Published in Nucleic Acids Res on May 08, 2007
Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes. Genome Biol (2008) 1.46
An integrative computational approach for prioritization of genomic variants. PLoS One (2014) 1.45
The C. savignyi genetic map and its integration with the reference sequence facilitates insights into chordate genome evolution. Genome Res (2008) 0.89
Whole-Genome rVISTA: a tool to determine enrichment of transcription factor binding sites in gene promoters from transcriptomic data. Bioinformatics (2013) 0.89
Transcription of the transforming growth factor beta activating integrin beta8 subunit is regulated by SP3, AP-1, and the p38 pathway. J Biol Chem (2010) 0.88
Conserved genomic structure of the Cyp1a1 and Cyp1a2 loci and their dioxin responsive elements cluster. Biochem Pharmacol (2008) 0.87
ModuleOrganizer: detecting modules in families of transposable elements. BMC Bioinformatics (2010) 0.82
Computational tools and resources for prediction and analysis of gene regulatory regions in the chick genome. Genesis (2013) 0.79
A conserved MRF4 promoter drives transgenic expression in Xenopus embryonic somites and adult muscle. Int J Dev Biol (2010) 0.75
KISSa: a strategy to build multiple sequence alignments from pairwise comparisons of very closely related sequences. BMC Res Notes (2009) 0.75
BLAT--the BLAST-like alignment tool. Genome Res (2002) 126.78
Human non-synonymous SNPs: server and survey. Nucleic Acids Res (2002) 50.45
Human-mouse alignments with BLASTZ. Genome Res (2003) 35.49
Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res (2004) 24.52
LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res (2003) 23.03
TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res (2006) 22.20
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2006) 18.84
VISTA: computational tools for comparative genomics. Nucleic Acids Res (2004) 13.52
VISTA : visualizing global DNA sequence alignments of arbitrary length. Bioinformatics (2000) 12.50
MATCH: A tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res (2003) 11.82
MAVID: constrained ancestral alignment of multiple sequences. Genome Res (2004) 5.83
Glocal alignment: finding rearrangements during alignment. Bioinformatics (2003) 4.88
Strategies and tools for whole-genome alignments. Genome Res (2003) 4.86
Close sequence comparisons are sufficient to identify human cis-regulatory elements. Genome Res (2006) 3.92
Automated whole-genome multiple alignment of rat, mouse, and human. Genome Res (2004) 2.64
Phylo-VISTA: interactive visualization of multiple DNA sequence alignments. Bioinformatics (2004) 1.97
Gene expression patterns define key transcriptional events in cell-cycle regulation by cAMP and protein kinase A. Proc Natl Acad Sci U S A (2005) 1.52
Mapping cis-regulatory domains in the human genome using multi-species conservation of synteny. Hum Mol Genet (2005) 1.49
Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons. Genome Biol (2007) 1.08
TreeQ-VISTA: an interactive tree visualization tool with functional annotation query capabilities. Bioinformatics (2007) 0.98
Primate-specific evolution of an LDLR enhancer. Genome Biol (2006) 0.94
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
The Sorghum bicolor genome and the diversification of grasses. Nature (2009) 14.62
The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Res (2007) 13.81
VISTA: computational tools for comparative genomics. Nucleic Acids Res (2004) 13.52
The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science (2007) 11.15
In vivo enhancer analysis of human conserved non-coding sequences. Nature (2006) 10.60
AVID: A global alignment program. Genome Res (2003) 10.06
Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res (2005) 8.38
The amphioxus genome and the evolution of the chordate karyotype. Nature (2008) 8.03
The integrated microbial genomes (IMG) system. Nucleic Acids Res (2006) 7.34
rVista for comparative sequence-based discovery of functional transcription factor binding sites. Genome Res (2002) 7.33
IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res (2007) 7.18
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17
VISTA Enhancer Browser--a database of tissue-specific human enhancers. Nucleic Acids Res (2006) 7.04
Visualizing genomes: techniques and challenges. Nat Methods (2010) 6.66
Glocal alignment: finding rearrangements during alignment. Bioinformatics (2003) 4.88
Strategies and tools for whole-genome alignments. Genome Res (2003) 4.86
The genome of the Western clawed frog Xenopus tropicalis. Science (2010) 4.70
Characterization of evolutionary rates and constraints in three Mammalian genomes. Genome Res (2004) 4.45
Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science (2009) 4.05
