Detection of coregulation in differential gene expression profiles.

[1]  G. Fogel,et al.  A statistical analysis of the TRANSFAC database. , 2005, Bio Systems.

[2]  David J. Arenillas,et al.  oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes , 2005, Nucleic acids research.

[3]  Bart De Moor,et al.  A genetic algorithm for the detection of new cis-regulatory modules in sets of coregulated genes , 2004, Bioinform..

[4]  Sonja J. Prohaska,et al.  Surveying phylogenetic footprints in large gene clusters: applications to Hox cluster duplications. , 2004, Molecular phylogenetics and evolution.

[5]  T. Meyer,et al.  Genome-wide gene-expression patterns of donor kidney biopsies distinguish primary allograft function , 2004, Laboratory Investigation.

[6]  Atul J. Butte,et al.  Quantifying the relationship between co-expression, co-regulation and gene function , 2004, BMC Bioinformatics.

[7]  Jacques van Helden,et al.  Metrics for comparing regulatory sequences on the basis of pattern counts , 2004, Bioinform..

[8]  Ting Wang,et al.  Combining phylogenetic data with co-regulated genes to identify regulatory motifs , 2003, Bioinform..

[9]  Daphne Koller,et al.  Genome-wide discovery of transcriptional modules from DNA sequence and gene expression , 2003, ISMB.

[10]  Saurabh Sinha,et al.  A probabilistic method to detect regulatory modules , 2003, ISMB.

[11]  Roded Sharan,et al.  CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments , 2003, ISMB.

[12]  Eric C. Rouchka,et al.  Gibbs Recursive Sampler: finding transcription factor binding sites , 2003, Nucleic Acids Res..

[13]  Alexander E. Kel,et al.  MATCHTM: a tool for searching transcription factor binding sites in DNA sequences , 2003, Nucleic Acids Res..

[14]  A. Sandelin,et al.  Identification of conserved regulatory elements by comparative genome analysis , 2003, Journal of biology.

[15]  B. De Moor,et al.  Toucan: deciphering the cis-regulatory logic of coregulated genes. , 2003, Nucleic acids research.

[16]  Jon D. McAuliffe,et al.  Phylogenetic Shadowing of Primate Sequences to Find Functional Regions of the Human Genome , 2003, Science.

[17]  Wyeth W. Wasserman,et al.  TFBS: Computational framework for transcription factor binding site analysis , 2002, Bioinform..

[18]  M. Blanchette,et al.  Discovery of regulatory elements by a computational method for phylogenetic footprinting. , 2002, Genome research.

[19]  G. Church,et al.  Identifying regulatory networks by combinatorial analysis of promoter elements , 2001, Nature Genetics.

[20]  Jun S. Liu,et al.  BioProspector: Discovering Conserved DNA Motifs in Upstream Regulatory Regions of Co-Expressed Genes , 2000, Pacific Symposium on Biocomputing.

[21]  G. Church,et al.  Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. , 2000, Journal of molecular biology.

[22]  G. Church,et al.  Systematic determination of genetic network architecture , 1999, Nature Genetics.

[23]  J. Fickett,et al.  Identification of regulatory regions which confer muscle-specific gene expression. , 1998, Journal of molecular biology.

[24]  E. Davidson,et al.  Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene. , 1998, Science.

[25]  G. Wray Promoter Logic , 1998, Science.

[26]  Robert D Clark,et al.  Neighborhood behavior: a useful concept for validation of "molecular diversity" descriptors. , 1996, Journal of medicinal chemistry.

[27]  K. Kinzler,et al.  Serial Analysis of Gene Expression , 1995, Science.

[28]  Jun S. Liu,et al.  Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. , 1993, Science.

[29]  T. D. Schneider,et al.  Sequence logos: a new way to display consensus sequences. , 1990, Nucleic acids research.

[30]  Wyeth W. Wasserman,et al.  JASPAR: an open-access database for eukaryotic transcription factor binding profiles , 2004, Nucleic Acids Res..

[31]  G. Fogel,et al.  Discovery of sequence motifs related to coexpression of genes using evolutionary computation. , 2004, Nucleic acids research.

[32]  Alexander E. Kel,et al.  TRANSFAC®: transcriptional regulation, from patterns to profiles , 2003, Nucleic Acids Res..

[33]  W. Miller,et al.  Distinguishing regulatory DNA from neutral sites. , 2003, Genome research.

[34]  Philipp Bucher,et al.  The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data , 2002, Nucleic Acids Res..

[35]  J. Blake,et al.  Creating the Gene Ontology Resource : Design and Implementation The Gene Ontology Consortium 2 , 2001 .

[36]  Gary D. Stormo,et al.  DNA binding sites: representation and discovery , 2000, Bioinform..

[37]  Thomas Werner,et al.  Regulatory modules shared within gene classes as well as across gene classes can be detected by the same in silico approach , 2000, Silico Biol..

[38]  S. P. Fodor,et al.  High density synthetic oligonucleotide arrays , 1999, Nature Genetics.

[39]  M. Eisen,et al.  Gene expression informatics —it's all in your mine , 1999, Nature Genetics.

[40]  Thomas Werner,et al.  Muscle actin genes: A first step towards computational classification of tissue specific promoters , 1998, Silico Biol..

[41]  Charles Elkan,et al.  The Value of Prior Knowledge in Discovering Motifs with MEME , 1995, ISMB.