| Fast gapped-read alignment with Bowtie 2 B Langmead, SL Salzberg Nature methods 9 (4), 357-359, 2012 | 58979 | 2012 |
| Ultrafast and memory-efficient alignment of short DNA sequences to the human genome B Langmead, C Trapnell, M Pop, SL Salzberg Genome biology 10 (3), R25, 2009 | 25576 | 2009 |
| HISAT: a fast spliced aligner with low memory requirements D Kim, B Langmead, SL Salzberg Nature methods 12 (4), 357-360, 2015 | 22397 | 2015 |
| The sequence of the human genome JC Venter, MD Adams, EW Myers, PW Li, RJ Mural, et al. Science 291 (5507), 1304-1351, 2001 | 21395 | 2001 |
| 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 | 16861 | 2010 |
| FLASH: fast length adjustment of short reads to improve genome assemblies T Magoč, SL Salzberg Bioinformatics 27 (21), 2957-2963, 2011 | 15162 | 2011 |
| 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 |
| TopHat: discovering splice junctions with RNA-Seq C Trapnell, L Pachter, SL Salzberg Bioinformatics 25 (9), 1105-1111, 2009 | 13856 | 2009 |
| Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype D Kim, JM Paggi, C Park, C Bennett, SL Salzberg Nature biotechnology 37 (8), 907-915, 2019 | 13127 | 2019 |
| 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 |
| Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. GI Arabidopsis Nature 408 (6814), 796, 2000 | 11705 | 2000 |
| 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 |
| Versatile and open software for comparing large genomes S Kurtz, A Phillippy, AL Delcher, M Smoot, M Shumway, C Antonescu, ... Genome biology 5 (2), R12, 2004 | 6080 | 2004 |
| 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 | 5774 | 2002 |
| Kraken: ultrafast metagenomic sequence classification using exact alignments DE Wood, SL Salzberg Genome biology 15 (3), R46, 2014 | 5188 | 2014 |
| The transcriptional landscape of the mammalian genome P Carninci, T Kasukawa, S Katayama, J Gough, MC Frith, N Maeda, ... science 309 (5740), 1559-1563, 2005 | 4125 | 2005 |
| 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), R7, 2008 | 3713 | 2008 |
| The complete sequence of a human genome S Nurk, S Koren, A Rhie, M Rautiainen, AV Bzikadze, A Mikheenko, ... Science 376 (6588), 44-53, 2022 | 3541 | 2022 |
| Identifying bacterial genes and endosymbiont DNA with Glimmer AL Delcher, KA Bratke, EC Powers, SL Salzberg Bioinformatics 23 (6), 673-679, 2007 | 3506 | 2007 |
Mihaela PerteaAssociate Professor, Johns Hopkins UniversityVerified email at jhu.edu
