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Cole Trapnell - Publications

Affiliations: 
2010 Computer Science University of Maryland, College Park, College Park, MD 
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69/119 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 Martin BK, Qiu C, Nichols E, Phung M, Green-Gladden R, Srivatsan S, Blecher-Gonen R, Beliveau BJ, Trapnell C, Cao J, Shendure J. Optimized single-nucleus transcriptional profiling by combinatorial indexing. Nature Protocols. PMID 36261634 DOI: 10.1038/s41596-022-00752-0  0.351
2022 Kim HJ, Booth G, Saunders L, Srivatsan S, McFaline-Figueroa JL, Trapnell C. Nuclear oligo hashing improves differential analysis of single-cell RNA-seq. Nature Communications. 13: 2666. PMID 35562344 DOI: 10.1038/s41467-022-30309-4  0.412
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  0.316
2020 Hasle N, Cooke A, Srivatsan S, Huang H, Stephany JJ, Krieger Z, Jackson D, Tang W, Pendyala S, Monnat RJ, Trapnell C, Hatch EM, Fowler DM. High-throughput, microscope-based sorting to dissect cellular heterogeneity. Molecular Systems Biology. 16: e9442. PMID 32500953 DOI: 10.15252/Msb.20209442  0.392
2020 Gabrovsek L, Collins KB, Aggarwal S, Saunders LM, Lau HT, Suh D, Sancak Y, Trapnell C, Ong SE, Smith FD, Scott JD. A-kinase-anchoring protein 1 (dAKAP1)-based signaling complexes coordinate local protein synthesis at the mitochondrial surface. The Journal of Biological Chemistry. PMID 32482893 DOI: 10.1074/Jbc.Ra120.013454  0.319
2020 McFaline-Figueroa JL, Trapnell C, Cuperus JT. The promise of single-cell genomics in plants. Current Opinion in Plant Biology. 54: 114-121. PMID 32388018 DOI: 10.1016/J.Pbi.2020.04.002  0.352
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  0.419
2020 Dorrity MW, Saunders LM, Queitsch C, Fields S, Trapnell C. Dimensionality reduction by UMAP to visualize physical and genetic interactions. Nature Communications. 11: 1537. PMID 32210240 DOI: 10.1038/S41467-020-15351-4  0.317
2020 Qiu X, Rahimzamani A, Wang L, Ren B, Mao Q, Durham T, McFaline-Figueroa JL, Saunders L, Trapnell C, Kannan S. Inferring Causal Gene Regulatory Networks from Coupled Single-Cell Expression Dynamics Using Scribe. Cell Systems. PMID 32135093 DOI: 10.1016/J.Cels.2020.02.003  0.379
2020 Sridhar A, Hoshino A, Finkbeiner CR, Chitsazan A, Dai L, Haugan AK, Eschenbacher KM, Jackson DL, Trapnell C, Bermingham-McDonogh O, Glass I, Reh TA. Single-Cell Transcriptomic Comparison of Human Fetal Retina, hPSC-Derived Retinal Organoids, and Long-Term Retinal Cultures. Cell Reports. 30: 1644-1659.e4. PMID 32023475 DOI: 10.1016/J.Celrep.2020.01.007  0.342
2019 Srivatsan SR, McFaline-Figueroa JL, Ramani V, Saunders L, Cao J, Packer J, Pliner HA, Jackson DL, Daza RM, Christiansen L, Zhang F, Steemers F, Shendure J, Trapnell C. Massively multiplex chemical transcriptomics at single cell resolution. Science (New York, N.Y.). PMID 31806696 DOI: 10.1126/Science.Aax6234  0.308
2019 Pliner HA, Shendure J, Trapnell C. Supervised classification enables rapid annotation of cell atlases. Nature Methods. PMID 31501545 DOI: 10.1038/S41592-019-0535-3  0.346
2019 Packer JS, Zhu Q, Huynh C, Sivaramakrishnan P, Preston E, Dueck H, Stefanik D, Tan K, Trapnell C, Kim J, Waterston RH, Murray JI. A lineage-resolved molecular atlas of embryogenesis at single-cell resolution. Science (New York, N.Y.). PMID 31488706 DOI: 10.1126/Science.Aax1971  0.336
