Mitchell R. Vollger

404 for me. Any chance you are ready to share broadly?

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.

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

It’s an issue but a similar policy at Princeton ruined my undergraduate experience. My cohort quickly established the top ~20% of performers and then for the next three years studied exclusively within the that group to protect their grades. Ruining the opportunity to learn from your best peers.

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]

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...

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

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 - Nature Biotechnology Single-molecule chromatin fiber sequencing exposes single-cell-level heterogeneity in the chromatin architecture of individual regulatory elements.

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

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

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 ...

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!

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.

It’s not totally up to date but still may be useful: fiberseq.github.io/index.html

@mollyschumer.bsky.social if the data is pre SPQR chemistry I would recommend fibertools. If it’s new data then you can use Jasmine from Pacbio, Andrew and I spent a fair amount of time looking at the Jasmine results and they look good. And it will all still work with downstream fibertools commands

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.

Ben Langmead promoted to full professor. Computer science.

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!

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...

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

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.

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.

🧬🧪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/...

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-...

You may be excited, @mrvollger.bsky.social, but we are even more so! I can't wait to be your colleague!

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

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

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...

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...

So who carried it? Hope you didn’t enlist Phil lol

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).

Alfred is the answer! (imo) www.alfredapp.com