@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
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.
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.
I wrote a primer on AI antibody design, published on Asimov press.
www.asimov.press/p/antibody-d...
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...
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.
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...
congress sounds cool i wish it was real
Funny how “doing things” never seems to include “writing documentation.”
Engineers will say “you can just do things” and then hand-roll the most cursed workflow language you’ve ever seen.
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...
📢 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...
🎉 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...
First, @tattabio.bsky.social is now on Bluesky!💙 and second, we launched mult-sequence CoSearch on SeqHub!
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.
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!
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.
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:
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
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
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...