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Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes dlvr.it/Sqvk60

Excited to introduce scKINETICS, an algorithm for joint inference of gene regulatory mechanism and cellular velocity, co-developed by the amazing duo of Cassandra Burdziak and Julia Zhao academic.oup.com/bioinformatics…

🔬🧬 Excited to share our latest study science.org/doi/10.1126/sc… Science Magazine developing ChromExM which uses expansion microscopy to visualize the chromatin, transcription, RNA POL II and pioneer factor Nanog during genome activation.

Sequence-based ML methods (Enformer, ChromBPNet...) are invaluable in genomics but the ecosystem for their *use* after training is less developed. Introducing, `tangermeme`: a PyTorch library for genomics discovery for everything-other-than-the-model. github.com/jmschrei/tange… 1.

Excited to share with the single-cell community the most recent work of Tomàs Montserrat Ayuso and AnnaEsteveCodina from CNAG, something we think will be a game-changer in #scRNAseq quality control: biorxiv.org/content/10.110… bioRxiv Get ready for the tweetorial! 1/10

By learning to embed DNA k-mers and cells into a joint space, CellSpace improves single-cell ATAC-seq analysis in multiple tasks such as latent structure discovery, transcription factor activity inference, and batch effect mitigation. nature.com/articles/s4159…

How can we better reveal cellular 🦠and sample🧍variation from large-scale scRNA-seq studies? We have released a new and improved deep generative model, #MrVI, in scvi-tools and on bioRxiv, accompanied by real-world use cases. A thread... 🧵1/ biorxiv.org/content/10.110…

Our work describing #TREM2 #macrophages in #obesity & #diabetes-associated #KidneyDisease is out. An exciting journey since first sighting #TREM2 macs in our kidney #scRNAseq in 2018 w Yiming, Katherine Anna Greka Broad Institute Huge 🙏🙏 to all coauthors dlvr.it/T7FFMb

Introducing pgBoost, by Elizabeth Dorans , using eQTL data to learn consensus variant-gene maps from 10x multiome data. pgBoost is particularly effective in mapping target genes to distal variants where genomic distance starts to underperform. Give it a read!

I am excited to share a part of my postdoctoral work that came out today in nature. We developed a single-cell nascent RNA sequencing method (scGRO-seq) that, among other applications, can help generate enhancer-gene maps. 🧵1/13 nature.com/articles/s4158…

Today we’re excited to freely share an early-version of, perhaps, the world’s most expansive genetics dataset: Logan. #bioinformatics #petabase #genetics #genomics #openscience biorxiv.org/content/10.110…

🧵 Thrilled to share our latest in nature! We’ve mapped fetal blood development in Down syndrome (DS) using single-cell multi-omics, studying why children with DS face a 150-fold higher leukemia risk and blood abnormalities at birth. nature.com/articles/s4158…

Hi all, I am currently on the academic job market. I am a postdoctoral researcher in Dr. Christina Leslie's lab at the Computational and Systems Biology Program at Memorial Sloan Kettering Cancer Center. My research focuses on deciphering causal and dynamic gene regulation

How are promoter interactions coordinated during cell differentiation? In our first paper, we investigate the temporal relationship between genome folding, transcription and histone modifications during ESC differentiation. (1)

Out in Nature Communications ! ChromaFold predicts 3D contact maps using single-cell ATAC-seq alone. nature.com/articles/s4146…

Excited to share our latest preprint, as part of ENCODE4, on a consensus variant-to-function (cV2F) score for functionally prioritizing variants for complex disease - led by Tabassum Fabiha and co-mentored with Alkes Price. biorxiv.org/content/10.110…