Adam Phillippy
@aphillippy.bsky.social
Finished a human genome, working on a few more 👨💻
Lab: https://genomeinformatics.github.io
Posts are my own
Lab: https://genomeinformatics.github.io
Posts are my own
Reposted by Adam Phillippy
Pregnancy loss is common in humans, and chromosomal abnormalities are the leading cause. Using genetic data from ~140,000 IVF embryos, we show that maternal variation in meiosis genes influences recombination and aneuploidy risk.
First authors: @saracarioscia.bsky.social & @aabiddanda.github.io
First authors: @saracarioscia.bsky.social & @aabiddanda.github.io
Common variation in meiosis genes shapes human recombination and aneuploidy - Nature
Analysis of data from pre-implantation genetic testing sheds light on the genetic basis of meiotic-origin aneuploidy, the leading cause of human pregnancy loss, identifying common genetic variants ass...
www.nature.com
January 21, 2026 at 9:14 PM
Pregnancy loss is common in humans, and chromosomal abnormalities are the leading cause. Using genetic data from ~140,000 IVF embryos, we show that maternal variation in meiosis genes influences recombination and aneuploidy risk.
First authors: @saracarioscia.bsky.social & @aabiddanda.github.io
First authors: @saracarioscia.bsky.social & @aabiddanda.github.io
Reposted by Adam Phillippy
Recently learned that I will be promoted to FULL PROFESSOR(!) this coming summer. So happy and thankful for those that have supported me along the way, including collaborators, mentors, colleagues, friends, family, trainees, and letter writers. #bighugs #youdabest #firstgen
January 21, 2026 at 10:26 AM
Recently learned that I will be promoted to FULL PROFESSOR(!) this coming summer. So happy and thankful for those that have supported me along the way, including collaborators, mentors, colleagues, friends, family, trainees, and letter writers. #bighugs #youdabest #firstgen
Reposted by Adam Phillippy
1,000 PacBio genomes in a prospectively designed clinical utility study.
This was the biggest and most important study that made us go live in diagnostics.
Long-read genomes as a genetic first tier test across many rare diseases!
www.medrxiv.org/content/10.6...
This was the biggest and most important study that made us go live in diagnostics.
Long-read genomes as a genetic first tier test across many rare diseases!
www.medrxiv.org/content/10.6...
Clinical long-read genome sequencing for rare disease diagnostics
Background Diagnostic evaluation of rare genetic disorders continues to rely on multiple test modalities, despite the increasing use of short-read exome or genome sequencing as first-tier tests. Long-...
www.medrxiv.org
January 19, 2026 at 8:30 AM
1,000 PacBio genomes in a prospectively designed clinical utility study.
This was the biggest and most important study that made us go live in diagnostics.
Long-read genomes as a genetic first tier test across many rare diseases!
www.medrxiv.org/content/10.6...
This was the biggest and most important study that made us go live in diagnostics.
Long-read genomes as a genetic first tier test across many rare diseases!
www.medrxiv.org/content/10.6...
Reposted by Adam Phillippy
very sad news. Peer Bork was one of the leaders of our field, a wonderful scientist, and he's much too young to be gone. www.embl.org/news/embl-an...
In remembrance of Peer Bork | EMBL
EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.
www.embl.org
January 16, 2026 at 6:33 PM
very sad news. Peer Bork was one of the leaders of our field, a wonderful scientist, and he's much too young to be gone. www.embl.org/news/embl-an...
T2T zebrafish annotation drop 🐟
Exciting genome news! For those interested, there is a prerelease of the Ensembl gene models for the new reference genomes GRCz12tu (GCA_049306965.1) and GRCz12ab (GCA_05204075.1) at ftp.ebi.ac.uk/pub/database...
You can download gff and gtf files there as well as softmasked genomes.
You can download gff and gtf files there as well as softmasked genomes.
Index of /pub/databases/ensembl/pre-release/Danio_rerio
ftp.ebi.ac.uk
January 13, 2026 at 10:56 PM
T2T zebrafish annotation drop 🐟
Mitchell is fantastic! Highly recommended!
I am hiring a staff bioinformatician for my new lab at the University of Utah! Please consider applying if you are on the hunt:
employment.utah.edu/salt-lake-ci...
employment.utah.edu/salt-lake-ci...
