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Mitchell R. Vollger

@mrvollger.bsky.social
280 followers 170 following 18 posts

vollgerlab.com

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Reposted by Mitchell R. Vollger
Vijay Ramani @vram142.bsky.social · 14/09/2026
Everything you wanted to know about single-molecule epigenomics but were too afraid to ask! Wonderful to co-write (h/t ENORMOUS lift by @arnaudkr.bsky.social) this primer on our nascent field. Also, a 💯 example of wonderful colleagues building something *together*, not in competition =)
nature.com
A practical guide to studying genome function using single-molecule genomics
Nature Reviews Molecular Cell Biology - Single-molecule genomics methods are used to study the activity of regulatory factors on individual DNA molecules genome-wide, thereby enabling...
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Reposted by Mitchell R. Vollger
bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 07/09/2026
Barking Up Inferred Trees: Detecting Signatures of Selection in Dog Genomes Using Ancestral Recombination Graphs www.biorxiv.org/content/10.64898/20…
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Aaron Quinlan (he/him) @aaronquinlan.bsky.social · 28/08/2026
I am delighted to announce that The Department of Human Genetics at the University of Utah is continuing a multi-year recruiting initiative for multiple tenure-track faculty positions at the rank of Assistant Professor. Please share and consider applying! utah.peopleadmin.com/postings/208...
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Matt Holt @holtjma.bsky.social · 27/08/2026
Our article introducing Aardvark for variant benchmarking is now published in Genome Biology! “Aardvark: sifting through differences in a mound of variants” DOI: doi.org/10.1186/s130... GitHub: github.com/PacificBiosc... Follow along for some highlights… 1/N
doi.org
Client Challenge
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Adam Phillippy @aphillippy.bsky.social · 24/08/2026
On our last day, the lab ran a pop-up coffee shop for our NHGRI colleagues, staffed by our own highly experienced baristas Suhani and Serge. Farewell NIH! Thanks for being a great home for the past 11 years 🥲 Watch for our next pop-up at Hopkins once we get properly equipped 😁
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Cell - a Cell Press journal @cp-cell.bsky.social · 06/08/2026
New issue alert👉https://cell.com/cell/current On the cover: The Telomere-to-Telomere Consortium has finished the complete, diploid genome of a person. The cover is inspired by a karyotype of the chromosomes in metaphase, representing the two haplotypes as different colors.
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Kristen Kwan @blockintheback.bsky.social · 03/08/2026
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!
healthcare.utah.edu
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...
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Reposted by Mitchell R. Vollger
Gokcumen Lab @gokcumenlab.bsky.social · 29/07/2026
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
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 29/07/2026
ImpuT2T: Pangenome-Based Patching for Human Genome Assemblies www.biorxiv.org/content/10.64898/20…
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 22/07/2026
HPRC2: A human pangenome reference with near-complete coverage of common genetic variation www.biorxiv.org/content/10.64898/20…
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Rajiv McCoy @rajivmccoy.bsky.social · 30/06/2026
Thank you to the Burroughs Wellcome Fund for supporting our research to understand the genetic causes of human pregnancy loss.
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Erik Garrison @thinks.lol · 17/06/2026
seqwish is now implemented in rust! github.com/pangenome/se... github.com/pangenome/se...
github.com
GitHub - pangenome/seqwish: alignment to variation graph inducer
alignment to variation graph inducer. Contribute to pangenome/seqwish development by creating an account on GitHub.
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Reposted by Mitchell R. Vollger
bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 30/05/2026
Memory-safe high-performance sequence mapping with rammap www.biorxiv.org/content/10.64898/20…
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Tom Sasani @tomsasani.bsky.social · 20/05/2026
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.
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Aaron Quinlan (he/him) @aaronquinlan.bsky.social · 15/02/2026
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)
forms.gle
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Maitreya Dunham @maitreya.bsky.social · 27/03/2026
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...
washington.edu
Four UW researchers named AAAS Fellows
Four University of Washington researchers have been named AAAS Fellows, according to an announcement by the American Association for the Advancement of Science. They are among 449 newly elected...
