Steven Salzberg
Steven Salzberg
Bloomberg Distinguished Professor, Johns Hopkins University
Verified email at - Homepage
Cited by
Cited by
Fast gapped-read alignment with Bowtie 2
B Langmead, SL Salzberg
Nature methods 9 (4), 357-359, 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
The sequence of the human genome
JC Venter, MD Adams, EW Myers, PW Li, RJ Mural, et al.
Science 291 (5507), 1304-1351, 2001
HISAT: a fast spliced aligner with low memory requirements
D Kim, B Langmead, SL Salzberg
Nature methods 12 (4), 357-360, 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
TopHat: discovering splice junctions with RNA-Seq
C Trapnell, L Pachter, SL Salzberg
Bioinformatics 25 (9), 1105-1111, 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
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
FLASH: fast length adjustment of short reads to improve genome assemblies
T Magoč, SL Salzberg
Bioinformatics 27 (21), 2957-2963, 2011
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.
GI Arabidopsis
Nature 408 (6814), 796, 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
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
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
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
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
Kraken: ultrafast metagenomic sequence classification using exact alignments
DE Wood, SL Salzberg
Genome biology 15, 1-12, 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
Identifying bacterial genes and endosymbiont DNA with Glimmer
AL Delcher, KA Bratke, EC Powers, SL Salzberg
Bioinformatics 23 (6), 673-679, 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
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
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