Cross-species sequence comparisons: a review of methods and available resources. Genome Res (2003) 3.90
The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proc Natl Acad Sci U S A (2007) 3.58
The genome portal of the Department of Energy Joint Genome Institute. Nucleic Acids Res (2011) 3.26
An experimental metagenome data management and analysis system. Bioinformatics (2006) 2.71
Automated whole-genome multiple alignment of rat, mouse, and human. Genome Res (2004) 2.64
Combinatorial regulation of endothelial gene expression by ets and forkhead transcription factors. Cell (2008) 2.60
MycoCosm portal: gearing up for 1000 fungal genomes. Nucleic Acids Res (2013) 2.60
RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. Nucleic Acids Res (2009) 2.53
Multiple whole-genome alignments without a reference organism. Genome Res (2009) 2.31
The DNA sequence and biology of human chromosome 19. Nature (2004) 2.29
The splicing regulatory element, UGCAUG, is phylogenetically and spatially conserved in introns that flank tissue-specific alternative exons. Nucleic Acids Res (2005) 2.20
Phylo-VISTA: interactive visualization of multiple DNA sequence alignments. Bioinformatics (2004) 1.97
RegTransBase--a database of regulatory sequences and interactions in a wide range of prokaryotic genomes. Nucleic Acids Res (2006) 1.95
A correlation with exon expression approach to identify cis-regulatory elements for tissue-specific alternative splicing. Nucleic Acids Res (2007) 1.94
A cis-regulatory signature in ascidians and flies, independent of transcription factor binding sites. Curr Biol (2010) 1.93
RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach. Nucleic Acids Res (2010) 1.81
Trends in prokaryotic evolution revealed by comparison of closely related bacterial and archaeal genomes. J Bacteriol (2008) 1.79
Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria. Genome Biol (2004) 1.78
RegPrecise 3.0--a resource for genome-scale exploration of transcriptional regulation in bacteria. BMC Genomics (2013) 1.61
Gene expression patterns define key transcriptional events in cell-cycle regulation by cAMP and protein kinase A. Proc Natl Acad Sci U S A (2005) 1.52
The genome portal of the Department of Energy Joint Genome Institute: 2014 updates. Nucleic Acids Res (2013) 1.50
Comparative genomics of regulation of fatty acid and branched-chain amino acid utilization in proteobacteria. J Bacteriol (2008) 1.45
ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes. Nucleic Acids Res (2008) 1.30
Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus. BMC Genomics (2011) 1.26
SNP-VISTA: an interactive SNP visualization tool. BMC Bioinformatics (2005) 1.21
RegTransBase--a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes. BMC Genomics (2013) 1.13
RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics. Nucleic Acids Res (2012) 1.06
Extensive parallelism in protein evolution. Biol Direct (2007) 1.00
TreeQ-VISTA: an interactive tree visualization tool with functional annotation query capabilities. Bioinformatics (2007) 0.98
Conservation patterns in different functional sequence categories of divergent Drosophila species. Genomics (2006) 0.97
Differential domain evolution and complex RNA processing in a family of paralogous EPB41 (protein 4.1) genes facilitate expression of diverse tissue-specific isoforms. Genomics (2004) 0.96
Whole-Genome rVISTA: a tool to determine enrichment of transcription factor binding sites in gene promoters from transcriptomic data. Bioinformatics (2013) 0.89
Variation in conserved non-coding sequences on chromosome 5q and susceptibility to asthma and atopy. Respir Res (2005) 0.88
Comparative genomics of the dormancy regulons in mycobacteria. J Bacteriol (2011) 0.88
Short sequence motifs, overrepresented in mammalian conserved non-coding sequences. BMC Genomics (2007) 0.87
Transcription factor family-based reconstruction of singleton regulons and study of the Crp/Fnr, ArsR, and GntR families in Desulfovibrionales genomes. J Bacteriol (2012) 0.86
VISTA Region Viewer (RViewer)--a computational system for prioritizing genomic intervals for biomedical studies. Bioinformatics (2011) 0.85
High-throughput translational medicine: challenges and solutions. Adv Exp Med Biol (2014) 0.81
Comparative genomics approaches to study organism similarities and differences. J Biomed Inform (2002) 0.80
SNPs in putative regulatory regions identified by human mouse comparative sequencing and transcription factor binding site data. Mamm Genome (2002) 0.79
New family of tungstate-responsive transcriptional regulators in sulfate-reducing bacteria. J Bacteriol (2013) 0.78
Obtaining comparative genomic data with the VISTA family of computational tools. Curr Protoc Bioinformatics (2009) 0.78
Tandem termination signal in plant mRNAs. Gene (2011) 0.76