Jobs | University of Utah
Founded in 1850, The University of Utah is the flagship institution of higher learning in Utah, and offers over 100 undergraduate and more than 90 graduate degree programs to over 30,000 students. Uni...
employment.utah.edu
January 12, 2026 at 9:20 PM
Mitchell is fantastic! Highly recommended!
Reposted by Adam Phillippy
if you're interested, note that the time is UK time. In the US, that will be 9:00am.
Science Seminar on Jan 8 at 2pm with Prof. Steven Salzberg (John Hopkins University) on Major data analysis errors invalidate cancer microbiome findings. Please register at shorturl.at/Ll78Z
@stevensalzberg.bsky.social @jhucompsci.bsky.social
@stevensalzberg.bsky.social @jhucompsci.bsky.social
January 7, 2026 at 7:03 PM
if you're interested, note that the time is UK time. In the US, that will be 9:00am.
Reposted by Adam Phillippy
Now published in Nature Biotechnology:
go.nature.com/44P7nSm
If you missed it, the TL;DR is in my April thread below
go.nature.com/44P7nSm
If you missed it, the TL;DR is in my April thread below
January 6, 2026 at 9:38 AM
Now published in Nature Biotechnology:
go.nature.com/44P7nSm
If you missed it, the TL;DR is in my April thread below
go.nature.com/44P7nSm
If you missed it, the TL;DR is in my April thread below
Reposted by Adam Phillippy
Now published in Algorithms for Molecular Biology: link.springer.com/article/10.1.... Key message: a tiny CNN model with 7k parameters can capture main splice signals across vertebrates+insect and halves the minimap2 & miniprot junction error rate. I always use this new feature now.
Preprint on "Improving spliced alignment by modeling splice sites with deep learning". It describes minisplice for modeling splice signals. Minimap2 and miniprot now optionally use the predicted scores to improve spliced alignment.
arxiv.org/abs/2506.12986
arxiv.org/abs/2506.12986
January 6, 2026 at 11:02 PM
Now published in Algorithms for Molecular Biology: link.springer.com/article/10.1.... Key message: a tiny CNN model with 7k parameters can capture main splice signals across vertebrates+insect and halves the minimap2 & miniprot junction error rate. I always use this new feature now.
Reposted by Adam Phillippy
Haplotype-Resolved Genomics Reveals Conserved Chromatin Architecture and Epigenetic Constraints of Human Neocentromeres https://www.biorxiv.org/content/10.64898/2025.12.23.696241v1
December 26, 2025 at 4:33 AM
Haplotype-Resolved Genomics Reveals Conserved Chromatin Architecture and Epigenetic Constraints of Human Neocentromeres https://www.biorxiv.org/content/10.64898/2025.12.23.696241v1
Reposted by Adam Phillippy
Congratulations, To you, Steven and Prajna. Super cool findings.
a group of gorillas are standing in a cage looking out of a hole .
ALT: a group of gorillas are standing in a cage looking out of a hole .
media.tenor.com
December 24, 2025 at 3:20 PM
Congratulations, To you, Steven and Prajna. Super cool findings.
Reposted by Adam Phillippy
I've been thinking about the "virtual cell" concept and wanted to write up a few thoughts. Specifically on how I think the prior experience in GWAS informs the most likely way these models will be useful.
andrewcarroll.github.io/2025/12/23/t...
andrewcarroll.github.io/2025/12/23/t...
The Virtual Cell Will Be More Like Gwas Than Alphafold
There has been significant discussion recently on the concept of the “virtual cell.” I want to summarize the key concepts regarding what the field wants from a virtual cell and the challenges we face....
andrewcarroll.github.io
December 24, 2025 at 1:52 AM
I've been thinking about the "virtual cell" concept and wanted to write up a few thoughts. Specifically on how I think the prior experience in GWAS informs the most likely way these models will be useful.
andrewcarroll.github.io/2025/12/23/t...
andrewcarroll.github.io/2025/12/23/t...
If you’ve heard me talk in the past ~5 years, you will know I have developed an obsession with acrocentric chromosomes. This is all of that, condensed into one paper. I will do a full thread in the new year, but for those that want something to read over the holidays, have at it. Such a cool story!
