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
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 🎣 🎣 🎉
Baym continues to make freakin' art. Must see thread/paper
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Intracellular competition shapes plasmid population dynamics
From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...
www.science.org
November 20, 2025 at 11:29 PM
Baym continues to make freakin' art. Must see thread/paper
Reposted by Adam Phillippy
Join us at this exciting Workshop on #LongReads with keynotes from @aphillippy.bsky.social @mydennis.bsky.social
co-organized by @christinebeck.bsky.social and Mark Adams @jacksonlab.bsky.social Register www.jax.org/longread
#RNA #genomics #bioinformatics #cancer #medicine #evolution #neuroscience
co-organized by @christinebeck.bsky.social and Mark Adams @jacksonlab.bsky.social Register www.jax.org/longread
#RNA #genomics #bioinformatics #cancer #medicine #evolution #neuroscience
Long-Read Sequencing Workshop
The program will involve sessions on Genome Evolution, Genome Regulation, Transcriptomics, Rare Diseases, Common Diseases, and Viral and Microbial Genomes. Committed speakers include Adam Phillipy (NH...
www.jax.org
November 14, 2025 at 7:57 PM
Join us at this exciting Workshop on #LongReads with keynotes from @aphillippy.bsky.social @mydennis.bsky.social
co-organized by @christinebeck.bsky.social and Mark Adams @jacksonlab.bsky.social Register www.jax.org/longread
#RNA #genomics #bioinformatics #cancer #medicine #evolution #neuroscience
co-organized by @christinebeck.bsky.social and Mark Adams @jacksonlab.bsky.social Register www.jax.org/longread
#RNA #genomics #bioinformatics #cancer #medicine #evolution #neuroscience
‼️ There are an unprecedented number of Institute Director vacancies at the NIH and many of the application windows close this week or next, including ones that are essential to genomics research in the US including NHGRI, NLM/NCBI, and NIGMS. Please spread the word: hr.nih.gov/careers/open...
hr.nih.gov
November 10, 2025 at 4:08 PM
‼️ There are an unprecedented number of Institute Director vacancies at the NIH and many of the application windows close this week or next, including ones that are essential to genomics research in the US including NHGRI, NLM/NCBI, and NIGMS. Please spread the word: hr.nih.gov/careers/open...
Reposted by Adam Phillippy
I was one of the Editorial Board Members at @gigascience.bsky.social who resigned from the Editorial Board.
🧪 🔓
⬇️
retractionwatch.com/2025/11/03/d...
🧪 🔓
⬇️
retractionwatch.com/2025/11/03/d...
Dozens of board members resign from big-data journal after mass staff firings
More than three-fifths of the editorial board of a biomedical sciences journal resigned after the publication’s operations moved from Hong Kong to Shenzhen, China, and the editors and software team…
retractionwatch.com
November 4, 2025 at 3:46 PM
I was one of the Editorial Board Members at @gigascience.bsky.social who resigned from the Editorial Board.
🧪 🔓
⬇️
retractionwatch.com/2025/11/03/d...
🧪 🔓
⬇️
retractionwatch.com/2025/11/03/d...
Reposted by Adam Phillippy
My former mentor, colleague, and friend Hamilton Smith passed away this week. He was a giant in science, a Nobel Laureate, but also one of the nicest people you could ever meet. He will be missed by many. www.jcvi.org/media-center...
Remembering Hamilton O. Smith
Hamilton O. Smith
August 31, 1931 – October 25, 2025
It is with profound sorrow that we announce the loss of Hamilton O. Smith, M.D., a...
www.jcvi.org
October 29, 2025 at 11:26 PM
My former mentor, colleague, and friend Hamilton Smith passed away this week. He was a giant in science, a Nobel Laureate, but also one of the nicest people you could ever meet. He will be missed by many. www.jcvi.org/media-center...
Reposted by Adam Phillippy
About half the GigaScience editorial board (incl me) just resigned (academic.oup.com/gigascience/... is not yet updated). I resigned because it is very unclear what is happening and why - see @scedmunds.bsky.social blog post gigasciencejournal.com/blog/and-its..., for eg
Editorial_Board
Editorial Team
Editor-in-Chief
Xun Xu, PhD; BGI Research, Shenzhen, China
Executive Editor
Hongling Zhou; GigaScience Press, BGI Shenzhen, China
Edito
academic.oup.com
October 29, 2025 at 4:03 PM
About half the GigaScience editorial board (incl me) just resigned (academic.oup.com/gigascience/... is not yet updated). I resigned because it is very unclear what is happening and why - see @scedmunds.bsky.social blog post gigasciencejournal.com/blog/and-its..., for eg
Reposted by Adam Phillippy
1/
WashU research news; excited to share our new paper on Chromosome 9p Syndromes 🧬 Hope you take the time to read it. Here is the link:
link.springer.com/article/10.1...
@washugenetics.bsky.social
WashU research news; excited to share our new paper on Chromosome 9p Syndromes 🧬 Hope you take the time to read it. Here is the link:
link.springer.com/article/10.1...
@washugenetics.bsky.social
Whole-genome sequencing reveals individual and cohort level insights into chromosome 9p syndromes - Genome Medicine
Background Previous genomic efforts on chromosome 9p deletion and duplication syndromes have utilized low-resolution strategies (i.e., karyotypes, chromosome microarrays). These studies have provided ...
link.springer.com
October 28, 2025 at 11:27 PM
1/
WashU research news; excited to share our new paper on Chromosome 9p Syndromes 🧬 Hope you take the time to read it. Here is the link:
link.springer.com/article/10.1...
@washugenetics.bsky.social
WashU research news; excited to share our new paper on Chromosome 9p Syndromes 🧬 Hope you take the time to read it. Here is the link:
link.springer.com/article/10.1...
@washugenetics.bsky.social
Reposted by Adam Phillippy
I am hiring! - looking for a Staff Scientist to co-run my research group with me. Staff Scientist is a senior professional scientist role at EMBL. Please forward to people you might know who could be interested! embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Staff Scientist
About EMBL-EBI EMBL’s European Bioinformatics Institute is a data powerhouse, utilised on a global scale to advance scientific discovery through bioinformatics and solutions to some of the world’s mos...
embl.wd103.myworkdayjobs.com
October 10, 2025 at 7:30 AM
I am hiring! - looking for a Staff Scientist to co-run my research group with me. Staff Scientist is a senior professional scientist role at EMBL. Please forward to people you might know who could be interested! embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Reposted by Adam Phillippy
We investigated Constellation from Illumina @bcmhgsc.bsky.social for rare disease cases @gregor-research.bsky.social from @bcmhouston.bsky.social.
We tested HG002-4 & sequenced 21 families. We could detangle complex SV & other interesting findings described here: www.medrxiv.org/content/10.1...
We tested HG002-4 & sequenced 21 families. We could detangle complex SV & other interesting findings described here: www.medrxiv.org/content/10.1...
Constellation illuminates rare disease genetics
Despite significant advances in genomic sequencing, the resolution of many rare disease cases is still hindered by variant detection limitations. Short reads struggle in homologous regions, and long r...
www.medrxiv.org
October 20, 2025 at 1:40 PM
We investigated Constellation from Illumina @bcmhgsc.bsky.social for rare disease cases @gregor-research.bsky.social from @bcmhouston.bsky.social.
We tested HG002-4 & sequenced 21 families. We could detangle complex SV & other interesting findings described here: www.medrxiv.org/content/10.1...
We tested HG002-4 & sequenced 21 families. We could detangle complex SV & other interesting findings described here: www.medrxiv.org/content/10.1...