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Thrilled to share our new paper, jointly with Sasha Rudensky, spearheaded by Ari Glasner, Sam Rose and Roshan Sharma. While deleting genes is the current rave, this paper shows the awesome power of deleting entire cell types, T-regs in this example: rdcu.be/da7x1

Favorite players right now: Musiala, Mitoma, Coman, Gavi, Odegaard

our paper out today in ⁦Science Magazine⁩ showing how plasticity in early cancer progression influences cells’ ability to communicate w/ their environment! huge thank you & congrats ⁦Direna Alonso-Curbelo⁩ ⁦⁦Lowe Lab⁩ ⁦dana_peer⁩! science.org/doi/10.1126/sc…

Excited to share a new preprint of my work in the Wysocka lab! We show how a composite DNA motif enables selective TF cooperativity between members of two of the largest TF families in humans to shape face and limb development. biorxiv.org/content/10.110… 1/

🎉Exciting News!🧬🔬 I’m starting a computational biology lab at Memorial Sloan Kettering Cancer Center in NYC! We're hiring at all levels to study how histological transformation and other forms of lineage plasticity drive progression across cancer types! joechanlab.org

RNA is informant and agent. Controlled RNA export from cells could enable cell-cell delivery of functional and non-destructive tracking of cell dynamics. Our new paper, led by brilliant Felix Horns, engineers RNA export for both capabilities: authors.elsevier.com/sd/article/S00…

Just breaking: I'm thrilled to announce that I have successfully defended my Ph.D.! 🎓 Thank you to everyone who supported me along the way. 🙏 #PhDGraduate #ProudMoment

Super excited to share the first preprint from Karuna Ganesh Lab! An amazing collaboration with dana_peer, led by the phenomenal andrew moorman @f_cambuli and Ellie Benitez Memorial Sloan Kettering Cancer Center. Progressive #Plasticity during #ColorectalCancer #Metastasis. biorxiv.org/content/10.110…

In Nature Reviews Genetics today, we discuss recent advances in computational methods for #3Dgenome analysis, pointing to an integrative future. Apologies for any missed refs. Joint w/ @NCITomMisteli Frank Alber Yang Zhang Lorenzo Boninsegna Muyu "Wendy" Yang. 4DNucleome nature.com/articles/s4157…

New in Nature Biotechnology, MSK’s Russell Zhang Kunes, Thomas Walle, dana_peer & team designed Spectra — an algorithm that combines user-provided gene programs with the detection of novel programs — to unravel heterogeneity in large-scale scRNA-seq studies. nature.com/articles/s4158…

Check out our paper and the accompanying perspective by Kuhlman published today in Science Magazine about the surprising role of short tandem repeats in regulating eukaryotic transcription! science.org/doi/10.1126/sc… science.org/doi/10.1126/sc… A thread (1/11):

Super excited to share the final publication of Spectra, fruit of the wonderful collaboration between Russell Zhang Kunes and Thomas Walle, a gene program factorization program that I hope will help many interpret and bring insight from their single-cell data -->

Because our genome is so much more than genes. A must-read for those eager to learn of the intricacies of non-coding sequences, in this case short tandem repeats, that define cell states: science.org/doi/abs/10.112…

What gets erased when you integrate #singlecell data across samples/studies, and can you get it back? When samples are from e.g. healthy & disease, should you simply massage cells together? FINALLY, I feel we can answer this question: doi.org/10.1101/2023.0…

With gratitude in my heart and fire in my belly, I am thrilled to receive an R37 MERIT award from National Cancer Institute NIH to understand how disordered chromatin in cohesin mutant MDS alters leukemia transformation Herbert Irving Comprehensive Cancer Center Columbia Medicine Columbia Stem Cell Initiative (CSCI) Columbia Genetics and Development Department @NCICancerBio

Memorial Sloan Kettering Cancer Center Columbia University DKFZ Universitätsklinikum Heidelberg VomLaborInDiePraxis HHMI dana_peer Russell Zhang Kunes Thomas Walle Spectra: new insights to improve immunotherapy treatments #NBTintheNews via Drug Target Review drugtargetreview.com/news/111866/sp…

Today starts a new era of genome engineering! We use RNA-only delivery to safely and efficiently deliver genes of interest to the human genome! Collins Lab UC Berkeley MCB A thread 🧵: nature.com/articles/s4158…

Is DNA all you need? Introducing Evo, a long context 7B foundation model for biology Evo has SOTA *zero-shot* prediction across DNA, RNA, and protein modalities Evo can generate DNA, RNA+proteins & make CRISPR-Cas systems for first time blog …n-model-tool-arc-institute.vercel.app/news/blog/evo

Super excited to announce that our work “Wasserstein Wormhole: Scalable Optimal Transport with Transformer” has been accepted to #ICML2024! Wormhole is method to find OT-preserving embeddings for massive cohorts of points clouds. arxiv.org/abs/2404.09411

I am thrilled to share with the world a new preprint, spearheaded by the truly amazing Jose Reyes in partnership with Lowe Lab. Focused on the benign to malignant transition in PDAC, uncovering roles of plasticity, tissue remodeling and P53 -> biorxiv.org/content/10.110…