2019 McFaline-Figueroa JL, Hill AJ, Qiu X, Jackson D, Shendure J, Trapnell C. A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition. Nature Genetics. 51: 1389-1398. PMID 31477929 DOI: 10.1038/S41588-019-0489-5  0.378
2019 Sharon N, Vanderhooft J, Straubhaar J, Mueller J, Chawla R, Zhou Q, Engquist EN, Trapnell C, Gifford DK, Melton DA. Wnt Signaling Separates the Progenitor and Endocrine Compartments during Pancreas Development. Cell Reports. 27: 2281-2291.e5. PMID 31116975 DOI: 10.1016/J.Celrep.2019.04.083  0.362
2019 Sinnamon JR, Torkenczy KA, Linhoff MW, Vitak SA, Mulqueen RM, Pliner HA, Trapnell C, Steemers FJ, Mandel G, Adey AC. The accessible chromatin landscape of the murine hippocampus at single-cell resolution. Genome Research. PMID 30936163 DOI: 10.1101/Gr.243725.118  0.34
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  0.422
2019 Cao J, Spielmann M, Qiu X, Huang X, Ibrahim DM, Hill AJ, Zhang F, Mundlos S, Christiansen L, Steemers FJ, Trapnell C, Shendure J. The single-cell transcriptional landscape of mammalian organogenesis. Nature. PMID 30787437 DOI: 10.1038/S41586-019-0969-X  0.379
2019 Hadland B, Varnum-Finney B, Dozono S, Dignum T, Nourigat-Mckay C, Jackson D, Rafii S, Trapnell C, Bernstein ID. Integrated Single Cell Transcriptomics Defines an Engineered Niche Supporting Hematopoietic Stem Cell Development Ex Vivo Blood. 134: 3699-3699. DOI: 10.1182/Blood-2019-126109  0.37
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  0.48
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  0.612
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  0.432
2018 Pliner HA, Packer JS, McFaline-Figueroa JL, Cusanovich DA, Daza RM, Aghamirzaie D, Srivatsan S, Qiu X, Jackson D, Minkina A, Adey AC, Steemers FJ, Shendure J, Trapnell C. Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data. Molecular Cell. PMID 30078726 DOI: 10.1016/J.Molcel.2018.06.044  0.377
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  0.422
2018 Packer J, Trapnell C. Single-Cell Multi-omics: An Engine for New Quantitative Models of Gene Regulation. Trends in Genetics : Tig. 34: 653-665. PMID 30007833 DOI: 10.1016/J.Tig.2018.06.001  0.464
2018 Mikheev AM, Mikheeva SA, Severs LJ, Funk CC, Huang L, McFaline-Figueroa JL, Schwensen J, Trapnell C, Price ND, Wong S, Rostomily RC. Targeting TWIST1 through loss of function inhibits tumorigenicity of human glioblastoma. Molecular Oncology. PMID 29754406 DOI: 10.1002/1878-0261.12320  0.335
2018 Mulqueen RM, Pokholok D, Norberg SJ, Torkenczy KA, Fields AJ, Sun D, Sinnamon JR, Shendure J, Trapnell C, O'Roak BJ, Xia Z, Steemers FJ, Adey AC. Highly scalable generation of DNA methylation profiles in single cells. Nature Biotechnology. PMID 29644997 DOI: 10.1038/Nbt.4112  0.348
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  0.604
2018 Cusanovich DA, Reddington JP, Garfield DA, Daza RM, Aghamirzaie D, Marco-Ferreres R, Pliner HA, Christiansen L, Qiu X, Steemers FJ, Trapnell C, Shendure J, Furlong EEM. The cis-regulatory dynamics of embryonic development at single-cell resolution. Nature. PMID 29539636 DOI: 10.1038/Nature25981  0.384
