You may have noticed that AlphaFold3 does not allow covalent bonds between/within polymer chains (protein, DNA, RNA) but allows it for ligands. We tried to go around this limitation by simply treating one of residues/nucleic acids as a ligand.

Enjoyed writing this review of synthetic lethality in drug discovery with @emanuelvgo.bsky.social and @davidjadams.bsky.social rdcu.be/eFBmw

The Garnett Lab is excited to launch DepMap Miner, a new tool to explore cancer dependency data! Built on the Sanger DepMap, the DepMap Miner brings together multi-omic and functional datasets for over 1300 cancer cell models. Start mining data now: dataminer.depmap.sanger.ac.uk

Doomscrolling pause to chat CRISPR libraries! Preprint describes our new, data-driven approach to combine on-target and off-target predictions much more intelligently for *selecting* guides, which we use to develop our newest Cas9 knockout library, Jacquere. Thread: www.biorxiv.org/content/10.1...

A nasal spray reduced the risk of Covid infections in a double blind, placebo controlled randomized trial jamanetwork.com/journals/jam...

🍹This Perspective discusses recent insights into #vimentin filament structure and function, as well as emerging findings that point to a role in #tumor invasion in #mesenchymal cells analogous to embryonic development and wound healing. 👉https://rdcu.be/eCOQp bit.ly/423dC3c

If this was a drug, it would be a blockbuster prevention vs Alzheimer's disease for APOE4 homozygotes, with 35% reduction of risk!

We recently performed SGE of RNU4-2 and identified functionally impactful variants underlying a new recessive disease. Today, the team led by @rociorius.bsky.social @alexblakes.bsky.social @cassimons.bsky.social & @nickywhiffin.bsky.social provide in-depth analysis of its clinical presentation. 🧵⬇️

Very promising news on the next seven-year EU budget, with a proposed substantial increase for Horizon Europe including the ERC. We are analysing the other parts of this proposal in more detail. @Vonderleyen @EZaharievaEU research-and-innovation.ec.europa.eu/news/all-res...

Second day of the Royal Soc Future of Science Publishing conference #FutureSciPub. This morning we start with a panel on leveraging digital infrastructure to go beyond traditional journal/article model.

New work out in @natgenet.nature.com from @davidjadams.bsky.social Lab @sangerinstitute.bsky.social (with a contribution from us led by A.Vinceti): CDS2 is a cancer dependency in uveal melanomas with low CDS1 expression: a synthetic lethal axis with broad potential 🔗 www.nature.com/articles/s41...

Não há palavras... talvez cantar seja a melhor recordação! www.reddit.com/r/PrimeiraLi...

Here: Baby KJ at home with his mom Nicole. This really happened, folks. Hundreds of people from 8 organizations (led by Rebecca Ahrens-nicklas and Kiran Musunuru) came together to make a bespoke gene editor for this kiddo. He was once in the 7th percentile of body weight. Look at him now! ❤️

🚀 We're launching quantms.org — new hub for all #quantms related projects. Explore its components #pmultiqc & #ibaqpy, and check all reanalysis we're sharing with the community: quantms.org/datasets Meet the Team and Labs behind the project 👉 quantms.org/about #OpenSource #Proteomics #ASMS2025

Ever wondered which method to use to infer kinase activities from phosphoproteomics data? 💻💭Our revised comprehensive evaluation of kinase activity inference tools, done in collaboration with the Zhang lab @bcmhouston.bsky.social, is now out @natcomms.nature.com 🔬 tinyurl.com/4twuc6z4

New @nature.com An ingenious way to track DNA replication patterns at the single-cell level that leads to cell heterogeneity and daughter cells that can potentially give rise to cancer www.nature.com/articles/s41...

Our work on deriving protein-protein (functional) associations across different human tissues from proteomics data is now published. There is quite a lot in this paper, so I will just touch on a few highlights: www.nature.com/articles/s41...

Six years after the discovery of WRN synthetic lethality in MSI cancers, WRN inhibitors hit center stage again today at #aacr25 with report of the first in human phase 1 trial data for RO7589831. Can’t wait to see it!

New blog post - State of the lab 12, yearly series on being a group leader in academia. This one reflects back on the transition from junior PI to a more established scientist www.evocellnet.com/2025/03/stat...

If teams forming around the 'Rewiring Cancer Cells' or 'TME Dynamics' Grand Challenges would like to include our high-throughput organoid co-culture signalling technologies please get in touch!

7 new Cancer Grand Challenges announced: www.cancergrandchallenges.org/new-challenges @cancergrand.bsky.social

Francis Collins is leaving NIH www.npr.org/sections/sho...

Major:

New paper from the Functional Genomics Centre! 🎉 Published in BMC Genomics describing our effort to minimize the size of genome-wide CRISPR-Cas9 libraries. Learn more here: rdcu.be/ebsN6

Today in BJC Reports, we summarise the outcomes from a multidisciplinary workshop focused on addressing cancer drug resistance. www.nature.com/articles/s44...

Hi all! Inspired by how easy ColabFold ( @sokrypton.org ) made prot structure prediction for me, I have started ColabRNA to facilitate making predictions with RNA-based models! Currently, the following models are available: - SpliceAI - Pangolin - SpliceTransformer - Borzoi Happy to get feedback!

