Today is a big day. After many years of work, I’m excited to finally share a paper describing a novel approach to identifying potential breakthroughs in biomedical research, up to twelve years before the breakthrough itself occurs. 1/15

🧮 Just out in Bioinformatics Advances: “FroM Superstring to Indexing: A space-efficient index for unconstrained k-mer sets using the Masked Burrows-Wheeler Transform (MBWT)”  Full article available: https://doi.org/10.1093/bioadv/vbaf290  Authors include: @pavelvesely.bsky.social, @brinda.eu

History will remember Claudia Sheinbaum as the idiot who demanded a government to say sorry for stuff that happened 500 years ago, while taking selfies with a nazi-pedophile. elpais.com/deportes/mun...

Selective RNA sequestration in biomolecular condensates directs cell fate transitions - @distefanolab.bsky.social @brumbaugh-lab.bsky.social go.nature.com/3X215du

Berlin’s senate invests >12 mio EUR for 3 NFL games in Berlin, at a time where they cut millions at the universities that are already underfunded, with collapsing buildings. They definitely seems to have priorities that are not mine. www.tagesspiegel.de/berlin/senat...

This is pure bullshit. You don’t need to run 200 LLM agents for >8 hours to do DE, GSEA and generate a couple of heatmaps. And if you do, just spend 2 weeks learning bioinformatics and you won’t need to give money to a company selling snake oil. arxiv.org/pdf/2511.02824

🚨 We're hiring! 🚨 Our lab at the University of Málaga, Spain🇪🇸 is looking for a bioinformatician researcher for a postdoc position (1+1 years). Check the ad, and if you're interested, get in touch! 📅 Starting date early 2026, with some flexibility. 🙏Please, RT!

My humble advice to 10X: Why don’t you invest a bit more on R&D and a little bit less on legal? www.genomeweb.com/business-new...

When I was an undergrad, I saw a talk by Oliver Sacks about music. During the Q&A, someone asked Sacks if he thought science would reveal the deepest mysteries of art. Sacks (a rare humanist among scientists) said that he doubted it, at which Eric Kandel (the host) leaped up and grabbed the mic.

What is RNA velocity in situ? ChatGPT kept getting it wrong... So I made this video explaining how RNA velocity in situ infers gene expression dynamics by distinguishing nuclear vs. cytoplasmic expression in spatial transcriptomics data: youtu.be/z9Oxf1hvum0 #AcademicSky

Just published an interactive article about a magical algorithm known as the Burrows-Wheeler Transform, which powers sequence alignment tools like bowtie and bwa: sandbox.bio/concepts/bwt It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.

Ca n'est pas si souvent, un article publié dans Nature met ma communauté à l'honneur (la bioinformatique des séquences). Je vous raconte ? www.nature.com/articles/d41...

How does a “universal” transcription factor evolve to do species-specific jobs? Our new preprint reveals how divergence in TBP’s domains shapes transcriptional specialization across eukaryotes. Read it here 👉 www.biorxiv.org/content/10.1... #MolecularEvolution #Transcription

Preliminary results show that the current framework of "AI" makes ppl less likely to help or seek help from other humans, or to seek to soothe conflict, and that people actively prefer that framework to any others, literally serving to make them more dependent on it.

Israel is a terrorist state.

SQLite que no pase hambre

We are thrilled to announce that our NEW Large Language Model will be released on 11.18.25.

1/4 Hash functions in genomic sequence analysis (tinyurl.com/4kk9ccmt) : a new survey written together with Ke Chen, Xiang Li, Qian Shi, and Mingfu Shao. Before submitting it, we are posting it online to get feedback from the community.

🔴 ÚLTIMA HORA | La mayoría de los países abandonan la Asamblea General de la ONU a la llegada de Netanyahu social.elpais.com/njzv3

Mr. Big Ears said at the UN today, “Thanks to the efforts of our intelligence service, this message is being streamed to every Gazan’s phone.”

We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics. www.biorxiv.org/content/10.1... (1/n)

IMSLP (imslp.org; the biggest public library for classical music) generated >4 TB of data over the last 20 years. Open-ST (rajewsky-lab.github.io/openst) can generate that from a 1x3x4 mm piece of human tissue in two days.

How come different people giving the same prompt to ChatGPT get different answers? A new article from ThinkingMachines explains why LLMs are nondeterministic, and it largely comes down to how parallelization and precision are handled. 🧵

A machine learning model can sort people with myalgic encephalomyelitis/chronic fatigue syndrome from healthy controls with 77% accuracy by sequencing the cell-free RNA in their plasma, suggesting a test for the condition may be on the horizon. In PNAS: www.pnas.org/doi/10.1073/...

