PhD candidate at @EMBL @EMBLBarcelona, previously @UniHeidelberg @saezlab. Also in Bluesky https://nitter.gq/t.co/2JDEEyNskj
Barcelona, España
Joined October 2019
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When I started this project as part of my master's programme, I didn't think I'd ever see it in press, but here we are! Very happy to share this work (now peer-reviewed) with you, big thanks to @JulioSaezRod @martingarridorc + rest of coauthors for their support and contributions
Our workflow, FLOP, exploring the impact of filtering, normalization, and differential expression on functional analysis is now published in @NAR_Open. doi.org/10.1093/nar/gkae552
Victor Paton retweeted
📢 Introducing CORNETO: a unified, knowledge-driven framework for multi-sample network learning & modeling via constrained optimization, supporting a wide variety of network methods and prior knowledge
💻Code: github.com/saezlab/corneto
📜Paper: doi.org/10.1101/2024.10.26.6…
🧵👇
ALT CORNETO: Unified knowledge-driven network inference from omics data
Victor Paton retweeted
After nearly two years of hard work, the paper I coauthored with my lifelong partner, and now fiancé, is out in @NatureNeuro 🎉 No podria estar més feliç d’haver-ho fet junts @Cels121 😊
Our work with @schirmerlab in multiple sclerosis (MS) is out today in @NatureNeuro. We investigated lesion progression and cell-cell communication events in MS using snRNA-seq and spatial transcriptomics 🧠 See below ⬇️
nature.com/articles/s41593-0…
Victor Paton retweeted
🚨 We're Hiring! 🚨
At EMBL Barcelona we build tissues to understand them, and we are looking for a Group Leader in Tissue Biology & Disease Modelling!
🔬 Lead independent research on 3D tissue dynamics & engineering
📅 Apply by 24 Nov 2024
More info: embl.org/jobs/position/BCN00…
Victor Paton retweeted
Very happy to have presented some of our methods at #SEBBM !!
Desde Heildeberg viene Martín Garrido para contarnos que puede hacer la #IA para la #BiologiaMolecular
#46congresoSEBBM
Victor Paton retweeted
📣 The much-revised manuscript of LIANA+, our all-in-one solution to study cell-cell communication from single-cell, spatial, and multi-omics technologies, is now published in @NatureCellBio nature.com/articles/s41556-0…
Victor Paton retweeted
Applications for the EMBL International PhD Programme are open! 👀
The programme offers fully funded PhD positions at EMBL’s six sites across Europe 🌍
Have a look at this opportunity to start your career in the life sciences here:
embl.org/about/info/embl-int…
Victor Paton retweeted
🎉Very happy to see this out in @BriefingBioinfo! Big thanks again to @DanielBDimitrov @DugourdAjf and @JulioSaezRod who is moving to @emblebi. Looking forward to seeing you more on campus💜
📢 Our paper on MetalinksDB, a comprehensive metabolite-mediated cell-cell communication database, is now published in @BriefingBioinfo doi.org/10.1093/bib/bbae347
Victor Paton retweeted
Are you interested in cis-regulatory DNA interactions?
In 2018, #Cicero introduced an algorithm for inferring cis-coaccessible networks from scATAC
I’m excited to share #Circe, a Python implementation that is 100x faster and uses 5x less memory!
@LauCan88 @JulioSaezRod
1/5
Victor Paton retweeted
📢 Our paper on MetalinksDB, a comprehensive metabolite-mediated cell-cell communication database, is now published in @BriefingBioinfo doi.org/10.1093/bib/bbae347
Victor Paton retweeted
Understanding complex diseases requires approaches that jointly analyze omic data across multiple biological layers. In our new preprint, we merge data-driven multiomic factor analysis with systematic integration of mechanistic knowledge using COSMOS+ 🧵👇 doi.org/10.1101/2024.07.15.6…
Victor Paton retweeted
Very happy to see this paper out in @NAR_Open !! Congrats to @vicpaton on his first publication, and big thanks to all coauthors and @JulioSaezRod for the opportunity to co-supervise this work
Our workflow, FLOP, exploring the impact of filtering, normalization, and differential expression on functional analysis is now published in @NAR_Open. doi.org/10.1093/nar/gkae552
Victor Paton retweeted
Our workflow, FLOP, exploring the impact of filtering, normalization, and differential expression on functional analysis is now published in @NAR_Open. doi.org/10.1093/nar/gkae552
Victor Paton retweeted
We welcome Julio Saez-Rodriguez @JulioSaezRod as our new Head of Research!
Associate Director for EMBL-EBI Services Jo McEntyre @jomcentyre has been promoted to Deputy Director of EMBL-EBI & Rolf Apweiler is stepping back to Associate Director as he looks towards retirement.
Super nice event! Big thanks to @flowuenne @kubranarci and others for organising it.
If you use Nextflow to process omics data, check the new nf-core module for decoupler-py that @nicnic025, @attila_gbr and I have developed in this hackathon! nf-co.re/modules/decoupler_d…
Day two of the nf-core hackathon in Heidelberg is off to a great start! Grateful for the support from @GHGA_DE and shoutout to the amazing organizers. Thanks everyone for joining us! Let's keep the #nextflow momentum going! 🚀 #nfcore #hackathon
Victor Paton retweeted
HuMMuS is finally out in Bioinformatics ! 🥳
doi.org/10.1093/bioinformati…
We provide new insights, notably on HuMMuS robustness, and methylation data contribution in identifying driver TFs.
The revision was a very interesting journey, thanks everyone for all the great feedbacks !😊
Finally out a new paper from the lab lead by @TrimbourR "Molecular mechanisms reconstruction from single-cell multi-omics data with HuMMuS"
doi.org/10.1093/bioinformati…
#singlecell #multilayernetworks
Victor Paton retweeted
👇Useful metabolite cell-cell communication database with interesting analysis in kidney diseases. Big thanks to fantastic supervisors @DanielBDimitrov @DugourdAjf @JulioSaezRod and @saezlab, great group with cool science and incredible team spirit🙌.
1) 📚 Looking for flexible and user-friendly resources on metabolite-mediated interactions in cell-cell communication? Check our new database, MetalinksDB, described in our recent preprint: tinyurl.com/mldbpprnt
Victor Paton retweeted
Multicellular Factor Analysis is now fully available in @eLife's website, including the editor's evaluation and our updated revision.
Estimate multicellular programs and perform unsupervised analysis of samples from cross-condition single cell atlases
elifesciences.org/articles/9…
Victor Paton retweeted
Previous studies have checked the differences between diff expression analysis pipelines at the single gene level, but to what extend do they affect gene set enrichment analysis? Led by @vicpaton, we have explored this question in our recent preprint, check it out here 👇
Results in diff expression analysis can vary depending on the processing pipeline used, but to what extent do they affect gene set enrichment?🤔 To answer this we present FLOP, a #nextflow workflow to perform & contrast RNA-seq results 🖥️ doi.org/10.1101/2023.09.13.5… 👇🧵
Very happy to share with you my first work as first author! Here, my colleagues and I at @saezlab aimed to determine to what extent RNAseq DE analysis pipelines actually alter gene set enrichment scores, usually the last step of a transcriptomics analysis.
The results:👇
Results in diff expression analysis can vary depending on the processing pipeline used, but to what extent do they affect gene set enrichment?🤔 To answer this we present FLOP, a #nextflow workflow to perform & contrast RNA-seq results 🖥️ doi.org/10.1101/2023.09.13.5… 👇🧵