Lightnews — Scholar-powered news

Michael Love @mikelove.bsky.social · 3h

If you're at #ASHG25 check out these talks!

And follow this group for a blend of #geneticepi #statgen #compbio

Arjun Bhattacharya @arjunbhattac.bsky.social · 5d

A few programming notes for #ashg25 from trainees in my group @mdanderson.bsky.social + a thread of me being a proud PI. Please drop by these sessions and talk to @taylorhead.bsky.social, @seantbres.bsky.social , @ytchang11.bsky.social, and me in Boston @geneticssociety.bsky.social next week!

Presentations for Taylor Head (Room 205ABC Level 2 at 11:15 am on 10/15), Sean Bresnahan (Room 253ABC Level 2 at 8:45 am), and poster for Yung-Han Chang (Board 1108T, 2:30-4:30 pm on 10/16)

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Johannes Hingerl @johahi.bsky.social · 1d

Happy to share that Flashzoi is now published!
We enhanced Borzoi with RoPE & FlashAttention for >3x faster training/inference & 2.4x reduction in memory usage.
This brings large-scale genomic analysis and fine-tuning within reach of academic budgets.
📄: doi.org/10.1093/bioi...

Flashzoi: an enhanced Borzoi for accelerated genomic analysis

AbstractMotivation. Accurately predicting how DNA sequence drives gene regulation and how genetic variants alter gene expression is a central challenge in

doi.org

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Michael Love @mikelove.bsky.social · 2d

Yes I checked this systematically

I also consider these basically equivalent

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Mark Peifer (He, him) @peiferlabunc.bsky.social · 2d

I'm very excited to announce that UNC Biology has 6 faculty positions open this year! The first is for an Asst Professor who studies organismal resilience using an integrative approach 1/n
unc.peopleadmin.com/postings/307...

Poster with QR code linking to the position

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Mark Peifer (He, him) @peiferlabunc.bsky.social · 2d

The six faculty positions open at UNC Biology also include 2 openings for Teaching Assistant Professors or Teaching Associate Professors. We seek instructors with expertise from any area of biology 1/n
unc.peopleadmin.com/postings/307...

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Angie Rasmussen @angierasmussen.bsky.social · 3d

For more information about the Friday night massacre at CDC, I wrote up an analysis of who got terminated and what that means for public health.

Grateful to @saveamericamvmt.bsky.social for supporting and amplifying. We are in really terrible trouble.

rasmussenretorts.substack.com/p/the-death-...

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Apoorva Mandavilli @apoorvanyt.bsky.social · 2d

The Trump administration on Saturday scrambled to rescind layoffs of hundreds of CDC scientists who were mistakenly fired on Friday night in what appeared to be a substantial procedural lapse.

www.nytimes.com/2025/10/11/h...

Trump Administration Is Bringing Back Scores of C.D.C. Experts Fired in Error

www.nytimes.com

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Sheryl Gay Stolberg @sherylnyt.bsky.social · 3d

BREAKING: Friday night massacre underway at CDC. Doznes of "disease detectives," high-level scientists, entire Washington staff and editors of the MMWR (Morbidity and Mortality Weekly Report) have all been RIFed and received the following notice:

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Jeremy Faust, MD @jeremyfaust.bsky.social · 3d

CDC leaders asked staff to report if they’d received RIF notices—plus details like years of service and whether they’d been reinstated before.

Why?

Because these decisions weren’t made inside the agency. They came from political operatives outside CDC, apparently.

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Rob Patro @robp.bsky.social · 4d

Hi bioinformatics, genomics and CS friends! Please help me spread the word. I'm hiring a postdoc! Come work on cutting edge method development in algorithmic genomics with me and my group at @umdscience.bsky.social! 🖥️🧬

Rob Patro @robp.bsky.social · 6d

And it's posted! If you're interested and eligible, please consider applying through the UMD portal: umd.wd1.myworkdayjobs.com/en-US/UMCP/j....

If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!

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Jeremy Simon @jeremymsimon.bsky.social · 4d

Incredible opportunity to go train with the Patro lab @umdscience.bsky.social and develop new genomic methods!

Rob Patro @robp.bsky.social · 4d

Hi bioinformatics, genomics and CS friends! Please help me spread the word. I'm hiring a postdoc! Come work on cutting edge method development in algorithmic genomics with me and my group at @umdscience.bsky.social! 🖥️🧬

Rob Patro @robp.bsky.social · 6d

And it's posted! If you're interested and eligible, please consider applying through the UMD portal: umd.wd1.myworkdayjobs.com/en-US/UMCP/j....

If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!

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Rob Patro @robp.bsky.social · 5d

The Metagraph paper is out in Nature; it showed up in my feeds today! Congratulations to Mikhail Karasikov, @gxxxr.bsky.social, @akkah21.bsky.social and all of the other authors (whom I'd love to follow on Bluesky if I can find you ;P) www.nature.com/articles/s41...

