We love to fetishize "top" researchers and give them special big pots of money. But we get far more science by spreading money among all researchers (closer to the NSERC DG model). This old post is magically relevant again... scientistseessquirrel.wordpress.com/2015/05/12/w...

The Ensembl website is so cool, there should be a version of it that works.

Why does anyone use the Wilcoxon test for anything? It's not even transitive. It's sensitive to things one most likely is not looking for (changes in distribution shape) and relatively insensitive to what one usually is looking for (change in location). www.sciencedirect.com/science/arti...

This is very exciting! I still haven’t found a super clean solution for integrating Bedtools and Python, so this functionality in Bedder is very interesting and I’m looking forward to trying it out.

I named my fists AUG and UGA because one starts it and the other finishes it.

#OpenCloning is a an Open Source alternative to SnapGene/Benchling that supports automation and integration with other software ✅ Free 🔓 Open Source 🧬 More cloning methods than SnapGene 🤖 Can be automated with python 👨‍🔬 Built by a researcher — for researchers! 👉 Check it out at opencloning.org

they’re saying you can still push to github if your heart is full of joy and whimsy, it’s true

Adding citations of people who might review the paper

SEATTLE!!! We’ve now taken the lead by 91 votes! 🤯 This thing is certainly not over! Over 1,000 ballots have been challenged, so if you haven’t tracked your ballot yet get on it! Our trusty volunteers have been working hard to "cure" ballots so they count! We're so close!

How do GWAS and rare variant burden tests rank gene signals? In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck! 🧬🧪🧵 www.nature.com/articles/s41...

Got with the times + made a BSky to share our new, large-scale spatial RNAseq study of adult human #locuscoeruleus! Co-1st auth and cryostat wizard @heenadivecha.bsky.social squeezed 85 tissue sections into 43 Visium arrays. (1/8) www.biorxiv.org/content/10.1...

Dismantling the Institutional Review Board (IRB), that oversees all human subjects research, is bad. Really bad.

He does bioinformatics now.

PD fellowship opportunity! New project ideas on medicinal plant engineering, cell type specific response to elicitation of biosynthesis, and epigenome/cloning evolution of long term cultured plant cells in the context of chemical production. www.simonsfoundation.org/grant/simons... Email me!

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.

📃 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.”

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.

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

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 🫠

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...

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.

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)

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.

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!

🚀 Reminder: Bioconductor Developer Forum is this Monday! 🧵 Topic: R & Rust in Bioinformatics 🗓️ July 28 | 🕚 11am EDT / 5pm CEST 🔗 Details + Zoom: blog.bioconductor.org/posts/2025-0... #Bioconductor #RStats #RustLang #OpenSource

How I sleep every night living in the Pacific Northwest:

I am looking to connect with my plant bio assistant professor cohort. If you know someone (or if it’s you!) please let me know. #PlantScience

Legend says the ancient Babylonians once tried to sequence and annotate God's own genome, and for their ambition and hubris they were forever cursed to have different annotation formats and standards so they could never do genomics with ease again.

Scientists, especially Seattle ones! One of my research scientists is heading to her PhD and we're looking to fill her spot, if not replace her. If you know someone looking to do cool and impactful translational research give them this: uwhires.admin.washington.edu/ENG/Candidat...

90% of your work in a zebrafish lab is basically this: