Week 9's reads: 🧬 RAEFISH: sequencing-free, whole-genome spatial profiling 🤖 SpatialRNA & gsMap: GNNs for tissue-level insights 🎯 GLACIER: causal inference meets spatial gene regulation open.substack.com/pub/behindtheb… #SingleCell #Bioinformatics #Genomics #SpatialOmics

Week 10: 🧠 SIMVI: disentangling spatial vs. intrinsic variation with deep generative models 🧬 scOMM: supervised integration of RNA & ATAC 🧹 OPT: catching off-target probe binding in Xenium spatial panels shorturl.at/fPzYP #SingleCell #Spatial #Bioinformatics

After a brief hiatus (sorry about that!), new deep dives on: -HyDrop v2: Low-cost scATAC-seq 💰 - ZEB2: Tumor macrophage master switch 🔍 - New spatial transcriptomics tools 🧩 - ecDNA micronucleation open.substack.com/pub/behindtheb… #Genomics #SingleCell #cancer #bioinformatics

New weekly reads! 📝 C2S-Scale: LLMs for gene expression → natural language 🔗 Bio-DTA: DNA + scRNA via dynamic token adaptation 🧪 Zero-shot eval: scGPT + Geneformer struggle w/o tuning 👉 open.substack.com/pub/behindtheb… #Bioinformatics #AI #Genomics #scRNAseq #FoundationModels

Weekly Reads: 📡 dominoSignal: differential cell–cell communication via TF activity 🧠 ChAIR: tri-omic single-cell + 3D genome maps across brain aging 🌲 Bonsai: tree-based, distortion-free visualizations open.substack.com/pub/behindtheb… #SingleCell #Bioinformatics #CancerBiology

Today in Science Magazine we report the development of a laboratory-evolved CRISPR-associated transposase (evoCAST) that supports therapeutically relevant levels of RNA-programmable gene insertion in human cells, a collaboration with Sternberg Lab. 1/13 drive.google.com/file/d/1I-UbCR…

How does tumour heterogeneity arise? How can we predict cancer cell plasticity? In 2 studies, we trace #glioblastoma heterogeneity to a spatial cancer cell trajectory w. atlassing bit.ly/4mkrWgs & predict plasticity w. snRNA/ATAC+deep learning bit.ly/3FbI6Ic 🧵

Weekly reads: 📉 CIN + cGAS–STING: instability fuels immune suppression in EAC 🌍 scCellFie: metabolic maps across 30M cells + tissues 🧫 BCR-MERFISH: in situ plasma cell clonality meets spatial transcriptomics shorturl.at/Wjfk2 #SingleCell #SpatialTranscriptomics #Cancer

Weekly reads 26/5/25 🧓 EPI-Clone: age-driven clonal drift in blood revealed by methylation 🧠 SFRP2⁺ CAFs & IL-33 macrophages: microenvironment blocks therapy 📊 Atlas Mapping Benchmarks: when your UMAP lies tinyurl.com/wr2606 #SingleCell #Spatial #Bioinformatics

Weekly Reads 1/6/25 🔥 Taurine fuels leukemia stem cells via glycolysis 🧼 SpotSweeper: spatial QC gets smarter 🌐 scVIVA: niche-aware modeling of cell states in tissue open.substack.com/pub/behindtheb… #SingleCell #SpatialTranscriptomics #CancerBiology #Bioinformatics #AI