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

Great resource, out today in @natneuro.nature.com: An integrated single-nucleus and spatial transcriptomics atlas reveals the molecular landscape of the human hippocampus @stephaniehicks.bsky.social @martinowk.bsky.social & colleagues 🧪🧠🧬 www.nature.com/articles/s41...

Hot take: I think the word “spatial” in spatial (transcript)-omics does not make any sense.

A recent paper reveals a surprising insight. The length of the cell cycle in a particular tissue determines the oncogenic transformation capacity of particular oncogenes, with tissues with shorter cell cycles most susceptible 3/n

T cells must preserve their structural integrity while migrating through dense environments. A central actin pool under confinement balances forward propulsion with shape integrity to protect nucleus from DNA damage @sciimmunology.bsky.social www.science.org/doi/10.1126/...

Single-cell polygenic risk scores dissect cellular and molecular heterogeneity of complex human diseases go.nature.com/3H6pAlr

Hey, it's out! doi.org/10.1016/j.ce... Aligning Big Brains and Atlases, ABBA in short, is published in Cell Reports @cp-cellreports.bsky.social . @biancasilvalab.bsky.social's lab added an analysis pipeline on top of it (BraiAn) and did all the relevant biological work. What is it ? Short thread:

🎉 The revised version of CORNETO, our unified Python framework for knowledge-driven network inference from omics data, is published in peer reviewed form 🔗 Paper: www.nature.com/articles/s42... 📖 News & Views: www.nature.com/articles/s42... 💻 Code: corneto.org 🧵 Thread 👇

What a wonderful story with a super powerful message: Tumor progression can be explained just by tumor and TME reshaping each other via cell-cell communication. No additional mutations required.

Happy to share a new preprint! W/ @zachgold.bsky.social, Haylee Oyler, Jonathan Levine and @nathanjbkraft.bsky.social. We use a spatially explicit experimental design to ask: do higher-order interactions structure the dynamics of annual plant communities? Link: www.biorxiv.org/content/10.1... 🧵

@astar-gis.bsky.social teams up with 10x Genomics to revolutionize drug discovery for #TISHUMAP! Using AI & spatial biology, this project will analyze thousands of tissue samples to fast-track drug target discovery in cancer & inflammatory diseases. A major step toward precision medicine! #Genomics

RNALens: Study on 5' UTR Modeling and Cell-Specificity https://www.biorxiv.org/content/10.1101/2025.07.20.665722v1

“treatment with X modestly reduced the levels of these cytokines, but the differences were not statistically significant” Please stop

I’m very happy.

Our latest work is now live on bioRxiv! We use copy number variation inference to uncover tumor clonality from imaging-based spatial transcriptomics data. Check it out: doi.org/10.1101/2025...

The UCSC genome browser team are a great lot and it’s nice to see them celebrated in this article. There are a couple of quotes from me in there, although Michael picked my more reserved comments - I recall gushing quite a lot more about magnificent genomics hippies www.nature.com/articles/d41...