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Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts
Derek Y Chiang, Alan M Moses, Manolis Kellis, Eric S Lander, Michael B Eisen
Genome Biol. 2003; 4(7): R43. Published online 2003 June 26. doi: 10.1186/gb-2003-4-7-r43
PMCID:
PMC193630
Abstract Full Text PDF–471K Supplementary Material
 Is Cited by the Following 19 Articles in this Archive:
ArrayPlex: distributed, interactive and programmatic access to genome sequence, annotation, ontology, and analytical toolsets
Patrick J Killion, Vishwanath R Iyer
Genome Biol. 2008; 9(11): R159. Published online 2008 November 12. doi: 10.1186/gb-2008-9-11-r159
PMCID:
PMC2614491
Abstract Full Text PDF–4.8M
Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences
Lucas D. Ward, Harmen J. Bussemaker
Bioinformatics. 2008 July 1; 24(13): i165–i171. doi: 10.1093/bioinformatics/btn154
PMCID:
PMC2718632
Abstract Full Text PDF–283K Supplementary Material
A Caenorhabditis motif compendium for studying transcriptional gene regulation
Christoph Dieterich, Ralf J Sommer
BMC Genomics. 2008; 9: 30. Published online 2008 January 23. doi: 10.1186/1471-2164-9-30
PMCID:
PMC2248174
Abstract Full Text PDF–684K Supplementary Material
Genomic Identification of Regulatory Elements by Evolutionary Sequence Comparison and Functional Analysis
Gabriela G. Loots
Adv Genet. Author manuscript; available in PMC 2010 June 8.
Published in final edited form as: Adv Genet. 2008; 61: 269–293. doi: 10.1016/S0065-2660(07)00010-7
PMCID:
PMC2882178
Abstract Full Text PDF–428K
Prediction of synergistic transcription factors by function conservation
Zihua Hu, Boyu Hu, James F Collins
Genome Biol. 2007; 8(12): R257. Published online 2007 December 5. doi: 10.1186/gb-2007-8-12-r257
PMCID:
PMC2246259
Abstract Full Text PDF–667K Supplementary Material
Determining Physical Constraints in Transcriptional Initiation Complexes Using DNA Sequence Analysis
Ryan K. Shultzaberger, Derek Y. Chiang, Alan M. Moses, Michael B. Eisen
PLoS ONE. 2007; 2(11): e1199. Published online 2007 November 21. doi: 10.1371/journal.pone.0001199
PMCID:
PMC2077805
Abstract Full Text PDF–793K
A Role for Sterol Levels in Oxygen Sensing in Saccharomyces cerevisiae
Brandon S. J. Davies, Jasper Rine
Genetics. 2006 September; 174(1): 191–201. doi: 10.1534/genetics.106.059964
PMCID:
PMC1569814
Abstract Full Text PDF–745K
Flexible promoter architecture requirements for coactivator recruitment
Derek Y Chiang, David A Nix, Ryan K Shultzaberger, Audrey P Gasch, Michael B Eisen
BMC Mol Biol. 2006; 7: 16. Published online 2006 April 28. doi: 10.1186/1471-2199-7-16
PMCID:
PMC1488866
Abstract Full Text PDF–1.0M Supplementary Material
XcisClique: analysis of regulatory bicliques
Amrita Pati, Cecilia Vasquez-Robinet, Lenwood S Heath, Ruth Grene, TM Murali
BMC Bioinformatics. 2006; 7: 218. Published online 2006 April 21. doi: 10.1186/1471-2105-7-218
PMCID:
PMC1513260
Abstract Full Text PDF–451K Supplementary Material
Genome-wide identification of the regulatory targets of a transcription factor using biochemical characterization and computational genomic analysis
Emmitt R Jolly, Chen-Shan Chin, Ira Herskowitz, Hao Li
BMC Bioinformatics. 2005; 6: 275. Published online 2005 November 18. doi: 10.1186/1471-2105-6-275
PMCID:
PMC1326232
Abstract Full Text PDF–779K Supplementary Material
Statistical methods for identifying yeast cell cycle transcription factors
Huai-Kuang Tsai, Henry Horng-Shing Lu, Wen-Hsiung Li
Proc Natl Acad Sci U S A. 2005 September 20; 102(38): 13532–13537. Published online 2005 September 12. doi: 10.1073/pnas.0505874102
PMCID:
PMC1224643
Abstract Full Text PDF–479K Supplementary Material
Ab initio identification of putative human transcription factor binding sites by comparative genomics
D Corà, C Herrmann, C Dieterich, F Di Cunto, P Provero, M Caselle
BMC Bioinformatics. 2005; 6: 110. Published online 2005 May 2. doi: 10.1186/1471-2105-6-110
PMCID:
PMC1097714
Abstract Full Text PDF–317K Supplementary Material
Genome-wide regulatory complexity in yeast promoters: Separation of functionally conserved and neutral sequence
Chen-Shan Chin, Jeffrey H. Chuang, Hao Li
Genome Res. 2005 February; 15(2): 205–213. doi: 10.1101/gr.3243305
PMCID:
PMC546519
Abstract Full Text PDF–281K
Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach
Olivier Elemento, Saeed Tavazoie
Genome Biol. 2005; 6(2): R18. Published online 2005 January 26. doi: 10.1186/gb-2005-6-2-r18
PMCID:
PMC551538
Abstract Full Text PDF–1.0M
Construction of predictive promoter models on the example of antibacterial response of human epithelial cells
Ekaterina Shelest, Edgar Wingender
Theor Biol Med Model. 2005; 2: 2. Published online 2005 January 12. doi: 10.1186/1742-4682-2-2
PMCID:
PMC546226
Abstract Full Text PDF–463K Supplementary Material
MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model
Alan M Moses, Derek Y Chiang, Daniel A Pollard, Venky N Iyer, Michael B Eisen
Genome Biol. 2004; 5(12): R98. Published online 2004 November 30. doi: 10.1186/gb-2004-5-12-r98
PMCID:
PMC545801
Abstract Full Text PDF–758K Supplementary Material
Conservation and Evolution of Cis-Regulatory Systems in Ascomycete Fungi
Audrey P Gasch, Alan M Moses, Derek Y Chiang, Hunter B Fraser, Mark Berardini, Michael B Eisen
PLoS Biol. 2004 December; 2(12): e398. Published online 2004 November 9. doi: 10.1371/journal.pbio.0020398
PMCID:
PMC526180
Abstract Full Text PDF–732K Supplementary Material
Interacting models of cooperative gene regulation
Debopriya Das, Nilanjana Banerjee, Michael Q. Zhang
Proc Natl Acad Sci U S A. 2004 November 16; 101(46): 16234–16239. Published online 2004 November 8. doi: 10.1073/pnas.0407365101
PMCID:
PMC528978
Abstract Full Text PDF–298K Supplementary Material
Rewiring the transcriptional regulatory circuits of cells
Devin R Scannell, Ken Wolfe
Genome Biol. 2004; 5(2): 206. Published online 2004 January 29.
PMCID:
PMC395740
Abstract Full Text PDF–84K
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