DNA methylation signatures of mismatch repair-deficient colorectal cancer www.biorxiv.org/content/10.64898/2026.04...

Scientists invented a fake disease. AI told people it was real Bixonimania doesn’t exist except in a clutch of obviously bogus academic papers. So why did AI chatbots warn people about this fictional illness?

This is quite extraordinary- scientists set a kind of trap for AI chat bots by inventing a fake disease. AI told people it was real and… the deliberately bogus preprints started being cited in peer reviewed literature 🫣
🧪 #MedSky

www.nature.com/articles/d41...

Exonic enhancers: proceed with caution in exome and genome sequencing studies Exonic enhancers (eExons) are coding exons that also function as enhancers of the gene in which they reside or (a) nearby gene(s). Mutations that affect the enhancer activity of these eExons have been associated with human disease. Therefore, eExon ...

If you have unsolved exome cases, go back and look at the synonymous variants you threw away.

Overlay with ChIP-seq or ATAC-seq for the relevant tissue.

The genetic code is multiplexed. Protein effect is one layer of many.

pmc.ncbi.nlm.nih.gov/articles/PM...

New preprint with Garnett lab 🚀: from descriptive → causal single-cell atlases in CRC.We build the largest CRC atlas (>300 pts, 1.5M cells) using continual learning, and link cell states to causal drivers via Tahoe-100M, validated in organoids! www.biorxiv.org/content/10.6...

Explainable Linear and Generalized Linear Models by the Predictions Plot Multiple linear regression is a basic statistical tool, yielding a prediction formula with the input variables, slopes, and an intercept. But is it really easy to see which terms have the largest e...

#rstats #dataviz

A new kid on the dataviz block is the predictions plot, showing how predictors in lm()/glm() contribute to
the predicted response. A novel and useful idea!

TAS: doi.org/10.1080/0003...
Implemented in the {classmap} package.

Remembrance of inflammations past Chronic inflammation increases the risk of colon cancer. This inflammation drives epigenetic changes in the nucleus of stem cells that promote tumour formation.

Chronic inflammation has long been linked to cancer, but how is that history retained in the tissue?

In a new #Nature study, Nagaraja et al show that colitis leaves a lasting epigenetic memory in colonic stem cells, which persists after inflammation resolves & primes for subsequent tumor growth 🧪🔬

SMAD4 loss drives chromosomal instability during tumourigenesis via translational reprogramming www.biorxiv.org/content/10.64898/2026.03...

AI-generated cartoon of a computational biologist and wet-lab biologist collaborating on a research project

✂️🧬preprint!

"Quantitative prediction of nonsense-mediated #mRNA decay across human genes by #genomic language #model & large-scale mutational scanning"

Fantastic teamwork by @IgnasiToledano 👨‍🔬and @MarcellVeiner👨‍💻. We combine massive experiment and sequence AI to elucidate NMD👇

Embracing Bayesian Methods in Clinical Trials This Perspective discusses the importance of the US Food and Drug Administration’s draft guidance on the use of bayesian methods in clinical trials because it underscores its commitment to modernizing...

Celebrating the draft FDA Bayesian guidance document with our perspective in @jama.com. Honored to co-author w/Jack Lee (MD Anderson), Lisa LaVange (past director of Office of Biostatistics FDA CDER&president of ASA),& my Bayesian inspiration Sir David Spiegelhalter jamanetwork.com/journals/jam...

This review explores the dual role of #Rloops—three-strand nucleic acid structures that regulate genes yet threaten #GenomeStability—highlighting their impact on #DNAdamage and repair as a promising avenue for therapeutic innovation.

#OpenAccess: doi.org/10.1016/j.ge...

Generalist biological artificial intelligence in modeling the language of life - Nature Biotechnology This Review discusses the promises and pitfalls of biological AI algorithms and presents a vision for generalist biological artificial intelligence, in which models can perform diverse tasks across bi...

AI to understand the language of life.
Our review just published
nature.com/articles/s41...
Free access rdcu.be/e89lQ

Real-world clinical utility of tumor whole-genome sequencing in solid cancers - Nature Medicine In a real-world cohort of 888 patients with solid cancers receiving whole-genome sequencing profiling, actionable biomarkers were identified in 73% of patients, and targeted therapies were associated ...

Why should tumor whole genome sequencing (WGS) be done for cancer?
In real practice of medicine study of 888 patients with solid cancers, WGS directly led to clinical consequences in over 40%
www.nature.com/articles/s41...

