Brad Bowles 🧬🔬💻
Genomics and RNA Bioinformatics. PhD Scientist @ Tempus Labs. Posting about personal projects and cool papers, views my own. Seattle ⬅️➡️ MN.
Coding with #Python, #R, and #Nextflow. Brad-bio.dev
- Reposted by Brad Bowles 🧬🔬💻Synovial sarcoma is driven almost exclusively by a single oncofusion – SS18-SSX For years, the assumptions on disease mechanisms were simple: ➡️ SS18-SSX works by hijacking SWI/SNF chromatin remodeling activity Our new study shows that assumption was wrong 🧵👇 www.biorxiv.org/content/10.6...
- Access to high-quality human genomics data can be a major barrier for bioinformatics learners, so I wanted to write a quick post plugging the 1000 genomes project as a source of practice data!
- Reposted by Brad Bowles 🧬🔬💻It’s been reported locally, but I’m not sure how much national notice this has gotten. As part of this invasion by shithead goons, they are putting ICE agents in jetbridges and other parts of the airport at Minneapolis-Saint Paul. If you are flying Delta via MSP, you are putting yourself at risk.
- Reposted by Brad Bowles 🧬🔬💻It seems a lot of people think they know Minneapolis now. Our flaws. Our faults. I hope my neighbors join me in reclaiming the narrative. Minneapolis, through the eyes of someone who actually lives here:
- Reposted by Brad Bowles 🧬🔬💻It’s easy to think that schools in Minneapolis are closed because the Feds murdered someone in the street but no, the actual reason is that while that was happening, the Feds were busy doing other heinous shit across the city like tear-gassing a school
- “The move came after officials at Roosevelt High School said armed U.S. Border Patrol officers came on school property during dismissal Wednesday and began tackling people, handcuffed two staff members and released chemical weapons on bystanders.” — www.mprnews.org/story/2026/0...
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- Reposted by Brad Bowles 🧬🔬💻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.
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- 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.
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- Reposted by Brad Bowles 🧬🔬💻#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
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- Reposted by Brad Bowles 🧬🔬💻Adding citations of people who might review the paper
- Reposted by Brad Bowles 🧬🔬💻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!
- Reposted by Brad Bowles 🧬🔬💻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...
- Reposted by Brad Bowles 🧬🔬💻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...
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- Reposted by Brad Bowles 🧬🔬💻Dismantling the Institutional Review Board (IRB), that oversees all human subjects research, is bad. Really bad.
- The entire HR department at the CDC is gone. Everyone at the IRB, which makes sure studies are conducted ethically and rigorously, and the ethics office, which oversee conflicts of interest for CDC leaders and advisory committee members, were also let go. www.theguardian.com/us-news/2025...
- He does bioinformatics now.
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- Reposted by Brad Bowles 🧬🔬💻📃 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).
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- Reposted by Brad Bowles 🧬🔬💻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...
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- Reposted by Brad Bowles 🧬🔬💻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.
- 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...
- 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 🧬🔬💻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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- Was just refused a COVID booster at my local Walgreens despite this change in policy 🫠
- Reposted by Brad Bowles 🧬🔬💻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...
- Reposted by Brad Bowles 🧬🔬💻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...
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- Reposted by Brad Bowles 🧬🔬💻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.
- 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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- Academics being assigned another unpaid volunteer role:
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- Reposted by Brad Bowles 🧬🔬💻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.
- Reposted by Brad Bowles 🧬🔬💻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! 🧵
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- I was also under this misconception 🙋♂️ thanks for sharing this mini review!
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- How I sleep every night living in the Pacific Northwest:
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- Reposted by Brad Bowles 🧬🔬💻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.
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- 90% of your work in a zebrafish lab is basically this:
- Reposted by Brad Bowles 🧬🔬💻As requested - A Starter Pack of PIs in Biology (or related fields) who are recruiting PHD STUDENTS! If you would like to be added, feel free to ask! go.bsky.app/Bf4DRFmat://did:plc:hsnbex4tim4ajhv3dmgr4x5a/app.bsky.graph.starterpack/3lub2nmqyzd2n
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- Much love for the UCSC genome browser team, it is a tool I use weekly and something I probably couldn’t live without 🫡
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- Reposted by Brad Bowles 🧬🔬💻Hello! Ever wonder what's "talking to" your favorite transcript, but were too scared to ask? In our review in @cp-cellreports.bsky.social, @mardakheh.bsky.social and I highlight new RNA-focused tools for discovering RNA interactions across organizational scales. Checkit! tinyurl.com/ydn6e3ac
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