2018 Hill AJ, McFaline-Figueroa JL, Starita LM, Gasperini MJ, Matreyek KA, Packer J, Jackson D, Shendure J, Trapnell C. On the design of CRISPR-based single-cell molecular screens. Nature Methods. PMID 29457792 DOI: 10.1038/Nmeth.4604  0.418
2018 Russell AB, Trapnell C, Bloom JD. Extreme heterogeneity of influenza virus infection in single cells. Elife. 7. PMID 29451492 DOI: 10.7554/Elife.32303  0.327
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  0.422
2017 Qiu X, Mao Q, Tang Y, Wang L, Chawla R, Pliner HA, Trapnell C. Reversed graph embedding resolves complex single-cell trajectories. Nature Methods. PMID 28825705 DOI: 10.1038/Nmeth.4402  0.326
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  0.488
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  0.481
2016 Zhang J, Ratanasirintrawoot S, Chandrasekaran S, Wu Z, Ficarro SB, Yu C, Ross CA, Cacchiarelli D, Xia Q, Seligson M, Shinoda G, Xie W, Cahan P, Wang L, Ng SC, ... ... Trapnell C, et al. LIN28 Regulates Stem Cell Metabolism and Conversion to Primed Pluripotency. Cell Stem Cell. PMID 27320042 DOI: 10.1016/J.Stem.2016.05.009  0.35
2016 Liu S, Trapnell C. Single-cell transcriptome sequencing: recent advances and remaining challenges. F1000research. 5. PMID 26949524 DOI: 10.12688/F1000Research.7223.1  0.464
2015 Hanchate NK, Kondoh K, Lu Z, Kuang D, Ye X, Qiu X, Pachter L, Trapnell C, Buck LB. Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis. Science (New York, N.Y.). PMID 26541607 DOI: 10.1126/Science.Aad2456  0.319
2015 Trapnell C. Defining cell types and states with single-cell genomics. Genome Research. 25: 1491-8. PMID 26430159 DOI: 10.1101/Gr.190595.115  0.354
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  0.591
2015 Cusanovich DA, Daza R, Adey A, Pliner HA, Christiansen L, Gunderson KL, Steemers FJ, Trapnell C, Shendure J. Epigenetics. Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing. Science (New York, N.Y.). 348: 910-4. PMID 25953818 DOI: 10.1126/Science.Aab1601  0.348
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  0.64
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  0.751
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  0.734
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  0.746
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  0.713
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  0.74
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  0.767
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  0.791
2012 Mortimer SA, Trapnell C, Aviran S, Pachter L, Lucks JB. SHAPE-Seq: High-Throughput RNA Structure Analysis. Current Protocols in Chemical Biology. 4: 275-97. PMID 23788555 DOI: 10.1002/9780470559277.Ch120019  0.46
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  0.795
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  0.672
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  0.7
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  0.787
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  0.75
2011 Roberts A, Pimentel H, Trapnell C, Pachter L. Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics (Oxford, England). 27: 2325-9. PMID 21697122 DOI: 10.1093/Bioinformatics/Btr355  0.513
2011 Aviran S, Trapnell C, Lucks JB, Mortimer SA, Luo S, Schroth GP, Doudna JA, Arkin AP, Pachter L. Modeling and automation of sequencing-based characterization of RNA structure. Proceedings of the National Academy of Sciences of the United States of America. 108: 11069-74. PMID 21642536 DOI: 10.1073/Pnas.1106541108  0.452
