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Reposted by Brad Bowles 🧬🔬💻

Ethan Holz @ethanholz.com · 12h

I wonder if we could leverage ORCID to create Bluesky verification records for researchers. It would allow for scientists to become validated by their own body of work and is something already used in the community.

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Reposted by Brad Bowles 🧬🔬💻

Pragati Kore @pragskore.bsky.social · 3d

📃 We’re excited to share our latest work, now published in Nature Communications — a major update to the Genome Aggregation Database (gnomAD) that improves allele frequency resolution for two gnomAD-defined genetic ancestry groups using local ancestry inference (LAI).

Improved allele frequencies in gnomAD through local ancestry inference - Nature Communications

This study incorporates local ancestry into the Genome Aggregation Database (gnomAD) to improve allele frequency estimates for admixed populations, enhancing variant interpretation and enabling more accurate and equitable genomic research and clinical care.

www.nature.com

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Daniel Litt @littmath.bsky.social · 10d

Oh, you have criticisms of my paper? Surely you noticed the part of the paper where we already rebutted your critique, by writing “Possible criticisms: the methodology of this paper is bad. We are aware of this.”

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Reposted by Brad Bowles 🧬🔬💻

Dr. Kat Napaaqtuk❄️ @napaaqtuk.bsky.social · 12d

Comment period ends on Monday for a proposed rule change that would terminate student visas after 4 years. It also puts limits on exchange visitors and reps of foreign media, and shortens the length of time at the end of the visa from 60 days to 30 days.

www.federalregister.gov/documents/20...

Establishing a Fixed Time Period of Admission and an Extension of Stay Procedure for Nonimmigrant Academic Students, Exchange Visitors, and Representatives of Foreign Information Media

Unlike most nonimmigrant classifications, which are admitted for a fixed time period, aliens in the F (academic student), J (exchange visitor), and most I (representatives of foreign information media...

www.federalregister.gov

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Francesca Finotello 🖥️🧬 @francescafinotello.bsky.social · 13d

🖥️🧬🧪 Publication Alert!

I’m very excited to share our latest paper: “NovumRNA: Accurate prediction of non-canonical #tumor #antigens from RNA #sequencing data”

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Reposted by Brad Bowles 🧬🔬💻

Matt Rockman @wormsrock.bsky.social · 15d

C. elegans is a real animal and we set out to understand how it comes to have its distinctive biogeography. Its ancestral center of diversity is in the higher elevation forests of Hawaii. Its closest relatives are spread across east Asia. Did they travel from Asia? [Preprint 🧵]

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Brad Bowles 🧬🔬💻 @bradbowles.bsky.social · 15d

┏┓
┃┃╱╲ In this
┃╱╱╲╲ house
╱╱╭╮╲╲ we pretend
▔▏┗┛▕▔ that hg38
╱▔▔▔▔▔▔▔▔▔▔╲
does not exist
╱╱┏┳┓╭╮┏┳┓ ╲╲
▔▏┗┻┛┃┃┗┻┛▕▔

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Brad Bowles 🧬🔬💻 @bradbowles.bsky.social · 17d

For comparison, the two studies cited in today’s FDA press release included 8,856 and 996 children respectively.

Joshua Weitz @joshuasweitz.bsky.social · 17d

Reminder: a large (2.5M+) sibling control study found "no evidence of increased risk of autism, ADHD, or intellectual disability associated with acetaminophen use". Precisely the kind of data that requires serious consideration before declaring mission accomplished.

jamanetwork.com/journals/jam...

Acetaminophen Use During Pregnancy and Children’s Risk of Autism, ADHD, and Intellectual Disability

This nationwide cohort study with sibling control analysis examines the association of acetaminophen use during pregnancy with children’s risk of autism, ADHD, and intellectual disability.

jamanetwork.com

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Brad Bowles 🧬🔬💻 @bradbowles.bsky.social · 17d

Full link: www.fda.gov/news-events/...

FDA Takes Action to Make a Treatment Available for Autism Symptoms

The U.S. Food and Drug Administration today initiated the approval of leucovorin calcium tablets for patients with cerebral folate deficiency (CFD), a neurological condition that affects folate (a vit...

www.fda.gov

Brad Bowles 🧬🔬💻 @bradbowles.bsky.social · 17d

I was unsurprised to see that the FDA announcement on leucovorin ... doesn't include a single peer-reviewed citation.

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Reposted by Brad Bowles 🧬🔬💻

Elizabeth Jacobs, PhD @elizabethjacobs.bsky.social · 21d

I think it is likely that Dr. Kuperwasser and Dr. El-Deiry will present misinformation about the SV40 promoter-enhancer in COVID19 vaccines tomorrow at ACIP.

I strongly recommend that you read @gorskon.bsky.social’s excellent work on the topic before the fearmongering begins.

VAERS and plasmid DNA "contamination" of COVID-19 vaccines: The nonsense continues

A new preprint is making the rounds falsely claiming to correlate "contamination" of COVID-19 vaccines with plasmid DNA to VAERS reports.

www.respectfulinsolence.com

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Alex Rubinsteyn @alexr.bsky.social · 21d

Is there something wrong with the HLA-II entries of the HLA Ligand Atlas?

Looked up the model PRAME epitope A2/SLLQHLIGL and found it's mostly detected on HLA-II alleles -- which doesn't make sense of a teeny little 9mer.

