Standout Papers

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome 2009 2026 2014 2020 16.0k
  1. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome (2009)
    Ben Langmead, Cole Trapnell et al. Genome biology
  2. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation (2010)
    Cole Trapnell, Brian A. Williams et al. Nature Biotechnology
  3. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions (2013)
    Daehwan Kim, Geo Pertea et al. Genome biology
  4. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks (2012)
    Cole Trapnell, Adam Roberts et al. Nature Protocols
  5. TopHat: discovering splice junctions with RNA-Seq (2009)
    Cole Trapnell, Lior Pachter et al. Bioinformatics
  6. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells (2014)
    Cole Trapnell, Davide Cacchiarelli et al. Nature Biotechnology
  7. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses (2011)
    Moran N. Cabili, Cole Trapnell et al. Genes & Development
  8. Differential analysis of gene regulation at transcript resolution with RNA-seq (2012)
    Cole Trapnell, David G. Hendrickson et al. Nature Biotechnology
  9. Reversed graph embedding resolves complex single-cell trajectories (2017)
    Xiaojie Qiu, Qi Mao et al. Nature Methods
  10. The single-cell transcriptional landscape of mammalian organogenesis (2019)
    Junyue Cao, Malte Spielmann et al. Nature
  11. Improving RNA-Seq expression estimates by correcting for fragment bias (2011)
    Adam Roberts, Cole Trapnell et al. Genome biology
  12. Single-cell mRNA quantification and differential analysis with Census (2017)
    Xiaojie Qiu, Andrew J. Hill et al. Nature Methods
  13. Comprehensive single-cell transcriptional profiling of a multicellular organism (2017)
    Junyue Cao, Jonathan S. Packer et al. Science
  14. Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing (2015)
    Darren A. Cusanovich, Riza M. Daza et al. Science
  15. Identification of novel transcripts in annotated genomes using RNA-Seq (2011)
    Adam Roberts, Harold Pimentel et al. Bioinformatics
  16. Computational methods for transcriptome annotation and quantification using RNA-seq (2011)
    Manuel Garber, Manfred Grabherr et al. Nature Methods
  17. Joint profiling of chromatin accessibility and gene expression in thousands of single cells (2018)
    Junyue Cao, Darren A. Cusanovich et al. Science
  18. Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre (2014)
    Ezgi Hacisuleyman, Loyal A. Goff et al. Nature Structural & Molecular Biology
  19. Defining cell types and states with single-cell genomics (2015)
    Cole Trapnell Genome Research
  20. A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility (2018)
    Darren A. Cusanovich, Andrew J. Hill et al. Cell
  21. Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data (2018)
    Hannah A. Pliner, Jonathan S. Packer et al. Molecular Cell
  22. A human cell atlas of fetal gene expression (2020)
    Junyue Cao, Diana R. O’Day et al. Science
  23. A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens (2019)
    Molly Gasperini, Andrew J. Hill et al. Cell
  24. Multiplexed RNA structure characterization with selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) (2011)
    Julius B. Lucks, Stefanie Mortimer et al. Proceedings of the National Academy of Sciences
  25. A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution (2019)
    Jonathan S. Packer, Qin Zhu et al. Science
  26. Dynamics of Gene Expression in Single Root Cells of Arabidopsis thaliana (2019)
    Ken Jean-Baptiste, José L. McFaline‐Figueroa et al. The Plant Cell

Immediate Impact

16 by Nobel laureates 56 from Science/Nature 202 standout
Sub-graph 1 of 16

Citing Papers

A noninflammatory mRNA vaccine for treatment of experimental autoimmune encephalomyelitis
2021 StandoutScienceNobel
Fibrosis: from mechanisms to medicines
2020 StandoutNature
79 intermediate papers

Works of Cole Trapnell being referenced

Joint profiling of chromatin accessibility and gene expression in thousands of single cells
2018 StandoutScience
Pulmonary macrophage transplantation therapy
2014 Nature
and 23 more

Author Peers

Author Last Decade Papers Cites
Cole Trapnell 57498 16372 3026 16023 100 82.8k
Simon Anders 49534 11349 3614 15138 53 83.9k
Michael I. Love 37348 8531 2821 10730 86 64.4k
Wolfgang Huber 64845 14172 4890 17108 228 105.3k
Ben Langmead 47882 8482 2363 17852 77 76.0k
Minoru Kanehisa 73697 11792 3561 13696 253 109.5k
Mentor Sopjani 33650 9444 6355 12774 78 65.5k
Ronald G. Tilton 34918 9821 7162 12758 128 73.0k
Yanchun Zhao 32197 9394 6191 12689 70 63.7k
Christian von Mering 43997 7284 3332 6730 132 66.8k
Lior Pachter 35321 7926 2098 12097 163 53.7k

All Works

Loading papers...

Rankless by CCL
2026