I am sincerely honored and excited to be named the Vice Chair for Vision Research at the @moraneyecenter.bsky.social at @utah.edu. I am thrilled to work with everyone to build upon the Moran's rich history in vision research. Stay tuned for much more to come - we will be growing!

Moran Eye Center Names Kristen M. Kwan, PhD, Vice Chair for Vision Research

The John A. Moran Eye Center at the University of Utah has named Kristen M. Kwan, PhD, Vice Chair for Vision Research. In this leadership role, she will help guide the strategic direction of the Moran...

healthcare.utah.edu

New paper with @rajivmccoy.bsky.social @ajhgnews.bsky.social. Bottom line: Polymorphic gene duplications absent in the reference genome can produce spurious trans-eQTLs, and we propose a method to identify these false positives. authors.elsevier.com/c/1nWChgeXHnOF

ImpuT2T: Pangenome-Based Patching for Human Genome Assemblies https://www.biorxiv.org/content/10.64898/2026.07.27.741037v1

HPRC2: A human pangenome reference with near-complete coverage of common genetic variation https://www.biorxiv.org/content/10.64898/2026.07.21.739710v1

Thank you to the Burroughs Wellcome Fund for supporting our research to understand the genetic causes of human pregnancy loss.

Johns Hopkins Arts & Sciences@jhuartssciences.bsky.social · last mo.

Congratulations to biology professor @rajivmccoy.bsky.social on being selected as a 2026 Next Gen Pregnancy Initiative recipient from the @bwfund.bsky.social for his project: Uncovering genetic mechanisms of pregnancy loss across parental and fetal genomes. www.bwfund.org/news/bwf-ann...

seqwish is now implemented in rust! github.com/pangenome/se... github.com/pangenome/se...

Memory-safe high-performance sequence mapping with rammap https://www.biorxiv.org/content/10.64898/2026.05.26.726289v1

Excited to announce that I'll be joining the Department of Genetics at UGA (@universityofga.bsky.social) in January! My lab will use model systems, DNA sequencing, and new computational tools to study mutation rate evolution across the tree of life.

We are holding our annual Rising Stars in Genetics and Genomics Postdoc Symposium on September 24-25, 2026! Please nominate postdocs who are conducting cutting edge, creative work, and are likely to be a leader in their field. Please nominate by April 30, 2026: forms.gle/85NZaxFezUk8... (1/2)

I’m so pleased to be named a AAAS Fellow! I remember opening the original email thinking wow, which of my awesome faculty won this nice thing (a perk of being chair is getting emails like that) but it was me! www.washington.edu/news/2026/03...

We've launched a department Trainee Emergency Fund, to help support EVERYONE BELONGING IN SCIENCE by meeting urgent financial needs of students and postdocs. Every gift will be matched, up to $1,000, by Nels Elde. Click to see a message from Aaron Quinlan and to donate! www.givecampus.com/s/w46xg1

Long reads carry multiple small vars and SVs and their phasing. LongcallD is the only caller that tightly integrates germline/mosaic small/structural vars/MEIs and their phasing in a single C program. One command line to get competitive small variant calls and better SVs. Led by Yan Gao.

bioRxiv Genomics@biorxiv-genomic.bsky.social · 5mo ago

LongcallD: joint calling and phasing of small, structural and mosaic variants from long reads https://www.biorxiv.org/content/10.64898/2026.03.20.713111v1

Another terminal based tool to interactively monitor all running #Snakemake workflows is #snkmt: github.com/cademirch/sn....

GitHub - cademirch/snkmt: A TUI for monitoring Snakemake workflows in real-time.

A TUI for monitoring Snakemake workflows in real-time. - cademirch/snkmt

github.com

Brent Pedersen, Mitchell Vollger and I have "posted" our preprint of the manuscript describing bedder, a complement to the functionality of bedtools. The "preprint server" we have chosen is google docs because it was rejected by biorxiv. docs.google.com/document/d/1...

bedder-manuscript.v10

Bioinformatics, 2026, 0–0 doi: 10.1093/bioinformatics/xxxxx Advance Access Publication Date: DD Month YYYY Genome Analysis Genome Analysis bedder: flexible genome interval intersection with user-defi...

docs.google.com

Anyone have a moment to help with a bioconda merge? github.com/bioconda/bio...

