Pablo Marin-Garcia
@pablomaring.bsky.social
Bioinformatician and eHealth consultant
Reposted by 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...
December 20, 2024 at 10:55 AM
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...
Reposted by Pablo Marin-Garcia
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...
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...
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.
www.nature.com
September 10, 2025 at 9:12 AM
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...
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...
Reposted by Pablo Marin-Garcia
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...
blog.genesmindsmachines.com/p/how-do-bic...
How do bicycles work?
Conservation of angular momentum plays a major role, but why is angular momentum conserved?
blog.genesmindsmachines.com
September 16, 2025 at 2:03 PM
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...
blog.genesmindsmachines.com/p/how-do-bic...
Reposted by Pablo Marin-Garcia
Tanehisi Coates writes with a clarity that is rare. This reflection is worth reading.
www.vanityfair.com/news/story/c...
www.vanityfair.com/news/story/c...
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.
www.vanityfair.com
September 17, 2025 at 2:15 PM
Tanehisi Coates writes with a clarity that is rare. This reflection is worth reading.
www.vanityfair.com/news/story/c...
www.vanityfair.com/news/story/c...
Reposted by Pablo Marin-Garcia
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...
Learn more and take the survey 👉 www.carpentries.org/blog/2025/09...
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...
www.carpentries.org
September 17, 2025 at 12:21 PM
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...
Learn more and take the survey 👉 www.carpentries.org/blog/2025/09...
Reposted by Pablo Marin-Garcia
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...
📆 First session: Getting Started with Positron: Quick Tour and Community Q&A on September 24th! Register here - events.zoom.us/ev/Ajss5j9Ve...
September 16, 2025 at 5:47 PM
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...
📆 First session: Getting Started with Positron: Quick Tour and Community Q&A on September 24th! Register here - events.zoom.us/ev/Ajss5j9Ve...
Reposted by Pablo Marin-Garcia
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...
jtibs.substack.com/p/if-all-the...
If all the world were a monorepo
The R ecosystem and the case for extreme empathy in software maintenance
jtibs.substack.com
September 14, 2025 at 11:29 PM
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...
jtibs.substack.com/p/if-all-the...
Reposted by Pablo Marin-Garcia
Naughty Grok must be taught not to tell the truth
September 14, 2025 at 9:18 PM
Naughty Grok must be taught not to tell the truth
Reposted by Pablo Marin-Garcia
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...
www.nature.com/articles/s41...
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
www.nature.com
September 13, 2025 at 7:20 PM
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...
www.nature.com/articles/s41...
How to effectively talk about political violence. Bernie Sanders nailed it again
youtu.be/HlIvH6ozvv4?...
youtu.be/HlIvH6ozvv4?...
In Wake of Charlie Kirk Murder, Sen. Bernie Sanders Addresses Rising Political Violence in America
YouTube video by Senator Bernie Sanders
youtu.be
September 13, 2025 at 6:06 PM
How to effectively talk about political violence. Bernie Sanders nailed it again
youtu.be/HlIvH6ozvv4?...
youtu.be/HlIvH6ozvv4?...
Reposted by Pablo Marin-Garcia
#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
Snakemake
snakemake.github.io
August 29, 2025 at 12:54 PM
#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
Reposted by Pablo Marin-Garcia
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
#academicsky #edusky #psychsky
August 23, 2025 at 1:24 PM
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
#academicsky #edusky #psychsky
Reposted by Pablo Marin-Garcia
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.
August 23, 2025 at 6:16 PM
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.
Reposted by Pablo Marin-Garcia
🚨 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.
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.
August 20, 2025 at 10:34 AM
🚨 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.
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.
Reposted by Pablo Marin-Garcia
Reposted by Pablo Marin-Garcia
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/...
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
academic.oup.com
August 15, 2025 at 3:56 PM
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/...
Reposted by Pablo Marin-Garcia
"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/...
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?
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...
journals.biologists.com
August 15, 2025 at 4:16 PM
"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/...
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/...
Reposted by Pablo Marin-Garcia
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...
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...
August 15, 2025 at 8:30 PM
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...
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...
Reposted by Pablo Marin-Garcia
August 14, 2025 at 6:05 PM
Reposted by Pablo Marin-Garcia
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.
Attempts to get Amazon to take these down have gone nowhere.
August 14, 2025 at 10:11 PM
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.
Attempts to get Amazon to take these down have gone nowhere.
Reposted by Pablo Marin-Garcia
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
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
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
academic.oup.com
August 14, 2025 at 1:10 PM
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
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
Reposted by Pablo Marin-Garcia
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.
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.
But how do AI videos actually work? | Guest video by @WelchLabsVideo
YouTube video by 3Blue1Brown
youtu.be
July 25, 2025 at 12:27 PM
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.
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.
Reposted by Pablo Marin-Garcia
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...
www.biorxiv.org/content/10.1...
July 6, 2025 at 5:05 PM
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...
www.biorxiv.org/content/10.1...
Reposted by Pablo Marin-Garcia
APAV: An advanced pangenome analysis and visualization toolkit
journals.plos.org/ploscompbiol...
journals.plos.org/ploscompbiol...
July 13, 2025 at 4:22 PM
APAV: An advanced pangenome analysis and visualization toolkit
journals.plos.org/ploscompbiol...
journals.plos.org/ploscompbiol...