Fodor S, Rava R, Huang X, Pease A, Holmes C, Adams C: Multiplexed biochemical assays with biological chips. Nature. 1993, 364: 555-556. 10.1038/364555a0.
Article
CAS
PubMed
Google Scholar
Schena M, Shalon D, Davis R, Brown P: Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 1995, 270 (5235): 467-470. 10.1126/science.270.5235.467.
Article
CAS
PubMed
Google Scholar
Tomancak P, Beaton A, Weiszmann R, Kwan E, Shu S, Lewis S, Richards S, Ashburner M, Hartenstein V, Celniker S et al: Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biol. 2002, 3 (12): RESEARCH0088-
Article
PubMed Central
PubMed
Google Scholar
Ren B, Robert F, Wyrick J, Aparicio O, Jennings E, Simon I, Zeitlinger J, Schreiber J, Hannett N, Kanin E et al: Genome-wide location and function of DNA binding proteins. Science's STKE. 2000, 290 (5500): 2306-
CAS
Google Scholar
Iyer V, Horak C, Scafe C, Botstein D, Snyder M, Brown P: Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature. 2001, 409 (6819): 533-538. 10.1038/35054095.
Article
CAS
PubMed
Google Scholar
Harbison C, Gordon D, Lee T, Rinaldi N, Macisaac K, Danford T, Hannett N, Tagne J, Reynolds D, Yoo J et al: Transcriptional regulatory code of a eukaryotic genome. Nature. 2004, 431 (7004): 99-104. 10.1038/nature02800.
Article
PubMed Central
CAS
PubMed
Google Scholar
Roth F, Hughes J, Estep P, Church G: Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nature biotechnology. 1998, 16 (10): 939-945. 10.1038/nbt1098-939.
Article
CAS
PubMed
Google Scholar
Hertz G, Stormo G: Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics. 1999, 15 (7): 563-577. 10.1093/bioinformatics/15.7.563.
Article
CAS
PubMed
Google Scholar
Bailey T, Elkan C, University of California SDDoCS, Engineering: Fitting a Mixture Model by Expectation Maximization to Discover Motifs in Bipolymers. 1994, Citeseer
Google Scholar
Lawrence C, Altschul S, Boguski M, Liu J, Neuwald A, Wootton J: Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science. 1993, 262 (5131): 208-214. 10.1126/science.8211139.
Article
CAS
PubMed
Google Scholar
Workman C, Stormo G: ANN-Spec: a method for discovering transcription factor binding sites with improved specificity. Pac Symp Biocomput. 2000, 467-478.
Google Scholar
Buhler J, Tompa M: Finding motifs using random projections. Journal of computational biology. 2002, 9 (2): 225-242. 10.1089/10665270252935430.
Article
CAS
PubMed
Google Scholar
Liu X, Brutlag D, Liu J: An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nature biotechnology. 2002, 20 (8): 835-839.
Article
CAS
PubMed
Google Scholar
Sinha S, Tompa M: YMF: a program for discovery of novel transcription factor binding sites by statistical overrepresentation. Nucleic acids research. 2003, 31 (13): 3586-3588. 10.1093/nar/gkg618.
Article
PubMed Central
CAS
PubMed
Google Scholar
van Helden J, André B, Collado-Vides J: Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. Journal of molecular biology. 1998, 281 (5): 827-842. 10.1006/jmbi.1998.1947.
Article
CAS
PubMed
Google Scholar
Brāzma A, Jonassen I, Vilo J, Ukkonen E: Predicting gene regulatory elements in silico on a genomic scale. Genome research. 1998, 8 (11): 1202-1215.
PubMed Central
PubMed
Google Scholar
Beer M, Tavazoie S: Predicting gene expression from sequence. Cell. 2004, 117 (2): 185-198. 10.1016/S0092-8674(04)00304-6.
Article
CAS
PubMed
Google Scholar
Elemento O, Slonim N, Tavazoie S: A universal framework for regulatory element discovery across all genomes and data types. Molecular cell. 2007, 28 (2): 337-350. 10.1016/j.molcel.2007.09.027.
Article
PubMed Central
CAS
PubMed
Google Scholar
Bussemaker H, Li H, Siggia E et al: Regulatory element detection using correlation with expression. Nature genetics. 2001, 27 (2): 167-171. 10.1038/84792.
