| 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 | 9026 | 2010 |
| 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 | 7470 | 2013 |
| 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 | 7462 | 2012 |
| Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs Fantom Consortium, ... Nature 420 (6915), 563, 2002 | 1766 | 2002 |
| 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 | 1468 | 2003 |
| 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 | 1291 | 2015 |
| 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 | 954 | 2009 |
| 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 | 780 | 2016 |
| 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 | 520 | 2001 |
| 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 | 389 | 2000 |
| 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 | 363 | 2010 |
| 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 | 354 | 2000 |
| 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 | 241 | 2005 |
| 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 | 239 | 2003 |
| 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 | 236 | 2003 |
| 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 | 200 | 2010 |
| 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 | 199 | 2002 |
| 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 | 191 | 2000 |
| 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 | 180 | 2015 |
| 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 | 144 | 2017 |