In case you missed it-- check out our Paper Skygest preprint! ⤵️

A complete set of canonical nucleobases in the carbonaceous asteroid (162173) Ryugu - Nature Astronomy Samples returned from the asteroid Ryugu contain all five canonical nucleobases (A, G, C, T and U). Their presence in Ryugu and Bennu supports the hypothesis that carbonaceous asteroids contributed…

A complete set of canonical nucleobases in the carbonaceous asteroid (162173) Ryugu 🧬🛸 www.nature.com/articles/s41...

How the classic computer game Doom became a tool for science The 1990s game has been run on bacteria and a satellite and played by neurons in a dish.

‘Can it run Doom?’ In the latest, scientists reported that they had taught neurons grown on a silicon chip to play the game
🧪
www.nature.com/articles/d41...

The AI co-scientist is here www.nature.com/articles/s41... 🧬💻🧪 rdcu.be/e8xmk

DNA methylation variability defines a fundamental dimension of tumor epigenomes linked to genomic instability, tumor aggressiveness, and clinical outcomes www.biorxiv.org/content/10.64898/2026.03...

Scientists show #lncRNA AC004854.2 drives #ColorectalCancer by disrupting the PUF60–FUBP1 complex to boost #cMYC transcription; forming a SOX4/AC004854.2/PUF60/c-MYC axis that promotes #tumor growth, attenuated by c-MYC inhibition.

#OpenAccess: doi.org/10.1016/j.ge...

How do authors want to use AI for review? - EMBO Reports EMBO Reports - A survey of researchers who compared AI-generated scientific reviews with journal-agnostic human peer review reveals that they overwhelmingly prefer using AI as a self-checking tool...

"AI is here to stay...From writing to reviewing...It is essential to engage with it [&] develop use cases that benefit the community...The clear winning option is use of AI review by authors prior to submission.” link.springer.com/article/10.1... via @tlemberger.bsky.social @odedrechavi.bsky.social

Gene regulatory networks: from correlative models to causal explanations www.nature.com/articles/s41... 🧬💻🧪 rdcu.be/e7DIE

How much does it pay to publish an open access academic book? Read this thread for my story and 💲💰 amounts. 🧵

www.routledge.com/9781032908724

Nucleosome spacing across cell types, diseases, and ages Abstract. Nucleosome spacing patterns in the genome form a unique signature of a given cell, reflecting its chromatin organization and gene expression. Rec

From @narjournal.bsky.social #NARCriticalReviewsAndPerspectives | #Nucleosome spacing across cell types, diseases, and ages | #Bioinformatics #NucleosomeMappingData #OpenScience #Review 🧬 🖥️🧪🔓
⬇️
academic.oup.com/nar/article/...

Wonder which tandem repeat genotyper to use on your Oxford Nanopore genomes? We benchmarked 7 tools on >100 ONT genomes. We assessed usability, assembly concordance, Mendelian consistency, and sensitivity to pathogenic expansions. www.biorxiv.org/content/10.6...
🖥️ 🧬
@cubiomedinfo.bsky.social

What Do Biological Foundation Models Compute? Sparse Autoencoders from Feature Recovery to Mechanistic Interpretability #SingleCell 🧪🧬🖥️
www.biorxiv.org/content/10.64898/2026.03...

AI can write genomes — how long until it creates synthetic life? The Evo2 genomic language model can generate short genome sequences, but scientists say further advances are needed to write genomes that will work inside living cells.

Ewen's writeup of the new Evo 2 paper in Nature is reliably good. I can imagine this foundation model will be useful for doing synthetic biology in microbes.
But it's important to recognize that making this work for eg humans is not just a scaling-up issue...
www.nature.com/articles/d41...

Genome modelling and design across all domains of life with Evo 2 www.nature.com/articles/s41...

A pan-cancer compendium of 1,294 plasma cell-free DNA methylomes and fragmentomes enabling multicancer detection www.nature.com/articles/s4...

This review examines lysine #crotonylation (Kcr) as a widespread #PostTranslationalModification regulating gene expression, #DNArepair, protein stability, and disease, highlighting crosstalk with #acetylation and other PTMs as therapeutic targets.

Read: doi.org/10.1016/j.ge...

This week's cover @thelancet.com

Multimodal foundation transformer models for multiscale genomics www.nature.com/articles/s4...