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Xian Chang @xian-chang.bsky.social · 7d

🦒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 · 7d

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

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Adam Phillippy @aphillippy.bsky.social · 16d

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

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Mike Inouye @mikeinouye.bsky.social · Jun 5

📣 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.

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Jouni Sirén @jltsiren.bsky.social · May 15

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

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Human Pangenome Reference Consortium @humanpangenome.bsky.social · May 12

📢 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...

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Adam Phillippy @aphillippy.bsky.social · May 12

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 · May 12

📢 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...

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The Serfs (youtube.com/theserfstv) @theserfstv.bsky.social · Apr 18

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?

@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

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Heng Li @lh3lh3.bsky.social · Apr 18

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

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Heng Li @lh3lh3.bsky.social · Apr 18

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

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Floris Barthel @florisbarthel.bsky.social · Apr 16

🚨 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. 🧬

🧵👇

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Adam Phillippy @aphillippy.bsky.social · Apr 9

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...

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

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Nature @nature.com · Apr 9

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

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Molly Jong-Fast @mollyjongfast.bsky.social · Apr 4

I kind of want to go

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Nikki McCann Ramírez @nikkimcr.bsky.social · Apr 4

"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.

www.rollingstone.com

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Nature Biotechnology @natbiotech.nature.com · Apr 4

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

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Ian Boudreau @ianboudreau.com · Apr 3

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

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News Eye @newseye.bsky.social · Apr 3

22 weeks apart.

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.

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Senator Mark Warner @markwarner.bsky.social · Mar 28

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.

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Heng Li @lh3lh3.bsky.social · Mar 24

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

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Xian Chang @xian-chang.bsky.social · Mar 21

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

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Sherry Pagoto, PhD @drsherrypagoto.bsky.social · Mar 12

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.

www.forbes.com

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Karen Miga @khmiga.bsky.social · Mar 7

#standupforscience #slugforscience

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Benedict Paten @benedictpaten.bsky.social · Mar 7

Standing up for science in the redwoods :)

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John Skiles Skinner @skiles.blue · Mar 1

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

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Senator Bernie Sanders @sanders.senate.gov · Feb 28

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.

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