2011 Lucks JB, Mortimer SA, Trapnell C, Luo S, Aviran S, Schroth GP, Pachter L, Doudna JA, Arkin AP. Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). Proceedings of the National Academy of Sciences of the United States of America. 108: 11063-8. PMID 21642531 DOI: 10.1073/Pnas.1106501108  0.465
2011 Garber M, Grabherr MG, Guttman M, Trapnell C. Computational methods for transcriptome annotation and quantification using RNA-seq. Nature Methods. 8: 469-77. PMID 21623353 DOI: 10.1038/Nmeth.1613  0.461
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  0.627
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  0.681
2010 Bradley RK, Li XY, Trapnell C, Davidson S, Pachter L, Chu HC, Tonkin LA, Biggin MD, Eisen MB. Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. Plos Biology. 8: e1000343. PMID 20351773 DOI: 10.1371/Journal.Pbio.1000343  0.359
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  0.454
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  0.554
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  0.665
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  0.701
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  0.749
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  0.578
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  0.546
Low-probability matches (unlikely to be authored by this person)
2019 Saunders LM, Mishra AK, Aman AJ, Lewis VM, Toomey MB, Packer JS, Qiu X, McFaline-Figueroa JL, Corbo JC, Trapnell C, Parichy DM. Thyroid hormone regulates distinct paths to maturation in pigment cell lineages. Elife. 8. PMID 31140974 DOI: 10.7554/Elife.45181  0.299
2022 Calderon D, Blecher-Gonen R, Huang X, Secchia S, Kentro J, Daza RM, Martin B, Dulja A, Schaub C, Trapnell C, Larschan E, O'Connor-Giles KM, Furlong EEM, Shendure J. The continuum of embryonic development at single-cell resolution. Science (New York, N.Y.). 377: eabn5800. PMID 35926038 DOI: 10.1126/science.abn5800  0.298
2019 Sharon N, Chawla R, Mueller J, Vanderhooft J, Whitehorn LJ, Rosenthal B, Gürtler M, Estanboulieh RR, Shvartsman D, Gifford DK, Trapnell C, Melton D. A Peninsular Structure Coordinates Asynchronous Differentiation with Morphogenesis to Generate Pancreatic Islets. Cell. PMID 30661759 DOI: 10.1016/J.Cell.2018.12.003  0.297
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  0.295
2020 Furlan SN, Singh K, Lopez C, Tkachev V, Hunt DJ, Hibbard J, Betz KM, Blazar BR, Trapnell C, Kean LS. IL-2 enhances ex vivo-expanded regulatory T-cell persistence after adoptive transfer. Blood Advances. 4: 1594-1605. PMID 32311015 DOI: 10.1182/Bloodadvances.2019001248  0.294
2018 Hadland B, Varnum-Finney B, Jackson D, Poulos M, Butler J, Rafii S, Bernstein I, Trapnell C. Single Cell Transcriptomics Reconstructs the Embryonic Emergence of HSC and Identifies Ligand-Receptor Interactions Regulating HSC Genesis in the Aorta-Gonad-Mesonephros Vascular Niche Experimental Hematology. 64: S69-S70. DOI: 10.1016/J.Exphem.2018.06.238  0.291
2023 Tresenrider A, Sridhar A, Eldred KC, Cuschieri S, Hoffer D, Trapnell C, Reh TA. Single-cell sequencing of individual retinal organoids reveals determinants of cell-fate heterogeneity. Cell Reports Methods. 3: 100548. PMID 37671011 DOI: 10.1016/j.crmeth.2023.100548  0.291
