Mitchell R. Vollger

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

This is the way

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...

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...

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...

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...

GitHub - PacificBiosciences/pb-StarPhase: A phase-aware pharmacogenomic diplotyper for PacBio datasets A phase-aware pharmacogenomic diplotyper for PacBio datasets - PacificBiosciences/pb-StarPhase

“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...

I do fear with the DAG that the filesystem is the rate limiting factor but I have never benchmarked it. I know executing the same pipeline in a totally empty directory can be much faster though.

I have felt the DAG pain, haven’t had issues on the slurm side but did have grid issues for years. I think the executor plugins while it has been buggy is a step in making distribution better.

I think Johannes has talked a few times about wanting to use rust for the DAG, I know I would want that.

Care to share any of the rough edges? I find that sharing my workflows is often hard but rarely have trouble getting what I need working in the Snakemake framework.

You probably already know about this but I use ssh controlmaster to mitigate this.

I went and “changed” it to what I remembered having it as originally. So not sure why it was ever invalid.

Thx! Not sure how that happened I never even tried the fancy website thing.

GitHub - prefix-dev/pixi: Package management made easy Package management made easy. Contribute to prefix-dev/pixi development by creating an account on GitHub.

Re rust conda solver, have you seen: github.com/prefix-dev/p...