Trapnell C - Search Results

1

Differential analysis of gene regulation at transcript resolution with RNA-seq.

Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L. Trapnell C, et al. Nat Biotechnol. 2013 Jan;31(1):46-53. doi: 10.1038/nbt.2450. Epub 2012 Dec 9. Nat Biotechnol. 2013. PMID: 23222703 Free PMC article.

2

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.

3

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.

4

TopHat: discovering splice junctions with RNA-Seq.

Trapnell C, Pachter L, Salzberg SL. Trapnell C, et al. Bioinformatics. 2009 May 1;25(9):1105-11. doi: 10.1093/bioinformatics/btp120. Epub 2009 Mar 16. Bioinformatics. 2009. PMID: 19289445 Free PMC article.

5

Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species.

Bradley RK, Li XY, Trapnell C, Davidson S, Pachter L, Chu HC, Tonkin LA, Biggin MD, Eisen MB. Bradley RK, et al. Among authors: trapnell c. PLoS Biol. 2010 Mar 23;8(3):e1000343. doi: 10.1371/journal.pbio.1000343. PLoS Biol. 2010. PMID: 20351773 Free PMC article.

6

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.

7

Improving RNA-Seq expression estimates by correcting for fragment bias.

Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter L. Roberts A, et al. Among authors: trapnell c. Genome Biol. 2011;12(3):R22. doi: 10.1186/gb-2011-12-3-r22. Epub 2011 Mar 16. Genome Biol. 2011. PMID: 21410973 Free PMC article.

8

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.

9

Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq).

Lucks JB, Mortimer SA, Trapnell C, Luo S, Aviran S, Schroth GP, Pachter L, Doudna JA, Arkin AP. Lucks JB, et al. Among authors: trapnell c. Proc Natl Acad Sci U S A. 2011 Jul 5;108(27):11063-8. doi: 10.1073/pnas.1106501108. Epub 2011 Jun 3. Proc Natl Acad Sci U S A. 2011. PMID: 21642531 Free PMC article.

10

Modeling and automation of sequencing-based characterization of RNA structure.

Aviran S, Trapnell C, Lucks JB, Mortimer SA, Luo S, Schroth GP, Doudna JA, Arkin AP, Pachter L. Aviran S, et al. Among authors: trapnell c. Proc Natl Acad Sci U S A. 2011 Jul 5;108(27):11069-74. doi: 10.1073/pnas.1106541108. Epub 2011 Jun 3. Proc Natl Acad Sci U S A. 2011. PMID: 21642536 Free PMC article.

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