Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]

📣 Latest from the lab: Performance of deep-learning-based approaches to improve polygenic scores www.nature.com/articles/s41... Its thought deep learning will substantially improve PGS but the reality is MANY have tried but no/little gain has been seen so far. Here we report our negative results.

A new preprint on indexing pangenome graphs using an FM-index of the haplotypes and a tag array. Joint work with Parsa Eskandar and @benedictpaten.bsky.social.

📢 HPRC Release 2 is here! Now with phased genomes from 200+ individuals, a 5x increase from Release 1. Explore sequencing data, assemblies, annotations & alignments in our interactive data explorer ⬇️: humanpangenome.org/hprc-data-re...

The human pangenome continues to grow and improve! Release 2 is here! Click through for the details, but this is a pretty amazing dataset including not just the phased assemblies, but PacBio HiFi, ONT Ultralong, Dovetail/Illumina Hi-C, PacBio Kinnex, and Illumina WGS for all samples

An innocent man who committed no crime but is the same race as the person who murdered your daughter should have to spend the rest of his life in a concentration camp is the argument?

Minimap2-2.29 released with the support of short RNA-seq read alignment. More explanation and results here: lh3.github.io/2025/04/18/s...

Preprint on hifiasm Nanopore-only assembly. Led by Haoyu Cheng: www.biorxiv.org/content/10.1...

🚨 Pre-print alert! 🚨 We generated chromosome-scale diploid genome assemblies for the widely used fibroblast lines BJ and IMR-90. These models of replicative senescence and telomere shortening now have fully resolved telomeres, subtelomeres, and centromeres. 🧬 🧵👇

A project five years in the making, we've now published complete "T2T" genomes for six additional ape species! It turns out that finishing (and analyzing) six genomes is slightly more work than one... doi.org/10.1038/s415...

Nature research paper: Complete sequencing of ape genomes https://go.nature.com/3EfWwqk

I kind of want to go

"The outcome of this is basically the creation of this transnational penal colony where a president, a head of state, can make a deal with President Bukele and disappear undesirables indefinitely.” Read my full report here: www.rollingstone.com/politics/pol...

Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing - @mishakolmogorov.bsky.social go.nature.com/3R334eH

Everyone wants there to be a grand scheme behind all of this but the terrible truth is that extremely stupid people are in charge and they have a fanatical devotion to wrong, childlike concepts of society and economics cooked up by right wing radio hosts in order to sell tainted dietary supplements

22 weeks apart.

We should all be terrified to live in an America where legal residents can be detained, held at gunpoint, or deported because of the color of their skin or because the President disagrees with their views.

longcallD is a new variant caller for genomic long reads. It jointly calls phased small and structural variants. Single binary, one command line for the whole process. Comparable accuracy to mainstream callers. Great work by Yan Gao. github.com/yangao07/lon...

I'm very excited to share that I defended my thesis this week! I helped develop algorithms to combat reference #bias and make genomics more #equitable and #representative by incorporating genetic #diversity into genomics pipelines

New report shows that NIH grants fueled $95 billion in economic activity and 407,782 jobs in 2024. That's not to mention the countless lives that biomedical research has saved. Show me a better investment than that. www.forbes.com/sites/michae...

#standupforscience #slugforscience

Standing up for science in the redwoods :)

I got laid off today, with the rest of 18F. 18F was an elite federal software shop. We made gov't websites work better, more efficiently for the American people. We saved taxpayers from getting screwed over by contractors. And were fired for it. We made this website to tell our story: 18f.org

Trump berates Zelensky, the leader of a democratic country courageously fighting Russian imperialism, while he allies himself with Putin, a dictator who started the bloodiest European war in 80 years. Sorry, President Trump. We believe in democracy, not authoritarianism.

By @katherinejwu.com "The NIH... supported 99 percent of the drugs approved in the U.S. from 2010 to 2019. The agency has had a hand in “nearly all of our major medical breakthroughs over the past several decades,” The NIH is in a struggle for its (and our) lives. This is existential to America:

Get in dorks, we're going protesting! STAND UP FOR SCIENCE WITH US ON MARCH 7TH, 2025 WASHINGTON DC AND EVERY STATE CAPITOL Because science is for everyone! Find us at www.standupforscience2025.org #standupforscience2025 #scienceforall #sciencenotsilence

Today, along with 2,000 other NIH employees, I had to clear out my office 😭 It was truly the honor of my life to work with such incredibly passionate people focused on improving human health. I’ve never experienced a more positive culture where *everyone* cared about their job and serving others.

