Pablo Marin-Garcia

Weekly Recap (Dec 2024, part 3): The Evo model for sequence modeling and design, AI agents in biomedical research, improving bioinfo software with teamwork, VCF manipulation, GWAS Catalog, designing+engineering synthetic genomes doi.org/10.59350/p4r...

Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.

Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...

How do bicycles work? Conservation of angular momentum plays a major role, but why is angular momentum conserved?

A post about Emmy Noether, one of the most influential mathematical physicists of the 20th century, who rarely gets the recognition she deserves.
blog.genesmindsmachines.com/p/how-do-bic...

Charlie Kirk, Redeemed: A Political Class Finds Its Lost Cause By ignoring the rhetoric and actions of the Turning Point USA founder, pundits and politicians are sanitizing his legacy.

Tanehisi Coates writes with a clarity that is rare. This reflection is worth reading.
www.vanityfair.com/news/story/c...

Where are the ubam nowadays? GATK promoted them long time ago

We're Almost There: Share Your Input on The Carpentries' New Membership Model The Carpentries is evolving — and so is our membership program. To remain a strong, sustainable community of practice, we are finalising a new model that reflects today’s realities, tomorrow’s opportu...

Help us put the final touches to the future of Carpentries membership. Share your feedback on programs, services, and community in our survey today.

Learn more and take the survey 👉 www.carpentries.org/blog/2025/09...

Over the next few months, we will be hosting a Workflow Demo Series to cover everything you'll need to know as you explore Positron firsthand.

📆 First session: Getting Started with Positron: Quick Tour and Community Q&A on September 24th! Register here - events.zoom.us/ev/Ajss5j9Ve...

If all the world were a monorepo The R ecosystem and the case for extreme empathy in software maintenance

Really insightful post from Julie Tibshirani (spotted in LinkedIn, can't find on Bsky) reflecting on #rstats 's unique governance structure and what can be learned for other languages

jtibs.substack.com/p/if-all-the...

Naughty Grok must be taught not to tell the truth

Glucagon-like Peptide-1 receptor agonists as emerging therapeutics in bipolar disorder: a narrative review of preclinical and clinical evidence - Molecular Psychiatry Molecular Psychiatry - Glucagon-like Peptide-1 receptor agonists as emerging therapeutics in bipolar disorder: a narrative review of preclinical and clinical evidence

We know GLP-1 drugs reduce brain inflammation. But I didn't anticipate bipolar disorder as a possible indication in the future
www.nature.com/articles/s41...

YouTube video by Senator Bernie Sanders In Wake of Charlie Kirk Murder, Sen. Bernie Sanders Addresses Rising Political Violence in America

How to effectively talk about political violence. Bernie Sanders nailed it again
youtu.be/HlIvH6ozvv4?...

#Snakemake 9.10 has been released. The major change is that it now supports scheduling plugins. By that your scheduling algorithm research becomes immediately usable with thousands of workflows by thousands of users. snakemake.github.io

Hey friends! Are you interested in the science of learning? Then check out all the cool SOL researchers in this starter pack! go.bsky.app/CBPm1dV

#academicsky #edusky #psychsky

Google Sign in is dunkin cereal milk gluten fr Al Overview +1 No, Dunkin' Cereal Milk is not gluten-free because it contains milk, which is a common allergen, and as a result, it is not suitable for those with celiac disease or gluten intolerance. However, coffee drinks, dairy milk, and non-dairy milks like oat, almond, and coconut milk are naturally gluten-free at Dunkin'.

In 25 years, every business school in the country will be doing case studies about how a long defunct company known as “Google” once had an unbeatable lock on online information retrieval and then started doing shit like this.

🚨 Imagine a bacterium that refuses to follow the textbook:
It grows as tangled filaments, divides unevenly, reshapes its own membranes… and even builds grappling hooks.
Meet Litorilinea aerophila — and here’s why it blew our minds.

reddit post screenshot. what’s the point of vibe coding if i still have to pay a dev to fix it? what’s the point of vibe coding if at the end of the day i still gotta pay a dev to look at the code anyway. sure it feels kinda cool while i’m typing, like i’m in some flow state or whatever, but when stuff breaks it’s just dead weight. i cant vibe my way through debugging, i cant ship anything that actually matters, and then i’m back to square one pulling out my wallet for someone who actually knows what they’re doing. makes me think vibe coding is just roleplay for guys who want to feel like hackers without doing the hard part. am i missing something here or is it really just useless once you step outside the fantasy

you’re so close

Prevalence of errors in lab-made plasmids across the globe Abstract. Plasmids are indispensable in life sciences research and therapeutics development. Currently, most labs custom-build their plasmids. As yet, no s

Friends don’t use friend’s plasmids without sequencing them. For some types of plasmids from academic and industrial labs, up to 40% contained mutations academic.oup.com/nar/article/...

