Brad Bowles 🧬🔬💻
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bradbowles.bsky.social
Brad Bowles 🧬🔬💻
@bradbowles.bsky.social
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
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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!
An Introduction to Sequence Alignments
How bioinformatics learners can use data from the 1,000 Genomes Project to practice basic alignment skills.
thetranscript.leaflet.pub
Reposted by Brad Bowles 🧬🔬💻
We have a 3-years position open in our facility. Come join us to do great science in a nice team!
jobs.unibas.ch/offene-stell...
Universität Basel: Bioinformatician (100%)
The Department of Biomedicine (DBM) is a joint effort between the University of Basel and the University Hospitals Basel. It unites basic and clinical scientists to advance our understanding of health...
jobs.unibas.ch
February 12, 2026 at 9:15 AM
Reposted by Brad Bowles 🧬🔬💻
📢 Hiring! Our group @ncmbm.bsky.social seeks a Research Scientist contributing to:
• Reproducible pipelines for large-scale genomics
• cisreg signature analysis in breast cancer
• Continued development of JASPAR
• Cross-disciplinary collaboration

Apply now 👉
www.jobbnorge.no/en/available...
February 12, 2026 at 9:34 AM
Reposted by Brad Bowles 🧬🔬💻
🎉 Registration for the nf-core hackathon is now open! Join us online or in-person on March 11-13 for collaborative coding, pipeline development, and community building 💻

Bring your own project or choose from our community issues.🔧 Every project has a lead to guide you! nf-co.re/events/hacka...
nf-core
Details of past and future hackathons around nf-core.
nf-co.re
February 9, 2026 at 1:50 PM
Reposted by Brad Bowles 🧬🔬💻
First, @tattabio.bsky.social is now on Bluesky!💙 and second, we launched mult-sequence CoSearch on SeqHub!
Many questions in biology aren’t about individual proteins...they’re about how proteins behave together.

This week we launched CoSearch in SeqHub: a user-requested analysis that lets you explore where multiple proteins co-occur across 132,000 microbial genomes, in seconds.
February 4, 2026 at 4:08 PM
This guy was kidnapped down the street from me. The ICE surge in Minnesota is not over, nor limited to the twin cities. Be safe and please do not be silent or pretend that ICE is de-escalating.
By late Friday afternoon, the Department of Homeland Security put out a statement saying authorities had received Abreu-Vasquez's medications and that ICE would work to ensure he received them.

