Emanuel Gonçalves
@emanuelvgo.bsky.social
Assistant Professor Instituto Superior Técnico (IST) and INESC-ID
https://web.tecnico.ulisboa.pt/emanuel.v.goncalves/
https://web.tecnico.ulisboa.pt/emanuel.v.goncalves/
Pinned
Emanuel Gonçalves
@emanuelvgo.bsky.social
· Nov 29
Synthetic augmentation of cancer cell line multi-omic datasets using unsupervised deep learning
Nature Communications - Multi-omics integration is often limited by data sparsity and heterogeneity. Here, the authors develop MOSA, a method designed to augment DepMap cell line data to...
rdcu.be
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
Reposted by Emanuel Gonçalves
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.
October 16, 2025 at 10:47 AM
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.
Reposted by Emanuel Gonçalves
Enjoyed writing this review of synthetic lethality in drug discovery with @emanuelvgo.bsky.social and @davidjadams.bsky.social rdcu.be/eFBmw
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...
rdcu.be
September 24, 2025 at 2:54 PM
Enjoyed writing this review of synthetic lethality in drug discovery with @emanuelvgo.bsky.social and @davidjadams.bsky.social rdcu.be/eFBmw
Reposted by Emanuel Gonçalves
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
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
September 20, 2025 at 7:43 AM
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
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
Reposted by Emanuel Gonçalves
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...
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 ...
www.biorxiv.org
September 7, 2025 at 5:02 PM
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...
Reposted by Emanuel Gonçalves
A nasal spray reduced the risk of Covid infections in a double blind, placebo controlled randomized trial
jamanetwork.com/journals/jam...
jamanetwork.com/journals/jam...
September 2, 2025 at 3:16 PM
A nasal spray reduced the risk of Covid infections in a double blind, placebo controlled randomized trial
jamanetwork.com/journals/jam...
jamanetwork.com/journals/jam...
Reposted by Emanuel Gonçalves
🍹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
👉https://rdcu.be/eCOQp
bit.ly/423dC3c
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...
bit.ly
August 28, 2025 at 6:35 AM
🍹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
👉https://rdcu.be/eCOQp
bit.ly/423dC3c
Reposted by Emanuel Gonçalves
If this was a drug, it would be a blockbuster prevention vs Alzheimer's disease for APOE4 homozygotes, with 35% reduction of risk!
August 26, 2025 at 2:00 PM
If this was a drug, it would be a blockbuster prevention vs Alzheimer's disease for APOE4 homozygotes, with 35% reduction of risk!
Reposted by Emanuel Gonçalves
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. 🧵⬇️
I am absolutely delighted to share our work describing a new *recessive* condition caused by variants in #RNU4-2. Yes, that #RNU4-2!
tinyurl.com/3j9r56s8
@rociorius.bsky.social @yuyangchen.bsky.social @gregfindlay.bsky.social @dgmacarthur.bsky.social @cassimons.bsky.social @nickywhiffin.bsky.social
tinyurl.com/3j9r56s8
@rociorius.bsky.social @yuyangchen.bsky.social @gregfindlay.bsky.social @dgmacarthur.bsky.social @cassimons.bsky.social @nickywhiffin.bsky.social
Biallelic variants in the non-coding RNA gene RNU4-2 cause a recessive neurodevelopmental syndrome with distinct white matter changes
Genetic variants in RNU4-2, which encodes U4, a key non-coding small nuclear RNA (snRNA) component of the major spliceosome, were recently shown to cause a prevalent neurodevelopmental disorder (NDD) ...
www.medrxiv.org
August 18, 2025 at 12:20 PM
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. 🧵⬇️
Reposted by Emanuel Gonçalves
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...
We are analysing the other parts of this proposal in more detail.
@Vonderleyen @EZaharievaEU
research-and-innovation.ec.europa.eu/news/all-res...
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...
research-and-innovation.ec.europa.eu
July 23, 2025 at 7:49 PM
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...
We are analysing the other parts of this proposal in more detail.
@Vonderleyen @EZaharievaEU
research-and-innovation.ec.europa.eu/news/all-res...
Reposted by Emanuel Gonçalves
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.
