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Brad Bowles 🧬

@bradbowles.bsky.social
1.3K followers 2.6K following 67 posts

Genomics and RNA Bioinformatics @ Tempus. 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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Reposted by Brad Bowles 🧬
Dr. Stephanie @punkrockscience.bsky.social · 12/10/2026
Interviewer: Can you explain this gap in your CV? Scientist: That’s the non-coding portion of my CV - we’re not yet sure what all of it does, but we keep discovering new reasons that it’s there.
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Jordan van der Hagen @thejvandy.bsky.social · 10/10/2026
Listen to the Leaves Rustle. Minneapolis, Minnesota
Autumn branches frame the Minneapolis skyline across the river, with a tall tower catching the morning sun.Autumn trees and bright yellow shrubs line a riverbank across from a teal storefront and pale stone building.Dark leaves and hanging vines frame a patch of river glowing orange in the morning light.A red neon Nye’s sign glows above a quiet sidewalk, with parked cars and sunlit buildings down the street.
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Armin Ronacher @mitsuhiko.at · 09/10/2026
In the process I learned there is no good open source contrast algorithm so we're doing a survey on contrast to make one. Would be cool if you could take some minutes out of your day and do it. For science! contrastsurvey.earendil.com
contrastsurvey.earendil.com
Which grey stands out more?
A five-minute experiment on how people see contrast on their own screens.
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Caroline Bartman @cbartman.bsky.social · 26/09/2026
Are there key discoveries made with spatial RNA seq? Or what are your favorite spatial rna seq papers? Pls reski!
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Nic Wise @fastchicken.co.nz · 26/09/2026
This is excellent - esp the "don't trust ZIRP-era advice". Not just for beginners.
seangoedecke.com
Advice to a beginning software engineer
In general, you should be suspicious of engineers who are trying to give you advice. Even during ordinary times, this industry is so wide and changes so quickly…
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Better Things Are Possible @internethippo.bsky.social · 19/07/2025
It's Friday night baby
Sleepy time bear
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Rob Patro @robp.bsky.social · 16/09/2026
New preprint led by Zoe Rudnick: bramble 🌿 RNA-seq quantification makes you pick a side. Align to the transcriptome and your quantifier is happy, but reads from unannotated transcripts get misassigned to annotated ones. Align to the genome and you keep discovery, but limit quantification choices.
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Alex Rubinsteyn @alexr.bsky.social · 20/07/2026
Late 2020s going to be full of breakthroughs communicated as tweets like “lol fine tuned SlopCoder-V7 and it proved P=NP” with a link to fully correct alien math
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Brad Bowles 🧬 @bradbowles.bsky.social · 04/09/2026
Insanity
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J. Emory Parker 🏳️‍🌈 @jaspar.bsky.social · 19/08/2026
BIG news this morning: Moderna and Merck say their mRNA cancer “vaccine” worked in a late-stage melanoma trial www.statnews.com/2026/08/19/m...
statnews.com
Moderna and Merck say mRNA cancer vaccine succeeded in late-stage melanoma trial
A personalized mRNA cancer vaccine succeeded in a late-stage melanoma study, results that could herald a new, powerful approach in oncology.
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UCSC Genome Browser @genomebrowser.bsky.social · 17/08/2026
ENCODE GRAMMAR is now on the UCSC Genome Browser! 🧬 Base-resolution deep learning predictions, sequence contribution scores & motif instances (BPNet, ChromBPNet, ProCapNet, ReporterNet) across thousands of ENCODE experiments. Explore on hg38: genome.ucsc.edu/s/Lo...
UCSC Genome Browser view on human genome hg38 at chr8:127,898,412-127,899,647, showing the ENCODE GRAMMAR track hub. Ten stacked blue signal tracks display ChromBPNet observed and predicted DNase-seq and ATAC-seq signal for the K562 cell line, plus bias-corrected predicted profiles that rise to a sharp central peak, and base-resolution sequence contribution scores. At the bottom, a row of colored blocks marks predicted transcription factor motif instances (including GATA, KLF-SP, ELF-GABP, and FOS-JUN) directly beneath the peak.
