Steve Thorn

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 🧬 🖥️ 🧪 🔓
⬇️
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...

1. Nature Methods point of view data visualization blogs.nature.com/methagora/2... the columns on color mapping and heatmap are very nice.

Stress-induced loss of CTCF reveals an alternative, promoter-based mode of cohesin looping https://www.biorxiv.org/content/10.64898/2025.12.19.695003v1

Below is an example of a “collider” model, in which X and Y collide at Z, inducing dependence conditional on Z.

2/2
journals.plos.org/plosbiology/...

The Gene Ontology knowledgebase in 2026 Abstract. The Gene Ontology (GO) knowledgebase (https://geneontology.org) is a comprehensive resource describing the functions of genes. The GO knowledgeba

From the @geneontology.bsky.social team in the @narjournal.bsky.social #NARDatabaseIssue | The Gene Ontology knowledgebase in 2026 | #Bioinformatics #Database #OpenScience #GO #Ontology #GeneOnlology #OpenData 🧬 🖥️🧪🔓
⬇️ academic.oup.com/nar/advance-...

Causal modelling of gene effects from regulators to programs to traits - Nature Approaches combining genetic association and Perturb-seq data that link genetic variants to functional programs to traits are described.

GWAS has been an incredible discovery tool for human genetics: it regularly identifies *causal* links from 1000s of SNPs to any given trait. But mechanistic interpretation is usually difficult.

Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:

Top ten news stories in 2025 - Nature Biotechnology This year’s most popular stories are a testament to biotech ingenuity and a cause for celebration: the gene editing triumph that cured ‘baby KJ’ of a rare genetic disorder in record time; the bispecif...

Top ten news stories in 2025 www.nature.com/articles/s41...

📢 How does #epigenetics fuel #chromosome #instability in #cancer?
Together with @IlioVitale and @deadoc80.bsky.social, we highlighted two recent papers from @NatGen and @CD_AACR in our newly published @cp-trendscancer.bsky.social Spotlight!
Check it out here 👉 www.sciencedirect.com/science/arti...

A review on m6A methylation regulation & its biological functions in the #ImmuneSystem, detailing its critical role in the #Pathogenesis of #AutoimmuneDiseases, identifying potential #Biomarkers & targets for their prevention & treatment.

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

Order in which cancer-driving mutations occur affects the chance of tumour development Randomly acquired mutations face strong negative selection, except on certain cancer-promoting backgrounds.

and the Research Briefing to go with it www.nature.com/articles/d41...

plinkQC: An Integrated Tool for Ancestry Inference, Sample Selection, and Quality Control in Population Genetics www.biorxiv.org/content/10.1... 🧬🖥️🧪 R package meyer-lab-cshl.github.io/plinkQC/ #Rstats

Snappy: fast identification of DNA methylation motifs based on Oxford Nanopore reads. #DNAmethylation #BacterialDNA @nanoporetech.com #Sequencing #Bioinformatics #Genomics @bioinfoadv.bsky.social
academic.oup.com/bioinformati...

new out in Nature www.nature.com/articles/s41...