It’s a good day to be a preventable disease

Courts *ordered* the Trump admin to stop its spending freeze Yet ProPublica found place after place where $ is still frozen -hot meals for elderly and disabled -groceries for those in need -maternal & child health services -a clinic that serves the poor www.propublica.org/article/trum...

1. Today the NIH director issued a new directive slashing overhead rates to 15%. I want to provide some context on what that means and why it matters. grants.nih.gov/grants/guide...

Decimating the NSF would be an act of violence against USA competitiveness in science, technology and innovation. Have any of these people seen Shanghai lately? arstechnica.com/science/2025...

Researchers at @ucsantacruz.bsky.social have demonstrated how long-read sequencing could improve detection of diseases that have eluded diagnosis, at a fraction of the cost. New clinical tests could be on the way. 🗞 news.ucsc.edu/2025/01/pate... 👏🏼👏🏿👏🏾 @khmiga.bsky.social @benedictpaten.bsky.social

The data is in. 2024 was the warmest year on record, and probably in the whole of human history – about 1.6°C warmer than the pre-industrial period. More than 1 billion individual thermometer measurements, made by thousands of people over many decades, have been condensed into a single number.

ABC, NBC & CBS dedicated about 16 minutes of airtime last night to the California wildfires without once mentioning climate change. Since the news failed do it's job, here's a short summary of the role of climate change and wildfire risk: www.noaa.gov/noaa-wildfir...

Calling all postdocs! We're hosting a symposium in beautiful Santa Cruz, CA, to showcase rising talent in genomics research. Travel expenses are covered for selected applicants ✈️😎🏖 The event will be held on April 15. Applications due Feb 15: bit.ly/NextWave25

Very excited to see Movi (by @mohsenzakeri.bsky.social) now out in iScience: www.cell.com/iscience/ful.... Movi builds on the "move structure" pangenome index, a compressed full-text index and close cousin to r-index. Compared to r-index, the move structure is simpler and more cache-efficient.

New @dockstore.org update! Our free registry for sharing analytical tools and workflows for bioinformatics has gotten even better with: 🤖 AI based automatic topic sentence generation. 📚 Automatic DOI generation and discovery 🔎 Improved search results genomics.wordpress.ucsc.edu/news/2024/11...

"The formation and propagation of human Robertsonian chromosomes" ROBs are the most common translocation in humans, approx. ~1 per 800 people. Last year we proposed a simple mechanism for ROB formation; This year we prove it by finishing some T2T! New preprint: www.biorxiv.org/content/10.1...

Note, also similar nice results and ideas from @benlangmead.bsky.social's lab: www.biorxiv.org/content/10.1...

Out today in Nature Methods, our first attempt make personalized pangenomes: rdcu.be/dTD3o In the future it will vital to subset pangenomes to just the relevant haplotypes for a compared sample. Work by Jouni Siren, Matteo Ungaro, Parsa Eskander, vg team (github.com/vgteam/vg), and many others.

Long reads for rare disease diagnosis; new preprint from lab+ Broad and DC Children's collaborators. TLDR: Long-read sequencing reveals a lot more of the genome but interpreting the added information requires removing short-read bias from our current knowledge + DBs www.medrxiv.org/content/10.1...

New experimental version of Shasta genome assembler for higher accuracy nanopore simplex: github.com/paoloshasta/... (also see: docs.google.com/presentation...)

Fancy discussing pangenomes in Switzerland this summer? Join us for IGGSY 2024 in Ascona: iggsy.org/registration

How do we make a pangenome maximally relevant for the study of a new sample? www.biorxiv.org/content/10.1...

Today we announce the first release of Severus: a new tool for somatic SV calling for long reads! It's designed for complex (and simple) rearrangements in cancer genomes, but also works well for germline github.com/KolmogorovLa...

Initial release of DeepSomatic, which identifies subclonal variants when given tumor and normal BAM files. Pre-trained models and case studies available for Illumina and PacBio. Development led by Kishwar Shafin which built off a framework by Pi-Chuan Chang. (github.com/google/deeps...)