Cole Trapnell - Publications

Affiliations: 
2010 Computer Science University of Maryland, College Park, College Park, MD 

35 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Qiu C, Cao J, Martin BK, Li T, Welsh IC, Srivatsan S, Huang X, Calderon D, Noble WS, Disteche CM, Murray SA, Spielmann M, Moens CB, Trapnell C, Shendure J. Systematic reconstruction of cellular trajectories across mouse embryogenesis. Nature Genetics. 54: 328-341. PMID 35288709 DOI: 10.1038/s41588-022-01018-x  0.307
2021 Bonora G, Ramani V, Singh R, Fang H, Jackson DL, Srivatsan S, Qiu R, Lee C, Trapnell C, Shendure J, Duan Z, Deng X, Noble WS, Disteche CM. Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation. Genome Biology. 22: 279. PMID 34579774 DOI: 10.1186/s13059-021-02432-w  0.314
2020 Cao J, Zhou W, Steemers F, Trapnell C, Shendure J. Sci-fate characterizes the dynamics of gene expression in single cells. Nature Biotechnology. PMID 32284584 DOI: 10.1038/S41587-020-0480-9  0.32
2019 Jean-Baptiste K, McFaline-Figueroa JL, Alexandre CM, Dorrity MW, Saunders L, Bubb KL, Trapnell C, Fields S, Queitsch C, Cuperus J. Dynamics of gene expression in single root cells of A. thaliana. The Plant Cell. PMID 30923229 DOI: 10.1105/Tpc.18.00785  0.323
2018 Gasperini M, Hill AJ, McFaline-Figueroa JL, Martin B, Kim S, Zhang MD, Jackson D, Leith A, Schreiber J, Noble WS, Trapnell C, Ahituv N, Shendure J. A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens. Cell. PMID 30612741 DOI: 10.1016/J.Cell.2018.11.029  0.328
2018 Cacchiarelli D, Qiu X, Srivatsan S, Manfredi A, Ziller M, Overbey E, Grimaldi A, Grimsby J, Pokharel P, Livak KJ, Li S, Meissner A, Mikkelsen TS, Rinn JL, Trapnell C. Aligning Single-Cell Developmental and Reprogramming Trajectories Identifies Molecular Determinants of Myogenic Reprogramming Outcome. Cell Systems. PMID 30195438 DOI: 10.1016/J.Cels.2018.07.006  0.593
2018 Cao J, Cusanovich DA, Ramani V, Aghamirzaie D, Pliner HA, Hill AJ, Daza RM, McFaline-Figueroa JL, Packer JS, Christiansen L, Steemers FJ, Adey AC, Trapnell C, Shendure J. Joint profiling of chromatin accessibility and gene expression in thousands of single cells. Science (New York, N.Y.). PMID 30166440 DOI: 10.1126/Science.Aau0730  0.33
2018 Cusanovich DA, Hill AJ, Aghamirzaie D, Daza RM, Pliner HA, Berletch JB, Filippova GN, Huang X, Christiansen L, DeWitt WS, Lee C, Regalado SG, Read DF, Steemers FJ, Disteche CM, ... Trapnell C, et al. A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility. Cell. PMID 30078704 DOI: 10.1016/J.Cell.2018.06.052  0.327
2018 Cesana M, Guo MH, Cacchiarelli D, Wahlster L, Barragan J, Doulatov S, Vo LT, Salvatori B, Trapnell C, Clement K, Cahan P, Tsanov KM, Sousa PM, Tazon-Vega B, Bolondi A, et al. A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development. Cell Stem Cell. 22: 575-588.e7. PMID 29625070 DOI: 10.1016/J.Stem.2018.03.012  0.559
2018 Hadland B, Varnum-Finney B, Dozono S, Jackson D, Rafii S, Bernstein ID, Trapnell C. Single Cell Transcriptomics Maps the Embryonic Emergence of HSC and Identifies Intercellular Interactions Regulating HSC Genesis Blood. 132: 5086-5086. DOI: 10.1182/Blood-2018-99-118772  0.313
2017 Cao J, Packer JS, Ramani V, Cusanovich DA, Huynh C, Daza R, Qiu X, Lee C, Furlan SN, Steemers FJ, Adey A, Waterston RH, Trapnell C, Shendure J. Comprehensive single-cell transcriptional profiling of a multicellular organism. Science (New York, N.Y.). 357: 661-667. PMID 28818938 DOI: 10.1126/Science.Aam8940  0.365
2017 Qiu X, Hill A, Packer J, Lin D, Ma YA, Trapnell C. Single-cell mRNA quantification and differential analysis with Census. Nature Methods. PMID 28114287 DOI: 10.1038/Nmeth.4150  0.366
2015 Cacchiarelli D, Trapnell C, Ziller MJ, Soumillon M, Cesana M, Karnik R, Donaghey J, Smith ZD, Ratanasirintrawoot S, Zhang X, Ho Sui SJ, Wu Z, Akopian V, Gifford CA, Doench J, et al. Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency. Cell. 162: 412-424. PMID 26186193 DOI: 10.1016/J.Cell.2015.06.016  0.564
2014 Trapnell C, Cacchiarelli D, Grimsby J, Pokharel P, Li S, Morse M, Lennon NJ, Livak KJ, Mikkelsen TS, Rinn JL. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nature Biotechnology. 32: 381-6. PMID 24658644 DOI: 10.1038/Nbt.2859  0.612
