🔗 Paper: doi.org/10.1093/bib/bb… 🌐 Catalogue: sysbiobig.gitlab.io/ccc-catalog In collaboration with Costa Lab - @costalab.bsky.social Enrica Calura #SingleCell #Bioinformatics #CellCellCommunication #CCC #ComputationalBiology

🔥Check out this very comprehensive review on cell-cell communication analysis lead by sysbiobigunipd team with contributions by James Shiniti Nagai and Vanessa !

[1/5] Data often has inherent geometric and topological properties that can be exploited by machine learning algorithms. Below are four areas of machine learning that explore this important aspect.

🔥It is a pleasure to announce CrossTalker2.0🔥. New features includes CCI statistical tests, new visualizations, intracellular signalling, pathway analysis, a python version & tutorials based on heart and bone marrow fibrosis data costalab.github.io/CrossTalkeR/ by Vanessa & James Shiniti Nagai

Our paper “Point-Level Representation Learning on Point Clouds” with Michael Schaub has been accepted at ICML 2025! 🎉 We link global topological descriptors back to individual points — connecting TDA & local geometry. arxiv.org/abs/2406.02300 See you in Vancouver next week!🇨🇦

🙏 Grateful for the great engagement at our #CellCellCommunication #tutorial at #ISMBECCB2025! See you next week in #Liverpool in person!👋 Organizers: Giulia Cesaro, James Shiniti Nagai, Mayra Ruiz, Costa Lab - @costalab.bsky.social , Giacomo Baruzzo, Barbara Di Camillo

Join our "Advances in Single-Cell Technologies" meeting in December in Freiburg, co-organised with Marco Prinz and Katrin Kierdorf. Excellent line-up of speakers covering spatial technologies, lineage tracing, computational methods, and more. uniklinik-freiburg.de/single-cell-te…

Amazing work by Victor Puelles on multiplex kidney pathology. Great to see this landmark method from Fibromap out there with our contribution by Mehdijoodaki on how Pilot can dissect disease trajectories in multiplex images.

Great about NicheSphere and on Myelofibrorsis PIC-seq by Mayra Ruiz in ISMB. Coll with Rebekka Schneider

A strong tour by Giulia Cesaro on cell cell Communication and intra celular signaling at ISMB

🔬 Ever wonder how your immune system ages? 📊 We used single-cell multi-omics (RNA + ATAC) + bulk ATAC on PBMCs to build a cell-by-cell map of aging. 🧠 Find out which genes fade, which chromatin gates close and why some immune systems age slower. 👉 Poster C-482 #ISMBECCB2025

Celebreting a busy & sucessfull #ISMBECCB2025

„Die #HightechAgendaDeutschland steht dafür, dass wir aus Forschung wieder Wohlstand machen“, stellt BM Dorothee Bär klar. Wir investieren in Schlüsseltechnologien von Bio- bis Quantentechnologie, von KI bis Fusion. 👉Mehr dazu hier: hightech-agenda-deutschland.de

🌟 Just back from an inspiring #ISMBECCB2025 in #Liverpool — full of insightful talks, fresh ideas, valuable feedback, and great networking! Our team was proud to contribute with an oral presentation, several posters, and a co-organized tutorial on #singlecell and #spatialdata.

🎤 #NetBio Oral Talk: Giulia Cesaro — Cell-specific #GraphOperation on Signaling Pathways (w/ Costa Lab - @costalab.bsky.social) 🧬 Poster @ #HiTSeq: Giacomo Baruzzo — Simulating #NGSReads from Tumor Samples (led by Francesca Longhin)

Nature research paper: Pathology-oriented multiplexing enables integrative disease mapping go.nature.com/450ovVy

To all of the folk saying we need deep learning for RNA-seq prediction...

Uh oh: deep learning models in genomics lose badly to very simple linear models. Could they have been over-hyped? (new paper by Simon Anders Constantin Ahlmann-Eltze (@const-ae.bsky.social) and Wolfgang Huber) nature.com/articles/s4159…

Excited to share our latest paper @NatureMethods We present a high-throughput framework to map cellular interactions at ultra-high scale – broadly applicable from whole-organism immune response mapping to personalized therapy response prediction (1/4). nature.com/articles/s4159…

Great to shown our work on how PILOT can be used for multi-scale analysis of pathomics data on the Computational Nephropathology Karman Conference #RWTH #DigitalPathology