Euxhen Hasanaj … Eric Xing conducted the first systematic pan-modal study of perturbation embeddings, with an emphasis on those derived from biological foundation models. ➡️ biorxiv.org/content/10.110… #singlecell #spatialomics #spatialbiology #spatialtranscriptomics

Qile Yang … Nick Borcherding presented scRepertoire 2, a substantial update to the R package for analyzing and visualizing single-cell immune receptor data. ➡️ journals.plos.org/ploscompbiol/a… #singlecell #spatialomics #spatialbiology #spatialtranscriptomics

Malte Luecken … Smita Krishnaswamy developed the Open Problems in Single-Cell Analysis platform, an open-source, extensible, living benchmarking framework that enables quantitative evaluation of best practices in single-cell analysis. ➡️ nature.com/articles/s4158… #singlecell

Denis Bienroth … Mirana Ramialison developed VR-Omics, a free, platform-agnostic software that provides end-to-end automated processing of multi-slice data through a biologist-friendly interface. ➡️ genomebiology.biomedcentral.com/articles/10.11… #singlecell #spatialomics #spatialbiology

Filip Karlsson … Simon Fredriksson presented the Proximity Network Assay (PNA), a DNA-based method for constructing three-dimensional nanoscale maps of 155 proteins in single cells without the use of optics. ➡️ biorxiv.org/content/10.110… #singlecell #spatialomics #spatialbiology

Pandey et al. developed a pan-cancer R package called TCGAimmunosurv that integrates bulk RNA-Seq data from The Cancer Genome Atlas (TCGA) with scRNA-Seq data to identify the genes to investigate mutation-specific immune dynamics: ➡️ sciencedirect.com/science/articl… #singlecell

Scoones et al. presented a comparative analysis of long-read scRNA-seq protocols on PacBio and Oxford Nanopore platforms, incorporating MAS-seq and targeted CRISPR-based depletion to remove highly expressed transcripts prior to sequencing ➡️ biorxiv.org/content/10.110… #singlecell

Zhiqiang Jia … Hanbin Ma developed an active-matrix digital microfluidic platform that realizes fully automated biological procedures for intelligent single-cell sample manipulation. ➡️ nature.com/articles/s4137… #singlecell #spatialomics #spatialbiology #spatialtranscriptomics

Patysheva et al. investigated systemic and local immune landscape of patients with triple-negative breast cancer during the first course of neoadjuvant chemotherapy (NAC) and identified factors contributing to chemotherapy resistance. ➡️nature.com/articles/s4154… #singlecell

Xiangyu Wang … Xiaofeng Gu developed molecular atlas of rice, one of the world’s major crops by applying single-cell multi-omics to over 116,000 cells from eight organs. ➡️ nature.com/articles/s4158… #singlecell #spatialomics #spatialbiology #spatialtranscriptomics

ASCA together with MGI and Helicon will hold the workshop “Stereo-seq: Spatial Transcriptomics” 📍Registration opens at July 14 📍Registration deadline is September 22 📍Workshop is being held on November 11-14, 2025 📍Tomsk, Russia ➡️ ascanet.org/events/ASCA-MG… #singlecell

Ji et al. introduced CAPTAIN, a multimodal foundational model pretrained on over four million single cells with concurrently measured transcriptomes and a curated repertoire of 382 surface proteins across diverse human and mouse tissues. ➡️ biorxiv.org/content/10.110… #singlecell

Dear colleagues! We are going on a short summer vacation. We wish you a bright and eventful summer! See you in August! 🌞 ASCA Team #ASCAinfo #singlecell

⚡Despite our short vacation, we are pleased to announce ASCA-SEEKGENE-SESANA Workshop "Single Cell Multiome ATAC and RNA-seq on a Genolab M platform". 📍October 27-29, 2025 📍Registration deadline is September 22, 2025 📍Tomsk, Russia ➡️ ascanet.org/events/ASCA-OC… #singlecell

⚡The First Master’s Program in Bioinformatics Focusing on Single Cell Multiomics is open. ➡️Application deadline: August 20, 2025 ➡️ master-omics.ru #ASCAinfo #singlecell #spatialomics

⚡After a vacation, we are ready to share news in the single cell and spatial world. Here, you can find a list of key discoveries published last month: ➡️ linkedin.com/feed/update/ur… #singlecell #spatialomics #spatialbiology #spatialtranscriptomics #singlecellanalysis

Dmitriy Semenov ... Elena Kuligina used scRNA-seq to compare transcriptional responses in human glioma cells, non-malignant brain cells, and immortalized glioblastoma U87 MG cells following infection with the oncolytic virus VV-GMCSF-Lact. ➡️ mdpi.com/1422-0067/26/1… #singlecell

Lee et al. presented a single-nucleus and spatial transcriptomic atlas of the model plant Arabidopsis spanning ten developmental stages, encompassing over 400,000 nuclei from all organ systems and tissues — from seeds to developing siliques ➡️ nature.com/articles/s4147… #singlecell

Sarah Dobner ... Laura de Rooij presented the Human Aging Endothelial Cell Atlas (HAECA), a harmonized single-cell transcriptomic compendium of over 375,000 endothelial cells from 12 human tissues throughout adulthood. ➡️ biorxiv.org/content/10.110… #singlecell #spatialomics

Furtwängler et al. leveraged recent technological advances in single-cell proteomics by Mass Spectrometry to generate a dataset of an in vivo differentiation hierarchy encompassing over 2500 human CD34+ hematopoietic stem and progenitor cells: science.org/doi/10.1126/sc… #singlecell