Discovery of a new biomarker (RNAPII) in cancer that denotes aggressiveness, increased risk of recurrence, shown in breast cancer and meningioma (<-Figure) @science.org www.science.org/doi/10.1126/...

It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS or other (non-LCH) dendritic or histiocytic sarcomas cases.

I just released version 0.9.7 of the #clustermq #rstats package: mschubert.github.io/clustermq/ _Run your code on HPC or via SSH via one line of code_ Please check it out; feedback is welcome!

This might be the best paper on applying sparse autoencoders to protein language models. The authors identify how neural networks trained on amino acid sequences "discover" different features, some specific to individual protein families, other for substructures www.biorxiv.org/content/10.1...

The submission deadline has been extended to *8 May 2025*! "Genome Biology is calling for submissions to our Collection on key genetic determinants and functional consequences of genome editing interventions in the context of cancer." #CRISPR www.biomedcentral.com/collections/...

(1/3) Excited to share our latest work using @depmap.org to uncover a new synthetic lethality in two distinct patient populations! We found that SKI complex inactivation through two independent genomic alterations creates a dependency on PELO #CancerResearch #SyntheticLethality #Genomics #DepMap

🚨The Taipale lab are hiring in our new home at the @sangerinstitute.bsky.social 🚨 We're looking for senior postdocs, postdocs and a tech specialist. Check out the jobs ads here and please share! 👇 shorturl.at/cZcEP shorturl.at/Edupy shorturl.at/R0ToY shorturl.at/KdVky

Come work at the European Molecular Biology Laboratory in the beautiful science & university city Heidelberg as a Research Software Engineer on R/Bioconductor tools for biological data science and AI ! embl.wd103.myworkdayjobs.com/EMBL/job/Hei...

JOB OPPORTUNITY: Join us as a scientific programmer to advance tools for multi-omics data at Heidelberg University. Details can be found at shorturl.at/OcnOa and please spread the word!

We will be hosting the International Conference on Systems Biology (ICSB) in Dublin this year – 5-9th October icsb2025.com/registration/ #ICSB2025

Modern GWAS can identify 1000s of significant hits but it can be hard to turn this into biological insight. What key cellular functions link genetic variation to disease? I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵

Every once in a while we publish a paper that moves a whole field forward. I think that's the case for this one from the Bugaj lab, where they describe proteins for THERMOGENETIC control of cellular behavior. www.nature.com/articles/s41...

This is an important shift - the long awaited new Ensembl web site is ready for beta testing - is smooth, scrollable genome loveliness +clean views of the complex information - but @ensembl.bsky.social needs your help to get all the use cases out. Come to the webinar, and check out beta.ensembl.org

Functional evaluation and clinical classification of BRCA2 variants www.nature.com/articles/s41...

How to do differential expression with scRNAseq data? State of the art is "pseudo-bulk" analysis with RNA-seq methods like edgeR or DESeq2, where "cell type" is encoded as discrete categories. Biologically, discrete categories are not always the most appropriate concept.(1/3) doi.org/10.1038/s415...

New metabolomic aging clock trained on 168 metabolites in UK Biobank (N=225,212)⏲️ 👉R2 up to 0.35 👉associations with frailty index, telomere length, self-rated health 👉prediction of all-cause mortality 1/3

1/🚀 Excited to share RegVelo, our new cell model combining RNA velocity with gene regulatory network (GRN) dynamics to model cellular changes and predict in silico perturbations. Here's how it works and why it matters! 🧵👇 biorxiv.org/content/10.1101/2024.12.11.627935v1

Tissue-specific adaptations to cytochrome c oxidase deficiency shape physiological outcomes 🧪 www.sciencedirect.com/science/arti... Congratulations to Milica Popovic and Lea Isermann from the Trifunovic lab for this nice work!

Thrilled to share our first dive into generative models, integrating 7 distinct omics to generate a complete Synthetic Cancer Dependency Map for +1,500 cancer cell lines! Excited for what’s ahead. rdcu.be/d1TgQ #GarnettLab #CMRI #ProCan #INESC-ID #IST @naturecomms.bsky.social

Excited to launch a new Gordon Research Conference on synthetic lethality in oncology. Great cutting edge program, superb speakers and lots of networking opportunities. Applications open. www.grc.org/synthetic-le...

A pair of graphs I think about a lot. On the topic of pooled CRISPR screens, the left is "replicate correlation" when simply examining the abundance of guide RNAs, i.e. log-normalized read counts. On the right is taking those same data and subtracting from a common starting point, i.e. pDNA.

Abstract submissions are still open for the CSHL Network Biology meeting in March 11 - 15 2025 (abstract deadline: Jan 10). A large fraction of talks will be selected from the abstracts. On behalf of the organizers, we look forward to welcoming you there. meetings.cshl.edu/meetings.asp...

A vertical takeoff of life science with #AI LLLMs. Publication of 10 new foundation models of Proteins, DNA, RNA, methylation, cells, and interactions, evolution, and design in the past couple of weeks! Unprecedented progress, reviewed in the new Ground Truths erictopol.substack.com/p/learning-t...