2018 Mucci A, Lopez-Rodriguez E, Hetzel M, Liu S, Suzuki T, Happle C, Ackermann M, Kempf H, Hillje R, Kunkiel J, Janosz E, Brennig S, Glage S, Bankstahl JP, Dettmer S, ... ... Trapnell C, et al. iPSC-Derived Macrophages Effectively Treat Pulmonary Alveolar Proteinosis in Csf2rb-Deficient Mice. Stem Cell Reports. PMID 30100408 DOI: 10.1016/J.Stemcr.2018.07.006  0.289
2018 Wray-Dutra MN, Chawla R, Thomas KR, Seymour BJ, Arkatkar T, Sommer KM, Khim S, Trapnell C, James RG, Rawlings DJ. Activated CARD11 accelerates germinal center kinetics, promoting mTORC1 and terminal differentiation. The Journal of Experimental Medicine. PMID 30127060 DOI: 10.1084/Jem.20180230  0.276
2022 Hadland B, Varnum-Finney B, Dozono S, Dignum T, Nourigat-McKay C, Heck AM, Ishida T, Jackson DL, Itkin T, Butler JM, Rafii S, Trapnell C, Bernstein ID. Engineering a niche supporting hematopoietic stem cell development using integrated single-cell transcriptomics. Nature Communications. 13: 1584. PMID 35332125 DOI: 10.1038/s41467-022-28781-z  0.268
2023 Huang X, Henck J, Qiu C, Sreenivasan VKA, Balachandran S, Amarie OV, Hrabě de Angelis M, Behncke RY, Chan WL, Despang A, Dickel DE, Duran M, Feuchtinger A, Fuchs H, Gailus-Durner V, ... ... Trapnell C, et al. Single-cell, whole-embryo phenotyping of mammalian developmental disorders. Nature. PMID 37968388 DOI: 10.1038/s41586-023-06548-w  0.265
2019 Saunders LM, Mishra AK, Aman AJ, Lewis VM, Toomey MB, Packer JS, Qiu X, McFaline-Figueroa JL, Corbo JC, Trapnell C, Parichy DM. Author response: Thyroid hormone regulates distinct paths to maturation in pigment cell lineages Elife. DOI: 10.7554/Elife.45181.040  0.262
2023 Dorrity MW, Saunders LM, Duran M, Srivatsan SR, Barkan E, Jackson DL, Sattler SM, Ewing B, Queitsch C, Shendure J, Raible DW, Kimelman D, Trapnell C. Proteostasis governs differential temperature sensitivity across embryonic cell types. Cell. 186: 5015-5027.e12. PMID 37949057 DOI: 10.1016/j.cell.2023.10.013  0.261
2020 Domcke S, Hill AJ, Daza RM, Cao J, O'Day DR, Pliner HA, Aldinger KA, Pokholok D, Zhang F, Milbank JH, Zager MA, Glass IA, Steemers FJ, Doherty D, Trapnell C, et al. A human cell atlas of fetal chromatin accessibility. Science (New York, N.Y.). 370. PMID 33184180 DOI: 10.1126/science.aba7612  0.26
2022 Rubin SA, Baron CS, Pessoa Rodrigues C, Duran M, Corbin AF, Yang SP, Trapnell C, Zon LI. Single-cell analyses reveal early thymic progenitors and pre-B cells in zebrafish. The Journal of Experimental Medicine. 219. PMID 35938989 DOI: 10.1084/jem.20220038  0.256
2020 Liu SX, Gustafson HH, Jackson DL, Pun SH, Trapnell C. Trajectory analysis quantifies transcriptional plasticity during macrophage polarization. Scientific Reports. 10: 12273. PMID 32703960 DOI: 10.1038/S41598-020-68766-W  0.254
2023 Qiu C, Martin BK, Welsh IC, Daza RM, Le TM, Huang X, Nichols EK, Taylor ML, Fulton O, Oâ Day DR, Gomes AR, Ilcisin S, Srivatsan S, Deng X, Disteche CM, ... ... Trapnell C, et al. A single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pup. Biorxiv : the Preprint Server For Biology. PMID 37066300 DOI: 10.1101/2023.04.05.535726  0.252