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Reposted by Brad Bowles 🧬
Chang M. Yun @chang-m-yun.bsky.social · 06/08/2026
Finally… Excited to share what I’ve been working on for the first half of my PhD! ENCODE GRAMMAR: One of the largest collections of regulatory DNA seq2func models to date (3,865 in total) trained across ENCODE, with full model interpretations and annotations tracks. Blog: tinyurl.com/3hmknhaa 1/
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Sarah Aitken @s-j-aitken.bsky.social · 27/07/2026
🧬NEW PAPER🧬 To what extent is cancer development deterministic? Does the germline genome affect that predictability? Find out in our #StrainDifferences paper @nature.com "Genetic background sets the trajectory of experimental cancer evolution" www.nature.com/articles/s41... 🧵[1/14]
nature.com
Genetic background sets the trajectory of experimental cancer evolution - Nature
Experimentally replaying tumour evolution in divergent mouse strains reveals the importance of interactions between genetic ancestry and acquired cancer-driving mutations in shaping the earliest stage...
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Brad Bowles 🧬 @bradbowles.bsky.social · 02/08/2026
I missed it at the time, but it looks like the July PyTorch 2.13 release introduced FlexAttention to Apple Silicon, which means that models with Flash Attention dependencies (for ex Evo2) have an easier path to be forked + deployed on Apple Silicon. Just a PSA for anyone else who missed this!
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Brad Bowles 🧬 @bradbowles.bsky.social · 21/07/2026
I love close.city and I used it to pick the first neighborhood I lived in when I moved to Seattle. Thanks for putting so much love into this effort @nathenry.com !
close.city
Close - Travel Time Map
Close travel time map. Find neighborhoods where you can walk, bike, or take public transit to the amenities that matter most to you.
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Memento (spooky) Morty 🌙 @mementomorty.bsky.social · 18/07/2026
i think all raccoons should be shaped like that actually
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The Great Pumpkin Papers 🎃🎃🎃 @professormusgrave.bsky.social · 17/06/2026
Yes, self promotion sucks, academics, but if you don’t do it nobody will find out about your work. The point is to publish and be read, not publish and hope you are discovered by fate, lifted out of a humble and pure obscurity so that you may be both famous and retiring
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Rob Patro @robp.bsky.social · 14/06/2026
salmon 2.0 (the rust re-write) is now live! It's also the version you get if you install via bioconda. This is a from-scratch rewrite in rust, and the base for future development. I'll post a more detailed thread tomorrow, but you can read the docs here combine-lab.github.io/salmon/
combine-lab.github.io
salmon
Fast, accurate transcript quantification from RNA-seq reads.
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Mark Peifer (He, him) @peiferlabunc.bsky.social · 02/06/2026
Russell Vought, Director of the OMB, has issued a set of proposed changes that would dramatically alter federal grant funding. However, we can each take action to prevent these from taking effect. Here's how, a 🧵 🧪 1/n www.science.org/content/arti...
science.org
White House seeks to tighten political oversight of grantmaking
Sweeping proposed rule, now open for comments, would also restrict foreign collaborations and remove federal funding for open-access fees
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Ryan Hill @ryanhillart.bsky.social · 29/05/2026
Painting Zucks megayacht on Lake Union last night 🔥
Me standing at my easel in front of Mark Zuckerberg's megayacht Launchpad docked on Lake Union in SeattleClose up of the easel showing the painting of yacht in flames
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Dr. Kat Napaaqtuk❄️ @napaaqtuk.bsky.social · 30/05/2026
If you are going to comment on the proposed changes to how science is done in the US, please use this guide. The rules specify that you have to mention the number associated with the proposed changes, and this blog has those. Here is where to comment: www.federalregister.gov/documents/20...
federalregister.gov
Regulation for Federal Financial Assistance
The Office of Management and Budget (OMB) proposes to revise the Guidance for Federal Financial Assistance to improve government- wide policies and requirements related to the management of grants, co...
