Haplotype-Resolved Genomics Reveals Conserved Chromatin Architecture and Epigenetic Constraints of Human Neocentromeres https://www.biorxiv.org/content/10.64898/2025.12.23.696241v1

Congratulations, To you, Steven and Prajna. Super cool findings.

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...

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!

The registration deadline is fast approaching for probgen 2026! Abstracts due by January 15, registration by January 31 probgen2026.github.io

Human acrocentric chromosome short arm de novo mutation and recombination https://www.biorxiv.org/content/10.64898/2025.12.16.694519v1

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

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...

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

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...

Mapping single-cell diploid chromatin fiber architectures using DAF-seq - @uwgenome.bsky.social @uwdeptmedicine.bsky.social go.nature.com/4rFTAHy

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

Preprint Alert! 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 !

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 🎣 🎣 🎉

Baym continues to make freakin' art. Must see thread/paper

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

‼️ 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...

I was one of the Editorial Board Members at @gigascience.bsky.social who resigned from the Editorial Board. 🧪 🔓 ⬇️ retractionwatch.com/2025/11/03/d...

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...

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

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

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...

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...

Read the preprint here with all the details, plus lots of other long-read powered analysis! www.medrxiv.org/content/10.1...

The T2T zebra finch genome has hatched! 🐣 🧬 @vertebrategenomes.bsky.social

For those interested in #Indigenous #Genomics and #ASHG25 in Boston, here are some interested posters/talks/events coming out of the Tsosie Lab, @nativebio.bsky.social, and @d4itdr.bsky.social. For those looking for Friday plans, attend our Ancillary Event, debuting a #Tribal #data repository!

Out today via @natgenet.nature.com, the first federally funded #Tribal #data repository, a revolutionary approach to data management and applied/operationalization of IDSov @d4itdr.bsky.social. Also, if you are at #ASHG25, come see us this morning in 205ABC www.nature.com/articles/s41...

actually it reminds me more of finding 1000s of human contaminants annotated as proteins within draft bacterial genomes in GenBank, which we published in 2018 (and @aphillippy.bsky.social knows this work): pubmed.ncbi.nlm.nih.gov/31064768/

A telomere-to-telomere map of somatic mutation burden and functional impact in cancer https://www.biorxiv.org/content/10.1101/2025.10.10.681725v1

Excited to share our new paper on predicting gene expression in yeast! We introduce "Shorkie," a supervised ML model that builds off a self-supervised foundation to interpret regulatory DNA. Preprint: www.biorxiv.org/content/10.1...

In honor of ASHG week (since I won’t be there), see "Choose your human genome reference wisely", in which Vivien Marx interviewed me @fergalmartin.bsky.social @lh3lh3.bsky.social @danrdanny.bsky.social @heidirehm.bsky.social and others on the state of the human reference rdcu.be/eJejg 🧵[1/10]

Now Hiring! Whitney Laboratory Assistant/Associate Professor in Marine Bioscience Apply & More Info - explore.jobs.ufl.edu/en-us/job/53... We seek a creative, collaborative scientist whose research harnesses or advances cutting-edge tools. Please help spread the word & reach out with any questions!

Big news! We're hiring lots of new faculty here at the University of Virginia School of Data Science @uvadatascience.bsky.social! You can find all our postings here: datascience.virginia.edu/faculty-jobs

🚨 New paper alert on telomeres! 🚨 Something different from the group! Thanks to Yuxin, a talented student in the lab, we used long-reads in 75 human trios to study telomeres and their inheritance.

Last week we were in the Washington Post for our characterization of Robertsonian chromosomes. This week we are entering our 10th day of being shut down and all of our research is on hold. To help me feel not-so-bad, here is a thread of some studies we released right before the shutdown 🧵 [1/n]...

Now that I'm settled in at @umasschan.bsky.social, I'm hiring at all levels: grad students, post-docs, and software engineers/bioinformaticians! The goal of my lab is to understand the regulatory role of every nucleotide in our genomes and how this changes across every cell in our bodies.

And it's posted! If you're interested and eligible, please consider applying through the UMD portal: umd.wd1.myworkdayjobs.com/en-US/UMCP/j.... If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!

Read ‘Sperm sequencing reveals extensive positive selection in the male germline’ from @sangerinstitute.bsky.social and collaborators in @nature.com below: nature.com/articles/s41...

I’m pleased as punch to share our hot off the presses article in @ajhgnews.bsky.social : A scalable approach for genomic-first rare disorder detection in a healthcare-based population Also presenting next week at #ashg25 #ashg2025 www.cell.com/ajhg/abstrac...

How Robertsonian chromosomes can lead to miscarriage or trisomy explained in one great figure from Human Molecular Genetics (Strachan and Read) that I have referred to many times

🚂 The T2T train keeps rolling: "The formation and propagation of human Robertsonian chromosomes" with Gerton and Garrison labs is out! What's a Robertsonian chromosome? Let Jen tell you herself in this great video, or read our paper: [1/3] 📺 youtu.be/JmlY5omxQVc 📄 www.nature.com/articles/s41...

New blog post! metaMDBG (@gaetanbenoit.bsky.social) and Myloasm (@jimshaw.bsky.social) have had recent releases, so I updated the benchmarks from the Autocycler paper: rrwick.github.io/2025/09/23/a... Both tools improved considerably! Time to update your conda environments 😄

More from HG002: This figure shows the incredible progress of de novo assembly over the past 5 years. Ash1 was a good "collapsed haplotype" assembly from 2020. Now we have single-tech solutions (ONT 6B4) that can produce nearly perfect diploid assemblies out of the (HERRO/Verkko) box 🤯

A couple editorial notes: (1) Element is Aviti UltraQ, ILMN is NovaSeq PCR-Free. (2) This is showing *per read* accuracy, which doesn't capture the randomness of the errors. Random (uniform) errors are better, but we couldn't decide on a metric for showing this. Suggestions welcome

Check this out! This is a big deal and helps lead the way for how we should think about analyzing genomes.

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]

hey bluesky 👋 visa hurdles mean I’m looking for opportunities outside the US. I’m a computational biologist (bacterial + phage genomics, postdoc in Koonin’s group @ NIH). I am interested in teaming up on funding apps. reach out if this resonates!

New blog post – A quick look at Roche's SBX lh3.github.io/2025/09/11/a...