C
Cole Trapnell
Researcher at University of Washington
Publications - 148
Citations - 101469
Cole Trapnell is an academic researcher from University of Washington. The author has contributed to research in topics: Biology & Gene. The author has an hindex of 57, co-authored 123 publications receiving 84590 citations. Previous affiliations of Cole Trapnell include Iowa State University & Massachusetts Institute of Technology.
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Journal ArticleDOI
Integrated Single Cell Transcriptomics Defines an Engineered Niche Supporting Hematopoietic Stem Cell Development Ex Vivo
Brandon Hadland,Brandon Hadland,Barbara Varnum-Finney,Stacey Dozono,Tessa Dignum,Cynthia Nourigat-Mckay,Dana Jackson,Shahin Rafii,Cole Trapnell,Irwin D. Bernstein,Irwin D. Bernstein +10 more
TL;DR: These studies enhance the understanding of the core signal pathways necessary for the embryonic development of functional HSC, with the potential to advance in vitro engineering of therapeutically relevant pluripotent stem cell-derived HSC in stromal cell-free culture.
Posted ContentDOI
Single-cell analysis of chromatin and expression reveals age- and sex-associated alterations in the human heart
David F. Read,Gregory T. Booth,Riza M. Daza,Dana Jackson,Rula J Green Gladden,Sanjay Srivatsan,Brent Ewing,Jennifer M. Franks,Cailyn H. Spurrell,Anne Roshella Gomes,Diana R. O’Day,Aishwarya A. Gogate,Beth Martin,Lea M. Starita,Yiing Lin,Jay Shendure,Shin Lin,Cole Trapnell +17 more
TL;DR: Predictive models of cell-type-specific RNA expression levels utilizing ATAC-Seq profiles to link distal regulatory sequences to promoters are trained, quantifying the predictive value of a simple TF-to-expression regulatory grammar and identifying cell- type-specific TFs.
Posted ContentDOI
Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies
Natasha Edman,Rachel L. Redler,Ashish Phal,Thomas Schlichthaerle,Sanjay Srivatsan,Ali Etemadi,Seong-Jun An,Andrew H. Favor,Devon D Ehnes,Zhe Li,Florian Praetorius,Max Gordon,Wei Yang,Brian Coventry,Derrick R. Hicks,Longxing Cao,N. Bethel,Piper Heine,Analisa Murray,Stacey Gerben,Lauren Carter,Marcos C. Miranda,Babak Negahdari,Sangwon Lee,Cole Trapnell,Lance Stewart,Damian C. Ekiert,Joseph Schlessinger,Jay Shendure,Gira Bhabha,Hannele Ruohola-Baker,D. Baker +31 more
TL;DR: In this paper , a de novo designed fibroblast growth-factor receptor (FGFR) binding module was incorporated into cyclic homo-oligomers with up to 8 subunits using repeat protein building blocks that can be modularly extended.
Posted ContentDOI
A single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pup
Chengxiang Qiu,Beth Martin,Ian C. Welsh,Riza M. Daza,Xingfan Huang,Eva Nichols,Diana R. O’Day,Anne Roshella Gomes,Saskia Ilcisin,Sanjay Srivatsan,Xinxian Deng,Christine M. Disteche,William Noble,Nobuhiko Hamazaki,David Kimelman,Junyue Cao,Alexander F. Schier,Malte Spielmann,Stephen A. Murray,Cole Trapnell,Jay Shendure +20 more
TL;DR: The authors applied single cell combinatorial indexing (sci-*) to profile the transcriptional states of 12.4 million nuclei from 83 precisely staged embryos spanning late gastrulation (embryonic day 8 or E8) to birth (postnatal day 0 or P0), with 2-hr temporal resolution during somitogenesis, 6-hr resolution through to birth, and 20-min resolution during the immediate postpartum period.
Xanthomonas spp. Specificity of Plant Pathogenic Offer Insight into Host and Tissue Two New Complete Genome Sequences
Jan E. Leach,Frank F. White,V. Sonti,Seiji Tsuge,Volker Brendel,Pamela C. Ronald,Valérie Verdier,J. Maxwell Dow,Boris Szurek,Casiana M. Vera-Cruz,Alok Pandey,Vikas Sharma,Steven A. Sullivan,Gopaljee Jha,Hiromichi Ishihara,George Dimitrov,R. Madupu,Daniel D. Sommer,Cole Trapnell,M. Phillippy,Daniela Puiu,Michael C. Schatz,Misha L. Rajaram,Arthur L. Delcher,Van Sluys,Robert P. Ryan,Damien F. Meyer,Samuel V. Angiuoli,Prabhu B. Patil,Adam J. Bogdanove,Ralf Koebnik,Hong Lu +31 more