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How we think and talk about mitochondria matters to our science and to newcomers in the field. The powerhouse analogy is expired and we need specific vocabulary to capture the beautiful complexity of mitochondrial biology. We propose a framework and some nomenclature.

Our preprint on the development of PerturbView, an Optical Pooled Screening (OPS) technology, is out! Massive thanks to Eric Lubeck for driving the project with me, along with our fantastic mentors, Orit Rozenblatt-Rosen, Levi A. Garraway and Aviv Regev biorxiv.org/content/10.110… 1/

Check out the new optical pooled screening (OPS) technology, PerturbView, from my fantastic mentor, Taka Kudo! ⬇️ PerturbView enables image-based perturbation screens in tissue with spatial transcriptomics phenotyping.

Spatial analysis is converging with pooled CRISPR screens in a recent series of preprints w/ different guide readouts: 1. RCA biorxiv.org/content/10.110… 2. in situ txn + FISH biorxiv.org/content/10.110… 3. in situ txn + in situ seq biorxiv.org/content/10.110… Exciting for tissue biology!

PerturbView enables in vivo CRISPR screens with single cell spatial resolution (biorxiv.org/content/10.110…). CRISPR sgRNA are uniquely identified over 6 rounds of in situ sequencing. Attached is an animation of in situ sequencing of sgRNAs in a tumor xenograft (1/4)

SC-VAE: A Supervised Contrastive Framework for Learning Disentangled Representations of Cell Perturbation Data biorxiv.org/content/10.110…

Our latest in nature: Convergence of coronary artery disease genes on endothelial cell programs nature.com/articles/s4158… Incredible work led by Gavin Schnitzler and Helen Kang — a long-standing partnership between our lab and Raj Gupta My comments below: 1/

🗣️wahoo!!! my doctoral work is out online in Cell: authors.elsevier.com/c/1ie1VL7PXqPm4!! couldn't have done it without my two wonderful labs and co-advisors Stanley Qi Lab & @MackallLab we developed a new RNA-targeting CRISPR platform (MEGA) to engineer better T cell therapies...🧵

So much to learn still about enhancer-promoter interactions! 🥸🤓

(1/2) New paper from KL Kim Gilbert J. Rahme (He/him/his) Brad Bernstein Gene Regulation Observatory with RCMC contribution from Viraat Goel ASHansen Lab sciencedirect.com/science/articl… Quantitative dissection of how loss of a CTCF insulator boundary in GIST causes aberrant enhancer-oncogene interactions

An elegant solution for 2-plex perturbation screens! And great care was put into minimizing lentiviral recombination. Great work 🤓

Excited to share Sarah's new review on BiDirectional Promoters (BDPs). Sarah discusses 6 molecular mechanisms that may account for unique transcriptional properties of BDP with a focus on noise regulation and co-expression: authors.elsevier.com/a/1jI5c,LqArU0…

Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment. nature.com/articles/s4158…

🧬GWAS is fundamental in drug discovery, linking disease to genetic variants. However, studying rare and uncommon diseases with GWAS is hard due to the huge sample sizes required. How can we use AI to help GWAS with small cohorts? In a multi-year collaboration GSK