Schwartz Lab https://validator.w3.org/feed/docs/rss2.html Richard Dong Richard presents his poster “SPAGHETTI enhances phase contrast microscopy quantitative analyses using large-scale H&E morphological models through a generative deep learning approach” at ISMB/ECCB 2025! Leo Cui Christie presents her poster “Does single-cell gene expression reflect RNA abundance?” at AACR 2025! Gregory presents at the Data Sciences Institute: AI in Genomics! The Schwartz Lab receives The Manchester-Melbourne-Toronto (MMT) Research Fund! Gregory presents at the Allan Slaight Breakthrough Forum: From Tumour Complexity to Translational Breakthroughs! The Schwartz Lab receives a Canadian Institutes of Health Research Project Grant! Gregory presents at the Manchester Cancer Research Centre! The Schwartz Lab receives TRANSCAN-3 funding as part of a multinational project for biliary tract cancer! Richard’s manuscript “SPAGHETTI leverages massive H&E morphological models for phase contrast microscopy images with a generative deep learning approach” is now on bioRxiv! Fatema, Deisha, Joshua, and Victoria’s article “CellNEST reveals cell–cell relay networks using attention mechanisms on spatial transcriptomics” is now published in Nature Methods! CellNEST reveals cell–cell relay networks using attention mechanisms on spatial transcriptomics Sabrina Xi Chloe Nichole Calica Viet Hoang Bruno Saleme Gregory is a co-author on “Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance” in collaboration with the Faryabi lab! Publications Lin, Ho Seok, and Gregory are co-authors on “An inflammatory state defines a high-risk T-lineage acute lymphoblastic leukemia subgroup” in collaboration with the Tikhonova lab! An inflammatory state defines a high-risk T-lineage acute lymphoblastic leukemia subgroup Team Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance Joshua Li News Conor, Christie, and Javier’s article “TooManyCellsInteractive: A visualization tool for dynamic exploration of single-cell data” is now published in GigaScience! TooManyCellsInteractive: A visualization tool for dynamic exploration of single-cell data SPAGHETTI leverages massive H&E morphological models for phase contrast microscopy images with a generative deep learning approach Attribution Fatema, Josh, and Deisha’s preprint “NEST: Spatially-mapped cell-cell communication patterns using a deep learning-based attention mechanism” is out now on bioRxiv! Richard, Almas, and Victoria receive Ontario Graduate Scholarships, congrats! Richard (Ph.D. student) and Victoria (Masters student) join the lab. Welcome! Tingxiao (Victoria) Gao Lin Yang Almas Khan Deisha Paliwal Ho Seok Lee Wendy Chen Christie Lau Deisha joins the lab as a Master’s student. Welcome! Deisha receives the Canada Graduate Scholarships – Master’s program! Way to go! In collaboration with the Faryabi lab, our new paper “AnnoSpat annotates cell types and quantifies cellular arrangements from spatial proteomics” is out on Nature Communications! Gregory presents at the Biophysics Seminar Series at the University of Toronto AnnoSpat annotates cell types and quantifies cellular arrangements from spatial proteomics NEST: Spatially-mapped cell-cell communication patterns using a deep learning-based attention mechanism TooManyCells identifies and visualizes relationships of single-cell clades. AnnoSpat annotates cell types and quantifies cellular arrangements from spatial proteomics NEST-Interactive NEST SCHWARTZ LAB