Benedict Paten
@benedictpaten.bsky.social
Professor of Biomolecular Engineering at the University of California, Santa Cruz; Associate Director, UC Santa Cruz Genomics Institute
Reposted by Benedict Paten
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.
October 18, 2025 at 4:00 PM
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.
Reposted by 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
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
Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe https://www.biorxiv.org/content/10.1101/2025.09.29.678807v1
October 2, 2025 at 6:28 AM
🦒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
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
Reposted by Benedict Paten
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 ...
www.biorxiv.org
September 22, 2025 at 5:01 PM
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]
Reposted by Benedict Paten
📣 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.
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.
June 5, 2025 at 1:37 PM
📣 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.
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.
Reposted by Benedict Paten
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...
www.biorxiv.org
May 15, 2025 at 8:22 PM
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.
Reposted by Benedict Paten
📢 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...
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...
May 12, 2025 at 1:15 PM
📢 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...
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...
Reposted by Benedict Paten
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
📢 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...
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...
May 12, 2025 at 1:52 PM
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
Reposted by Benedict Paten
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?
April 18, 2025 at 7:44 PM
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?
Reposted by Benedict Paten
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
April 18, 2025 at 9:53 PM
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...
Reposted by Benedict Paten
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...
www.biorxiv.org
April 18, 2025 at 9:54 PM
Preprint on hifiasm Nanopore-only assembly. Led by Haoyu Cheng: www.biorxiv.org/content/10.1...
Reposted by Benedict Paten
🚨 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. 🧬
🧵👇
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. 🧬
🧵👇
April 16, 2025 at 6:05 PM
🚨 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. 🧬
🧵👇
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. 🧬
🧵👇
Reposted by Benedict Paten
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...
April 9, 2025 at 9:31 PM
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...
Reposted by Benedict Paten
Reposted by Benedict Paten
I kind of want to go
April 4, 2025 at 9:42 PM
I kind of want to go
Reposted by Benedict Paten
"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...
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.
www.rollingstone.com
April 4, 2025 at 11:12 PM
"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...
Read my full report here: www.rollingstone.com/politics/pol...
Reposted by Benedict Paten
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
April 4, 2025 at 4:04 PM
Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing - @mishakolmogorov.bsky.social go.nature.com/3R334eH
Reposted by Benedict Paten
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
April 3, 2025 at 2:11 PM
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
Reposted by Benedict Paten
Reposted by Benedict Paten
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.
March 28, 2025 at 2:16 PM
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.
Reposted by Benedict Paten
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
March 24, 2025 at 4:53 PM
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...
Reposted by Benedict Paten
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
March 21, 2025 at 11:00 PM
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
Reposted by Benedict Paten
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...
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.
www.forbes.com
March 12, 2025 at 8:47 PM
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...
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...
Reposted by Benedict Paten
March 7, 2025 at 8:33 PM
Standing up for science in the redwoods :)
March 7, 2025 at 8:26 PM
Standing up for science in the redwoods :)
Reposted by Benedict Paten
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
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
March 1, 2025 at 10:38 PM
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
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