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.
Coding with #Python, #R, and #Nextflow.
Pinned
When you send a sample for sequencing, I’m actually one of the people who sorts through the reads. We just put them in a big pile on the table and all gather round. I like long reads because they’re easier to pick up with my hands.
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
✅ 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
#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
✅ 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
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
they’re saying you can still push to github if your heart is full of joy and whimsy, it’s true
Reposted by Brad Bowles 🧬🔬💻
Adding citations of people who might review the paper
November 14, 2025 at 10:06 AM
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!
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
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!
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...
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
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...
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...
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
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...
www.biorxiv.org/content/10.1...
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...
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
Dismantling the Institutional Review Board (IRB), that oversees all human subjects research, is bad. Really bad.
He does bioinformatics now.
October 16, 2025 at 3:04 PM
He does bioinformatics now.
Reposted by Brad Bowles 🧬🔬💻
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!
Email me!
Simons Postdoctoral Fellowships in Plant Biology
Simons Postdoctoral Fellowships in Plant Biology on Simons Foundation
www.simonsfoundation.org
October 14, 2025 at 12:45 PM
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!
Email me!
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).
Improved allele frequencies in gnomAD through local ancestry inference - Nature Communications
This study incorporates local ancestry into the Genome Aggregation Database (gnomAD) to improve allele frequency estimates for admixed populations, enhancing variant interpretation and enabling more accurate and equitable genomic research and clinical care.
www.nature.com
October 6, 2025 at 6:31 PM
📃 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).
Reposted by Brad Bowles 🧬🔬💻
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.”
September 30, 2025 at 1:52 AM
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.”
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...
www.federalregister.gov/documents/20...
Establishing a Fixed Time Period of Admission and an Extension of Stay Procedure for Nonimmigrant Academic Students, Exchange Visitors, and Representatives of Foreign Information Media
Unlike most nonimmigrant classifications, which are admitted for a fixed time period, aliens in the F (academic student), J (exchange visitor), and most I (representatives of foreign information media...
www.federalregister.gov
September 27, 2025 at 12:18 PM
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...
www.federalregister.gov/documents/20...
Reposted by Brad Bowles 🧬🔬💻
🖥️🧬🧪 Publication Alert!
I’m very excited to share our latest paper: “NovumRNA: Accurate prediction of non-canonical #tumor #antigens from RNA #sequencing data”
I’m very excited to share our latest paper: “NovumRNA: Accurate prediction of non-canonical #tumor #antigens from RNA #sequencing data”
September 26, 2025 at 12:13 PM
🖥️🧬🧪 Publication Alert!
I’m very excited to share our latest paper: “NovumRNA: Accurate prediction of non-canonical #tumor #antigens from RNA #sequencing data”
I’m very excited to share our latest paper: “NovumRNA: Accurate prediction of non-canonical #tumor #antigens from RNA #sequencing data”
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 🧵]
September 24, 2025 at 8:33 PM
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
╱╱┏┳┓╭╮┏┳┓ ╲╲
▔▏┗┻┛┃┃┗┻┛▕▔
┃┃╱╲ In this
┃╱╱╲╲ house
╱╱╭╮╲╲ we pretend
▔▏┗┛▕▔ that hg38
╱▔▔▔▔▔▔▔▔▔▔╲
does not exist
╱╱┏┳┓╭╮┏┳┓ ╲╲
▔▏┗┻┛┃┃┗┻┛▕▔
September 24, 2025 at 9:52 PM
┏┓
┃┃╱╲ In this
┃╱╱╲╲ house
╱╱╭╮╲╲ we pretend
▔▏┗┛▕▔ that hg38
╱▔▔▔▔▔▔▔▔▔▔╲
does not exist
╱╱┏┳┓╭╮┏┳┓ ╲╲
▔▏┗┻┛┃┃┗┻┛▕▔
┃┃╱╲ 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...
jamanetwork.com/journals/jam...
Acetaminophen Use During Pregnancy and Children’s Risk of Autism, ADHD, and Intellectual Disability
This nationwide cohort study with sibling control analysis examines the association of acetaminophen use during pregnancy with children’s risk of autism, ADHD, and intellectual disability.
jamanetwork.com
September 23, 2025 at 3:04 AM
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.
September 23, 2025 at 1:32 AM
I was unsurprised to see that the FDA announcement on leucovorin ... doesn't include a single peer-reviewed citation.
Reposted by Brad Bowles 🧬🔬💻
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.
I strongly recommend that you read @gorskon.bsky.social’s excellent work on the topic before the fearmongering begins.
VAERS and plasmid DNA "contamination" of COVID-19 vaccines: The nonsense continues
A new preprint is making the rounds falsely claiming to correlate "contamination" of COVID-19 vaccines with plasmid DNA to VAERS reports.
www.respectfulinsolence.com
September 18, 2025 at 2:50 PM
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.
I strongly recommend that you read @gorskon.bsky.social’s excellent work on the topic before the fearmongering begins.
Reposted by Brad Bowles 🧬🔬💻
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)
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)
September 18, 2025 at 10:54 AM
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)
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)
Reposted by Brad Bowles 🧬🔬💻
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...
Turns out, yes!
Protein Language Models Capture Structural and Functional Epistasis in a Zero-Shot Setting
www.biorxiv.org/content/10.1...
September 18, 2025 at 12:01 AM
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...
Turns out, yes!
Protein Language Models Capture Structural and Functional Epistasis in a Zero-Shot Setting
www.biorxiv.org/content/10.1...
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
Ie: it's not us (Samtools team)! Be warned
September 15, 2025 at 8:40 AM
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
Ie: it's not us (Samtools team)! Be warned
Reposted by Brad Bowles 🧬🔬💻
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...
Research Laboratory Job: Postdoctoral Research Fellow - Computational Biologist at Dana-Farber Cancer Institute in 450 Brookline Ave, Boston, MA
Postdoctoral Research Fellow - Computational Biologist job
careers.dana-farber.org
September 15, 2025 at 10:57 AM
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 🫠
Minnesota Governor Tim Walz has issued an executive order to protect COVID vaccine access.
Link: content.govdelivery.com/attachments/...
Link: content.govdelivery.com/attachments/...
September 14, 2025 at 9:16 PM
Was just refused a COVID booster at my local Walgreens despite this change in policy 🫠