Pertea G[au] - Search Results

Year	Number of Results
2000	3
2001	3
2002	3
2003	3
2005	1
2006	1
2007	1
2009	2
2010	2
2011	1
2012	1
2013	1
2015	2
2016	1
2017	3
2018	2
2019	2
2020	2
2021	1
2022	1
2023	1
2024	0

1

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown.

Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL. Pertea M, et al. Among authors: pertea gm. Nat Protoc. 2016 Sep;11(9):1650-67. doi: 10.1038/nprot.2016.095. Epub 2016 Aug 11. Nat Protoc. 2016. PMID: 27560171 Free PMC article.

2

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads.

Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL. Pertea M, et al. Among authors: pertea gm. Nat Biotechnol. 2015 Mar;33(3):290-5. doi: 10.1038/nbt.3122. Epub 2015 Feb 18. Nat Biotechnol. 2015. PMID: 25690850 Free PMC article.

3

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. Among authors: pertea g. 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.

4

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. Among authors: pertea g. Nat Protoc. 2012 Mar 1;7(3):562-78. doi: 10.1038/nprot.2012.016. Nat Protoc. 2012. PMID: 22383036 Free PMC article.

5

GFF Utilities: GffRead and GffCompare.

Pertea G, Pertea M. Pertea G, et al. F1000Res. 2020 Apr 28;9:ISCB Comm J-304. doi: 10.12688/f1000research.23297.2. eCollection 2020. F1000Res. 2020. PMID: 32489650 Free PMC article.

6

Transcriptome assembly from long-read RNA-seq alignments with StringTie2.

Kovaka S, Zimin AV, Pertea GM, Razaghi R, Salzberg SL, Pertea M. Kovaka S, et al. Among authors: pertea gm. Genome Biol. 2019 Dec 16;20(1):278. doi: 10.1186/s13059-019-1910-1. Genome Biol. 2019. PMID: 31842956 Free PMC article.

7

Improved transcriptome assembly using a hybrid of long and short reads with StringTie.

Shumate A, Wong B, Pertea G, Pertea M. Shumate A, et al. Among authors: pertea g. PLoS Comput Biol. 2022 Jun 1;18(6):e1009730. doi: 10.1371/journal.pcbi.1009730. eCollection 2022 Jun. PLoS Comput Biol. 2022. PMID: 35648784 Free PMC article.

8

The TIGR Maize Database.

Chan AP, Pertea G, Cheung F, Lee D, Zheng L, Whitelaw C, Pontaroli AC, SanMiguel P, Yuan Y, Bennetzen J, Barbazuk WB, Quackenbush J, Rabinowicz PD. Chan AP, et al. Among authors: pertea g. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D771-6. doi: 10.1093/nar/gkj072. Nucleic Acids Res. 2006. PMID: 16381977 Free PMC article.

9

Genetic and environmental contributions to ancestry differences in gene expression in the human brain.

Benjamin KJM, Chen Q, Eagles NJ, Huuki-Myers LA, Collado-Torres L, Stolz JM, Pertea G, Shin JH, Paquola ACM, Hyde TM, Kleinman JE, Jaffe AE, Han S, Weinberger DR. Benjamin KJM, et al. Among authors: pertea g. bioRxiv [Preprint]. 2023 Oct 5:2023.03.28.534458. doi: 10.1101/2023.03.28.534458. bioRxiv. 2023. PMID: 37034760 Free PMC article. Preprint.

10

Ballgown bridges the gap between transcriptome assembly and expression analysis.

Frazee AC, Pertea G, Jaffe AE, Langmead B, Salzberg SL, Leek JT. Frazee AC, et al. Among authors: pertea g. Nat Biotechnol. 2015 Mar;33(3):243-6. doi: 10.1038/nbt.3172. Nat Biotechnol. 2015. PMID: 25748911 Free PMC article. No abstract available.

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