Emanuel Gonçalves

Synthetic lethality in cancer drug discovery: challenges and opportunities Nature Reviews Drug Discovery - This Review outlines recent advances in synthetic lethality, from CRISPR-based discovery and machine learning-guided prioritization of gene pairs to new phenotypic...

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

depmap miner logo

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

Balancing off-target and on-target considerations for optimized Cas9 CRISPR knockout library design The continued development of high-dimensional CRISPR screen readouts, such as single-cell RNA sequencing and high-content imaging, necessitates compact libraries to enable functional interrogation at ...

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...

Vimentin intermediate filaments as structural and mechanical coordinators of mesenchymal cells - Nature Cell Biology This Perspective presents recent insights into vimentin filament structure and function and discusses emerging findings that point to a role in tumour invasion in mesenchymal cells analogous to embryo...

🍹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. 🧵⬇️

Horizon Europe 2028 - 2034: twice bigger, simpler, faster and more impactful Research and innovation news alert: As part of the next long-term EU budget 2028-2034, the Commission is proposing to double the budget of the research and innovation framework programme to €175 billi...

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.

The synthetic lethal interaction between CDS1 and CDS2 is a vulnerability in uveal melanoma and across multiple tumor types - Nature Genetics This study employs a functional genomic approach to identify a synthetic lethal interaction between CDS1 and CDS2 in uveal melanoma and other cancers, which may represent a potential therapeutic targe...

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...

From the PrimeiraLiga community on Reddit: Diogo Jota 20 Explore this post and more from the PrimeiraLiga community

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...

A tissue-specific atlas of protein–protein associations enables prioritization of candidate disease genes - Nature Biotechnology Protein–protein interactions specific to 11 individual tissues are presented in a comprehensive resource.

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!

New challenges Explore the challenges currently open for Expressions of Interest.

7 new Cancer Grand Challenges announced:

www.cancergrandchallenges.org/new-challenges
@cancergrand.bsky.social

Legendary former NIH director retires from embattled agency Dr. Francis Collins is leaving the National Institutes of Health, where he served as director from 2009 to 2021. The agency is facing cutbacks and restrictions under the Trump administration.

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

Breaking barriers: we need a multidisciplinary approach to tackle cancer drug resistance - BJC Reports BJC Reports - Breaking barriers: we need a multidisciplinary approach to tackle cancer drug resistance

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

GitHub - MiqG/ColabRNA: Making RNA-based models accessible to all. Making RNA-based models accessible to all. Contribute to MiqG/ColabRNA development by creating an account on GitHub.

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!

A range of features identified from sparse autoencoders trained on different layers on ESM2-650M

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/...