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Can not believe that it is my first week as a @PI at St. Anna Children's Cancer Research Institute CCRI ! I feel very welcomed and super excited about the future. We plan to work on mystery of pediatric cancer initiation, cell fate decisions modeled in @organoids. Will be announcing the PhD positions soon! 👩🏻‍🔬 🧫🔬🎉

Excited to share our latest paper led by Rachel Glenn. We generated a genetically diverse mouse pluripotent stem cell panel from the Diversity Outbred stock and outline experimental approaches for "population-scale" in vitro directed differentiation. biorxiv.org/content/10.110…

Excited to share our lab’s latest preprint exploring how mutations and transcriptional cell states cooperate to drive therapeutic resistance in Ph+ B cell acute lymphoblastic leukemia (Ph+ ALL)! (1/14) biorxiv.org/content/10.110…

Tomorrow, 2024-06-24, at 18:00 CEST will be another community meeting! Louis Faure will talk about about scFates (github.com/LouisFaure/scF…), a scalable Python suite for fast tree inference and advanced pseudotime downstream analysis, with a focus on fate biasing.

Excited to share our newest pre-print by Xueqian Zhuang on how aging suppresses tumorigenesis and stemness in the lung by promoting a functional iron insufficiency in the alveolar epithelium. Interestingly, this renders aged cells resistant to ferroptosis: biorxiv.org/content/10.110…

Clonal expansions can remodel entire tissues even when they appear normal, but what mechanisms drive this? And how do these processes differ from tumorigenesis? Out nature, we identify distinct TNF programs during tumor evolution. 🧵 nature.com/articles/s4158…

Excited to share our preprint "Multiome Perturb-seq unlocks scalable discovery of integrated perturbation effects on the transcriptome & epigenome". This work extends single-cell CRISPR screens to simultaneously profile gene expression & chromatin accessibility.

On bioRxiv today, we raise serious concerns over a recent @nature paper describing ReDeeM, a new single-cell mitochondrial DNA (mtDNA) sequencing / analysis method. Here are three things that you need to know: 1/n biorxiv.org/content/10.110…

Can we recreate the transcriptional states seen in single-cell atlas projects? In our new preprint we try to do this using large-scale Perturb-seq experiments. Along the way we discuss off-target effects of CRISPR epigenetic editors and identify drivers of key fibroblast states.

new out in Nature nature.com/articles/s4158…

Our latest preprint is out! 🚨We discovered that intestinal stem cells actively fight bacterial infections. Learn more about it in our new study by Sacha LEBON in collaboration with Matan biorxiv.org/content/10.110…

Out today, our exciting study showing how TGFb secretion by Tet2-mutant CH macrophages is a druggable resistance mechanism in Anaplastic Thyroid Cancer. Ross Levine Pablo Sánchez Vela Richard Koche Memorial Sloan Kettering Cancer Center

🎉Excited to present our latest work out today nature 1.What gives a leukemia its phenotype – the oncogenic driver or the differentiation stage of the cell-of-origin? 2.Why do RAS mutations always happen late in AML? 3.Who will relapse after VEN? nature.com/articles/s4158…

Thrilled to share our paper now out nature delineating #plasticity during #CRC #metastasis, a fantastic collaboration led by Andrew Moorman Ellie Benitez, and @f_cambuli from the Karuna Ganesh Lab and @dana_per lab! nature.com/articles/s4158… rdcu.be/dYAVK. A 🧵

(1) How can we build complex structures from a limited set of progenitors and cell types? In our new preprint, we describe patterns of cell fate decisions during early development and (in some cases) identify molecular correlates of different behaviors. biorxiv.org/content/10.110…

Several years in the making (and aging), Xueqian Zhuang 's study on aging is out today nature. She finds, surprisingly, that aging suppresses tumorigenesis and stemness in the lung by promoting a functional iron insufficiency in the alveolar epithelium. nature.com/articles/s4158…

PERFF-seq is out today in Nature Genetics! Our recent thread summarizes why we are excited about the prospects of programmable nucleic acid cytometry for studying rare cell states. nature.com/articles/s4158…

I’m excited to share my work over the last few years with Jason Buenrostro! Chronic inflammation creates an epigenetic memory in colonic stem cells, priming them for tumor growth: tinyurl.com/ColitisNagaraj…. Here’s a walkthrough of what we found (🧵)

What protects individuals from developing blood cancers? Thrilled to share my work in Vijay Sankaran lab, describing inherited resilience protecting blood stem cells from clonal hematopoiesis by modifying RNA regulation. 🧵👇(1/n) biorxiv.org/content/10.110…

Finally out in Nature our collaboration with the Velten Lab 🥰 Enjoy the reading! nature.com/articles/s4158…