• Publications
  • Influence
Basic local alignment search tool.
A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP)Expand
  • 71,815
  • 8594
  • PDF
A Greedy Algorithm for Aligning DNA Sequences
We introduce a new greedy alignment algorithm with particularly good performance and show that it computes the same alignment as does a certain dynamic programming algorithm, while executing over 10 times faster on appropriate data. Expand
  • 3,755
  • 542
  • PDF
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.
We have conducted a comprehensive search for conserved elements in vertebrate genomes, using genome-wide multiple alignments of five vertebrate species (human, mouse, rat, chicken, and FuguExpand
  • 3,119
  • 263
  • PDF
Complete genome sequence of Salmonella enterica serovar Typhimurium LT2
Salmonella enterica subspecies I, serovar Typhimurium (S. typhimurium), is a leading cause of human gastroenteritis, and is used as a mouse model of human typhoid fever. The incidence of non-typhoidExpand
  • 1,697
  • 194
Galaxy: a platform for interactive large-scale genome analysis.
Accessing and analyzing the exponentially expanding genomic sequence and functional data pose a challenge for biomedical researchers. Here we describe an interactive system, Galaxy, that combines theExpand
  • 1,915
  • 158
  • PDF
PipMaker--a web server for aligning two genomic DNA sequences.
PipMaker (http://bio.cse.psu.edu) is a World-Wide Web site for comparing two long DNA sequences to identify conserved segments and for producing informative, high-resolution displays of the resultingExpand
  • 1,217
  • 135
  • PDF
Human-mouse alignments with BLASTZ.
The Mouse Genome Analysis Consortium aligned the human and mouse genome sequences for a variety of purposes, using alignment programs that suited the various needs. For investigating issues regardingExpand
  • 1,270
  • 125
  • PDF
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These dataExpand
  • 4,613
  • 124
  • PDF
Aligning multiple genomic sequences with the threaded blockset aligner.
We define a "threaded blockset," which is a novel generalization of the classic notion of a multiple alignment. A new computer program called TBA (for "threaded blockset aligner") builds a threadedExpand
  • 1,287
  • 97
  • PDF