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Reposted by Mitchell R. Vollger
Ellen Leffler @ellenleffler.bsky.social · 24/03/2026
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
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Reposted by Mitchell R. Vollger
Heng Li @lh3lh3.bsky.social · 23/03/2026
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.
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Reposted by Mitchell R. Vollger
Johannes Köster @johanneskoester.bsky.social · 16/03/2026
Another terminal based tool to interactively monitor all running #Snakemake workflows is #snkmt: github.com/cademirch/sn....
github.com
GitHub - cademirch/snkmt: A TUI for monitoring Snakemake workflows in real-time.
A TUI for monitoring Snakemake workflows in real-time. - cademirch/snkmt
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Reposted by Mitchell R. Vollger
Aaron Quinlan (he/him) @aaronquinlan.bsky.social · 12/03/2026
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...
docs.google.com
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...
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Mitchell R. Vollger @mrvollger.bsky.social · 05/03/2026
Anyone have a moment to help with a bioconda merge? github.com/bioconda/bio...
github.com
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 ...
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Mitchell R. Vollger @mrvollger.bsky.social · 18/02/2026
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.
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Reposted by Mitchell R. Vollger
Aaron Quinlan (he/him) @aaronquinlan.bsky.social · 10/02/2026
New lab photo for the first time in too many years. I am so proud of this team's curiosity, camaraderie, and collabative energy.
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Žiga Avsec @avsecz.bsky.social · 28/01/2026
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
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Adam Phillippy @aphillippy.bsky.social · 02/02/2026
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]
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Rajiv McCoy @rajivmccoy.bsky.social · 21/01/2026
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
nature.com
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...
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Mitchell R. Vollger @mrvollger.bsky.social · 12/01/2026
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
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...
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Reposted by Mitchell R. Vollger
Nature Biotechnology @natbiotech.nature.com · 03/12/2025
Mapping single-cell diploid chromatin fiber architectures using DAF-seq - @uwgenome.bsky.social @uwdeptmedicine.bsky.social go.nature.com/4rFTAHy
go.nature.com
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.
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Aaron Quinlan (he/him) @aaronquinlan.bsky.social · 02/12/2025
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
quinlanlab.org
Intro to Bedder – The Quinlan Lab
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Shawn Fayer @shawnfayer.bsky.social · 22/11/2025
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!
medrxiv.org
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 ...
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Megan Dennis @mydennis.bsky.social · 07/10/2025
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.
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Ben Langmead @benlangmead.bsky.social · 09/09/2025
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.
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Mitchell R. Vollger @mrvollger.bsky.social · 17/08/2025
@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.
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JHU Computer Science @jhucompsci.bsky.social · 22/07/2025
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. 🧬
Ben Langmead promoted to full professor. Computer science.
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Daniela C. Soto @dcsoto.bsky.social · 21/07/2025
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!
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Megan Dennis @mydennis.bsky.social · 21/07/2025
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...
authors.elsevier.com
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Dr. Jean Fan @jef.works · 08/07/2025
How it started vs. How it's going #Tenured Grateful to all those who've been a part of this journey so far. But the fun is just getting started 💪 Curious to find out just what this privilege of tenure can enable. Let's see how we can put it to the test. Feel free to share ideas 😉 #AcademicSky
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Kristen Kwan @blockintheback.bsky.social · 04/07/2025
Some personal news: amid everything going on, I’ve been promoted to Professor. I am so deeply grateful to all of the past and present members of the lab, who allowed me to be a part of their journey. I am so honored to call all of you my colleagues.
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Emadden @emadden.bsky.social · 18/06/2025
🧬🧪Fiber-seq was developed and originally published by Andrew Stergachis (now at @uwdeptmedicine.bsky.social) in 2020. It's a very cool method for adding chromatin accessibility data to native LRS experiments. You should definitely check out the original paper: www.science.org/doi/10.1126/...
science.org
Single-molecule regulatory architectures captured by chromatin fiber sequencing
Fiber-seq translates single-molecule chromatin stencils into a readout of the primary architecture of chromatin.
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Jenna Norton @jenna-m-norton.bsky.social · 10/06/2025
Today, my NIH colleagues and I did something scary but really important. We spoke up about egregious harms we are seeing happen to research participants and public health through thoughtless and politicized policies at NIH. 🧵1/3 apnews.com/article/nih-...
