| Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. GI Arabidopsis Nature 408 (6814), 796, 2000 | 11072 | 2000 |
| 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 | 8488 | 2015 |
| Genome sequence of the human malaria parasite Plasmodium falciparum MJ Gardner, N Hall, E Fung, O White, M Berriman, RW Hyman, JM Carlton, ... Nature 419 (6906), 498-511, 2002 | 5409 | 2002 |
| 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 | 4736 | 2016 |
| Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments BJ Haas, SL Salzberg, W Zhu, M Pertea, JE Allen, J Orvis, O White, ... Genome biology 9, 1-22, 2008 | 2524 | 2008 |
| The ENCODE (ENCyclopedia of DNA elements) project EA Feingold, PJ Good, MS Guyer, S Kamholz, L Liefer, K Wetterstrand, ... Science 306 (5696), 636-640, 2004 | 2364 | 2004 |
| Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus WC Nierman, A Pain, MJ Anderson, JR Wortman, HS Kim, J Arroyo, ... Nature 438 (7071), 1151-1156, 2005 | 1665 | 2005 |
| TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders WH Majoros, M Pertea, SL Salzberg Bioinformatics 20 (16), 2878-2879, 2004 | 1475 | 2004 |
| Genome Sequence of Aedes aegypti, a Major Arbovirus Vector V Nene, JR Wortman, D Lawson, B Haas, C Kodira, Z Tu, B Loftus, Z Xi, ... Science 316 (5832), 1718-1723, 2007 | 1333 | 2007 |
| The genome of the blood fluke Schistosoma mansoni M Berriman, BJ Haas, PT LoVerde, RA Wilson, GP Dillon, GC Cerqueira, ... Nature 460 (7253), 352-358, 2009 | 1213 | 2009 |
| 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, 1-13, 2019 | 1010 | 2019 |
| Draft Genome Sequence of the Sexually Transmitted Pathogen Trichomonas vaginalis JM Carlton, RP Hirt, JC Silva, AL Delcher, M Schatz, Q Zhao, JR Wortman, ... Science 315 (5809), 207-212, 2007 | 998 | 2007 |
| Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii JM Carlton, SV Angiuoli, BB Suh, TW Kooij, M Pertea, JC Silva, ... Nature 419 (6906), 512-519, 2002 | 904 | 2002 |
| GFF utilities: GffRead and GffCompare G Pertea, M Pertea F1000Research 9, 2020 | 884 | 2020 |
| The Genome of the Basidiomycetous Yeast and Human Pathogen Cryptococcus neoformans BJ Loftus, E Fung, P Roncaglia, D Rowley, P Amedeo, D Bruno, ... Science 307 (5713), 1321-1324, 2005 | 852 | 2005 |
| GeneSplicer: a new computational method for splice site prediction M Pertea, X Lin, SL Salzberg Nucleic acids research 29 (5), 1185-1190, 2001 | 738 | 2001 |
| Draft genome of the filarial nematode parasite Brugia malayi E Ghedin, S Wang, D Spiro, E Caler, Q Zhao, J Crabtree, JE Allen, ... Science 317 (5845), 1756-1760, 2007 | 718 | 2007 |
| Chromosome 2 Sequence of the Human Malaria Parasite Plasmodium falciparum MJ Gardner, H Tettelin, DJ Carucci, LM Cummings, L Aravind, EV Koonin, ... Science 282 (5391), 1126-1132, 1998 | 582 | 1998 |
| Broad CTL response is required to clear latent HIV-1 due to dominance of escape mutations K Deng, M Pertea, A Rongvaux, L Wang, CM Durand, G Ghiaur, J Lai, ... Nature 517 (7534), 381-385, 2015 | 572 | 2015 |
| Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes MJ Gardner, R Bishop, T Shah, EP De Villiers, JM Carlton, N Hall, Q Ren, ... Science 309 (5731), 134-137, 2005 | 390 | 2005 |
