Benedict Paten

🦒Long read giraffe is out!🦒
Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2

A complete diploid human genome benchmark for personalized genomics Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...

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.

Lossless Pangenome Indexing Using Tag Arrays Pangenome graphs represent the genomic variation by encoding multiple haplotypes within a unified graph structure. However, efficient and lossless indexing of such structures remains challenging due t...

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

@ABC Patty Morin, whose daughter Rachel was murdered by a migrant without legal status in 2023, criticized her senator, Chris Van Hollen, for flying to El Salvador to advocate for Kilmar Abrego Garcia in an unrelated immigration case. https://abcnews.link/vxXfL69

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...

Efficient near telomere-to-telomere assembly of Nanopore Simplex reads Telomere-to-telomere (T2T) assembly is the ultimate goal for de novo genome assembly. Existing algorithms capable of near T2T assembly all require Oxford Nanopore Technologies (ONT) ultra-long reads w...

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 phylogeny of the 7 ape genomes that have now been completed from "T2T", with Homer Simpson representing mankind.

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...

Complete sequencing of ape genomes - Nature Complete sequences of chromosomes telomere-to-telomere from chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan and siamang provide a comprehensive and valuable resource for future evolutionary comparisons.

Nature research paper: Complete sequencing of ape genomes

https://go.nature.com/3EfWwqk

I kind of want to go

The 'Judicial Black Hole' of El Salvador's Prisons Is a Warning for Americans Donald Trump is cementing a partnership with El Salvador President Nayib Bukele, whose assault on civil rights is being mirrored in the U.S.

"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 - Nature Biotechnology Complex structural variations and rearrangements in cancer are identified using long-read sequencing.

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

Two front pages of the Economist. The first is dated October 25, 2024 and says “The Envy of the Workd” and has dollars bill rocketing into the sky in celebration of the US economy. The second front page is dated this week April 5th. It’s headline is “Ruination Day” and pictures Trump sawing a hole in the group the shape of the US.

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.

GitHub - yangao07/longcallD: A local-haplotagging-based small and structural variant caller A local-haplotagging-based small and structural variant caller - yangao07/longcallD

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

NIH Grants Fueled $95 Billion In FY 2024 Economic Activity, Finds New Report National Institutes of Health grants generated almost $95 billion in economic activity nationwide in FY 2024 according to a new report by United for Medical Research.

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.

Inside the Collapse at NIH Administration officials pressured NIH to avoid clear advice from the agency’s own lawyers to restart grant funding now.

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

Office desk without any personal items or decor

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

The Courts Blocked Trump’s Federal Funding Freeze. Agencies Are Withholding Money Anyway. Agencies continue to suspend funding, despite multiple court orders blocking the federal freeze. Experts say the Trump administration’s actions set the stage for challenges to Congress’ authority — an...

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...