Cole Trapnell Lab, cole-trapnell-lab has 36 repositories available.

Cole Trapnell Lab, Identify new marker genes. Cole Trapnell Associate Professor, Dept. Gautier et al. io/monocle3/docs/trajectories Monocle3の基本的な使い方 それでは実際にMonocle3を使っていきます。 まずはMonocle3でUMAPとt-SNEを描画するところまでやってみます。 データロード Cao & Packerらの線虫データをロードしていきます。 Pseudotime analysis To model differentiation trajectories, we performed trajectory analysis using Monocle 2 (http://cole-trapnell-lab. Many researchers are using single-cell RNA-Seq to discover new cell types. identify the YAP/TAZ-TEAD4-FOSL2 complex as a core regulatory circuitry in mesenchymal neuroblastoma cells and demonstrate its central role in plasticity from noradrenergic to mesenchymal states. The mission of the Trapnell lab is to understand how our genome encodes the program of our development and the role this program plays in disease. We develop and apply genomic tools, especially single-cell sequencing, to a variety of in vitro and animal model systems. We are grateful to Sharif Bordbar, Chris Zhu, Amy Wagers and the Broad RNAi platform for technical assistance, and Magali Soumillon for helpful discussions. His lab combines experimental and computational approaches to dissect gene regulatory networks. [5] The Trapnell Lab at the Allen Institute develops computational and experimental approaches to study gene regulation and cell differentiation — building tools and open datasets that power single-cell biology. Cole Trapnell is a Damon Runyon Postdoctoral Fellow. Apr 19, 2024 · Supporting healthy pregnancy outcomes requires a comprehensive understanding of the molecular and cellular programs of peri-implantation development, when most pregnancy failure occurs. io/monocle-release/docs, version 2. Scientific Co-Director, Seattle Hub for Synthetic Biology; Associate Professor of Genome Sciences, University of Washington at Allen Institute 3 days ago · The Brotman Baty Institute & The Seattle Hub for Synthetic Biology Jay Shendure, Cole Trapnell, Marion Pepper, Sud Pinglay, Nobuhiko (Nobu) Hamazaki Lea Starita, Doug Fowler, Jay Shendure, Andrew Stergachis. Here, we present single-cell transcriptomes of bovine peri-implantation embryo development at day 12, 14, 16, and 18 post-fertilization. github. Our work spans three broad areas illustrated below. cole-trapnell-lab has 36 repositories available. We defined the cellular composition and gene expression of The mission of the Trapnell lab is to understand how our genome encodes the program of our development and the role this program plays in disease. edu - Homepage single-cell genomics developmental genetics gene regulation Mar 27, 2024 · Summary Supporting healthy pregnancy outcomes requires a comprehensive understanding of the molecular and cellular programs of peri-implantation development, when most pregnancy failure occurs. At the University of Washington, his lab will focus on finding genes that govern stem cell maintenance and cell differentiation, primarily through single-cell genomics. Follow their code on GitHub. We defined the cellular composition and gene expression of 3 days ago · The Brotman Baty Institute & The Seattle Hub for Synthetic Biology Jay Shendure, Cole Trapnell, Marion Pepper, Sud Pinglay, Nobuhiko (Nobu) Hamazaki Lea Starita, Doug Fowler, Jay Shendure, Andrew Stergachis Dec 29, 2024 · https://cole-trapnell-lab. Monocle can help you purify them or characterize them further by identifying key marker genes that you can use in follow up experiments such as immunofluorescence or flow sorting. By rewiring the super-enhancer and transcriptomic landscape, these factors drive the acquisition of an invasive and drug-resistant phenotype in tumor cells. of Genome Sciences, University of Washington Verified email at uw. 0) as previously published 53. A UMI counts matrix was used as the input. 22. May 24, 2024 · The Trapnell Lab at the University of Washington's Department of Genome Sciences studies how genomes encode the program of vertebrate development and how that program goes awry in disease. Trapnell's research focuses on developing computational and genomic technologies to study how cells make fate decisions during development and disease. We defined the cellular composition and gene expression of embryonic disc Contribute to cole-trapnell-lab/monocle3 development by creating an account on GitHub. Cell lineage trajectories of FAPs were inferred and characterized at the single-nucleus level. The lab will operate at the interface between genomics and experimental cell biology to answer how cells make fate decisions. Mar 27, 2024 · Summary Supporting healthy pregnancy outcomes requires a comprehensive understanding of the molecular and cellular programs of peri-implantation development, when most pregnancy failure occurs. Monocle was originally built by Cole Trapnell and Davide Cacchiarelli, with substantial design input John Rinn and Tarjei Mikkelsen. 3h5, gkjz, ylijz, ux8t, ml4n, 2yzn, 2m4, hm0p, gotcr, sue6i6,