| 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), 511-515, 2010 | 16493 | 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 | 14137 | 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), 562-578, 2012 | 13863 | 2012 |
| 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), 290-295, 2015 | 12715 | 2015 |
| 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), 1650-1667, 2016 | 6483 | 2016 |
| Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs RIKEN Genome Exploration Research Group Phase I Team: Carninci P. 2 Hayatsu ... Nature 420 (6915), 563-573, 2002 | 2203 | 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 | 2024 | 2003 |
| Transcriptome assembly from long-read RNA-seq alignments with StringTie2 S Kovaka, AV Zimin, GM Pertea, R Razaghi, SL Salzberg, M Pertea Genome biology 20 (1), 278, 2019 | 1885 | 2019 |
| GFF utilities: GffRead and GffCompare G Pertea, M Pertea F1000Research 9, ISCB Comm J-304, 2020 | 1773 | 2020 |
| 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 | 1433 | 2009 |
| 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), 243-246, 2015 | 820 | 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), 498-502, 2017 | 662 | 2017 |
| 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 | 558 | 2001 |
| 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, L Ann Blomberg, ... PLoS biology 8 (9), e1000475, 2010 | 490 | 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), 239-240, 2000 | 425 | 2000 |
| 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 | 425 | 2000 |
| 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 | 411 | 2010 |
| Improved transcriptome assembly using a hybrid of long and short reads with StringTie A Shumate, B Wong, G Pertea, M Pertea PLoS computational biology 18 (6), e1009730, 2022 | 406 | 2022 |
| CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise M Pertea, A Shumate, G Pertea, A Varabyou, FP Breitwieser, YC Chang, ... Genome biology 19 (1), 208, 2018 | 357 | 2018 |
| 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 | 272 | 2005 |
