Benedict Paten
@benedictpaten.bsky.social
Professor of Biomolecular Engineering at the University of California, Santa Cruz; Associate Director, UC Santa Cruz Genomics Institute
A video of Alex Pretti reading out the final salute of an unnamed veteran he cared for until the end of his life in the ICU, posted to Facebook by his son.
I saw a tragically AI-generated version of this poster, so I have recreated a 100% human-made version for all your protest sign needs.
🦒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
bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 10mo agoRapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe https://www.biorxiv.org/content/10.1101/2025.09.29.678807v1
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]
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 ...
biorxiv.org
📣 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.
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...
biorxiv.org
📢 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
Human Pangenome Reference Consortium@humanpangenome.bsky.social · last yr.📢 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...
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...
Short RNA-seq read alignment with minimap2
lh3.github.io
Preprint on hifiasm Nanopore-only assembly. Led by Haoyu Cheng: www.biorxiv.org/content/10.1...
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...
biorxiv.org
🚨 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
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.
go.nature.com
"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...
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.
rollingstone.com
Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing - @mishakolmogorov.bsky.social go.nature.com/3R334eH
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.
go.nature.com
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
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...
GitHub - yangao07/longcallD: A local-haplotagging-based small and structural variant caller
A local-haplotagging-based small and structural variant caller - yangao07/longcallD
github.com
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...
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.
forbes.com
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
We're not done yet | 18F
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:
Inside the Collapse at NIH
Administration officials pressured NIH to avoid clear advice from the agency’s own lawyers to restart grant funding now.
theatlantic.com
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