But on Sunday afternoon, his wife told MPR News that he still hadn't received the life-saving medication.
Kidney recipient arrested by ICE in Rochester last week still isn't getting needed medications
The wife of a kidney transplant recipient tells MPR News that four days after his arrest, the man still has not received the medications he needs to keep his body from rejecting the kidney.
www.mprnews.org
February 8, 2026 at 9:12 PM
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...
SS18-SSX co-opts P300 to sustain oncogenic transcription independent of SWI/SNF activity
Synovial sarcoma is driven by the SS18-SSX fusion oncoprotein, which has been assumed to promote tumorigenesis through its incorporation into the SWI/SNF chromatin remodeling complexes. Accordingly, therapeutic efforts have focused on targeting SS18-SSX containing SWI/SNF assemblies, yet these approaches have produced limited clinical benefit. Here, we demonstrate that SS18-SSX sustains oncogenic transcription independent of SWI/SNF activity. Despite efficient degradation and dismantling of SWI/SNF complexes, fusion occupancy at target loci and associated gene expression programs remain largely intact. Instead, we identify the acetyltransferase P300 as an essential co-factor supporting SS18-SSX chromatin binding and transcriptional activation. Targeting P300 displaces the fusion from chromatin, suppresses its transcriptional output, compromising synovial sarcoma viability. Notably, dual PROTAC mediated degradation of P300 and SWI/SNF produces strong synergistic effects, broadly disrupting SS18-SSX localization and function. These findings redefine the mechanistic basis of synovial sarcoma and reveal a mechanistically anchored therapeutic strategy for targeting its core oncogenic driver. ### Competing Interest Statement C.R.V. has been a consultant for Flare Therapeutics, Roivant Sciences and C4 Therapeutics; has served on the advisory boards of KSQ Therapeutics, Syros Pharmaceuticals and Treeline Biosciences; has received research funding from Boehringer Ingelheim and Treeline Biosciences; and owns stock in Treeline Biosciences. S.A.A. has been a consultant and/or shareholder for Neomorph, Imago Biosciences, Hyku Therapeutics, C4 Therapeutics, Accent Therapeutics and Nimbus Therapeutics; and has received research support from Janssen and Syndax. N.O.C. is a co-founder, shareholder and management consultant for PhenoTherapeutics Ltd; and a shareholder in Amplia Therapeutics Ltd All other authors declare no financial interests UKRI, EP/X039633/1 Worldwide Cancer Research, https://ror.org/031tfbz57, 21-0271 Science Foundation Ireland, https://ror.org/0271asj38, 18/SIRG/5573
www.biorxiv.org
January 28, 2026 at 9:54 AM
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!
An Introduction to Sequence Alignments
How bioinformatics learners can use data from the 1,000 Genomes Project to practice basic alignment skills.
thetranscript.leaflet.pub
January 19, 2026 at 5:16 PM
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.
ICE agents to begin checking documents at MSP airport, patrol jet bridges - Minneapolis / St. Paul Business Journal
U.S. Immigration and Customs Enforcement agents will begin checking documents of travelers and workers at MSP airport, with patrols inside jet bridges.
www.bizjournals.com
January 16, 2026 at 4:11 AM
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:
January 14, 2026 at 3:07 PM
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...
Minneapolis schools cancel classes after Border Patrol clash disrupts dismissal at Roosevelt
Minneapolis schools closed for the week citing safety concerns after an encounter involving armed Border Patrol agents near Roosevelt High School.
www.mprnews.org
January 8, 2026 at 1:31 PM
Reposted by Brad Bowles 🧬🔬💻
Teaching Transcriptomics in a Master’s in Informatics! 🧬 I’m curious about your take on the best format for students: 1️⃣ Practical/Code-heavy + autonomous theory? 2️⃣ A traditional hybrid approach? What works best for informatics profiles? Let’s discuss below! 👇 #Bioinformatics #Transcriptomics
January 5, 2026 at 3:26 PM
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...
December 12, 2025 at 3:42 PM
The Ensembl website is so cool, there should be a version of it that works.
December 11, 2025 at 6:11 PM
Reposted by Brad Bowles 🧬🔬💻
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...
December 10, 2025 at 9:36 AM
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.
We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen.

1/n
Intro to Bedder – The Quinlan Lab
quinlanlab.org
December 2, 2025 at 4:19 AM
Reposted by Brad Bowles 🧬🔬💻
I named my fists AUG and UGA because one starts it and the other finishes it.
I named my fists Master and Commander, because together they’re gonna send you to the far side of the world.
I named my fists Pride and Prejudice, because it is a truth universally acknowledged that a single man in possession of two fists must be in want of whupping ass
December 1, 2025 at 3:39 PM
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
November 24, 2025 at 4:57 PM
Reposted by Brad Bowles 🧬🔬💻
they’re saying you can still push to github if your heart is full of joy and whimsy, it’s true
November 18, 2025 at 9:27 PM
Reposted by Brad Bowles 🧬🔬💻
Adding citations of people who might review the paper
November 14, 2025 at 10:06 AM
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!
November 11, 2025 at 12:16 AM
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...
Specificity, length and luck drive gene rankings in association studies - Nature
Genetic association tests prioritize candidate genes based on different criteria.
www.nature.com
November 7, 2025 at 12:05 AM
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...
Impact of Alzheimer's disease risk factors and local neuromelanin content on the transcriptomic landscape of the human locus coeruleus
The locus coeruleus (LC) is a small noradrenergic nucleus in the dorsal pons that sends projections across the brain regulating sleep, arousal, attention, stress responses, and some forms of cognition...
www.biorxiv.org
October 31, 2025 at 3:42 PM
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...
‘Instability and confusion’ as CDC slashes 1,300 jobs before reinstating half
Trump administration says 700 notices were sent in error, while top CDC officer says ‘they didn’t think through what they were doing’
www.theguardian.com
October 19, 2025 at 4:00 PM
He does bioinformatics now.
October 16, 2025 at 3:04 PM