2020 Hanchate NK, Lee EJ, Ellis A, Kondoh K, Kuang D, Basom R, Trapnell C, Buck LB. Connect-seq to superimpose molecular on anatomical neural circuit maps. Proceedings of the National Academy of Sciences of the United States of America. PMID 32034095 DOI: 10.1073/Pnas.1912176117  0.251
2014 Suzuki T, Arumugam P, Sakagami T, Lachmann N, Chalk C, Sallese A, Abe S, Trapnell C, Carey B, Moritz T, Malik P, Lutzko C, Wood RE, Trapnell BC. Pulmonary macrophage transplantation therapy. Nature. 514: 450-4. PMID 25274301 DOI: 10.1038/Nature13807  0.25
2020 Cao J, O'Day DR, Pliner HA, Kingsley PD, Deng M, Daza RM, Zager MA, Aldinger KA, Blecher-Gonen R, Zhang F, Spielmann M, Palis J, Doherty D, Steemers FJ, Glass IA, ... Trapnell C, et al. A human cell atlas of fetal gene expression. Science (New York, N.Y.). 370. PMID 33184181 DOI: 10.1126/science.aba7721  0.247
2018 Furlan SN, Lopez C, Tkachev V, Betz K, Hunt DJ, Hibbard J, Blazar BR, Trapnell C, Kean L. IL2 and Rapamycin Enhance Persistence of Adoptively-Transferred Ex-Vivo Expanded T Regulatory Cells Blood. 132: 2049-2049. DOI: 10.1182/Blood-2018-99-120254  0.246
2017 Cao J, Packer J, Waterston R, Trapnell C, Shendure J, Rajaram S, Wu LF, Altschuler SJ, Liang J, O'Brien LE, Eizenberg-Magar I, Rimer J, Friedman N, Metzl-Raz E, Kafri M, et al. Principles of Systems Biology, No. 21 : Editorial Cell Systems. 5: 158-160. PMID 28957648 DOI: 10.1016/J.Cels.2017.09.005  0.244
2023 Tresenrider A, Sridhar A, Eldred KC, Cuschieri S, Hoffer D, Trapnell C, Reh TA. Single-cell sequencing of individual retinal organoids reveals determinants of cell fate heterogeneity. Biorxiv : the Preprint Server For Biology. PMID 37398481 DOI: 10.1101/2023.05.31.543087  0.244
2024 Qiu C, Martin BK, Welsh IC, Daza RM, Le TM, Huang X, Nichols EK, Taylor ML, Fulton O, O'Day DR, Gomes AR, Ilcisin S, Srivatsan S, Deng X, Disteche CM, ... ... Trapnell C, et al. A single-cell time-lapse of mouse prenatal development from gastrula to birth. Nature. PMID 38355799 DOI: 10.1038/s41586-024-07069-w  0.241
2013 Altschul S, Demchak B, Durbin R, Gentleman R, Krzywinski M, Li H, Nekrutenko A, Robinson J, Rasband W, Taylor J, Trapnell C. The anatomy of successful computational biology software. Nature Biotechnology. 31: 894-7. PMID 24104757 DOI: 10.1038/Nbt.2721  0.24
2020 Hanchate N, Lee EJ, Ellis A, Kondoh K, Kuang D, Basom R, Trapnell C, Buck L. SUN-LB55 Connect-seq to Superimpose Molecular on Anatomical Neural Circuit Maps Journal of the Endocrine Society. 4. DOI: 10.1210/Jendso/Bvaa046.2259  0.236
2023 Tresenrider A, Hooper M, Todd L, Kierney F, Blasdel N, Trapnell C, Reh TA. A multiplexed, single-cell sequencing screen identifies compounds that increase neurogenic reprogramming of murine Muller glia. Biorxiv : the Preprint Server For Biology. PMID 37808650 DOI: 10.1101/2023.09.26.559569  0.233
2019 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. 176: 1516. PMID 30849375 DOI: 10.1016/j.cell.2019.02.027  0.222
2014 Altschul S, Demchak B, Durbin R, Gentleman R, Krzywinski M, Li H, Nekrutenko A, Robinson J, Rasband W, Taylor J, Trapnell C. Erratum: The anatomy of successful computational biology software Nature Biotechnology. 32: 592-592. DOI: 10.1038/Nbt0614-592B  0.221
2018 Russell AB, Trapnell C, Bloom JD. Author response: Extreme heterogeneity of influenza virus infection in single cells Elife. DOI: 10.7554/Elife.32303.045  0.211