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Chenxin Li, PhD @chenxinli2.bsky.social · 30/05/2026
Dear colleagues, PLEASE submit a comment against OMB's proposed rule. Elizabeth wrote great guide on drafting a comment. To submit it, go to www.regulations.gov/search and search for OMB-2026-0034. It will take time & effort to write a good comment, but a worthwhile effort to save our profession.
regulations.gov
Regulations.gov
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Tami Gjorgjieva @tamigj.bsky.social · 18/05/2026
If you are interested in volunteering as a mentor, please apply ASAP at forms.gle/mBEZs98z4XMU... and no later than Friday, May 22. (We really appreciate early applications as we are actively matching mentors to mentees based on needs/expertise.) (4/n)
forms.gle
MERIT Mentor Interest Form 2026
Hey there, Thanks for your interest in serving as a mentor for the MERIT (Mentorship and Research Individualized Training) program between Stanford and the Tanzania Human Genetics Organization. The go...
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Jeffrey Pullin @jeffreypullin.bsky.social · 18/05/2026
tinyurl.com/reuxynmc Very excited to see this work I was a small part of published! We analysed two large scale colocalisation datasets: OpenTargets data and an analysis of immune-mediated disease GWAS/immune cell eQTLs seeking to understand the "colocalisation gap". Some highlights:
journals.plos.org
Design and interpretation of eQTL-GWAS colocalisation studies: Lessons from a large-scale evaluation
Author summary Most of the genetic variants associated with complex traits are located outside genes, limiting functional interpretation. Genetic colocalisation helps identify candidate causal genes b...
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Brad Bowles 🧬 @bradbowles.bsky.social · 15/05/2026
Incredibly disappointing to hear that this is even being considered.
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Christine Mayr @christinemayr.bsky.social · 08/05/2026
If you want to know what 3′UTRs with long conserved sequence stretches do, check out our BioRxiv preprint doi.org/10.64898/202.... They form functional intermolecular 3′UTR-3′UTR interactions that enable co-folding of proteins to rapidly induce transcriptional programs.
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Adam Auton @adamauton.bsky.social · 07/05/2026
Population geneticists! Come work at 23andMe! New role just posted. 23andme.wd5.myworkdayjobs.com/23/job/Palo-...
23andme.wd5.myworkdayjobs.com
Scientist, Population Genetics
23andMe is looking for a quantitative scientist with extensive experience in population genetics and statistical modeling of human genetics data to join our R&D team. You will leverage your expert...
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Reposted by Brad Bowles 🧬
Ali Seleit @aliseleit.bsky.social · 05/05/2026
(1/15) Thrilled to share new Evo-Devo work where we address the molecular, cellular & morphometric basis of an extreme axis segmentation program in the Japanese eel — an animal that forms 120 vertebrae.
biorxiv.org
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Erik Sontheimer 🇺🇸💙🇺🇦 @eriksontheimer.bsky.social · 29/04/2026
Site-specific, multi-kilobase insertions and over-writes in mammalian cells, without DSBs, HDR, recombinases, integrases, transposases, or active cell cycling? Using fully or predominantly single-stranded DNA donors? 1/15
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Karolin Luger @nucleosomepolice.bsky.social · 17/04/2026
there goes the central dogma, i guess. is nothing sacred anymore?
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Paul Markus Müller 🏳️‍🌈 @pm-mueller.bsky.social · 16/04/2026
Original image from 2011 of what I just had seen under the microscope when I ran into @oliverrocks.bsky.social’s office to show him. Turned out he’d observed this too, had no idea what it was either, but was just as stunned and curious as I was. This is how it all started... /1
Hela cell transfected with Cdc42 showing a bright and long rod structure spanning the whole cell. DIC image below shows the same rod structure with high contrast.
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Thiago Carvalho @cyrilpedia.bsky.social · 11/04/2026
Buckle up 'So let’s finally talk about peptides. And I don’t mean peptides as chemists and biologists understand them (short chains of amino acids) I mean “Peptides!”, the hot new wonder drugs that you can order by mail. Oh man.' www.science.org/content/blog...
science.org
Ah, Peptides. Where to Begin?
