Remi Trimbour
@TrimbourR
MD-PhD student at @institutpasteur and @saezlab Working in computational biology Follow me on BlueSky or GitHub instead 😇
HuMMuS is finally out in Bioinformatics ! 🥳 doi.org/10.1093/bioinf… 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/bioinf… #singlecell #multilayernetworks
What are the key disrupted multicellular processes in heart failure? In our new work we combine 23 years of molecular data with recent single-cell atlases to draw a cross-study patient map. How did we navigate the heart failure space? 🧵⬇️ doi.org/10.1101/2024.1…
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/s4159…
I had the opportunity to present #HuMMuS at @ECCBinfo — amazing experience! Huge thanks to the organisers for their formidable job. 🫶 And special mention for the food and fresh hummus! Perfectly on-point snack reminder 😋🧆
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/bioinf… #singlecell #multilayernetworks
After a very constructive back and forth with editors and reviewers of @NatureComms, scConfluence has now been published @LauCan88 @gabrielpeyre ! I'll present it this afternoon at the poster session of @ECCBinfo (P296) Published version: nature.com/articles/s4146…
🥳 I’m very happy to announce our preprint biorxiv.org/content/10.110… ! scConfluence combines uncoupled autoencoders with Inverse Optimal Transport to integrate unpaired multimodal single-cell data in shared low dimensional latent space. @LauCan88 @gabrielpeyre
🚨🚨 AI in Bio release 🧬 Very happy to share my work on a Large Cell Model for Gene Network Inference. It is for now just a preprint and more is to come. We are asking the question: “What can 50M cells tell us about gene networks?” ❓Behind it, other questions arose like:…
🎉 New preprint! biorxiv.org/content/10.110… STORIES learns a differentiation potential from spatial transcriptomics profiled at several time points using Fused Gromov-Wasserstein, an extension of Optimal Transport. @gabrielpeyre @LauCan88
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/gk…
Writing this piece has been quite fulfilling (and scary). I spent half of last year putting in order some of my thoughts regarding how to study multicellular coordination with single-cell and spatial data. If you are interested please read the manuscript below. 😊
How to link single-cell diversity and the emergence and maintenance of robust multicellular processes in developed tissues? 🤔 What can we learn about multicellular coordination in tissues from single-cell omics data? Read about our view: arxiv.org/abs/2403.06753
If you like MISTy doi.org/10.1186/s13059…, you'll really like Kasumi doi.org/10.1101/2024.0…. Kasumi is a multi-view explainable representation learning approach, capturing localized relationship-based patterns in tissues across conditions aiming towards facilitating translation
Local heterogeneity of tissues can define their function and predict clinical outcomes. We introduce Kasumi 💻biorxiv.org/content/10.110… to identify spatially localized neighborhoods of intra and intercellular relationships from spatial omics persistent across samples & conditions
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/bioinf… #singlecell #multilayernetworks
A great paper to read, and an amazing tool to use if you have unpaired multi-omics data to integrate 🤩 Congrats for this amazing work Jules !
🥳 I’m very happy to announce our preprint biorxiv.org/content/10.110… ! scConfluence combines uncoupled autoencoders with Inverse Optimal Transport to integrate unpaired multimodal single-cell data in shared low dimensional latent space. @LauCan88 @gabrielpeyre
Looking for a postdoc to join my team @institutpasteur @CNRS @InstitutPrairie. The candidate will develop machine learning methods for single-cell omics data. Project funded by the #ERCStG MULTI-viewCELL
📢We are hiring! I am searching for an administrative assistant to be primarly asssociated to my team "Machine Learning for Integrative Genomics" (research.pasteur.fr/en/team/machin…) @institutpasteur For all details on the offer ➡️emploi.pasteur.fr/job/emploi-ass…