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Aaron Quinlan (he/him) @aaronquinlan.bsky.social · 05/06/2025
You may be excited, @mrvollger.bsky.social, but we are even more so! I can't wait to be your colleague!
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Mitchell R. Vollger @mrvollger.bsky.social · 05/06/2025
Very excited to share I’ll be starting my own group at University of Utah in the Department of Human Genetics in the new year! Reach out if you are interested! vollgerlab.com
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Alex Hoischen @ahoischen.bsky.social · 26/05/2025
Had the privilege to also see the magnificent session S10 - on the non-coding genome. Again top-notch science with great presentations and style of bring complex matters to a broad audience! What a treat! Thanks @mrvollger.bsky.social; @elfridedebaere.bsky.social and Musa Mhlanga @eshg.bsky.social
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Rajiv McCoy @rajivmccoy.bsky.social · 03/03/2025
In work led by @lalli.bsky.social, we present recombination maps and a diverse haplotype reference panel (1000 Genomes Project) for the T2T-CHM13 human reference genome. These resources improve the accuracy of phasing and imputation, especially around common CNVs. www.biorxiv.org/content/10.1...
biorxiv.org
A T2T-CHM13 recombination map and globally diverse haplotype reference panel improves phasing and imputation
The T2T-CHM13 complete human reference genome contains ~200 Mb of newly resolved sequence, improving read mapping and variant calling compared to GRCh38. However, the benefits of using complete refere...
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Megan Dennis @mydennis.bsky.social · 05/02/2025
Check out our new preprint describing CiFi - a method that couples 3C and PacBio HiFi sequencing with low input requirements. We apply it to human GM12878 to better characterize chromatin across repetitive regions, as well as single insect samples (a mosquito and a Mediterranean fruit fly).
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Adam Phillippy @aphillippy.bsky.social · 29/01/2025
This is the way
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Eric Topol @erictopol.bsky.social · 29/01/2025
The "kitchen sink" of omics to solve the basis for an undiagnosed disease: long read genome , transcriptome, methytome, epigenome, all synchronized (a first) www.nature.com/articles/s41...
nature.com
Synchronized long-read genome, methylome, epigenome and transcriptome profiling resolve a Mendelian condition - Nature Genetics
Simultaneous profiling of the genome, methylome, epigenome and transcriptome using single-molecule chromatin fiber sequencing and multiplexed arrays isoform sequencing identifies the genetic and molec...
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Megan Dennis @mydennis.bsky.social · 09/01/2025
The biggest congrats to former Dennis lab grad student Daniela Soto being named an HHMI Hanna Gray fellow!!! Soooooooo freaking proud and beyond-the-moon happy for her to have received this super well-deserved honor 🤩 www.hhmi.org/news/hhmi-na...
hhmi.org
HHMI Names the 2024 Hanna Gray Fellows | HHMI
The cohort includes early career scientists working in research areas ranging from treatment-resistant cancers to how animals evolved to live on land. The HHMI Hanna H. Gray Fellows Program provides e...
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Matt Holt @holtjma.bsky.social · 11/12/2024
“StarPhase: Comprehensive Phase-Aware Pharmacogenomic Diplotyper for Long-Read Sequencing Data” is now on biorxiv! In this work, we explore the use of long-read sequencing (#PacBio #HiFi) for #pharmacogenomics #PGx. 1/N Pre-print: doi.org/10.1101/2024... Repo: github.com/PacificBiosc...
github.com
GitHub - PacificBiosciences/pb-StarPhase: A phase-aware pharmacogenomic diplotyper for PacBio datasets
A phase-aware pharmacogenomic diplotyper for PacBio datasets - PacificBiosciences/pb-StarPhase
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Megan Dennis @mydennis.bsky.social · 27/09/2024
Check out our recent preprint, co-led by two former PhD students in the lab Daniela Soto and José Uribe-Salazar, in which we identify and characterize human duplicated genes implicated in brain evolution. www.biorxiv.org/content/10.1...
biorxiv.org
Gene expansions contributing to human brain evolution
Genomic drivers of human-specific neurological traits remain largely undiscovered. Duplicated genes expanded uniquely in the human lineage likely contributed to brain evolution, including the increase...
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