists are too eager to believe their own hype

In my latest column, I explain some of my reasons for being deeply skeptical about AI models that claim to understand DNA, genes, and genomes: stevensalzberg.substack.com/p/ai-is-star...

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.

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

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.

Trippy Memphis bridge https://pangenome.github.io/MemPanG26/

Level up your #pangenomics game! Workshop, conference & biohackathon in #Memphis, May 11-15, 2026. Join us and get your hands dirty with sequence alignment, explicit and implicit graphs, cutting-edge methods, and AI. Register now! pangenome.github.io/MemPanG26/ #Bioinformatics #MemPanG26

Guarracino Lab | Pangenome Research We develop methods to build and analyze pangenomes, with applications in cancer and complex disease. Translational Genomics Research Institute, Phoenix, AZ.

Looking for a postdoc to build my new lab at TGen (Phoenix, AZ) focused on pangenome methods for cancer and complex disease. Full stack — from pangenome assembly and compression to association studies and somatic variant discovery. Reach out if interested! guarracinolab.github.io#join

Common variation in meiosis genes shapes human recombination and aneuploidy - Nature Analysis of data from pre-implantation genetic testing sheds light on the genetic basis of meiotic-origin aneuploidy, the leading cause of human pregnancy loss, identifying common genetic variants ass...

Pregnancy loss is common in humans, and chromosomal abnormalities are the leading cause. Using genetic data from ~140,000 IVF embryos, we show that maternal variation in meiosis genes influences recombination and aneuploidy risk.

First authors: @saracarioscia.bsky.social & @aabiddanda.github.io

We just released a fairly substantial update to HiPhase that enables (beta) support for RNA (isoseq) datasets. There are some incidental improvements to WGS phasing as well!

Full release notes here: github.com/PacificBiosc...

I am looking for a postdoc to develop high-performance algorithms in computational genomics. Email or DM me if interested. For more information, see hlilab.github.io/vacancies. RTs appreciated!

I am hiring a staff bioinformatician for my new lab at the University of Utah! Please consider applying if you are on the hunt:
employment.utah.edu/salt-lake-ci...

Now published in Algorithms for Molecular Biology: link.springer.com/article/10.1.... Key message: a tiny CNN model with 7k parameters can capture main splice signals across vertebrates+insect and halves the minimap2 & miniprot junction error rate. I always use this new feature now.

I've been thinking about the "virtual cell" concept and wanted to write up a few thoughts. Specifically on how I think the prior experience in GWAS informs the most likely way these models will be useful.

andrewcarroll.github.io/2025/12/23/t...

If you’ve heard me talk in the past ~5 years, you will know I have developed an obsession with acrocentric chromosomes. This is all of that, condensed into one paper. I will do a full thread in the new year, but for those that want something to read over the holidays, have at it. Such a cool story!

There's an opening in our CompBio group at #PacBio. Apply below if you're interested in method / tool development for long-read sequencing applications! #Bioinformatics

pacbio.wd12.myworkdayjobs.com/PacBio-/job/...

GitHub - lh3/human-asm: A collection of high-quality human genomes A collection of high-quality human genomes. Contribute to lh3/human-asm development by creating an account on GitHub.

579 high-quality human genomes from @humanpangenome.bsky.social, Arab Pangenome and individual papers (CHM13, CN1, KSA001, I002C, YAO and KOREF1). Sequences available in the AGC format (3.7GB) and FM-index in the ropebwt3 format (20.3GB). For details, see github.com/lh3/human-asm

We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen.

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GREGoR: accelerating genomics for rare diseases - Nature The GREGoR consortium provides foundational resources and substrates for the future of rare disease genomics.

New in @nature.com! “GREGoR: Accelerating Genomics for Rare Diseases” highlights how the GREGoR Consortium is advancing rare disease discovery through data sharing, multi-omics, and next-gen sequencing across 7,500+ individuals in 3,000+ families.

🧬 www.nature.com/articles/s41...

Just found out #Nextflow supports job arrays 😅
Add `array <integer>` inside the `process { ... }` block, and it fixes “You have reached the rate limit of jobs submitted per hour” error.

Locityper enables targeted genotyping of complex polymorphic genes www.nature.com/articles/s41... (🔓https://rdcu.be/eLxCC 🧬🖥️🧪 github.com/tprodanov/lo...

I’ll be presenting a poster on Mitorsaw for #PacBio HiFi mitochondrial analysis today! Come see me this afternoon at #ASHG25 poster #4050 to chat about that or other topics!

In honor of ASHG week (since I won’t be there), see "Choose your human genome reference wisely", in which Vivien Marx interviewed me @fergalmartin.bsky.social @lh3lh3.bsky.social @danrdanny.bsky.social @heidirehm.bsky.social and others on the state of the human reference rdcu.be/eJejg 🧵[1/10]

Efficient and accurate search in petabase-scale sequence repositories - Nature MetaGraph enables scalable indexing of large sets of DNA, RNA or protein sequences using annotated de Bruijn graphs.

After years of research and continuous refinement, we’re thrilled to share that our paper on the MetaGraph framework — enabling Petabase-scale search across sequencing data — has been published today in Nature (www.nature.com/articles/s41...)

Staff Scientist About EMBL-EBI EMBL’s European Bioinformatics Institute is a data powerhouse, utilised on a global scale to advance scientific discovery through bioinformatics and solutions to some of the world’s mos...

I am hiring! - looking for a Staff Scientist to co-run my research group with me. Staff Scientist is a senior professional scientist role at EMBL. Please forward to people you might know who could be interested! embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

Hi bioinformatics, genomics and CS friends! Please help me spread the word. I'm hiring a postdoc! Come work on cutting edge method development in algorithmic genomics with me and my group at @umdscience.bsky.social! 🖥️🧬

I'm excited to share our pre-print about a new variant benchmarking tool we've been working on for the past few months!

Aardvark: Sifting through differences in a mound of variants
GitHub: github.com/PacificBiosc...

Some highlights in this thread:
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