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
Improving RNA-Seq expression estimates by correcting for fragment bias
Adam B Roberts,Cole Trapnell,Cole Trapnell,Julie Donaghey,John L. Rinn,John L. Rinn,Lior Pachter +6 more
TL;DR: Improvements in expression estimates as measured by correlation with independently performed qRT-PCR are found and correction of bias leads to improved replicability of results across libraries and sequencing technologies.
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Computational methods for transcriptome annotation and quantification using RNA-seq
TL;DR: The major conceptual and practical challenges of high-throughput RNA sequencing, the general classes of solutions for each category, and the interdependence between these categories are highlighted and discussed.
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Single-cell mRNA quantification and differential analysis with Census
TL;DR: The Census algorithm is introduced to convert relative RNA-seq expression levels into relative transcript counts without the need for experimental spike-in controls and it is demonstrated that Census enabled robust analysis at multiple layers of gene regulation.
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Comprehensive single-cell transcriptional profiling of a multicellular organism
Junyue Cao,Jonathan S. Packer,Vijay Ramani,Darren A. Cusanovich,Chau Huynh,Ray A. M. Daza,Xiaojie Qiu,Choli Lee,Scott N. Furlan,Scott N. Furlan,Scott N. Furlan,Frank J. Steemers,Andrew Adey,Andrew Adey,Robert H. Waterston,Cole Trapnell,Jay Shendure,Jay Shendure +17 more
TL;DR: The authors profiled almost 50,000 single cells from an individual Caenorhabditis elegans larval stage and were able to identify and recover information from different, even rare, cell types and develop combinatorial indexing strategies to profile the transcriptomes of single cells or nuclei.
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Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing.
Darren A. Cusanovich,Riza M. Daza,Andrew Adey,Hannah A. Pliner,Lena Christiansen,Kevin L. Gunderson,Frank J. Steemers,Cole Trapnell,Jay Shendure +8 more
TL;DR: Combinatorial cellular indexing, a strategy for multiplex barcoding of thousands of single cells per experiment, was successfully used to investigate the genome-wide chromatin accessibility landscape in each of over 15,000 single cells, avoiding the need for compartmentalization of individual cells.