Origin and evolution of acrocentric chromosomes in human and great apes https://www.biorxiv.org/content/10.64898/2025.12.22.696095v1
December 24, 2025 at 3:59 AM
If you’ve heard me talk in the past ~5 years, you will know I have developed an obsession with acrocentric chromosomes. This is all of that, condensed into one paper. I will do a full thread in the new year, but for those that want something to read over the holidays, have at it. Such a cool story!
Reposted by Adam Phillippy
The registration deadline is fast approaching for probgen 2026! Abstracts due by January 15, registration by January 31
probgen2026.github.io
probgen2026.github.io
Home - ProbGen 2026
Your Site Description
probgen2026.github.io
December 18, 2025 at 5:09 PM
The registration deadline is fast approaching for probgen 2026! Abstracts due by January 15, registration by January 31
probgen2026.github.io
probgen2026.github.io
Reposted by Adam Phillippy
Human acrocentric chromosome short arm de novo mutation and recombination https://www.biorxiv.org/content/10.64898/2025.12.16.694519v1
December 18, 2025 at 7:32 AM
Human acrocentric chromosome short arm de novo mutation and recombination https://www.biorxiv.org/content/10.64898/2025.12.16.694519v1
Reposted by Adam Phillippy
Complete genomes of a multi-generational pedigree to expand studies of genetic and epigenetic inheritance https://www.biorxiv.org/content/10.64898/2025.12.14.693655v1
December 17, 2025 at 5:32 AM
Complete genomes of a multi-generational pedigree to expand studies of genetic and epigenetic inheritance https://www.biorxiv.org/content/10.64898/2025.12.14.693655v1
Reposted by Adam Phillippy
Absolutely thrilled to share the latest work from my lab focused on the variation and evolution of human centromeres among global populations! We assembled 2,110 human centromeres, identifying 226 new major haplotypes and 1,870 α-satellite HOR variants. www.biorxiv.org/content/10.6...
December 16, 2025 at 4:06 PM
Absolutely thrilled to share the latest work from my lab focused on the variation and evolution of human centromeres among global populations! We assembled 2,110 human centromeres, identifying 226 new major haplotypes and 1,870 α-satellite HOR variants. www.biorxiv.org/content/10.6...
Reposted by Adam Phillippy
We're hiring an Assistant/Associate Professor of #Genomics & #Bioinformatics, #PhD, #MD, or both #Computational #Biology
Come work with us at the Institute for Genome Sciences
@medschool.umaryland.edu in #Baltimore!
Learn more/Apply: bit.ly/GenoBioinfo
Come work with us at the Institute for Genome Sciences
@medschool.umaryland.edu in #Baltimore!
Learn more/Apply: bit.ly/GenoBioinfo
December 11, 2025 at 4:16 PM
We're hiring an Assistant/Associate Professor of #Genomics & #Bioinformatics, #PhD, #MD, or both #Computational #Biology
Come work with us at the Institute for Genome Sciences
@medschool.umaryland.edu in #Baltimore!
Learn more/Apply: bit.ly/GenoBioinfo
Come work with us at the Institute for Genome Sciences
@medschool.umaryland.edu in #Baltimore!
Learn more/Apply: bit.ly/GenoBioinfo
Reposted by Adam Phillippy
If you ever need to fuzzy search some DNA, sassy is your tool.
Please spread the word; I think many people just outside my own circle could benefit from this :)
cc @rickbitloo.bsky.social
github.com/RagnarGrootK...
Please spread the word; I think many people just outside my own circle could benefit from this :)
cc @rickbitloo.bsky.social
github.com/RagnarGrootK...
December 10, 2025 at 3:50 PM
If you ever need to fuzzy search some DNA, sassy is your tool.
Please spread the word; I think many people just outside my own circle could benefit from this :)
cc @rickbitloo.bsky.social
github.com/RagnarGrootK...
Please spread the word; I think many people just outside my own circle could benefit from this :)
cc @rickbitloo.bsky.social
github.com/RagnarGrootK...