Update repository URLs in meta.yaml by mrvollger · Pull Request #63144 · bioconda/bioconda-recipes

Rustybam has moved from mrvollger to vollgerlab. Please read the guidelines for Bioconda recipes before opening a pull request (PR). General instructions If this PR adds or updates a recipe, use ...

github.com

It’s 5 years late but I had some time to update and finally write a little about rustybam. Its unique features really center on liftover operations that preserve the underlying alignment which can be composed in a surprising number of useful ways.

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 6mo ago

rustybam: a composable toolkit for alignment analysis and visualization with SafFire https://www.biorxiv.org/content/10.64898/2026.02.16.706142v1

New lab photo for the first time in too many years. I am so proud of this team's curiosity, camaraderie, and collabative energy.

AlphaGenome is out in @nature.com today along with model weights! 🧬 📄 Paper: www.nature.com/articles/s41... 💻 Weights: github.com/google-deepm... Getting here wasn’t a straight path. We discussed the story behind the model, paper & API in the following roundtable: youtu.be/V8lhUqKqzUc

Time for a thread on our Christmas preprint “Origin and evolution of acrocentric chromosomes in human and great apes”. I had so much fun with this project and paper. It will be hard to summarize in a thread, but I’ll try www.biorxiv.org/content/10.6... [1/21]

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

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...

nature.com

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...

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

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

The effects of genetic variants primarily occur in differentiated cells meaning we need to access these cell types to measure variant effects for most disease genes. We developed saturation genome editing in stem cells (iPSC-SGE) to enable phenotyping in diverse genetic and cell contexts at scale!

Editing stem cell genomes at scale to measure variant effects in diverse cell and genetic contexts

Multiplexed assays of variant effect (MAVEs) systematically measure variant function but have been limited to cancer cell lines rather than disease-relevant cell types. We developed saturation genome ...

medrxiv.org

Happy to share work spearheaded by former grad student Colin Shew testing shared duplicated cis regulatory elements (CREs) using an MPRA. While we find some high effect CREs, collectively paralog differences represent modest effects accounting for observed gene expression divergence.

bioRxiv Genomics@biorxiv-genomic.bsky.social · 10mo ago

Influence of cis-regulatory elements on regulatory divergence in human segmental duplications https://www.biorxiv.org/content/10.1101/2025.10.03.680410v1

More youtube videos coming soon to www.youtube.com/BenLangmead! New recording setup. I've got a couple videos in the editing phase and hope to keep up a rhythm of 1 new video per week.

@uwmedicine.bsky.social what is this? Trying to get your patients and employees with insurance to pay for full medical bills during check in before billing insurance… Disappointing and wrong.

Congratulations to @benlangmead.bsky.social on his promotion to full professor! 🎉 Prof. Langmead is recognized across the computational and life sciences fields for his innovative methods helping to transform how biomedical researchers and other life scientists access and use DNA sequencing data. 🧬

Thrilled that our study on human gene duplications and brain evolution is out! It was a true labor of love, with special shout-outs to my co-first author @jmuribescr.bsky.social and my PhD mentor @mydennis.bsky.social. Huge thanks as well to @aidaandres.bsky.social for all the popgen wisdom!

Megan Dennis@mydennis.bsky.social · last yr.

Check out our latest work co-led by @dcsoto.bsky.social and @jmuribescr.bsky.social identifying hundreds of human duplicated gene families using the new T2T-CHM13 assembly, with a focus on those potentially contributing to brain evolution 🧪: authors.elsevier.com/a/1lTQtL7PXu...

Check out our latest work co-led by @dcsoto.bsky.social and @jmuribescr.bsky.social identifying hundreds of human duplicated gene families using the new T2T-CHM13 assembly, with a focus on those potentially contributing to brain evolution 🧪: authors.elsevier.com/a/1lTQtL7PXu...