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
Yesterday in Valencia Dr. @nlbigas.bsky.social received the 2025 Premio Rei Jaume I in Biomedical Research. Her work on how cancer mutations arise and evolve has earned major recognition!
Congratulations, Núria! 🙌
#ReiJaumeI #CancerResearch
@cerca.cat @icreacommunity.bsky.social @bbglab.bsky.social
Congratulations, Núria! 🙌
#ReiJaumeI #CancerResearch
@cerca.cat @icreacommunity.bsky.social @bbglab.bsky.social
November 26, 2025 at 1:30 PM
Yesterday in Valencia Dr. @nlbigas.bsky.social received the 2025 Premio Rei Jaume I in Biomedical Research. Her work on how cancer mutations arise and evolve has earned major recognition!
Congratulations, Núria! 🙌
#ReiJaumeI #CancerResearch
@cerca.cat @icreacommunity.bsky.social @bbglab.bsky.social
Congratulations, Núria! 🙌
#ReiJaumeI #CancerResearch
@cerca.cat @icreacommunity.bsky.social @bbglab.bsky.social
Reposted by Emanuel Gonçalves
Finally the scary example. The image of a western blot with a time course experiment, staining a protein of interest, showing the increase of protein over time and a second staining with a control antibody that does not change over time
November 21, 2025 at 1:14 PM
Finally the scary example. The image of a western blot with a time course experiment, staining a protein of interest, showing the increase of protein over time and a second staining with a control antibody that does not change over time
Reposted by Emanuel Gonçalves
The second was about drawing the EGF pathway. I also asked to create an SVG of the EGF pathway drawing which worked but with much lower quality.
November 21, 2025 at 1:14 PM
The second was about drawing the EGF pathway. I also asked to create an SVG of the EGF pathway drawing which worked but with much lower quality.
Reposted by Emanuel Gonçalves
I tried the updated Gemini image generator on scientific related image prompts that have failed in the past and I am really impressed by the quality of the outputs. The first is drawing a diagram for a pocket prediction algorithm using Voronoi diagram, Delaunay triangulation and alpha shapes
November 21, 2025 at 1:14 PM
I tried the updated Gemini image generator on scientific related image prompts that have failed in the past and I am really impressed by the quality of the outputs. The first is drawing a diagram for a pocket prediction algorithm using Voronoi diagram, Delaunay triangulation and alpha shapes
Reposted by Emanuel Gonçalves
The last session starts with Lodewyk Wessels from @nkinl.bsky.social sharing the work on perturbation response models!
November 20, 2025 at 3:56 PM
The last session starts with Lodewyk Wessels from @nkinl.bsky.social sharing the work on perturbation response models!
Reposted by Emanuel Gonçalves
And we finish this session with @epetsalaki.bsky.social showing the potential of using CRISPR data to study context specific signalling and drug responses
November 20, 2025 at 4:18 PM
And we finish this session with @epetsalaki.bsky.social showing the potential of using CRISPR data to study context specific signalling and drug responses
Reposted by Emanuel Gonçalves
Next we have @emanuelvgo.bsky.social , presenting the work on Minimal Libraries and use of AI-Synthetic Augmentation of CRISPR-Cas9 Screens for Drug Target Discovery
November 20, 2025 at 2:17 PM
Next we have @emanuelvgo.bsky.social , presenting the work on Minimal Libraries and use of AI-Synthetic Augmentation of CRISPR-Cas9 Screens for Drug Target Discovery
Reposted by Emanuel Gonçalves
@emanuelvgo.bsky.social insisting the metaphors used in @eurocancerdepmap.bsky.social presentations have strong Portuguese representation 😄
November 20, 2025 at 2:21 PM
@emanuelvgo.bsky.social insisting the metaphors used in @eurocancerdepmap.bsky.social presentations have strong Portuguese representation 😄
Reposted by Emanuel Gonçalves
The Synthetic Lethality and Innovations in CRISPR Screening session begins with @manuelkaulich.bsky.social telling us about exciting CRISPR libraries they have developed and how nuclear mRNA processing can mask the CRISPRko phenotypes @eurocancerdepmap.bsky.social
November 20, 2025 at 10:50 AM
The Synthetic Lethality and Innovations in CRISPR Screening session begins with @manuelkaulich.bsky.social telling us about exciting CRISPR libraries they have developed and how nuclear mRNA processing can mask the CRISPRko phenotypes @eurocancerdepmap.bsky.social
Reposted by Emanuel Gonçalves
We are looking for a postdoc to join our team! If you're interested in translating a cutting edge genomics technology (www.nature.com/articles/s41...) to real-life applications in hematology, this is for you. We offer a unique working environment ON THE BEACH: recruitment.crg.eu/content/jobs...
November 20, 2025 at 9:36 AM
We are looking for a postdoc to join our team! If you're interested in translating a cutting edge genomics technology (www.nature.com/articles/s41...) to real-life applications in hematology, this is for you. We offer a unique working environment ON THE BEACH: recruitment.crg.eu/content/jobs...
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