Reposted by Adam Phillippy
Mapping single-cell diploid chromatin fiber architectures using DAF-seq - @uwgenome.bsky.social @uwdeptmedicine.bsky.social go.nature.com/4rFTAHy
Mapping single-cell diploid chromatin fiber architectures using DAF-seq - Nature Biotechnology
Single-molecule chromatin fiber sequencing exposes single-cell-level heterogeneity in the chromatin architecture of individual regulatory elements.
go.nature.com
December 3, 2025 at 7:43 PM
Mapping single-cell diploid chromatin fiber architectures using DAF-seq - @uwgenome.bsky.social @uwdeptmedicine.bsky.social go.nature.com/4rFTAHy
Reposted by Adam Phillippy
579 high-quality human genomes from @humanpangenome.bsky.social, Arab Pangenome and individual papers (CHM13, CN1, KSA001, I002C, YAO and KOREF1). Sequences available in the AGC format (3.7GB) and FM-index in the ropebwt3 format (20.3GB). For details, see github.com/lh3/human-asm
GitHub - lh3/human-asm: A collection of high-quality human genomes
A collection of high-quality human genomes. Contribute to lh3/human-asm development by creating an account on GitHub.
github.com
December 3, 2025 at 3:44 AM
579 high-quality human genomes from @humanpangenome.bsky.social, Arab Pangenome and individual papers (CHM13, CN1, KSA001, I002C, YAO and KOREF1). Sequences available in the AGC format (3.7GB) and FM-index in the ropebwt3 format (20.3GB). For details, see github.com/lh3/human-asm
Reposted by Adam Phillippy
Preprint Alert!
We present new strategies to accelerate large-scale document comparison using MinHash-like sketches.
A thread:
We present new strategies to accelerate large-scale document comparison using MinHash-like sketches.
A thread:
Compressed inverted indexes for scalable sequence similarity https://www.biorxiv.org/content/10.1101/2025.11.21.689685v1
December 1, 2025 at 2:59 PM
Preprint Alert!
We present new strategies to accelerate large-scale document comparison using MinHash-like sketches.
A thread:
We present new strategies to accelerate large-scale document comparison using MinHash-like sketches.
A thread:
"Sure, bedtools is great and happily used by literally everyone, but, it could be bedder" That takes some serious courage. Kudos Brent and @aaronquinlan.bsky.social !
We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen.
1/n
1/n
Intro to Bedder – The Quinlan Lab
quinlanlab.org
December 2, 2025 at 3:59 PM
"Sure, bedtools is great and happily used by literally everyone, but, it could be bedder" That takes some serious courage. Kudos Brent and @aaronquinlan.bsky.social !
Reposted by Adam Phillippy
On the importance of this genome assembly: "T2T or telomere-to-telomere assemblies are the emerging gold-standard of sequencing technologies. For the first time, the zebrafish community has fully complete genomes of its two most used WT strains: Tu & AB. This is groundbreaking!" #ZebrafishFunFacts 🧪
Folks, it is finally out! Our paper on T2T assemblies of the zebrafish genome is on BioRxiv:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.biorxiv.org
December 2, 2025 at 11:29 AM
On the importance of this genome assembly: "T2T or telomere-to-telomere assemblies are the emerging gold-standard of sequencing technologies. For the first time, the zebrafish community has fully complete genomes of its two most used WT strains: Tu & AB. This is groundbreaking!" #ZebrafishFunFacts 🧪
With @burgesslab.bsky.social, not one, but TWO freshly caught T2T zebrafish reference genomes for the Tübingen and AB strains 🎣 🎣 🎉
🎉 Excited to share our new preprint presenting a complete de novo assembly of the zebrafish genome; a major advance for zebrafish genomics and research! 🧬
Full paper: www.biorxiv.org/content/10.1...
@zebrafishrock.bsky.social @izfs.bsky.social @zfinmod.bsky.social @modelzebrafish.bsky.social
Full paper: www.biorxiv.org/content/10.1...
@zebrafishrock.bsky.social @izfs.bsky.social @zfinmod.bsky.social @modelzebrafish.bsky.social
doi.org
November 26, 2025 at 2:51 PM
With @burgesslab.bsky.social, not one, but TWO freshly caught T2T zebrafish reference genomes for the Tübingen and AB strains 🎣 🎣 🎉