A just-published paper in Nature Biotechnology from the lab of C4E Director Bing Ren describes a novel technique, Droplet Hi-C, for profiling chromatin both more effectively and at a lower cost. The paper also sheds new light on extra-chromosomal DNA.

how does PCA projection work? How do KNN and MNN for label transferring work in Seurat? A blog post on how I attempt to understand it at a low level. #singlecell #bioinformatics RT if you like it! divingintogeneticsandgenomics.com/post/pca-proje…

Delighted to share new work from our lab: MultiPerturb-seq 🎛️❌📥📤 Over the last few years, we've been combining CRISPR screens with multimodal readouts of gene expression (RNA) and chromatin accessibility (DNA). In this study, we bring those together within the same cells.

Happy to see this was published yesterday! It was great working on this with Shankar and Shifaan Thowfeequ. And thank you to the great editorial team at Nature Reviews Molecular Cell Biology.

Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling nature.com/articles/s4158…

VACANCY: Postdoctoral Research Scientist Join the Rugg-Gunn lab as they seek to understand early human development. Deadline: 5th January babrahaminstitute.livevacancies.co.uk/#/job/details/…

2. learning-bioinformatics-at-home github.com/harvardinforma… I started this repo 5 years ago at Harvard FAS informatics.

Modeling early gastrulation in human blastoids with DNA methylation patterns of natural blastocysts: Cell Stem Cell cell.com/cell-stem-cell…

We present MethylTree to accurately infer cellular lineages based on DNA methylation epimutations, which really enables noninvasive lineage tracing in humans and non-human primates. Thanks specially to shouwen wang. nature.com/articles/s4159…

dscHi-C allows us to investigate chromatin reorganization during mouse brain aging, while dscHi-C-Multiome reveals the complex relationship between genome structure and gene regulation. Learn more here: nature.com/articles/s4142…

Super excited to share our new study from the Jason Buenrostro Lab in nature! We developed a computational method for tracking transcription factor and nucleosome binding using single-cell ATAC-seq and deep learning. Paper: nature.com/articles/s4158…

📢 CUT&Tag version 3 Sometimes the preprint to paper route can be quite the odyssey. And so in that vein, we are delighted to give you version 3 of our CUT&Tag optimization and benchmarking manuscript: biorxiv.org/content/10.110…

happy to see our cell2fate model out at Nature Methods. It is a completely new take on RNA velocity to disentangle complex cell trajectories from scRNA data & we have some very cool applications coming up! nature.com/articles/s4159…

Interested in single cell genomics but need help getting started? Check out the full agenda for our Single Cell Genomics Day on Friday 4/25. All talks will be live-streamed (no registration required) at satijalab.org/scgd25

How can causal machine learning be applied to single-cell genomics to understand the true biological mechanisms underlying cellular processes?Nature Genetics TU München "Causal machine learning for single-cell genomics" • Advances in single-cell '-omics' technologies combined

Multiomics single-cell optimal transport moscot.spatiotemporal An #OptimalTransport-based common coordinate framework to map & align #SpatialTranscriptomics with single-cell/-nucleus omics data scalable for millions of cells across multiple time points vs Tangram gimVI

Absolutely thrilled to share with you the final version of EPIclone, out now (open access) in nature. This has been an amazing collaboration with the lab of Lars Velten (@larsplus) at Centre for Genomic Regulation (CRG) nature.com/articles/s4158…

Evaluating methods for the prediction of cell-type-specific enhancers in the mammalian cortex dlvr.it/TKvngd

Expansion in situ genome sequencing links nuclear abnormalities to aberrant chromatin regulation science.org/doi/10.1126/sc… Science Magazine Jason Buenrostro Ajay Labade Caroline Comenho

Now out in the July 10th issue of Cell LoxCode in vivo barcoding reveals epiblast clonal fate bias to fetal organs: Cell cell.com/cell/fulltext/…