Cole Trapnell

Summary

Publications

  1. pmc Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
    Cole Trapnell
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Protoc 7:562-78. 2012
  2. pmc Improving RNA-Seq expression estimates by correcting for fragment bias
    Adam Roberts
    Department of Computer Science, 387 Soda Hall, UC Berkeley, Berkeley, CA 94720, USA
    Genome Biol 12:R22. 2011
  3. pmc Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre
    Ezgi Hacisuleyman
    1 Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA 2 Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA 3 Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA 4
    Nat Struct Mol Biol 21:198-206. 2014
  4. pmc Long noncoding RNAs regulate adipogenesis
    Lei Sun
    Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 110:3387-92. 2013
  5. pmc Differential analysis of gene regulation at transcript resolution with RNA-seq
    Cole Trapnell
    Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
    Nat Biotechnol 31:46-53. 2013
  6. pmc Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
    Moran N Cabili
    Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
    Genes Dev 25:1915-27. 2011
  7. ncbi request reprint The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
    Cole Trapnell
    1 Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA 2 The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA 3
    Nat Biotechnol 32:381-6. 2014
  8. pmc Transcriptional and epigenetic dynamics during specification of human embryonic stem cells
    Casey A Gifford
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Cell 153:1149-63. 2013
  9. doi request reprint Computational methods for transcriptome annotation and quantification using RNA-seq
    Manuel Garber
    Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
    Nat Methods 8:469-77. 2011

Collaborators

Detail Information

Publications9

  1. pmc Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
    Cole Trapnell
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Protoc 7:562-78. 2012
    ..The protocol's execution time depends on the volume of transcriptome sequencing data and available computing resources but takes less than 1 d of computer time for typical experiments and ∼1 h of hands-on time...
  2. pmc Improving RNA-Seq expression estimates by correcting for fragment bias
    Adam Roberts
    Department of Computer Science, 387 Soda Hall, UC Berkeley, Berkeley, CA 94720, USA
    Genome Biol 12:R22. 2011
    ..We find improvements in expression estimates as measured by correlation with independently performed qRT-PCR and show that correction of bias leads to improved replicability of results across libraries and sequencing technologies...
  3. pmc Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre
    Ezgi Hacisuleyman
    1 Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA 2 Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA 3 Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA 4
    Nat Struct Mol Biol 21:198-206. 2014
    ..Thus, our data suggest a model in which lncRNAs such as Firre can interface with and modulate nuclear architecture across chromosomes. ..
  4. pmc Long noncoding RNAs regulate adipogenesis
    Lei Sun
    Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 110:3387-92. 2013
    ..RNAi-mediated loss of function screens identified functional lncRNAs with varying impact on adipogenesis. Collectively, we have identified numerous lncRNAs that are functionally required for proper adipogenesis...
  5. pmc Differential analysis of gene regulation at transcript resolution with RNA-seq
    Cole Trapnell
    Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
    Nat Biotechnol 31:46-53. 2013
    ..Cuffdiff 2 performs robust differential analysis in RNA-seq experiments at transcript resolution, revealing a layer of regulation not readily observable with other high-throughput technologies...
  6. pmc Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
    Moran N Cabili
    Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
    Genes Dev 25:1915-27. 2011
    ..Our integrated, comprehensive, yet conservative reference catalog of human lincRNAs reveals the global properties of lincRNAs and will facilitate experimental studies and further functional classification of these genes...
  7. ncbi request reprint The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
    Cole Trapnell
    1 Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA 2 The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA 3
    Nat Biotechnol 32:381-6. 2014
    ..Monocle can in principle be used to recover single-cell gene expression kinetics from a wide array of cellular processes, including differentiation, proliferation and oncogenic transformation. ..
  8. pmc Transcriptional and epigenetic dynamics during specification of human embryonic stem cells
    Casey A Gifford
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Cell 153:1149-63. 2013
    ....
  9. doi request reprint Computational methods for transcriptome annotation and quantification using RNA-seq
    Manuel Garber
    Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
    Nat Methods 8:469-77. 2011
    ..Finally, we highlight the interdependence between these categories and discuss the benefits for different biological applications...