Trapnell C - Search Results

1

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

Garber M, Grabherr MG, Guttman M, Trapnell C. Garber M, et al. Among authors: trapnell c. Nat Methods. 2011 Jun;8(6):469-77. doi: 10.1038/nmeth.1613. Epub 2011 May 27. Nat Methods. 2011. PMID: 21623353 Free article. Review.

2

Predicting cellular responses to complex perturbations in high-throughput screens.

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, Günnemann S, Trapnell C, Lopez-Paz D, Theis FJ. Lotfollahi M, et al. Among authors: trapnell c. Mol Syst Biol. 2023 Jun 12;19(6):e11517. doi: 10.15252/msb.202211517. Epub 2023 May 8. Mol Syst Biol. 2023. PMID: 37154091 Free PMC article.

3

Transcriptomic profiling of tissue environments critical for post-embryonic patterning and morphogenesis of zebrafish skin.

Aman AJ, Saunders LM, Carr AA, Srivatasan S, Eberhard C, Carrington B, Watkins-Chow D, Pavan WJ, Trapnell C, Parichy DM. Aman AJ, et al. Among authors: trapnell c. Elife. 2023 Sep 11;12:RP86670. doi: 10.7554/eLife.86670. Elife. 2023. PMID: 37695017 Free PMC article.

4

Dystrophin deficiency impairs cell junction formation during embryonic myogenesis.

Mozin E, Massouridès E, Mournetas V, Lièvre C, Bourdon A, Jackson DL, Packer JS, Seong J, Trapnell C, Le Guiner C, Adjali O, Pinset C, Mack DL, Dupont JB. Mozin E, et al. Among authors: trapnell c. bioRxiv [Preprint]. 2024 Apr 8:2023.12.05.569919. doi: 10.1101/2023.12.05.569919. bioRxiv. 2024. Update in: iScience. 2024 Jun 11;27(7):110242. doi: 10.1016/j.isci.2024.110242. PMID: 38106055 Free PMC article. Updated. Preprint.

5

Single-cell transcriptomic profiling of the zebrafish inner ear reveals molecularly distinct hair cell and supporting cell subtypes.

Shi T, Beaulieu MO, Saunders LM, Fabian P, Trapnell C, Segil N, Crump JG, Raible DW. Shi T, et al. Among authors: trapnell c. Elife. 2023 Jan 4;12:e82978. doi: 10.7554/eLife.82978. Elife. 2023. PMID: 36598134 Free PMC article.

6

High-capacity sample multiplexing for single cell chromatin accessibility profiling.

Booth GT, Daza RM, Srivatsan SR, McFaline-Figueroa JL, Gladden RG, Mullen AC, Furlan SN, Shendure J, Trapnell C. Booth GT, et al. Among authors: trapnell c. BMC Genomics. 2023 Dec 4;24(1):737. doi: 10.1186/s12864-023-09832-1. BMC Genomics. 2023. PMID: 38049719 Free PMC article.

7

Proteostasis governs differential temperature sensitivity across embryonic cell types.

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. Dorrity MW, et al. Among authors: trapnell c. Cell. 2023 Nov 9;186(23):5015-5027.e12. doi: 10.1016/j.cell.2023.10.013. Cell. 2023. PMID: 37949057 Free PMC article.

8

Single-cell sequencing of individual retinal organoids reveals determinants of cell-fate heterogeneity.

Tresenrider A, Sridhar A, Eldred KC, Cuschieri S, Hoffer D, Trapnell C, Reh TA. Tresenrider A, et al. Among authors: trapnell c. Cell Rep Methods. 2023 Aug 9;3(8):100548. doi: 10.1016/j.crmeth.2023.100548. eCollection 2023 Aug 28. Cell Rep Methods. 2023. PMID: 37671011 Free PMC article.

9

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

Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Trapnell C, et al. Nat Biotechnol. 2010 May;28(5):511-5. doi: 10.1038/nbt.1621. Epub 2010 May 2. Nat Biotechnol. 2010. PMID: 20436464 Free PMC article.

10

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

Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Trapnell C, et al. Nat Protoc. 2012 Mar 1;7(3):562-78. doi: 10.1038/nprot.2012.016. Nat Protoc. 2012. PMID: 22383036 Free PMC article.

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