Steven Salzberg

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Mihaela PerteaAssociate Professor, Johns Hopkins UniversityVerified email at jhu.edu
Ben LangmeadAssociate Professor of Computer Science, Johns Hopkins UniversityVerified email at cs.jhu.edu
Daehwan KimUniversity of Texas Southwestern Medical CenterVerified email at UTSouthwestern.edu
Cole TrapnellAssociate Professor, Dept. of Genome Sciences, University of WashingtonVerified email at uw.edu
Daniela PuiuJohns Hopkins UniversityVerified email at jhu.edu
Aleksey V ZiminResearch Scientist, Department of Biomedical Engineering, Johns Hopkins UnviersityVerified email at jhu.edu
Mihai PopProfessor of Computer Science, University of Maryland, College ParkVerified email at umd.edu
Owen WhiteDirector of Bioinformatics, Institute for Genome Sciences, Professor, Department of Epidemiology and Preventative, University ofVerified email at som.umaryland.edu
Adam M. PhillippyDirector, Center for Genomics and Data Science Research, NHGRI, NIHVerified email at nih.gov
Florian P BreitwieserPrincipal Software Engineer at SOPHiA GeneticsVerified email at jhu.edu
Michael C. SchatzBloomberg Distinguished Professor, Johns Hopkins UniversityVerified email at cs.jhu.edu
David R KelleyCalico LabsVerified email at calicolabs.com
David NealeUniversity California, Davis USDAVerified email at ucdavis.edu
James YorkeDist. Univ. Research Prof of Math and Physics, Univ. of MarylandVerified email at umd.edu
Jennifer Lu, Ph. D.Staff Scientist, Johns Hopkins UniversityVerified email at jhmi.edu
Brian HaasBroad InstituteVerified email at broadinstitute.org
Charles H. LangleyProfessor, University of California - DavisVerified email at ucdavis.edu
Jonathan A. EisenProfessor, University of California, Davis (UC Davis), Department of Evolution and EcologyVerified email at ucdavis.edu
Sreerama MurthyCEO & Chief Data Scientist, QuadratyxVerified email at quadratyx.com
Derrick WoodVeridian InformaticsVerified email at cs.jhu.edu

Steven Salzberg

Bloomberg Distinguished Professor, Johns Hopkins University

Verified email at jhu.edu - Homepage

Computational Biology Genomics Bioinformatics Metagenomics Biomedical Data Science


Title Sort by citations Sort by year Sort by title	Cited by Cited by	Year
Fast gapped-read alignment with Bowtie 2 B Langmead, SL Salzberg Nature methods 9 (4), 357-359, 2012	49951	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	23966	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	20772	2001
HISAT: a fast spliced aligner with low memory requirements D Kim, B Langmead, SL Salzberg Nature methods 12 (4), 357-360, 2015	18399	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	15844	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, 1-13, 2013	13528	2013
TopHat: discovering splice junctions with RNA-Seq C Trapnell, L Pachter, SL Salzberg Bioinformatics 25 (9), 1105-1111, 2009	13487	2009
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	13163	2012
FLASH: fast length adjustment of short reads to improve genome assemblies T Magoč, SL Salzberg Bioinformatics 27 (21), 2957-2963, 2011	13055	2011
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. GI Arabidopsis Nature 408 (6814), 796, 2000	11262	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	9786	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	8731	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	5683	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	5544	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	5291	2016
Kraken: ultrafast metagenomic sequence classification using exact alignments DE Wood, SL Salzberg Genome biology 15, 1-12, 2014	4474	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	4124	2005
Identifying bacterial genes and endosymbiont DNA with Glimmer AL Delcher, KA Bratke, EC Powers, SL Salzberg Bioinformatics 23 (6), 673-679, 2007	3240	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	2996	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	2863	2008

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