Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts
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* Corresponding author: Michael B Eisen mbeisen@lbl.gov
Genome Biology 2003, 4:R43 doi:10.1186/gb-2003-4-7-r43
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BioMed Central: 11 citations
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Software
Patrick J Killion, Vishwanath R Iyer Genome Biology 2008, 9:R159 (12 November 2008) ArrayPlex is a software package that centrally provides a large number of flexible toolsets useful for functional genomics. |
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Database
A Caenorhabditis motif compendium for studying transcriptional gene regulation Christoph Dieterich, Ralf J Sommer BMC Genomics 2008, 9:30 (23 January 2008) |
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Method
Prediction of synergistic transcription factors by function conservation Zihua Hu, Boyu Hu, James F Collins Genome Biology 2007, 8:R257 (5 December 2007) A new strategy is proposed for identifying synergistic transcription factors by function conservation, leading to the identification of 51 homotypic transcription-factor combinations. |
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Research article
Flexible promoter architecture requirements for coactivator recruitment Derek Y Chiang, David A Nix, Ryan K Shultzaberger, Audrey P Gasch, Michael B Eisen BMC Molecular Biology 2006, 7:16 (28 April 2006) |
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Software
XcisClique: analysis of regulatory bicliques Amrita Pati, Cecilia Vasquez-Robinet, Lenwood S Heath, Ruth Grene, TM Murali BMC Bioinformatics 2006, 7:218 (21 April 2006) |
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Methodology article
Emmitt R Jolly, Chen-Shan Chin, Ira Herskowitz, Hao Li BMC Bioinformatics 2005, 6:275 (18 November 2005) A new method combining biochemical characterisation with computational genomic analysis has been used successfully to identify targets of the yeast sporulation transcription factor, Ndt80.
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Research article
D Corà, C Herrmann, C Dieterich, F Di Cunto, P Provero, M Caselle BMC Bioinformatics 2005, 6:110 (2 May 2005) |
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Method
Olivier Elemento, Saeed Tavazoie Genome Biology 2005, 6:R18 (26 January 2005) The authors describe a powerful approach for discovering globally conserved regulatory elements between two genomes that does not require alignments. Its application to pairs of yeasts, worm, flies and mammals, yields a large number of known and novel putative regulatory elements, many of which show surprising conservation across large phylogenetic distances. |
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Research
Ekaterina Shelest, Edgar Wingender Theoretical Biology and Medical Modelling 2005, 2:2 (12 January 2005) |
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Method
Alan M Moses, Derek Y Chiang, Daniel A Pollard, Venky N Iyer, Michael B Eisen Genome Biology 2004, 5:R98 (30 November 2004) MONKEY is a new method for identifying conserved transcription-factor binding sites from multiple-sequence alignments. |
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Minireview
Rewiring the transcriptional regulatory circuits of cells Devin R Scannell, Ken Wolfe Genome Biology 2004, 5:206 (29 January 2004) New data from yeast species show that both changing the |