2023 Booth GT, Daza RM, Srivatsan SR, McFaline-Figueroa JL, Gladden RG, Mullen AC, Furlan SN, Shendure J, Trapnell C. High-capacity sample multiplexing for single cell chromatin accessibility profiling. Bmc Genomics. 24: 737. PMID 38049719 DOI: 10.1186/s12864-023-09832-1  0.204
2023 Booth GT, Daza RM, Srivatsan SR, McFaline-Figueroa JL, Gladden RG, Furlan SN, Shendure J, Trapnell C. High-Capacity Sample Multiplexing for Single Cell Chromatin Accessibility Profiling. Biorxiv : the Preprint Server For Biology. PMID 36945538 DOI: 10.1101/2023.03.05.531201  0.204
2023 Saunders LM, Srivatsan SR, Duran M, Dorrity MW, Ewing B, Linbo TH, Shendure J, Raible DW, Moens CB, Kimelman D, Trapnell C. Embryo-scale reverse genetics at single-cell resolution. Nature. 623: 782-791. PMID 37968389 DOI: 10.1038/s41586-023-06720-2  0.204
2021 O'Connor SA, Feldman HM, Arora S, Hoellerbauer P, Toledo CM, Corrin P, Carter L, Kufeld M, Bolouri H, Basom R, Delrow J, McFaline-Figueroa JL, Trapnell C, Pollard SM, Patel A, et al. Neural G0: a quiescent-like state found in neuroepithelial-derived cells and glioma. Molecular Systems Biology. 17: e9522. PMID 34101353 DOI: 10.15252/msb.20209522  0.2
2023 Shi T, Beaulieu MO, Saunders LM, Fabian P, Trapnell C, Segil N, Crump JG, Raible DW. Single-cell transcriptomic profiling of the zebrafish inner ear reveals molecularly distinct hair cell and supporting cell subtypes. Elife. 12. PMID 36598134 DOI: 10.7554/eLife.82978  0.199
2021 Dignum T, Varnum-Finney B, Srivatsan SR, Dozono S, Waltner O, Heck AM, Ishida T, Nourigat-McKay C, Jackson DL, Rafii S, Trapnell C, Bernstein ID, Hadland B. Multipotent progenitors and hematopoietic stem cells arise independently from hemogenic endothelium in the mouse embryo. Cell Reports. 36: 109675. PMID 34525376 DOI: 10.1016/j.celrep.2021.109675  0.197
2021 Cable J, Elowitz MB, Domingos AI, Habib N, Itzkovitz S, Hamidzada H, Balzer MS, Yanai I, Liberali P, Whited J, Streets A, Cai L, Stergachis AB, Hong CKY, Keren L, ... ... Trapnell C, et al. Single cell biology-a Keystone Symposia report. Annals of the New York Academy of Sciences. PMID 34605044 DOI: 10.1111/nyas.14692  0.192
2024 McFaline-Figueroa JL, Srivatsan S, Hill AJ, Gasperini M, Jackson DL, Saunders L, Domcke S, Regalado SG, Lazarchuck P, Alvarez S, Monnat RJ, Shendure J, Trapnell C. Multiplex single-cell chemical genomics reveals the kinase dependence of the response to targeted therapy. Cell Genomics. 100487. PMID 38278156 DOI: 10.1016/j.xgen.2023.100487  0.19
2023 McFaline-Figueroa JL, Srivatsan S, Hill AJ, Gasperini M, Jackson DL, Saunders L, Domcke S, Regalado SG, Lazarchuck P, Alvarez S, Monnat RJ, Shendure J, Trapnell C. Multiplex single-cell chemical genomics reveals the kinase dependence of the response to targeted therapy. Biorxiv : the Preprint Server For Biology. PMID 37398090 DOI: 10.1101/2023.03.10.531983  0.182
2015 Cusanovich DA, Daza R, Adey A, Pliner HA, Christiansen L, Gunderson KL, Steemers FJ, Trapnell C, Shendure J. Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing Science. 348: 910-914. DOI: 10.1126/science.aab1601  0.176
2023 Itkin T, Houghton S, Schreiner R, Lin Y, Badwe CR, Voisin V, Murison A, Seyedhassantehrani N, Kaufmann KB, Garcia-Prat L, Booth GT, Geng F, Liu Y, Gomez-Salinero JM, Shieh JH, ... ... Trapnell C, et al. Transcriptional Activation of Regenerative Hematopoiesis via Vascular Niche Sensing. Biorxiv : the Preprint Server For Biology. PMID 37034724 DOI: 10.1101/2023.03.27.534417  0.174
