User profiles for Steven Salzberg
Steven SalzbergBloomberg 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 …
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 …
series of tests on Haemophilus influenzae, Helicobacter pylori and other complete microbial …
TopHat: discovering splice junctions with RNA-Seq
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’…
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 …
reads. Even with very deep genome coverage, short read lengths cause problems in de …
HISAT: a fast spliced aligner with low memory requirements
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 …
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 …
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?
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
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. …
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
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 …
reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie …
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
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 …
sequences. We introduce StringTie, a computational method that applies a network flow …