I am in London this week for the Royal Society Future of science publishing conference. I think publishing will get worse before it gets better, but the organizers have invited ppl with equally spicy opinions so should be fun royalsociety.org/science-even...
July 15, 2025 at 8:37 AM
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.
Reposted by Emanuel Gonçalves
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...
🔗 www.nature.com/articles/s41...
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...
www.nature.com
July 6, 2025 at 3:14 PM
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...
🔗 www.nature.com/articles/s41...
Não há palavras... talvez cantar seja a melhor recordação! www.reddit.com/r/PrimeiraLi...
From the PrimeiraLiga community on Reddit: Diogo Jota 20
Explore this post and more from the PrimeiraLiga community
www.reddit.com
July 3, 2025 at 6:49 PM
Não há palavras... talvez cantar seja a melhor recordação! www.reddit.com/r/PrimeiraLi...
Reposted by Emanuel Gonçalves
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! ❤️
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! ❤️
June 4, 2025 at 10:43 AM
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! ❤️
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! ❤️
Reposted by Emanuel Gonçalves
🚀 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
Meet the Team and Labs behind the project
👉 quantms.org/about
#OpenSource #Proteomics #ASMS2025
quantms - Quantitative Mass Spectrometry Analysis
A bioinformatics best-practice analysis pipeline for Quantitative Mass Spectrometry (MS)
quantms.org
June 2, 2025 at 3:39 PM
🚀 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
Meet the Team and Labs behind the project
👉 quantms.org/about
#OpenSource #Proteomics #ASMS2025
Reposted by Emanuel Gonçalves
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
May 23, 2025 at 7:38 AM
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
Reposted by Emanuel Gonçalves
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...
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...
May 21, 2025 at 5:17 PM
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...
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...
Reposted by Emanuel Gonçalves
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...
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.
www.nature.com
May 2, 2025 at 10:31 AM
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...
www.nature.com/articles/s41...
Reposted by Emanuel Gonçalves
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!
April 27, 2025 at 2:38 PM
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!
Reposted by Emanuel Gonçalves
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...
State of the lab 12 - Becoming an established scientist
This blog post is part of a (nearly) yearly series on running a research group in academia. This post summarizes year 12, the 3rd year afte...
www.evocellnet.com
March 16, 2025 at 1:37 PM
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...
Reposted by Emanuel Gonçalves
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!
Just announced! Seven new Cancer Grand Challenges – with awards of up to £20m – available for research teams around the world to tackle the biggest questions in cancer research.
Read more: cruk.ink/4ha3LgZ 1/2
Read more: cruk.ink/4ha3LgZ 1/2
March 6, 2025 at 8:44 AM
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!
Reposted by Emanuel Gonçalves
7 new Cancer Grand Challenges announced:
www.cancergrandchallenges.org/new-challenges
@cancergrand.bsky.social
www.cancergrandchallenges.org/new-challenges
@cancergrand.bsky.social
New challenges
Explore the challenges currently open for Expressions of Interest.
www.cancergrandchallenges.org
March 5, 2025 at 3:16 PM
7 new Cancer Grand Challenges announced:
www.cancergrandchallenges.org/new-challenges
@cancergrand.bsky.social
www.cancergrandchallenges.org/new-challenges
@cancergrand.bsky.social
Reposted by Emanuel Gonçalves
Francis Collins is leaving NIH www.npr.org/sections/sho...
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.
www.npr.org
March 1, 2025 at 6:22 PM
Francis Collins is leaving NIH www.npr.org/sections/sho...
Reposted by Emanuel Gonçalves
Major:
Finland is making a significant investment in the future of machine learning / artificial intelligence by hiring 20 professors (at various levels) www.ellisinstitute.fi/ellis-instit...
PI positions | ELLIS Institute Finland
ELLIS Institute Finland PI positions
www.ellisinstitute.fi
February 28, 2025 at 9:10 AM
Major:
Reposted by Emanuel Gonçalves
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
A benchmark comparison of CRISPRn guide-RNA design algorithms and generation of small single and dual-targeting libraries to boost screening efficiency
rdcu.be
February 27, 2025 at 1:44 PM
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