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Emanuel Gonçalves

@emanuelvgo.bsky.social

200 followers 220 following 4 posts

Assistant Professor Instituto Superior Técnico (IST) and INESC-ID https://web.tecnico.ulisboa.pt/emanuel.v.goncalves/

web.tecnico.ulisboa.pt

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Emanuel Gonçalves @emanuelvgo.bsky.social · Nov 29

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

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

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Reposted by Emanuel Gonçalves

Colm Ryan @colmr.bsky.social · 14d

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

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Mathew Garnett @mgarnett.bsky.social · 19d

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

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John Doench @johndoench.bsky.social · Sep 7

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

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Eric Topol @erictopol.bsky.social · Sep 2

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

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Nature Cell Biology @natcellbio.nature.com · Aug 28

🍹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

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

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Eric Topol @erictopol.bsky.social · Aug 26

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

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Greg Findlay @gregfindlay.bsky.social · Aug 18

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. 🧵⬇️

alexblakes.bsky.social @alexblakes.bsky.social · Aug 18

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

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

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Maria Leptin @marialep.bsky.social · Jul 23

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...

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

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Richard McElreath 🐈‍⬛ @rmcelreath.bsky.social · Jul 15

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.

Richard McElreath 🐈‍⬛ @rmcelreath.bsky.social · Jul 14

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...

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IorioLab @ioriolab.bsky.social · Jul 6

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...

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

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Emanuel Gonçalves @emanuelvgo.bsky.social · Jul 3

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

Reposted by Emanuel Gonçalves

Fyodor Urnov @urnov.bsky.social · Jun 4

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! ❤️

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Yasset Perez-Riverol @ypriverol.bsky.social · Jun 2

🚀 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

quantms - Quantitative Mass Spectrometry Analysis

A bioinformatics best-practice analysis pipeline for Quantitative Mass Spectrometry (MS)

quantms.org

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Reposted by Emanuel Gonçalves

Saez-Rodriguez Group @saezlab.bsky.social · May 23

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

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Eric Topol @erictopol.bsky.social · May 21

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...

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Pedro Beltrao @pedrobeltrao.bsky.social · May 2

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...

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

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Mathew Garnett @mgarnett.bsky.social · Apr 27

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!

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Pedro Beltrao @pedrobeltrao.bsky.social · Mar 16

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

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Chris Tape @christophertape.bsky.social · Mar 6

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!

Cancer Research UK @cancerresearchuk.org · Mar 5

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

Blue square graphic, with black and white text which reads, ‘Breaking news: Announcing seven new Cancer Grand Challenges’

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Nicolas Robine @nicorobine.bsky.social · Mar 5

7 new Cancer Grand Challenges announced:

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

New challenges

Explore the challenges currently open for Expressions of Interest.

www.cancergrandchallenges.org

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Tim Stearns @stearnslab.bsky.social · Mar 1

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

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Reposted by Emanuel Gonçalves

Wolfgang Huber @wkhuber.bsky.social · Feb 28

Major:

Desmond Elliott @delliott.bsky.social · Feb 28

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

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David Walter @david-walter.bsky.social · Feb 27

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

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Matt Coelho @mattcoelho.bsky.social · Feb 28

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

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

www.nature.com

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Miquel Anglada-Girotto @m1quelag.bsky.social · Feb 15

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!

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.

github.com

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