This is how generative A.I. could be used to design far better, more potent mRNAs (linear and circular) for the future for genome editing, engineered T cells, cancer therapy, vaccines www.science.org/doi/10.1126/... @science.org

Adding layers of information to scRNA-seq data using pre-trained language models https://www.biorxiv.org/content/10.1101/2025.08.23.671699v1

el futuro está siendo lo que siempre soñé que sería: que al buscar algo en google te salga arriba del todo una puta chorrada de mierda de los cojones.

Deep-tissue transcriptomics and subcellular imaging at high spatial resolution🔓 pmc.ncbi.nlm.nih.gov/articles/PMC...

We're excited to present our latest article in Nature Machine Intelligence - Boosting the predictive power of protein representations with a corpus of text annotations. Link: www.nature.com/articles/s42... [1/4]

SpatialFinder: A Human-in-the-Loop Vision-Language Framework for Prioritizing High-Value Regions in Spatial Transcriptomics https://www.biorxiv.org/content/10.1101/2025.08.16.670684v1

Stereo-cell is a DNA nanoball array-based method that enables scalable, spatially resolved single-cell sequencing across diverse cell types and sizes with multimodal integration capabilities. #NBThighlight www.science.org/doi/10.1126/...

Automated optogenetic control of hundreds of cells in parallel. Each cell is individually steered, collectively acting as a "tissue printer". Preprint & code out! www.biorxiv.org/content/10.1...

Three-dimensional spatial transcriptomics at isotropic resolution enabled by generative deep learning [new] AI maps 3D genes from 2D data. Modeling enables isotropic resolution, revealing gradients.

Novel Predictive Spatial Biomarker in Non-Small Cell Lung Carcinoma: The Diversity of Niches Unlocking Treatment Sensitivity (DONUTS) https://www.biorxiv.org/content/10.1101/2025.08.13.665980v1

for the love of all that you hold dear, no. A lot of bioinformatics is already blind plug-in play and making this easier is just going to lead to even shittier analysis.

My generation had to deal with datasets where Excel had autocorrected gene names to dates. Future generations are going to have to deal with the hallucinations of slopbots.

FlyBase, a Drosophila database, will lose a third of its team in early October because the Harvard grant that covered the employees’ salaries was canceled. Scientists warn that losing FlyBase could devastate fly research. By @claudia-lopez.bsky.social www.thetransmitter.org/community/ha...

“Nobody with intellectual integrity should still believe that pure scaling will get us to AGI.” Amazing piece by @garymarcus.bsky.social (IMO, also applies to the FM for biology bs) garymarcus.substack.com/p/gpt-5-over...

"PhD-level experts in your back pocket" is a completely nonsensical description of AI but a pretty good description of social media if you follow the right people

Likening PhD holders to a (non-functional) algorithm is a form of dehumanisation & anti-intellectualism that is a bellwether for contemporary fascism. Essentially it's a typical — if not the archetypal — first step towards fascism: to dehumanise, deskill, defund, and, ultimately, fire the academics.

🧬🧬🧬 New review from the lab: Evolution of comparative transcriptomics: biological scales, phylogenetic spans, and modeling frameworks authors.elsevier.com/sd/article/S... By @mattezambon.bsky.social & @fedemantica.bsky.social, together with @jonnyfrazer.bsky.social & Mafalda Dias.

@ukbiobank.bsky.social just dropped their article on whole genome analysis of 490K human samples. Illumina sequencing and DRAGEN to help power the analysis of all those samples www.nature.com/articles/s41...

Imagine if Bach had composed a Stabat Mater.

An analysis shows that current deep learning models do not beat linear baselines in predicting gene perturbation effects, thus emphasizing the importance of further method development and evaluation. @const-ae.bsky.social @wkhuber.bsky.social @s-anders.bsky.social www.nature.com/articles/s41...

Maria João Pires always makes me smile. Always.

Beautiful spatial transcriptomics of developing meninges and meningiomas. Hints into the origins of meningiomas arising from the dural border 🤩🧐

Next up was @tatsuyanobori.bsky.social who gave a fantastic talk on how his lab is unraveling plant-microbe interactions utilizing cutting-edge tools spatial transcriptomics (MERFISH) and multiplexed 3D gene expression (PHYTOMap). A compelling story brought to life by stunning visuals. #pb2025