Why would anyone want to be a scientist? It is difficult to fathom why anyone intelligent enough to be a scientist would actually choose to be one. Doing good science requires the utmost exertion of body, mind and spirit, yet is consistently...

"why [would] anyone intelligent enough to be a scientist choose to be one [given] the unfavorable risk-to-reward ratio "?

One of the most intelligent people you could meet offers some answers: having ideas, watching them develop, and sharing them journals.biologists.com/jcs/article/...

Why would anyone want to be a scientist? There are the pleasures of:
1. Having the initial idea or insight,
2. Watching the idea develop into new experiments or a new model, and
3. Telling others.
Martin A. Schwartz
Check out also his Night Science podcast episode: podcasts.apple.com/us/podcast/7...

Defending US democracy: the role of scientists
@science.org
www.science.org/doi/10.1126/...

FRAUD ALERT: I have nothing to do with these phony books using my name on the cover. I have not written a memoir or partnered/inspired any cookbooks!
Attempts to get Amazon to take these down have gone nowhere.

Oncodrive3D: fast and accurate detection of structural clusters of somatic mutations under positive selection Abstract. Identifying the genes capable of driving tumorigenesis in different tissues is one of the central goals of cancer genomics. Computational methods

New paper from our lab - ‪@bbglab.bsky.social‬.

Oncodrive3D: fast and accurate detection of structural clusters of somatic mutations under positive selection

academic.oup.com/nar/article/...

Kudos to Stefano, Olivia, @fmuinos.bsky.social and Abel

YouTube video by 3Blue1Brown But how do AI videos actually work? | Guest video by @WelchLabsVideo

New video on the details of diffusion models: youtu.be/iv-5mZ_9CPY

Produced by Welch Labs, this is the first in a short series of 3b1b this summer. I enjoyed providing editorial feedback throughout the last several months, and couldn't be happier with the result.

Unbiased whole genome comparison of Pan paniscus (bonobo) and Homo sapiens (human) through a novel sequence match-based approach. #WGS #GenomeComparison #Genomics #Bioinformatics @biorxiv-bioinfo.bsky.social 🧬 🖥️
www.biorxiv.org/content/10.1...

Fig 1. Overview of APAV pipeline. (A) Workflow for PAV calling and consequent analysis. The coordinates of the target region are first extracted from a GFF file or BED file. The coverage of both the whole region and the element region is calculated based on the BAM files. The PAVs are determined according to their coverage, and interactive reports are generated. Subsequent analyses can be performed using the PAV tables, including genome size estimation, classification and statistical analysis, phenotypic association analysis, and visualization of elements. (B) Interactive analysis reports. The PAV report presents PAV tables, coverage data, pangenome sequences, genome annotation, and sequence alignments. The sample report presents sample tables, phenotype information, and real-time PAV analysis results. https://doi.org/10.1371/journal.pcbi.1013288.g001

APAV: An advanced pangenome analysis and visualization toolkit
journals.plos.org/ploscompbiol...

Header text: "HEY YOU! YES YOU! TAKE THIS SHIT OUT OF LINKS!" This is followed by a couple example urls, with a red square highlighting the sections with source identifiers. The rest of the text is as follows: Source identifiers are used to track your activity on a site. Where you came from, what device you use, and even who you talk to. Whether it's written clearly in the url or tied to a random string of characters, it's assigned to your activity. When you send a link containing a source identifier to somebody and they click it, it signals to the website that you two are connected. And that data goes right back to the website operators, and thus their advertisers. Whenever you select "share" or "copy link" on a social app or website, it creates a link like this. If you give even the smallest shit about online privacy, it's important to remove them. Everything after the "?" symbol can be removed without issue, especially sections starting with "si=" or "utm_source="

I saw an infographic a couple years ago about how to remove source identifiers from links and why it's important, but I can't find it again and too many people I know are sending me links with them so here's an infographic straight from the oven

Caine-Hackman!!

Join the Bioconductor Developer Forum - R & Rust in Bioinformatics

🗓️ 28 July, 17:00–18:00 CEST

Discussing extendr, Rust packages, and real-world use cases.

🔗 blog.bioconductor.org/posts/2025-0...

#Bioconductor #RStats #RustLang #Bioinformatics

Indeed