Article
CAS
PubMed
Google Scholar
Foat B, Houshmandi S, Olivas W, Bussemaker H: Profiling condition-specific, genome-wide regulation of mRNA stability in yeast. Proceedings of the National Academy of Sciences of the United States of America. 2005, 102 (49): 17675-10.1073/pnas.0503803102.
Article
PubMed Central
CAS
PubMed
Google Scholar
Pilpel Y, Sudarsanam P, Church G: Identifying regulatory networks by combinatorial analysis of promoter elements. Nature genetics. 2001, 29 (2): 153-159. 10.1038/ng724.
Article
CAS
PubMed
Google Scholar
Kellis M, Patterson N, Endrizzi M, Birren B, Lander E et al: Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature. 2003, 423 (6937): 241-254. 10.1038/nature01644.
Article
CAS
PubMed
Google Scholar
Cliften P, Sudarsanam P, Desikan A, Fulton L, Fulton B, Majors J, Waterston R, Cohen B, Johnston M: Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science. 2003, 301 (5629): 71-76. 10.1126/science.1084337.
Article
CAS
PubMed
Google Scholar
Pritsker M, Liu Y, Beer M, Tavazoie S: Whole-genome discovery of transcription factor binding sites by network-level conservation. Genome research. 2004, 14: 99-108.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wang T, Stormo G: Combining phylogenetic data with co-regulated genes to identify regulatory motifs. Bioinformatics. 2003, 19 (18): 2369-2380. 10.1093/bioinformatics/btg329.
Article
CAS
PubMed
Google Scholar
Blanchette M, Tompa M: Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome research. 2002, 12 (5): 739-748. 10.1101/gr.6902.
Article
PubMed Central
CAS
PubMed
Google Scholar
Lenhard B, Sandelin A, Mendoza L, Engström P, Jareborg N, Wasserman W: Identification of conserved regulatory elements by comparative genome analysis. Journal of Biology. 2003, 2 (2): 13-10.1186/1475-4924-2-13.
Article
PubMed Central
PubMed
Google Scholar
Krivan W, Wasserman W: A predictive model for regulatory sequences directing liver-specific transcription. Genome Research. 2001, 11 (9): 1559-1566. 10.1101/gr.180601.
Article
PubMed Central
CAS
PubMed
Google Scholar
Oeltjen J, Malley T, Muzny D, Miller W, Gibbs R, Belmont J: Large-scale comparative sequence analysis of the human and murine Bruton's tyrosine kinase loci reveals conserved regulatory domains. Genome Research. 1997, 7 (4): 315-329.
CAS
PubMed
Google Scholar
Hardison R: Conserved noncoding sequences are reliable guides to regulatory elements. Trends in Genetics. 2000, 16 (9): 369-372. 10.1016/S0168-9525(00)02081-3.
Article
CAS
PubMed
Google Scholar
Loots G, Locksley R, Blankespoor C, Wang Z, Miller W, Rubin E, Frazer K: Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science. 2000, 288 (5463): 136-140. 10.1126/science.288.5463.136.
Article
CAS
PubMed
Google Scholar
Wasserman W, Palumbo M, Thompson W, Fickett J, Lawrence C et al: Human-mouse genome comparisons to locate regulatory sites. Nature genetics. 2000, 26 (2): 225-228. 10.1038/79965.
Article
CAS
PubMed
Google Scholar
Qiu P, Qin L, Sorrentino R, Greene J, Wang L: Comparative promoter analysis and its application in analysis of PTH-regulated gene expression. Journal of molecular biology. 2003, 326 (5): 1327-1336. 10.1016/S0022-2836(03)00053-6.
Article
CAS
PubMed
Google Scholar
Brohée S, Janky R, Abdel-Sater F, Vanderstocken G, André B, van Helden J: Unraveling networks of co-regulated genes on the sole basis of genome sequences. Nucleic acids research. 2011, 39 (15): 6340-6358. 10.1093/nar/gkr264.
Article
PubMed Central
PubMed
Google Scholar
Thomas-Chollier M, Defrance M, Medina-Rivera A, Sand O, Herrmann C, Thiery D, van Helden J: RSAT 2011: regulatory sequence analysis tools. Nucleic Acids Res. 2011, 39: W86-W91. 10.1093/nar/gkr377.
