Lelli KM, Slattery M, Mann RS: Disentangling the many layers of eukaryotic transcriptional regulation. Annual review of genetics. 2012, 46: 43-68. 10.1146/annurev-genet-110711-155437.
Article
PubMed Central
CAS
PubMed
Google Scholar
Lawrence CE, Altschul SF, Boguski MS, Liu JS, Neuwald AF, Wootton JC: 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
Hertz GZ, Stormo GD: Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics (Oxford, England). 1999, 15 (7-8): 563-577.
Article
CAS
Google Scholar
Price A, Ramabhadran S, Pevzner PA: Finding subtle motifs by branching from sample strings. Bioinformatics (Oxford, England). 2003, ii149-155. 19 Suppl 2
Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, et al: Assessing computational tools for the discovery of transcription factor binding sites. Nature biotechnology. 2005, 23 (1): 137-144. 10.1038/nbt1053.
Article
CAS
PubMed
Google Scholar
Olson WK, Gorin AA, Lu XJ, Hock LM, Zhurkin VB: DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proceedings of the National Academy of Sciences of the United States of America. 1998, 95 (19): 11163-11168. 10.1073/pnas.95.19.11163.
Article
PubMed Central
CAS
PubMed
Google Scholar
Rohs R, West SM, Sosinsky A, Liu P, Mann RS, Honig BCINNO, Pmid: The role of DNA shape in protein-DNA recognition. Nature. 2009, 461 (7268): 1248-1253. 10.1038/nature08473.
Article
PubMed Central
CAS
PubMed
Google Scholar
Rohs R, West SM, Liu P, Honig B: Nuance in the double-helix and its role in protein-DNA recognition. Current opinion in structural biology. 2009, 19 (2): 171-177. 10.1016/j.sbi.2009.03.002.
Article
PubMed Central
CAS
PubMed
Google Scholar
Perez-Martin J, Rojo F, de Lorenzo V: Promoters responsive to DNA bending: a common theme in prokaryotic gene expression. Microbiological reviews. 1994, 58 (2): 268-290.
PubMed Central
CAS
PubMed
Google Scholar
Abeel T, Saeys Y, Bonnet E, Rouze P, Van de Peer Y: Generic eukaryotic core promoter prediction using structural features of DNA. Genome research. 2008, 18 (2): 310-323. 10.1101/gr.6991408.
Article
PubMed Central
CAS
PubMed
Google Scholar
Florquin K, Saeys Y, Degroeve S, Rouze P, Van de Peer Y: Large-scale structural analysis of the core promoter in mammalian and plant genomes. Nucleic acids research. 2005, 33 (13): 4255-4264. 10.1093/nar/gki737.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ueguchi C, Kakeda M, Yamada H, Mizuno T: An analogue of the DnaJ molecular chaperone in Escherichia coli. Proc Natl Acad Sci USA. 1994, 91 (3): 1054-1058. 10.1073/pnas.91.3.1054.
Article
PubMed Central
CAS
PubMed
Google Scholar
Mazin A, Milot E, Devoret R, Chartrand P: KIN17, a mouse nuclear protein, binds to bent DNA fragments that are found at illegitimate recombination junctions in mammalian cells. Molecular & general genetics: MGG. 1994, 244 (4): 435-438.
Article
CAS
Google Scholar
Parker SC, Hansen L, Abaan HO, Tullius TD, Margulies EH: Local DNA topography correlates with functional noncoding regions of the human genome. Science (New York, NY). 2009, 324 (5925): 389-392. 10.1126/science.1169050.
Article
CAS
Google Scholar
Broos S, Soete A, Hooghe B, Moran R, van Roy F, De Bleser P: PhysBinder: improving the prediction of transcription factor binding sites by flexible inclusion of biophysical properties. Nucleic Acids Res. 2013, 41: W531-534. 10.1093/nar/gkt288.
Article
PubMed Central
PubMed
Google Scholar
Hooghe B, Broos S, van Roy F, De Bleser P: A flexible integrative approach based on random forest improves prediction of transcription factor binding sites. Nucleic acids research. 2012, 40 (14): e106-10.1093/nar/gks283.
