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Reposted by Mitchell R. Vollger

Megan Dennis @mydennis.bsky.social · 2d

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 · 3d

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

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Mitchell R. Vollger @mrvollger.bsky.social · 9d

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

Home - The computational guide to Fiber-seq

fiberseq.github.io

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Mitchell R. Vollger @mrvollger.bsky.social · 9d

@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

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Reposted by Mitchell R. Vollger

Ben Langmead @benlangmead.bsky.social · 29d

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 · Aug 17

@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.

Reposted by Mitchell R. Vollger

JHU Computer Science @jhucompsci.bsky.social · Jul 22

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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Reposted by Mitchell R. Vollger

Daniela C. Soto @dcsoto.bsky.social · Jul 21

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 · Jul 21

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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Reposted by Mitchell R. Vollger

Megan Dennis @mydennis.bsky.social · Jul 21

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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Reposted by Mitchell R. Vollger

Dr. Jean Fan @jef.works · Jul 8

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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Reposted by Mitchell R. Vollger

Kristen Kwan @blockintheback.bsky.social · Jul 3

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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Reposted by Mitchell R. Vollger

Emily Madden @emadden.bsky.social · Jun 18

🧬🧪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/...

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.

www.science.org

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Reposted by Mitchell R. Vollger

Jenna Norton @jenna-m-norton.bsky.social · Jun 10

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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Reposted by Mitchell R. Vollger

Aaron Quinlan (he/him) @aaronquinlan.bsky.social · Jun 5

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

Mitchell R. Vollger @mrvollger.bsky.social · Jun 5

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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Mitchell R. Vollger @mrvollger.bsky.social · Jun 5

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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Reposted by Mitchell R. Vollger

Alex Hoischen @ahoischen.bsky.social · May 26

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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Reposted by Mitchell R. Vollger

Rajiv McCoy @rajivmccoy.bsky.social · Mar 3

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...

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...

www.biorxiv.org

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Mitchell R. Vollger @mrvollger.bsky.social · Feb 12

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

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Reposted by Mitchell R. Vollger

Megan Dennis @mydennis.bsky.social · Feb 5

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).

bioRxiv Genomics @biorxiv-genomic.bsky.social · Feb 5

CiFi: Accurate long-read chromatin conformation capture with low-input requirements https://www.biorxiv.org/content/10.1101/2025.01.31.635566v1

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Mitchell R. Vollger @mrvollger.bsky.social · Jan 30

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

Alfred - Productivity App for macOS

Alfred is a productivity application for macOS, which boosts your efficiency with hotkeys, keywords and text expansion. Search your Mac and the web, and control your Mac using custom actions with the ...

www.alfredapp.com

Reposted by Mitchell R. Vollger

Adam Phillippy @aphillippy.bsky.social · Jan 29

This is the way

Eric Topol @erictopol.bsky.social · Jan 29

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...

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...

www.nature.com

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Reposted by Mitchell R. Vollger

Eric Topol @erictopol.bsky.social · Jan 29

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...

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...

www.nature.com

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Reposted by Mitchell R. Vollger

Megan Dennis @mydennis.bsky.social · Jan 9

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 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...

www.hhmi.org

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Reposted by Mitchell R. Vollger

Matt Holt @holtjma.bsky.social · Dec 11

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

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

github.com

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Mitchell R. Vollger @mrvollger.bsky.social · Dec 6

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.

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Mitchell R. Vollger @mrvollger.bsky.social · Dec 6

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.

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