Brad Bowles 🧬🔬💻

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.

A cloning strategy as depicted in the OpenCloning website

#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

A photo of Katie Wilson seated in a wooden chair beside a white brick fireplace smiling at the camera with her hands folded

an image of the election results from King County

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!

Specificity, length and luck drive gene rankings in association studies - Nature Genetic association tests prioritize candidate genes based on different criteria.

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...

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...

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...

My two cents is that providing a GitHub repo with model code, plus making the model command-line executable in some way (ie a Bash, R script, etc) goes a long way to making your model portable. A list of dependencies or a containerization is a great add on as well!

Dismantling the Institutional Review Board (IRB), that oversees all human subjects research, is bad. Really bad.

A cat at a computer, classic internet stuff.

He does bioinformatics now.

Simons Postdoctoral Fellowships in Plant Biology Simons Postdoctoral Fellowships in Plant Biology on Simons Foundation

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!

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.

📃 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).

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.”

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...

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...

🖥️🧬🧪 Publication Alert!

I’m very excited to share our latest paper: “NovumRNA: Accurate prediction of non-canonical #tumor #antigens from RNA #sequencing data”

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.

FDA Takes Action to Make a Treatment Available for Autism Symptoms The U.S. Food and Drug Administration today initiated the approval of leucovorin calcium tablets for patients with cerebral folate deficiency (CFD), a neurological condition that affects folate (a vit...

Full link: www.fda.gov/news-events/...

I was unsurprised to see that the FDA announcement on leucovorin ... doesn't include a single peer-reviewed citation.

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.

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)

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...

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

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

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 🫠

UCSC Genome Browser User Satisfaction Survey | SurveyMars I have posted a survey titled 'UCSC Genome Browser User Satisfaction Survey' on SurveyMars. Please help me by filling it out. Thank you very much!

Please take a moment to tell us how you use the Genome Browser: surveymars.com/q/mnb...

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