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D-Index & Metrics

Genetics

D-Index
73
Citations
138501
World Ranking
1989
National Ranking
905

Research.com Recognitions

  • 2015 - Fellow of Alfred P. Sloan Foundation

Overview

Cole Trapnell is affiliated with the University of Washington in the United States. Their research primarily falls within Biochemistry, Genetics and Molecular Biology, where they have contributed to 201 publications. Within this main field, their work touches on several subfields including Molecular Biology, Immunology, Cell Biology, Biophysics, and Cancer Research.

The scientist's research topics prominently include Single-cell and spatial transcriptomics, Zebrafish Biomedical Research Applications, RNA Research and Splicing, Genomics and Chromatin Dynamics, Cell Image Analysis Techniques, Congenital heart defects research, and Retinal Development and Disorders.

Recent papers authored or co-authored by Cole Trapnell demonstrate a focus on cellular and developmental biology at high resolution. These include:

  • A human cell atlas of fetal gene expression, 2020, Science
  • A human cell atlas of fetal chromatin accessibility, 2020, Science
  • Single-Cell Transcriptomic Comparison of Human Fetal Retina, hPSC-Derived Retinal Organoids, and Long-Term Retinal Cultures, 2020, Cell Reports
  • Embryo-scale, single-cell spatial transcriptomics, 2021, Science
  • Dimensionality reduction by UMAP to visualize physical and genetic interactions, 2020, Nature Communications

Their frequent co-authors include Jay Shendure, Sanjay Srivatsan, Dana L. Jackson, Lauren M. Saunders, and Brandon Hadland, indicating active collaboration within a network of researchers in related fields.

Cole Trapnell's publications are often found in venues such as bioRxiv (Cold Spring Harbor Laboratory), eLife, Science, SSRN Electronic Journal, and Experimental Hematology, reflecting a pattern of dissemination across high-impact journals as well as preprint servers.

The researcher received the title of Fellow of the Alfred P. Sloan Foundation in 2015, which is an acknowledgment of their contributions within their scientific domain.

Best Publications

  • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

    Ben Langmead;Cole Trapnell;Mihai Pop;Steven L Salzberg

  • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

    Cole Trapnell;Cole Trapnell;Brian A Williams;Geo Pertea;Ali Mortazavi

  • TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

    Daehwan Kim;Daehwan Kim;Geo Pertea;Cole Trapnell;Cole Trapnell;Harold Pimentel

  • TopHat: discovering splice junctions with RNA-Seq

    Cole Trapnell;Lior Pachter;Steven L. Salzberg

  • Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

    Cole Trapnell;Adam Roberts;Loyal Goff;Loyal Goff;Loyal Goff;Geo Pertea

  • The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

    Cole Trapnell;Davide Cacchiarelli;Davide Cacchiarelli;Jonna L Grimsby;Prapti Pokharel

  • Differential analysis of gene regulation at transcript resolution with RNA-seq

    Cole Trapnell;David G Hendrickson;David G Hendrickson;Martin Sauvageau;Martin Sauvageau;Loyal Goff;Loyal Goff

  • Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

    Moran N. Cabili;Cole Trapnell;Cole Trapnell;Loyal Goff;Magdalena J. Koziol;Magdalena J. Koziol

  • Reversed graph embedding resolves complex single-cell trajectories.

    Xiaojie Qiu;Qi Mao;Ying Tang;Li Wang

  • The single-cell transcriptional landscape of mammalian organogenesis

    Junyue Cao;Malte Spielmann;Xiaojie Qiu;Xingfan Huang

  • 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

  • Single-cell mRNA quantification and differential analysis with Census

    Xiaojie Qiu;Andrew J Hill;Jonathan S Packer;Dejun Lin

  • Computational methods for transcriptome annotation and quantification using RNA-seq

    Manuel Garber;Manfred G Grabherr;Mitchell Guttman;Cole Trapnell;Cole Trapnell

  • Comprehensive single-cell transcriptional profiling of a multicellular organism

    Junyue Cao;Jonathan S. Packer;Vijay Ramani;Darren A. Cusanovich

  • Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing.

    Darren A. Cusanovich;Riza Daza;Andrew Adey;Hannah A. Pliner

  • Identification of novel transcripts in annotated genomes using RNA-Seq

    Adam Roberts;Harold Pimentel;Cole Trapnell;Lior Pachter

  • Joint profiling of chromatin accessibility and gene expression in thousands of single cells

    Junyue Cao;Darren A. Cusanovich;Vijay Ramani;Delasa Aghamirzaie

  • Defining cell types and states with single-cell genomics.

    Cole Trapnell

  • A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

    Darren A. Cusanovich;Andrew J. Hill;Delasa Aghamirzaie;Riza M. Daza

  • Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data.

    Hannah A. Pliner;Jonathan S. Packer;José L. McFaline-Figueroa;Darren A. Cusanovich

Frequent Co-Authors

Jay Shendure
Jay Shendure University of Washington
John L. Rinn
John L. Rinn University of Colorado Boulder
Loyal A. Goff
Loyal A. Goff Johns Hopkins University School of Medicine
Steven L. Salzberg
Steven L. Salzberg Johns Hopkins University
Lior Pachter
Lior Pachter California Institute of Technology
Tarjei S. Mikkelsen
Tarjei S. Mikkelsen Arsenal Biosciences (United States)
Irwin D. Bernstein
Irwin D. Bernstein Fred Hutchinson Cancer Research Center
Alexander Meissner
Alexander Meissner Max Planck Institute for Molecular Genetics
Michael C. Schatz
Michael C. Schatz Johns Hopkins University
Eric S. Lander
Eric S. Lander Broad Institute

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