Trapnell C - Search Results

1

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.

2

Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre.

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, Flavell R, Raj A, Rinn JL. Hacisuleyman E, et al. Among authors: trapnell c. Nat Struct Mol Biol. 2014 Feb;21(2):198-206. doi: 10.1038/nsmb.2764. Epub 2014 Jan 26. Nat Struct Mol Biol. 2014. PMID: 24463464 Free PMC article.

3

Targeted RNA sequencing reveals the deep complexity of the human transcriptome.

Mercer TR, Gerhardt DJ, Dinger ME, Crawford J, Trapnell C, Jeddeloh JA, Mattick JS, Rinn JL. Mercer TR, et al. Among authors: trapnell c. Nat Biotechnol. 2011 Nov 13;30(1):99-104. doi: 10.1038/nbt.2024. Nat Biotechnol. 2011. PMID: 22081020 Free PMC article.

4

Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A.

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, Aparna G, Jha G, Pandey A, Patil PB, Ishihara H, Meyer DF, Szurek B, Verdier V, Koebnik R, Dow JM, Ryan RP, Hirata H, Tsuyumu S, Won Lee S, Seo YS, Sriariyanum M, Ronald PC, Sonti RV, Van Sluys MA, Leach JE, White FF, Bogdanove AJ. Salzberg SL, et al. Among authors: trapnell c. BMC Genomics. 2008 May 1;9:204. doi: 10.1186/1471-2164-9-204. BMC Genomics. 2008. PMID: 18452608 Free PMC article.

5

How to map billions of short reads onto genomes.

Trapnell C, Salzberg SL. Trapnell C, et al. Nat Biotechnol. 2009 May;27(5):455-7. doi: 10.1038/nbt0509-455. Nat Biotechnol. 2009. PMID: 19430453 Free PMC article.

6

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Langmead B, Trapnell C, Pop M, Salzberg SL. Langmead B, et al. Among authors: trapnell c. Genome Biol. 2009;10(3):R25. doi: 10.1186/gb-2009-10-3-r25. Epub 2009 Mar 4. Genome Biol. 2009. PMID: 19261174 Free PMC article.

7

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.

8

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.

9

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.

Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. Kim D, et al. Among authors: trapnell c. Genome Biol. 2013 Apr 25;14(4):R36. doi: 10.1186/gb-2013-14-4-r36. Genome Biol. 2013. PMID: 23618408 Free PMC article.

10

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.

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