2023 Mozin E, Massouridès E, Mournetas V, Lièvre C, Bourdon A, Jackson DL, Packer JS, Trapnell C, Guiner CL, Adjali O, Pinset C, Mack DL, Dupont JB. Dystrophin deficiency impairs cell junction formation during embryonic myogenesis. Biorxiv : the Preprint Server For Biology. PMID 38106055 DOI: 10.1101/2023.12.05.569919  0.163
2021 Vanderwall ER, Barrow KA, Rich LM, Read DF, Trapnell C, Okoloko O, Ziegler SF, Hallstrand TS, White MP, Debley JS. Airway epithelial interferon response to SARS-CoV-2 is inferior to rhinovirus and heterologous rhinovirus infection suppresses SARS-CoV-2 replication. Biorxiv : the Preprint Server For Biology. PMID 34845445 DOI: 10.1101/2021.11.20.469409  0.163
2023 Aman AJ, Saunders LM, Carr AA, Srivatasan S, Eberhard C, Carrington B, Watkins-Chow D, Pavan WJ, Trapnell C, Parichy DM. Transcriptomic profiling of tissue environments critical for post-embryonic patterning and morphogenesis of zebrafish skin. Elife. 12. PMID 37695017 DOI: 10.7554/eLife.86670  0.157
2023 Lotfollahi M, Klimovskaia Susmelj A, De Donno C, Hetzel L, Ji Y, Ibarra IL, Srivatsan SR, Naghipourfar M, Daza RM, Martin B, Shendure J, McFaline-Figueroa JL, Boyeau P, Wolf FA, Yakubova N, ... ... Trapnell C, et al. Predicting cellular responses to complex perturbations in high-throughput screens. Molecular Systems Biology. e11517. PMID 37154091 DOI: 10.15252/msb.202211517  0.156
2021 Srivatsan SR, Regier MC, Barkan E, Franks JM, Packer JS, Grosjean P, Duran M, Saxton S, Ladd JJ, Spielmann M, Lois C, Lampe PD, Shendure J, Stevens KR, Trapnell C. Embryo-scale, single-cell spatial transcriptomics. Science (New York, N.Y.). 373: 111-117. PMID 34210887 DOI: 10.1126/science.abb9536  0.147
2022 Vanderwall ER, Barrow KA, Rich LM, Read DF, Trapnell C, Okoloko O, Ziegler SF, Hallstrand TS, White MP, Debley JS. Airway epithelial interferon response to SARS-CoV-2 is inferior to rhinovirus and heterologous rhinovirus infection suppresses SARS-CoV-2 replication. Scientific Reports. 12: 6972. PMID 35484173 DOI: 10.1038/s41598-022-10763-2  0.142
2023 Hasegawa Y, Franks JM, Tanaka Y, Uehara Y, Read DF, Williams C, Srivatsan S, Pitstick LB, Nikolaidis NM, Shaver CM, Wu H, Gardner JC, Osterburg AR, Yu JJ, Kopras EJ, ... ... Trapnell C, et al. Pulmonary osteoclast-like cells in silica induced pulmonary fibrosis. Biorxiv : the Preprint Server For Biology. PMID 36824953 DOI: 10.1101/2023.02.17.528996  0.137
2023 Edman NI, Redler RL, Phal A, Schlichthaerle T, Srivatsan SR, Etemadi A, An S, Favor A, Ehnes D, Li Z, Praetorius F, Gordon M, Yang W, Coventry B, Hicks DR, ... ... Trapnell C, et al. Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies. Biorxiv : the Preprint Server For Biology. PMID 36993355 DOI: 10.1101/2023.03.14.532666  0.097
2022 Shima K, Arumugam P, Sallese A, Horia Y, Ma Y, Trapnell C, Wessendarp M, Chalk C, McCarthy C, Carey BC, Trapnell BC, Suzuki T. A Murine Model of Hereditary Pulmonary Alveolar Proteinosis Caused by Homozygous Csf2ra Gene Disruption. American Journal of Physiology. Lung Cellular and Molecular Physiology. PMID 35043685 DOI: 10.1152/ajplung.00175.2021  0.093
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