Pablo Marin-Garcia

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

The reports of Bluesky’s death have been greatly exaggerated

The human pangenome continues to grow and improve! Release 2 is here! Click through for the details, but this is a pretty amazing dataset including not just the phased assemblies, but PacBio HiFi, ONT Ultralong, Dovetail/Illumina Hi-C, PacBio Kinnex, and Illumina WGS for all samples

🧬 Excited to share our poster at The 3rd International Electronic Conference on Biomedicines:

“Comprehensive Analysis of Genetic and Environmental Factors Influencing Type 2 Diabetes in the Spanish Population with NGS and the SEQENS Algorithm”

DOI: 10.13140/RG.2.2.35970.59846

Now known as one of the most cited "recent" (last 2 years?) papers in Systematic Biology!

The email I received says AE @wrightam.bsky.social is the first author though hahaha. We and the 22 coauthors and ALL of the crabs can all celebrate this much needed good news! 🦀🧪

RFK Jr and Statistics:

Internet sleuths have discovered that the "You Wouldn't Steal a Car" anti-piracy campaign pirated its font and did not pay for its commercial use.

(Read more: Sky News)

If you want to check if a human gene has copy-number changes or lands in a complex region, try pangene.bioinweb.org. Recently updated with more and better assemblies.

Tennis Balls xkcd.com/3080

PhD Timeline xkcd.com/3081

What memories .... Murrell's book was my R graphics bible of that time. As a literacy programming fan, I moved later to anything that follows "the grammar of graphics" but all this makes sense only if you understand the low levels of how a graphic is constructed.

If image processing was about bubbles... 🫧

Transcriptomics in the era of long-read sequencing Nature Reviews Genetics, Published online: 28 March 2025; doi:10.1038/s41576-025-00828-zAdvances in long-read sequencing are driving the implementation of these technologies for transcriptome profiling. The authors provide a comprehensive guide to long-read RNA sequencing, including experimental and computational tools, current applications, challenges and opportunities.

FYI: New online! Transcriptomics in the era of long-read sequencing

Technogeek friends... I'm looking for a way to build a WebAssembly display library or framework that would let me draw and layout gene regulatory network things. Happiest if it interfaces nicely with Rust or Python, ofc. Any tips?

Minimap2-2.29 released with the support of short RNA-seq read alignment. More explanation and results here: lh3.github.io/2025/04/18/s...

Efficient near telomere-to-telomere assembly of Nanopore Simplex reads Telomere-to-telomere (T2T) assembly is the ultimate goal for de novo genome assembly. Existing algorithms capable of near T2T assembly all require Oxford Nanopore Technologies (ONT) ultra-long reads w...

Preprint on hifiasm Nanopore-only assembly. Led by Haoyu Cheng: www.biorxiv.org/content/10.1...

Review
@brandontwchen.bsky.social
@lyssiotislab.bsky.social
Mitochondria-organelle crosstalk in establishing compartmentalized metabolic homeostasis
www.cell.com/molecular-ce...

CoverM: Read alignment statistics for metagenomics AbstractSummary. Genome-centric analysis of metagenomic samples is a powerful method for understanding the function of microbial communities. Calculating r

CoverM is published!

CoverM: Read alignment statistics for metagenomics academic.oup.com/bioinformati... #jcampubs

Efficient and robust search of microbial genomes via phylogenetic compression Nature Methods - Phylogenetic compression achieves performant and lossless compression of massive collections of microbial genomes, facilitating fast BLAST-like search and versatile alignment tasks.

Our latest paper, in which @brinda.eu (along with @zaminiqbal.bsky.social and others) introduces phylogenetic compression for storage and search of enormous microbial genome libraries, was published today in @naturemethods.bsky.social:

rdcu.be/eg4OA

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Tariffs xkcd.com/3073

Radial tree diagram displaying all Marvel films by series. Each film is shown as a circle and sized by its total box office income. Each series (and its films) has a dedicated color. The most successful series is Avengers, followed by Spider Man and Black PantherRadial tree diagram displaying all Marvel films by series. Each film is shown as a circle and sized by its total box office income. Each series (and its films) has a dedicated color. The most successful series is Avengers, followed by Spider Man and Black Panther

You want to create a bespoke graph in python? It's probably possible - with a bit of time and perserverance.🤓

Meet a radial tree diagram of Marvel film box office performance. 100% made in python using numpy, #matplotlib and bezier curves. Dont judge the code 😅 github.com/Lisa-Ho/smal...

#dataviz

Terrific paper by post-doc @aclark.bsky.social in @plos.org
Comp Biol. This tutorial enables students and biologists to simulate biological networks with our tool Netflux, no programming required! #sysbio #cardiosky 🧪

Bronze statues of a duck and her ducklings. They each have a little white sign

Adorable. The Boston ducks have protest signs #handsoff

‘Hands Off’ protests take off across US to oppose Trump agenda – live More than a thousand events expected in a show of defiance against US president’s ‘authoritarian overreach’

www.theguardian.com/world/live/2...