User profiles for Steven Salzberg

Steven Salzberg

Bloomberg Distinguished Professor, Johns Hopkins University
Verified email at jhu.edu
Cited by 341197

The sequence of the human genome

…, B Neelam, D Nusskern, DB Rusch, S Salzberg… - science, 2001 - science.org
A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human
genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion …

Microbial gene identification using interpolated Markov models

SL Salzberg, AL Delcher, S Kasif… - Nucleic acids …, 1998 - academic.oup.com
This paper describes a new system, GLIMMER, for finding genes in microbial genomes. In a
series of tests on Haemophilus influenzae, Helicobacter pylori and other complete microbial …

TopHat: discovering splice junctions with RNA-Seq

C Trapnell, L Pachter, SL Salzberg - Bioinformatics, 2009 - academic.oup.com
Motivation: A new protocol for sequencing the messenger RNA in a cell, known as RNA-Seq,
generates millions of short sequence fragments in a single run. These fragments, or ‘reads’…

FLASH: fast length adjustment of short reads to improve genome assemblies

T Magoč, SL Salzberg - Bioinformatics, 2011 - academic.oup.com
Motivation: Next-generation sequencing technologies generate very large numbers of short
reads. Even with very deep genome coverage, short read lengths cause problems in de …

HISAT: a fast spliced aligner with low memory requirements

D Kim, B Langmead, SL Salzberg - Nature methods, 2015 - nature.com
HISAT (hierarchical indexing for spliced alignment of transcripts) is a highly efficient system
for aligning reads from RNA sequencing experiments. HISAT uses an indexing scheme …

Bioinformatics challenges of new sequencing technology

M Pop, SL Salzberg - Trends in genetics, 2008 - cell.com
New DNA sequencing technologies can sequence up to one billion bases in a single day at
low cost, putting large-scale sequencing within the reach of many scientists. Many …

How to map billions of short reads onto genomes

C Trapnell, SL Salzberg - Nature biotechnology, 2009 - nature.com
Mapping the vast quantities of short sequence fragments produced by next-generation
sequencing platforms is a challenge. What programs are available and how do they work?

[HTML][HTML] TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

…, C Trapnell, H Pimentel, R Kelley, SL Salzberg - Genome biology, 2013 - Springer
TopHat is a popular spliced aligner for RNA-sequence (RNA-seq) experiments. In this paper,
we describe TopHat2, which incorporates many significant enhancements to TopHat. …

[HTML][HTML] Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

B Langmead, C Trapnell, M Pop, SL Salzberg - Genome biology, 2009 - Springer
Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence
reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie …

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

…, TC Chang, JT Mendell, SL Salzberg - Nature …, 2015 - nature.com
Methods used to sequence the transcriptome often produce more than 200 million short
sequences. We introduce StringTie, a computational method that applies a network flow …