The Herbert and Florence Irving Institute for Cancer Dynamics will continue its seminar series on the topic of mathematical sciences underpinning cancer research. The monthly seminars take place on the second Wednesday of the month, 2:00-3:00 PM EST. The presentations are open to the Columbia community (in person and online) and to researchers outside Columbia (via Zoom).
On Wednesday, January 15th (2:00 PM ET), IICD welcomes Cole Trapnell, Associate Professor, Department of Genome Sciences, University of Washington. Seminar hosted by José McFaline-Figueroa. The seminar will take place in person in Schermerhorn Hall 603 (Morningside Heights campus). If you wish to attend the seminar remotely, please register using the following link: https://columbiauniversity.zoom.us/meeting/register/tJEvcuCqrD8jGdyUzycUFquK7lEvmqMvfOWc
Title: Embryo-Scale Single-Cell Chemical Transcriptomics Reveals Dependencies Between Cell Types and Signaling Pathways
Abstract: Organogenesis is a highly organized process that is conserved across vertebrates and is heavily dependent on intercellular signaling to achieve cell type identity. We lack a detailed understanding of how developing cell types in each organ and tissue depend on developmental signaling pathways. To address this gap in knowledge, we applied highly multiplexed, scalable and temporally controlled in vivo chemical perturbations to comprehensively dissect individual signaling pathways’ (BMP, FGF, Notch, RA, Shh, TGF-β & Wnt) roles during organogenesis in the zebrafish embryo, allowing us to detect signaling pathway regulation even in very rare cell types. Focusing
on the development of the pectoral fin, for example, we show how this database leads to novel understandings of cell type specification by intercellular signaling during development. This resource will be widely applicable for investigators wanting to quickly assess the role of the major signaling pathways during the formation of their tissue of interest.
Bio: Cole Trapnell is a Professor of Genome Sciences at the University of Washington. He received his PhD in Computer Science at the University of Maryland and has formal training in both computational and experimental biology. As a graduate student with Steven Salzberg and Lior Pachter, Dr. Trapnell wrote “TopHat” and “Cufflinks”, two widely used tools for transcriptome sequencing (RNA-seq) analysis. He also co-developed (with Ben Langmead) the ultrafast short read alignment program “Bowtie”. As a postdoctoral fellow, Dr. Trapnell augmented his computational work with experimental training focused on analysis of cell differentiation, and developed “single-cell trajectory analysis”, an approach for studying cell differentiation using single-cell RNA-Seq. Dr. Trapnell’s lab has introduced computational tools extracting biological insights from single-cell data, such as “Monocle”, as well as experimental workflows for ultra- scalable single-cell molecular profiling experiments. The lab has used these tools to explore pancreatic islet development, olfactory neurogenesis, and thyroid hormone-dependent pigmentation, and is currently applying them to dissect the genetic program of zebrafish embryonic development. Dr Trapnell is a recipient of ISCB Overton Prize (2018), NIH Director’s New Innovator Award and Alfred P. Sloan Foundation Research Fellowship (2015), and Damon Runyon Dale F. Frey Award for Breakthrough Scientist (2014).