Fast gapped-read alignment with Bowtie 2 B Langmead, SL Salzberg Nature methods 9 (4), 357-359, 2012 | 46244 | 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, 1-10, 2009 | 23311 | 2009 |
The sequence of the human genome JC Venter, MD Adams, EW Myers, PW Li, RJ Mural, et al. Science 291 (5507), 1304-1351, 2001 | 20448 | 2001 |
HISAT: a fast spliced aligner with low memory requirements D Kim, B Langmead, SL Salzberg Nature methods 12 (4), 357-360, 2015 | 16615 | 2015 |
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 | 15381 | 2010 |
TopHat: discovering splice junctions with RNA-Seq C Trapnell, L Pachter, SL Salzberg Bioinformatics 25 (9), 1105-1111, 2009 | 13278 | 2009 |
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, 1-13, 2013 | 13167 | 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 | 12798 | 2012 |
FLASH: fast length adjustment of short reads to improve genome assemblies T Magoč, SL Salzberg Bioinformatics 27 (21), 2957-2963, 2011 | 12190 | 2011 |
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. GI Arabidopsis Nature 408 (6814), 796, 2000 | 11090 | 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 | 8571 | 2015 |
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 | 7107 | 2019 |
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 | 5483 | 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 | 5420 | 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 | 4772 | 2016 |
Kraken: ultrafast metagenomic sequence classification using exact alignments DE Wood, SL Salzberg Genome biology 15, 1-12, 2014 | 4147 | 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 | 4077 | 2005 |
Identifying bacterial genes and endosymbiont DNA with Glimmer AL Delcher, KA Bratke, EC Powers, SL Salzberg Bioinformatics 23 (6), 673-679, 2007 | 3126 | 2007 |
Improved microbial gene identification with GLIMMER AL Delcher, D Harmon, S Kasif, O White, SL Salzberg Nucleic acids research 27 (23), 4636-4641, 1999 | 2959 | 1999 |
Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi CM Fraser, S Casjens, WM Huang, GG Sutton, R Clayton, R Lathigra, ... Nature 390 (6660), 580-586, 1997 | 2624 | 1997 |