Article
PubMed Central
CAS
PubMed
Google Scholar
Gasch A, Spellman P, Kao C, Carmel-Harel O, Eisen M, Storz G, Botstein D, Brown P: Genomic expressionprograms in the response of yeast cells to environmental changes. Mol Biol Cell. 2000, 11: 4241-4257. 10.1091/mbc.11.12.4241.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ruan J, Perez J, Hernandez B, Sunter G, Sponsel V: Systematic construction and analysis of co-expression networks for identification of functional modules and cis-regulatory elements. 9th International Workshop on Data Mining in Bioinformatics, in conjuction with SIGKDD'10. 2010, Washington DC, USA: ACM
Google Scholar
Spellman P, Sherlock G, Zhang M, Iyer V, Anders K, Eisen M, Brown P, Botstein D, Futcher B: Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Molecular biology of the cell. 1998, 9 (12): 3273-3297. 10.1091/mbc.9.12.3273.
Article
PubMed Central
CAS
PubMed
Google Scholar
Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Schölkopf B, Weigel D, Lohmann J: A gene expression map of Arabidopsis development. Nat Genet. 2005, 37: 501-506. 10.1038/ng1543.
Article
CAS
PubMed
Google Scholar
Kilian J, Whitehead D, Horak J, Wanke D, Weinl S, Batistic O, D'Angelo , Bornberg-Bauer E, Kudla J, Harter K: The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant J. 2007, 50: 347-363. 10.1111/j.1365-313X.2007.03052.x.
Article
CAS
PubMed
Google Scholar
Wingender E, Dietze P, Karas H, Knüppel R: TRANSFAC: a database on transcription factors and theirDNA binding sites. Nucleic acids research. 1996, 24: 238-241. 10.1093/nar/24.1.238.
Article
PubMed Central
CAS
PubMed
Google Scholar
Simonis N, Wodak S, Cohen G, Van Helden J: Combining pattern discovery and discriminant analysis to predict gene co-regulation. Bioinformatics. 2004, 20 (15): 2370-2379. 10.1093/bioinformatics/bth252.
Article
CAS
PubMed
Google Scholar
Hosack D, Dennis G, Sherman B, Lane H, Lempicki R et al: Identifying biological themes within lists of genes with EASE. Genome Biol. 2003, 4 (10): R70-10.1186/gb-2003-4-10-r70.
Article
PubMed Central
PubMed
Google Scholar
Zhu C, Byers KJRP, McCord RP, Shi Z, Berger MF, Newburger DE, Saulrieta K, Smith Z, Shah MV, Radhakrishnan M, Philippakis AA, Hu Y, De Masi F, Pacek M, Rolfs A, Murthy T, LaBaer J, Bulyk ML: High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Research. 2009, 19 (4): 556-566. 10.1101/gr.090233.108.
Article
PubMed Central
CAS
PubMed
Google Scholar
Badis G, Chan ET, van Bakel H, Pena-Castillo L, Tillo D, Tsui K, Carlson CD, Gossett AJ, Hasino MJ, Warren CL, Gebbia M, Talukder S, Yang A, Mnaimneh S, Terterov D, Coburn D, Yeo AL, Yeo ZX, Clarke ND, Lieb JD, Ansari AZ, Nislow C, Hughes TR: A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Molecular Cell. 2008, 32 (6): 878-887. 10.1016/j.molcel.2008.11.020.
Article
PubMed Central
CAS
PubMed
Google Scholar
Dwight S, Balakrishnan R, Christie K, Costanzo M, Dolinski K, Engel S, Feierbach B, Fisk D, Hirschman J, Hong E, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld C, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Weng S, Botstein D, Cherry J: Saccharomyces genome database: underlying principlesand organisation. Brief Bioinform. 2004, 5: 9-22. 10.1093/bib/5.1.9.
Article
PubMed Central
CAS
PubMed
Google Scholar
Higo K, Ugawa Y, Iwamoto M, Korenaga T: Plant cis-acting regulatory DNA elements (PLACE) database:1999. Nucleic Acids Res. 1999, 27: 297-300. 10.1093/nar/27.1.297.
Article
PubMed Central
CAS
PubMed
Google Scholar
Tatematsu K, Ward S, Leyser O, Kamiya Y, Nambara E: Identification of cis-elements that regulate gene expression during initiation of axillary bud outgrowth in Arabidopsis. Plant Physiol. 2005, 138 (2): 757-766. 10.1104/pp.104.057984.
Article
PubMed Central
CAS
PubMed
Google Scholar