Steve Thorn

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 🧬 🖥️🧪🔓
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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 🧪🧬🖥️
https://www.biorxiv.org/content/10.64898/2026.03.04.709491v1

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...

Annotating genomes at increased scale and resolution Nature Reviews Genetics, Published online: 17 February 2026; doi:10.1038/s41576-026-00937-3In this Review, Ji et al. overview how rapidly advancing experimental and computational methods are enabling improved and automated annotation of gene structure and function, providing researchers with genome annotation resources of unprecedented scale and resolution.

ICYMI: New online! Annotating genomes at increased scale and resolution

A pan-cancer compendium of 1,294 plasma cell-free DNA methylomes and fragmentomes enabling multicancer detection - Nature Cancer Zeng et al. analyzed cfDNA methylation and fragmentomic data from 1,294 patient plasma samples across 14 major cancer types to present a comprehensive landscape of pancancer and cancer-specific cell-f...

🌟New Resource article

Read about the pancancer landscape of cancer-specific cell-free DNA methylation and fragmentomic features from plasma samples from 1,294 patients

✒️Yong Zeng, @matlupien.bsky.social, @pughlab.bsky.social, Housheng Hansen He & colleagues

www.nature.com/articles/s43...

M-PACT leverages cell-free DNA methylomes to achieve robust classification of pediatric brain tumors - Nature Cancer Smith et al. present M-PACT, a deep neural network leveraging low-input cell-free DNA methylation profiles to achieve robust classification of pediatric brain tumors and enable cellular deconvolution ...

⭐Technical Report out today at Nature Cancer

The deep neural network M-PACT uses low-input cell-free DNA methylation profiles to classify pediatric brain tumors
@doctorpauln77.bsky.social

www.nature.com/articles/s43...

Advancing regulatory variant effect prediction with AlphaGenome - Nature AlphaGenome, a deep learning model that inputs 1-Mb DNA sequence to predict functional genomic tracks at single-base resolution across diverse modalities, outperforms existing models in variant effect...

From @avsecz.bsky.social and colleagues in @nature.com | Advancing regulatory variant effect prediction with AlphaGenome | #AI #Bioinformatics #Genomics #ML #OpenScience 🧬 🖥️ 🧪 🔓
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www.nature.com/articles/s41...

Mutational scanning reveals oncogenic CTNNB1 mutations have diverse effects on signaling - Nature Genetics Saturation genome editing of a cancer mutation hotspot in CTNNB1, the gene encoding β-catenin, reveals a gradient of effects of missense mutations on Wnt signaling.

Delighted to contribute to this seminal study of a critical oncogene! A long journey but worth it in the end :-)
www.nature.com/articles/s41...

The largest randomized trial of medical A.I.
—Over 100,000 women in Sweden
—radiologist + AI vs 2 radiologists, in follow-up
—AI added led to 29% more cancer detected, 44% reduced workload, and
—Less cancer dx in subsequent 2 years, and, when found, less aggressive
thelancet.com/journals/lan...

A comprehensive survey of genome language models in bioinformatics. #GenomeLanguageModels #gMLs #ModelsReview #Bioinformatics #Genomics #BriefingsInBioinformatics
academic.oup.com/bib/article/...

A hypothesis is a liability Genome Biology -

9/
Or the paper where researchers missed a gorilla in the data.
genomebiology.biomedcentral.com/articles/10...
They did not see it because they did not plot it

Nous-209 neoantigen vaccine for cancer prevention in Lynch syndrome carriers: a phase 1b/2 trial - Nature Medicine In a phase 1b/2 trial, an off-the-shelf vaccine using gorilla adenoviral and modified vaccinia Ankara vectors with over 200 mutated peptides known to be present in persons with mismatch-repair-deficie...

A vaccine to prevent colon cancer.
Proof-of-concept for strong immune response and safety via neoantigens given to people carrying mutations for Lynch syndrome
nature.com/articles/s41...

New UK Wnt paper out in @natgenet.nature.com from the Owen Sansom group at @cruk-si.bsky.social showing the RNA-binding protein NPM1 supports WNT-driven intestinal and liver tumorigenesis.

www.nature.com/articles/s41...

DNA sequence quantitatively encodes CTCF-binding affinity at genome scale www.biorxiv.org/content/10....

Insights into DNA repeat expansions among 900,000 biobank participants www.nature.com/articles/s4...

The #E3ligase #UBR5 suppresses #ColorectalCancer by driving #ubiquitin‑mediated degradation of #Snail, limiting #EpithelialMesenchymalTransition & invasion; low UBR5 predicts poor prognosis, highlighting the UBR5–Snail axis as a #TherapeuticTarget.

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

An overview of key online resources for human genomics: a powerful and open toolbox for in silico research academic.oup.com/bfg/advance-...

Review: DNA methylation in mammalian development and disease www.nature.com/articles/s41... (free: rdcu.be/dUbb8)

Unique Signatures of Highly Constrained Genes Across Publicly Available Genomic Databases www.biorxiv.org/content/10.1...