Ah, Peptides. Where to Begin?
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Mayor Katie B. Wilson @mayor.seattle.gov · 02/04/2026
Reporting for duty 🫡
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Gergely Orosz @gergely.pragmaticengineer.com · 27/03/2026
If you use GitHub (especially if you pay for it!!) consider doing this *immediately* Settings -> Privacy -> Disallow GitHub to train their models on your code. GitHub opted *everyone* into training. No matter if you pay for the service (like I do). WTH github.com/settings/cop...
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the beggars out of here getter @milesklee.bsky.social · 25/03/2026
Elizabeth Holmes and that little blood capsule she loved so much
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Sky Marchini @sky.skymarchini.net · 22/03/2026
I’ve been resistant to calling Americans/developed world more broadly politicans/voters “decadent”, but like if you keep knocking loadbearing pillars out of your economy for aesthetic reasons because you don’t care about the consequences - then there really isn’t any other word to use for it
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Goldy @goldy.horsesass.org · 13/03/2026
I just had surgery to remove an orange-sized cyst from inside my chest, and the thoracic surgeon and absolutely every RN & NAC has been an immigrant or child/grandchild of immigrants. The U.S. would have no healthcare system without immigration. We’re so fortunate these people made America home.
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Stegle Lab @steglelab.bsky.social · 12/03/2026
How do immune disease-relevant variants rewire gene regulation in CD4+ T cells? In a collaboration led by Daniel Schraivogel and Lars Steinmetz at @embl.org, we combined two large-scale CRISPRi screens (4.1M cells) to map the downstream cascades of thousands of SNPs.
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Brian Naughton @btnaughton.bsky.social · 11/03/2026
I wrote a primer on AI antibody design, published on Asimov press. www.asimov.press/p/antibody-d...
asimov.press
How to Design Antibodies
A step-by-step guide to making de novo binders.
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Jordy F. Botello @jbotello.bsky.social · 10/03/2026
Some molecular machines, like ribosomes, can persist for long periods of time in cells. Could molecular aging of ribosomes shape how proteins are made? In our new preprint we track ribosomes as they age in cells and uncover unexpected effects on translation (1/10) www.biorxiv.org/content/10.6...
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tomate 🍅 @jascha.ohai.social.ap.brid.gy · 03/03/2026
When someone says „Scientists do not want you to know“ you can dismiss everything from there on. Scientists want you to know. They are desperate that you know. They can’t shut up about what they found out and want you to know.
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Julia Rühle @juruehle.bsky.social · 04/03/2026
The main project of my PhD 🧬🔬 is out: we developed single-cell lentiMPRA, a lentivirus-based method to measure enhancer activity and transcriptomes at single-cell resolution. We then applied sc-lentiMPRA to fully synthetic enhancers 🧩... 🔗 doi.org/10.64898/202...
doi.org
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Marisa Kabas @marisakabas.bsky.social · 28/02/2026
congress sounds cool i wish it was real
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Brad Bowles 🧬 @bradbowles.bsky.social · 24/02/2026
Engineers will say “you can just do things” and then hand-roll the most cursed workflow language you’ve ever seen.
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Julien Roux @julienroux.bsky.social · 12/02/2026
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...
jobs.unibas.ch
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...
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Anthony Mathelier @amathelier.bsky.social · 12/02/2026
📢 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...
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nf-core @nf-co.re · 09/02/2026
🎉 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-co.re
nf-core
Details of past and future hackathons around nf-core.
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Yunha Hwang @microyunha.bsky.social · 04/02/2026
First, @tattabio.bsky.social is now on Bluesky!💙 and second, we launched mult-sequence CoSearch on SeqHub!
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Brad Bowles 🧬 @bradbowles.bsky.social · 08/02/2026
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.
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Gerry Brien @gerrybrien.bsky.social · 28/01/2026
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...
biorxiv.org
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
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