Article
PubMed Central
CAS
PubMed
Google Scholar
Meysman P, Dang TH, Laukens K, De Smet R, Wu Y, Marchal K, Engelen K: Use of structural DNA properties for the prediction of transcription-factor binding sites in Escherichia coli. Nucleic acids research. 2011, 39 (2): e6-10.1093/nar/gkq1071.
Article
PubMed Central
PubMed
Google Scholar
Bauer AL, Hlavacek WS, Unkefer PJ, Mu F: Using sequence-specific chemical and structural properties of DNA to predict transcription factor binding sites. PLoS computational biology. 2010, 6 (11): e1001007-10.1371/journal.pcbi.1001007.
Article
PubMed Central
PubMed
Google Scholar
Greenbaum JA, Parker SC, Tullius TD: Detection of DNA structural motifs in functional genomic elements. Genome research. 2007, 17 (6): 940-946. 10.1101/gr.5602807.
Article
PubMed Central
CAS
PubMed
Google Scholar
Maienschein-Cline M, Dinner AR, Hlavacek WS, Mu F: Improved predictions of transcription factor binding sites using physicochemical features of DNA. Nucleic acids research. 2012, 40 (22): e175-10.1093/nar/gks771.
Article
PubMed Central
CAS
PubMed
Google Scholar
Dai Z, Dai X: Gene expression divergence is coupled to evolution of DNA structure in coding regions. PLoS Comput Biol. 2011, 7 (11): e1002275-10.1371/journal.pcbi.1002275.
Article
PubMed Central
CAS
PubMed
Google Scholar
Pedersen AG, Jensen LJ, Brunak S, Staerfeldt HH, Ussery DW: A DNA structural atlas for Escherichia coli. Journal of molecular biology. 2000, 299 (4): 907-930. 10.1006/jmbi.2000.3787.
Article
CAS
PubMed
Google Scholar
Liao GC, Rehm EJ, Rubin GM: Insertion site preferences of the P transposable element in Drosophila melanogaster. Proceedings of the National Academy of Sciences of the United States of America. 2000, 97 (7): 3347-3351. 10.1073/pnas.97.7.3347.
Article
PubMed Central
CAS
PubMed
Google Scholar
Baldi P, Baisnee PF: Sequence analysis by additive scales: DNA structure for sequences and repeats of all lengths. Bioinformatics (Oxford, England). 2000, 16 (10): 865-889. 10.1093/bioinformatics/16.10.865.
Article
CAS
Google Scholar
Goodsell DS, Dickerson RE: Bending and curvature calculations in B-DNA. Nucleic Acids Res. 1994, 22 (24): 5497-5503. 10.1093/nar/22.24.5497.
Article
PubMed Central
CAS
PubMed
Google Scholar
MacIsaac KD, Wang T, Gordon DB, Gifford DK, Stormo GD, Fraenkel E: An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC bioinformatics. 2006, 7: 113-10.1186/1471-2105-7-113.
Article
PubMed Central
PubMed
Google Scholar
GuhaThakurta D: Computational identification of transcriptional regulatory elements in DNA sequence. Nucleic acids research. 2006, 34 (12): 3585-3598. 10.1093/nar/gkl372.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wingender E, Chen X, Hehl R, Karas H, Liebich I, Matys V, Meinhardt T, Pruss M, Reuter I, Schacherer F: TRANSFAC: an integrated system for gene expression regulation. Nucleic acids research. 2000, 28 (1): 316-319. 10.1093/nar/28.1.316.
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, Hasinoff MJ, Warren CL, et al: 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
Gordan R, Murphy KF, McCord RP, Zhu C, Vedenko A, Bulyk ML: Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights. Genome biology. 2011, 12 (12): R125-10.1186/gb-2011-12-12-r125.
Article
PubMed Central
CAS
PubMed
Google Scholar
Greenbaum JA, Pang B, Tullius TD: Construction of a genome-scale structural map at single-nucleotide resolution. Genome research. 2007, 17 (6): 947-953. 10.1101/gr.6073107.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hirschman JE, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hong EL, Livstone MS, Nash R, et al: Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome. Nucleic Acids Res. 2006, 34: D442-445. 10.1093/nar/gkj117.
Article
PubMed Central
CAS
PubMed
Google Scholar