🌟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...

⭐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...

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...

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/...

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

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/...

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-...

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 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...

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...

ICYMI: New online! Establishing cancer registries in Africa — focus on hepatopancreatobiliary cancers

A systematic review highlights that many pathogenic DDR gene variants arose in recent #HumanEvolution, suggesting today’s cancer risks linked to DDR PVs are the by-product of human evolution. #medsky #OpenAccess: www.sciencedirect.com/science/arti...

Circular DNA has a ticket to ride chromosomes www.nature.com/articles/d41...

A vaccine targeting mutant IDH1 induces antitumour immunity www.nature.com/articles/nat...

A new pre-print with some cool results from my PhD! www.medrxiv.org/content/10.1...

Thank you @natrevcancer.nature.com for the invitation to talk about this really cool study by Lu and collaborators! www.nature.com/articles/s41... Thank you as well to my coauthor @pbasurto.bsky.social 😄

📍 Latest OmniPath paper is out now! ➡️ academic.oup.com/nar/advance-...

Our paper is out in @nature.com! Oncogenes are often copy-number amplified on extrachromosomal DNA (ecDNA) in cancer, but how is ecDNA inherited by dividing cells? Here we identified elements within ecDNA that promote its retention in dividing cells. 1/11 www.nature.com/articles/s41...

Review: Linking tumour angiogenesis and tumour immunity

SigRescueR: A Pan-System Framework for Noise Correction and Mutational Signature Identification Across Sequencing Platforms https://www.biorxiv.org/content/10.1101/2025.11.14.688578v1

Mapping chromatin structure at base-pair resolution unveils a unified model of cis-regulatory element interactions www.sciencedirect.com/science/arti... #genomics #dna #biochemistry #biophysics

New @natgenet.nature.com paper from the brilliant @eszterlakatos.bsky.social presents evidence that chromatin alterations disrupt antigen presentation & neoantigens in colorectal cancer. Also that immune escape is part of the "Big Bang", at the outset of CRC growth. www.nature.com/articles/s41...

New online! Decoding the regulatory genome with large-scale deep learning

PhD training needs a reboot in an AI world www.nature.com/articles/d41... 🧬🖥️🧪

This review highlights the dual nature of R-loops in #GeneRegulation and #GenomeInstability, emphasizing their impact on #DNADamage responses and potential as #therapeutic targets. #medsky #OpenAccess: www.sciencedirect.com/science/arti...

Now online in Cancer Discovery @aacrjournals.bsky.social: A Prognostic Signature for Lung Adenocarcinoma in Patients Who Have Never Smoked - by Wei Zhao, Maria Teresa Landi, and colleagues doi.org/10.1158/2159...

The first time I saw this approach was this post by @fabiocrameri.ch: x.com/fcrameri/sta... Some more serious examples are featured in his paper "The misuse of colour in science communication" 👉 www.nature.com/articles/s41...

Reproducible processing of TCGA regulatory networks academic.oup.com/gigascience/... 🧬🖥️🧪

What makes PhD students happy? Good supervision - Supervisors who invest in positive mentoring relationships with their PhD candidates also reap the benefits for their own research www.nature.com/articles/d41... #mentoring #phd #gradschool #commonsense #true #education #meded

GraphComm predicts cell cell communication using a graph based deep learning method in single cell RNA sequencing data www.nature.com/articles/s41... 🧬🖥️🧪 github.com/bhklab/Graph...