cisRED: a database system for genome-scale computational discovery of regulatory elements

Database resources of the National Center for Biotechnology Information: update

2003 • 10,877 citations

Fitting a mixture model by expectation maximization to discover motifs in biopolymers.

1994 • 4,818 citations

The KEGG resource for deciphering the genome

2003 • 4,678 citations

NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

2006 • 4,425 citations

The Gene Ontology (GO) database and informatics resource

2003 • 4,254 citations

OPTICS

1999 • 3,622 citations

The ENCODE (ENCyclopedia Of DNA Elements) Project

2004 • 2,327 citations

Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals

2005 • 1,895 citations

The UCSC Genome Browser Database

2003 • 1,872 citations

NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

2004 • 1,523 citations

DNA binding sites: representation and discovery

2000 • 1,503 citations

Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner

2004 • 1,473 citations

Assessing computational tools for the discovery of transcription factor binding sites

2005 • 1,289 citations

Identifying DNA and protein patterns with statistically significant alignments of multiple sequences.

1999 • 1,272 citations

Applied bioinformatics for the identification of regulatory elements

2004 • 1,210 citations

Coexpression Analysis of Human Genes Across Many Microarray Data Sets

2004 • 778 citations

Inparanoid: a comprehensive database of eukaryotic orthologs

2004 • 756 citations

Database resources of the National Center for Biotechnology Information

2004 • 410 citations

A Gibbs Sampling Method to Detect Overrepresented Motifs in the Upstream Regions of Coexpressed Genes

2002 • 353 citations

Ensembl 2005

2004 • 344 citations

Computational prediction of transcription-factor binding site locations

2015 • 289 citations

Computational prediction of transcription-factor binding site locations.

2003 • 238 citations

TRANSCompel(R): a database on composite regulatory elements in eukaryotic genes

2002 • 137 citations

Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach.

2005 • 129 citations

Discovering functional transcription-factor combinations in the human cell cycle

2005 • 89 citations

A Gibbs sampling method to detect over-represented motifs in the upstream regions of co-expressed genes

2001 • 71 citations

Identification of sparsely distributed clusters of cis-regulatory elements in sets of co-expressed genes

2004 • 61 citations

TRANSFAC, TRANSPATH and CYTOMER as starting points for an ontology of regulatory networks.

2004 • 55 citations

Assessment and integration of publicly available SAGE, cDNA microarray, and oligonucleotide microarray expression data for global coexpression analyses

2005 • 47 citations

Sockeye: A 3D Environment for Comparative Genomics

2004 • 41 citations

ArrayProspector: a web resource of functional associations inferred from microarray expression data

2004 • 31 citations