Efficient and accurate search in petabase-scale sequence repositories - Nature

MetaGraph enables scalable indexing of large sets of DNA, RNA or protein sequences using annotated de Bruijn graphs.

www.nature.com

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Rob Patro @robp.bsky.social · 6d

Have you recently completed (or finishing soon) a PhD in CS or a related discipline? Do you want to do research advancing the theory & practice of algorithmic genomics & build tools that people love to use? I'll be looking to hire a postdoc! Official ad coming soon:
docs.google.com/document/d/1...

Postdoc Description.docx

Title: Postdoctoral Associate Summary statement: The postdoctoral research associate is responsible for developing novel computational methodology for high-throughput sequence genomics tasks, as well ...

docs.google.com

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Michael Love @mikelove.bsky.social · 5d

Well deserved Michelle! Congratulations!

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Michelle Itano @michelleitano.bsky.social · 5d

So humbled and grateful for this opportunity, but want to emphasize that none of this would be possible without @marianadeniz.bsky.social who not only had the idea and did the work for the nomination, but saw in me something that I did not. It has been an honor to work with and learn from her. (1/2)

Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 5d

Now that I can say it publicly - huge congratulations to @michelleitano.bsky.social , winner of this year's @bioimagingna.bsky.social Michael W Davidson award for "Community contributions, in any of the areas of Engagement, Education, Mentorship, and Standardization". So well deserved! #GBIxBINA2025

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 5d

Now that I can say it publicly - huge congratulations to @michelleitano.bsky.social , winner of this year's @bioimagingna.bsky.social Michael W Davidson award for "Community contributions, in any of the areas of Engagement, Education, Mentorship, and Standardization". So well deserved! #GBIxBINA2025

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Wolfgang Huber @wkhuber.bsky.social · 5d

Multiple hypothesis testing is easier to understand than single hypothesis testing. Yet it is often taught the wrong way round.

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Jörg Vogel @jorg-vogel-lab.bsky.social · 5d

Two group leader positions available in the broader areas of RNA science, RNA technologies, and RNA medicine. Attractive packages and a great environment. Come and join us at Helmholtz RNA Würzburg, Bavaria.

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Claus Wilke @clauswilke.com · 7d

Biology is much more complicated than most non-biologists can imagine. And AI is not going to change this anytime soon.
blog.genesmindsmachines.com/p/we-still-c...

We still can’t predict much of anything in biology

Biology is hard. Yes, even for AI.

blog.genesmindsmachines.com

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Johannes Rainer @jorainer.bsky.social · 8d

Reminder 👇

Interested in improving our R tools for #MassSpectrometry data analysis and integrating them into Galaxy?

⏲️ 3 year position
📍 Bolzano, 🇮🇹

👉 apply if you like:

- #rstats SW development
- @bioconductor.bsky.social
- large-scale #metabolomics data analysis
- hiking ⛰️

🔗 bit.ly/46AMawx

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bioRxiv Genomics @biorxiv-genomic.bsky.social · 7d

Taming the reference genome jungle: the refget sequence collection standard https://www.biorxiv.org/content/10.1101/2025.10.06.680641v1

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Megan Dennis @mydennis.bsky.social · 7d

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 · 8d

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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Edda Schulz @eddaschulz.bsky.social · 8d

⚠️ Paper alert: Using a novel CRISPR screening approach, we mapped the entire regulatory network controlling Xist—key for X-chromosome inactivation.
👉 We discover how sex and development signals are decoded at a single gene locus.
www.nature.com/articles/s41...
👇 Bluetorial

Reporter CRISPR screens decipher cis-regulatory and trans-regulatory principles at the Xist locus - Nature Structural & Molecular Biology

Here Schwämmle et al. develop CRISPR reporter screens to map transcription-factor-regulatory element interactions at the Xist locus, revealing a two-step mechanism integrating developmental and X-dosage signals to initiate X-chromosome inactivation.

www.nature.com

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John Bull @garius.bsky.social · Jan 5

If you ask someone today to name the builder of Hadrian's Wall, they would give you a funny look. But historical memory is odd, and right up to the 1800s we forgot who built it.

Until in 1840 John Hodgson, an obscure Northumbrian clergyman, published the LONGEST footnote in history... 1/22

long stretch of worked roman stone on Hadrian's Wall.

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Kaur Alasoo @kauralasoo.bsky.social · 12d

Happy to share that this work together with @opentargets.org is now out at Nature Communications.

Open Targets @opentargets.org · 12d

Out now in Nature Comms: the largest trans-eQTL meta-analysis in a single cell type!

An Open Targets team led by Krista Freimann and @kauralasoo.bsky.social analysed 3,734 lymphoblastoid cell line samples across nine cohorts, identifying four robust loci

www.nature.com/articles/s41...

Trans-eQTL mapping prioritises USP18 as a negative regulator of interferon response at a lupus risk locus - Nature Communications | Open Targets

Out now in Nature Comms: the largest trans-eQTL meta-analysis in a single cell type! An Open Targets team led by Krista Freimann and Kaur Alasoo analysed 3,734 lymphoblastoid cell line samples across...

www.linkedin.com

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