Brad Bowles 🧬🔬💻

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.

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.

📃 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).

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.”

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...

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...

🖥️🧬🧪 Publication Alert!

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

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 🧵]

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

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

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...

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

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

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.

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)

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...

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

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

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...

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

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!

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.

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...

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...

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...

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.

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.

Image of now stolen salsa vaya

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.

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)

A very sad Donald trump

Academics being assigned another unpaid volunteer role:

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.

It’s also sickening to watch Silicon Valley market their mediocre AI product as “PhD’s in your pocket” when their pals in the White House are destroying the institutions that mint actual human PhD’s

RFK Jr. backs down all the time when he gets push back, so if anyone wants to call, here's the HHS number 1-877-696-6775.
I'd also call your senators/reps as well.

Beeswarm plot of the prediction error across different methods of double perturbations showing that all methods (scGPT, scFoundation, UCE, scBERT, Geneformer, GEARS, and CPA) perform worse than the additive baseline.

Line plot of the true positive rate against the false discovery proportion showing that none of the methods is better at finding non additive interactions than simply predicting no change.

Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉

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

We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!

🧵

bioRxiv bat signal going up. We have a big backlog of submissions. If any affiliates have time to do some screening, we (and all the authors) would be immensely grateful! 🙏

I was also under this misconception 🙋‍♂️ thanks for sharing this mini review!