(it's also weird to see it so much on healthy samples)

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Reposted by Brad Bowles 🧬🔬💻

ananthannambiar.bsky.social @ananthannambiar.bsky.social · 22d

We were wondering: Do protein language models learn epistatic signals during pretraining?
Turns out, yes!
Protein Language Models Capture Structural and Functional Epistasis in a Zero-Shot Setting
www.biorxiv.org/content/10.1...

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Reposted by Brad Bowles 🧬🔬💻

James Bonfield @jbonfield.bsky.social · 24d

Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.

Ie: it's not us (Samtools team)! Be warned

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Johannes Köster @johanneskoester.bsky.social · 24d

Open postdoc position in my former lab at @danafarber.bsky.social and @harvard.edu Medical School (CFCE). A working environment full of nice and smart people! careers.dana-farber.org/job/12169/po...

Research Laboratory Job: Postdoctoral Research Fellow - Computational Biologist at Dana-Farber Cancer Institute in 450 Brookline Ave, Boston, MA

Postdoctoral Research Fellow - Computational Biologist job

careers.dana-farber.org

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Brad Bowles 🧬🔬💻 @bradbowles.bsky.social · 25d

Was just refused a COVID booster at my local Walgreens despite this change in policy 🫠

Dr. Lucky Tran @luckytran.com · Sep 8

Minnesota Governor Tim Walz has issued an executive order to protect COVID vaccine access.

Link: content.govdelivery.com/attachments/...

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Reposted by Brad Bowles 🧬🔬💻

UCSC Genome Browser @genomebrowser.bsky.social · Sep 5

Please take a moment to tell us how you use the Genome Browser: surveymars.com/q/mnb...

Your feedback supports future improvements and our continued funding.

UCSC Genome Browser User Satisfaction Survey | SurveyMars

I have posted a survey titled 'UCSC Genome Browser User Satisfaction Survey' on SurveyMars. Please help me by filling it out. Thank you very much!

surveymars.com

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Brad Bowles 🧬🔬💻 @bradbowles.bsky.social · Sep 4

Since the article is paywalled, the study (Interagency Coordinating Committee on the Prevention of Underage Drinking draft report) is here: www.federalregister.gov/documents/20...

Reposted by Brad Bowles 🧬🔬💻

Sean Carroll @seanmcarroll.bsky.social · Sep 3

A proposed new rule would limit international students on F1 or J1 visas to stays in the US of no longer than 4 years. This effectively means that intl. students will no longer come to graduate school here (time to PhD is 5-6 years). You can comment here:

www.federalregister.gov/documents/20...

Establishing a Fixed Time Period of Admission and an Extension of Stay Procedure for Nonimmigrant Academic Students, Exchange Visitors, and Representatives of Foreign Information Media

Unlike most nonimmigrant classifications, which are admitted for a fixed time period, aliens in the F (academic student), J (exchange visitor), and most I (representatives of foreign information media...

www.federalregister.gov

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Reposted by Brad Bowles 🧬🔬💻

Isabel @isabelott.bsky.social · Aug 29

RFK must go. Please contact your congresspeople about this. Ask them why RFK was allowed to unilaterally fire a senate appointee because she contacted senators – the appropriate oversight body – after the HHS secretary demanded that she break the law & betray Americans’ public health.

As long as he stays in office, the American public has to assume that their public health is being actively threatened. A current CDC employee put it starkly:
People will die because of this. We won't be able to get out guidance or get out funding for public health departments or get out vaccines.
We're going to be sicker as a country, not as effective, waste resources. And for what? I don't understand.

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Tom Pepinsky @tompepinsky.com · Aug 28

This is absolutely catastrophic for U.S. higher education, and for U.S. global leadership. Just the latest in a series of senseless acts of self-sabotage by a malevolent administration bent on making the United States weak and poor.

Oren Samet @osamet.bsky.social · Aug 28

I know there's a lot happening today, but this is sneaking in under the radar. This proposed new rule would absolutely crush foreign PhD students, potentially making it impossible for them to enroll with any certainty of their ability to finish www.politico.com/news/2025/08...

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Kelli Refer @kellireef.bsky.social · Aug 21

My bicycle was just stolen in Capitol Hill Seattle. Please keep an eye out for a small sized Salsa Vaya, green bicycle with a rear rack, steel fenders, dynamo hubs, 26” wheels.

Parked at a bike rack at 15th and Pike. Saw my lock cut and thrown on the ground.

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Reposted by Brad Bowles 🧬🔬💻

Diego del Alamo @delalamo.xyz · Aug 17

Anyone know what program & settings was used to make these figs? I assume it isn't pymol or chimera (pic from @asimovpress.bsky.social on the other site)

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Brad Bowles 🧬🔬💻 @bradbowles.bsky.social · Aug 16

Academics being assigned another unpaid volunteer role:

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Reposted by Brad Bowles 🧬🔬💻

Geeka 🧬 🖥️🧪 @geeka.bsky.social · Aug 11

My lab is going to be imminently looking for a computer scientist or a biologist with deep understanding of R to develop and give bioinformatic education to postdocs. This is perfect for someone who likes teaching. You'd need to be in the Pittsburgh area. Feel free to reach out with questions.

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