2014 Hacisuleyman E, Goff LA, Trapnell C, Williams A, Henao-Mejia J, Sun L, McClanahan P, Hendrickson DG, Sauvageau M, Kelley DR, Morse M, Engreitz J, Lander ES, Guttman M, Lodish HF, et al. Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. Nature Structural & Molecular Biology. 21: 198-206. PMID 24463464 DOI: 10.1038/Nsmb.2764  0.77
2014 Silverman IM, Li F, Alexander A, Goff L, Trapnell C, Rinn JL, Gregory BD. RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome. Genome Biology. 15: R3. PMID 24393486 DOI: 10.1186/Gb-2014-15-1-R3  0.719
2014 Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Erratum: Corrigendum: Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks Nature Protocols. 9: 2513-2513. DOI: 10.1038/Nprot1014-2513A  0.77
2013 Gifford CA, Ziller MJ, Gu H, Trapnell C, Donaghey J, Tsankov A, Shalek AK, Kelley DR, Shishkin AA, Issner R, Zhang X, Coyne M, Fostel JL, Holmes L, Meldrim J, et al. Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. Cell. 153: 1149-63. PMID 23664763 DOI: 10.1016/J.Cell.2013.04.037  0.696
2013 Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biology. 14: R36. PMID 23618408 DOI: 10.1186/Gb-2013-14-4-R36  0.734
2013 Sun L, Goff LA, Trapnell C, Alexander R, Lo KA, Hacisuleyman E, Sauvageau M, Tazon-Vega B, Kelley DR, Hendrickson DG, Yuan B, Kellis M, Lodish HF, Rinn JL. Long noncoding RNAs regulate adipogenesis. Proceedings of the National Academy of Sciences of the United States of America. 110: 3387-92. PMID 23401553 DOI: 10.1073/Pnas.1222643110  0.786
2013 Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nature Biotechnology. 31: 46-53. PMID 23222703 DOI: 10.1038/Nbt.2450  0.806
2012 Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protocols. 7: 562-78. PMID 22383036 DOI: 10.1038/Nprot.2012.016  0.804
2012 Mercer TR, Gerhardt DJ, Dinger ME, Crawford J, Trapnell C, Jeddeloh JA, Mattick JS, Rinn JL. Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nature Biotechnology. 30: 99-104. PMID 22081020 DOI: 10.1038/Nbt.2024  0.6
2012 Cabili M, Lander E, Sabeti P, Regev A, Rinn JL, Rinn JL, Rinn JL, Trapnell C, Trapnell C, Goff L, Goff L, Broadbent K, Broadbent K, Guttman M. Abstract IA4: Linking RNA to human health and disease Cancer Research. 72: IA4-IA4. DOI: 10.1158/1538-7445.Nonrna12-Ia4  0.658
2011 Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes & Development. 25: 1915-27. PMID 21890647 DOI: 10.1101/Gad.17446611  0.766
2011 Bogdanove AJ, Koebnik R, Lu H, Furutani A, Angiuoli SV, Patil PB, Van Sluys MA, Ryan RP, Meyer DF, Han SW, Aparna G, Rajaram M, Delcher AL, Phillippy AM, Puiu D, ... ... Trapnell C, et al. Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp. Journal of Bacteriology. 193: 5450-64. PMID 21784931 DOI: 10.1128/Jb.05262-11  0.764
2011 Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter L. Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biology. 12: R22. PMID 21410973 DOI: 10.1186/Gb-2011-12-3-R22  0.559
2010 Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology. 28: 511-5. PMID 20436464 DOI: 10.1038/Nbt.1621  0.606
2009 Trapnell C, Schatz MC. Optimizing Data Intensive GPGPU Computations for DNA Sequence Alignment. Parallel Computing. 35: 429-440. PMID 20161021 DOI: 10.1016/j.parco.2009.05.002  0.441
2009 Trapnell C, Salzberg SL. How to map billions of short reads onto genomes Nature Biotechnology. 27: 455-457. PMID 19430453 DOI: 10.1038/Nbt0509-455  0.485
2009 Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics (Oxford, England). 25: 1105-11. PMID 19289445 DOI: 10.1093/Bioinformatics/Btp120  0.578
2009 Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology. 10: R25. PMID 19261174 DOI: 10.1186/Gb-2009-10-3-R25  0.703
2008 Salzberg SL, Sommer DD, Schatz MC, Phillippy AM, Rabinowicz PD, Tsuge S, Furutani A, Ochiai H, Delcher AL, Kelley D, Madupu R, Puiu D, Radune D, Shumway M, Trapnell C, et al. Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A. Bmc Genomics. 9: 204. PMID 18452608 DOI: 10.1186/1471-2164-9-204  0.757
2008 Salzberg SL, Sommer DD, Schatz MC, Phillippy AM, Rabinowicz PD, Tsuge S, Furutani A, Ochiai H, Delcher AL, Kelley D, Madupu R, Puiu D, Radune D, Shumway M, Trapnell C, et al. Erratum to: Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99 A Bmc Genomics. 9: 534. DOI: 10.1186/1471-2164-9-534  0.503
2007 Schatz MC, Trapnell C, Delcher AL, Varshney A. High-throughput sequence alignment using Graphics Processing Units. Bmc Bioinformatics. 8: 474. PMID 18070356 DOI: 10.1186/1471-2105-8-474  0.463
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