Lightnews — Scholar-powered news

Reposted by Michael Love

James Goldie @jamesgoldie.dev · 3h

Real excited that @vscode.dev can do OS notifications when Tasks finish now. I've been wanting this one for years — plenty of #rstats devs who want to be able to minimise their code editor while a chunky analysis runs!

Screenshot of Visual Studio Code changlog says:

Tasks
OS notification for long-running task completion
Setting: task.notifyWindowOnTaskCompletion
When a user-initiated, long-running task completes while the VS Code window is not focused, an OS badge and notification toast are shown. Selecting the notification focuses the window where the task completed. You can configure this behavior with the task. notifyWindowOnTaskCompletion setting.

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Reposted by Michael Love

Ben Langmead @benlangmead.bsky.social · 7h

New tool "bwt-svg" for making illustrations of the BWT and the many auxiliary arrays and other structures related to it. Pyodide-based no-installation-necessary interface here: benlangmead.github.io/bwt-svg/. (H/t to @robert.bio for pointing me to pyodide!) Full repo: github.com/benlangmead/....

Illustration of Burrows-Wheeler Transform and many auxiliary structures from the input string how$now$brown$cow$#

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Reposted by Michael Love

Polly Fordyce @pollyfordyce.bsky.social · 8h

Applications are due tomorrow! Apply to come and join us @stanford-chemh.bsky.social -- it's a truly wonderful place to launch a career in interdisciplinary molecular research.

Sarafan ChEM-H @stanford-chemh.bsky.social · Aug 26

Open faculty position!
We're seeking applicants for a tenure-track faculty position at the junior level (Assistant or untenured Associate Professor) with research programs that exist at the interface between molecular science and computation. Apply here: stanford.io/45MF3Qa

Open Faculty Position: Assistant or Associate (Untenured) Professor

Application deadline: 11:55 PM on Wednesday, October 15, 2025

Sarafan ChEM-H is seeking candidates with research programs that exist at the interface between molecular science and computation.

Click the link above to learn more & apply!

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Michael Love @mikelove.bsky.social · 14h

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 · 6d

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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Reposted by Michael Love

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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Reposted by Michael Love

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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Reposted by Michael Love

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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Reposted by Michael Love

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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Reposted by Michael Love

Apoorva Mandavilli @apoorvanyt.bsky.social · 3d

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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Reposted by Michael Love

Sheryl Gay Stolberg @sherylnyt.bsky.social · 4d

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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Reposted by Michael Love

Jeremy Faust, MD @jeremyfaust.bsky.social · 4d

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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Reposted by Michael Love

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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Reposted by Michael Love

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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Reposted by Michael Love

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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Reposted by Michael Love

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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Reposted by Michael Love

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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Reposted by Michael Love

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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Reposted by Michael Love

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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Reposted by Michael Love

Jörg Vogel @jorg-vogel-lab.bsky.social · 6d

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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Reposted by Michael Love

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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Reposted by Michael Love

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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Reposted by Michael Love

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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Reposted by Michael Love

Megan Dennis @mydennis.bsky.social · 8d

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 · 9d

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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