Geo Pertea
Geo Pertea
Software Engineer, Johns Hopkins University
Verified email at jhu.edu
TitleCited byYear
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
C Trapnell, BA Williams, G Pertea, A Mortazavi, G Kwan, MJ Van Baren, ...
Nature biotechnology 28 (5), 511, 2010
89732010
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
D Kim, G Pertea, C Trapnell, H Pimentel, R Kelley, SL Salzberg
Genome biology 14 (4), R36, 2013
74062013
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
C Trapnell, A Roberts, L Goff, G Pertea, D Kim, DR Kelley, H Pimentel, ...
Nature protocols 7 (3), 562, 2012
73952012
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs
Fantom Consortium, ...
Nature 420 (6915), 563, 2002
17562002
TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets
G Pertea, X Huang, F Liang, V Antonescu, R Sultana, S Karamycheva, ...
Bioinformatics 19 (5), 651-652, 2003
14622003
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
M Pertea, GM Pertea, CM Antonescu, TC Chang, JT Mendell, SL Salzberg
Nature biotechnology 33 (3), 290, 2015
12482015
A whole-genome assembly of the domestic cow, Bos taurus
AV Zimin, AL Delcher, L Florea, DR Kelley, MC Schatz, D Puiu, ...
Genome biology 10 (4), R42, 2009
9482009
Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown
M Pertea, D Kim, GM Pertea, JT Leek, SL Salzberg
Nature protocols 11 (9), 1650, 2016
7482016
The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species
J Quackenbush, J Cho, D Lee, F Liang, I Holt, S Karamycheva, B Parvizi, ...
Nucleic Acids Research 29 (1), 159-164, 2001
5182001
The TIGR gene indices: reconstruction and representation of expressed gene sequences
J Quackenbush, F Liang, I Holt, G Pertea, J Upton
Nucleic acids research 28 (1), 141-145, 2000
3892000
Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis
RA Dalloul, JA Long, AV Zimin, L Aslam, K Beal, LA Blomberg, P Bouffard, ...
PLoS biology 8 (9), e1000475, 2010
3622010
Gene index analysis of the human genome estimates approximately 120,000 genes
F Liang, I Holt, G Pertea, S Karamycheva, SL Salzberg, J Quackenbush
Nature genetics 25 (2), 239, 2000
3532000
The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes
Y Lee, J Tsai, S Sunkara, S Karamycheva, G Pertea, R Sultana, ...
Nucleic acids research 33 (suppl_1), D71-D74, 2005
2412005
Enrichment of gene-coding sequences in maize by genome filtration
CA Whitelaw, WB Barbazuk, G Pertea, AP Chan, F Cheung, Y Lee, ...
Science 302 (5653), 2118-2120, 2003
2372003
Comparative analyses of potato expressed sequence tag libraries
CM Ronning, SS Stegalkina, RA Ascenzi, O Bougri, AL Hart, TR Utterbach, ...
Plant Physiology 131 (2), 419-429, 2003
2362003
Cross-referencing eukaryotic genomes: TIGR orthologous gene alignments (TOGA)
Y Lee, R Sultana, G Pertea, J Cho, S Karamycheva, J Tsai, B Parvizi, ...
Genome Research 12 (3), 493-502, 2002
1992002
Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms
C Trapnell, BA Williams, G Pertea, A Mortazavi, G Kwan, MJ van Baren, ...
Nature biotechnology 28 (5), 511, 2010
1982010
An optimized protocol for analysis of EST sequences
F Liang, I Holt, G Pertea, S Karamycheva, SL Salzberg, J Quackenbush
Nucleic acids research 28 (18), 3657-3665, 2000
1912000
Ballgown bridges the gap between transcriptome assembly and expression analysis
AC Frazee, G Pertea, AE Jaffe, B Langmead, SL Salzberg, JT Leek
Nature biotechnology 33 (3), 243, 2015
1762015
Genome sequence of the progenitor of the wheat D genome Aegilops tauschii
MC Luo, YQ Gu, D Puiu, H Wang, SO Twardziok, KR Deal, N Huo, T Zhu, ...
Nature 551 (7681), 498, 2017
1402017
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Articles 1–20