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Volumn 6, Issue 1, 2011, Pages

GRISOTTO: A greedy approach to improve combinatorial algorithms for motif discovery with prior knowledge

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EID: 79955017149     PISSN: None     EISSN: 17487188     Source Type: Journal    
DOI: 10.1186/1748-7188-6-13     Document Type: Article
Times cited : (2)

References (42)
  • 1
    • 28444484981 scopus 로고    scopus 로고
    • GANN: Genetic Algorithm Neural Networks for the detection of conserved combinations of features in DNA
    • 10.1073/pnas.0505147102, 1297658, 16301543
    • Beiko RG, Charlebois RL. GANN: Genetic Algorithm Neural Networks for the detection of conserved combinations of features in DNA. Proc. Natl Acad Sci USA 2005, 102:17400-17405. 10.1073/pnas.0505147102, 1297658, 16301543.
    • (2005) Proc. Natl Acad Sci USA , vol.102 , pp. 17400-17405
    • Beiko, R.G.1    Charlebois, R.L.2
  • 3
    • 0032864396 scopus 로고    scopus 로고
    • Conformational and physicochemical DNA features specific for transcription factor binding sites
    • 10.1093/bioinformatics/15.7.654, 10487873
    • Ponomarenko JV, Ponomarenko MP, Frolov AS, Vorobiev DG, Overton GC, Kolchanov NA. Conformational and physicochemical DNA features specific for transcription factor binding sites. Bioinformatics 1999, 15(7):654-668. 10.1093/bioinformatics/15.7.654, 10487873.
    • (1999) Bioinformatics , vol.15 , Issue.7 , pp. 654-668
    • Ponomarenko, J.V.1    Ponomarenko, M.P.2    Frolov, A.S.3    Vorobiev, D.G.4    Overton, G.C.5    Kolchanov, N.A.6
  • 4
    • 17044403375 scopus 로고    scopus 로고
    • Macromolecular recognition
    • 10.1016/j.sbi.2005.01.018, 15837175
    • Deremble C, Lavery R. Macromolecular recognition. Current Opinion in Structural Biology 2005, 15:171-175. 10.1016/j.sbi.2005.01.018, 15837175.
    • (2005) Current Opinion in Structural Biology , vol.15 , pp. 171-175
    • Deremble, C.1    Lavery, R.2
  • 5
    • 19544366293 scopus 로고    scopus 로고
    • Non-additivity in protein-DNA binding
    • 10.1093/bioinformatics/bti361, 15746285
    • O'Flanagan RA, Paillard G, Lavery R, Sengupta AM. Non-additivity in protein-DNA binding. Bioinformatics 2005, 21(10):2254-2263. 10.1093/bioinformatics/bti361, 15746285.
    • (2005) Bioinformatics , vol.21 , Issue.10 , pp. 2254-2263
    • O'Flanagan, R.A.1    Paillard, G.2    Lavery, R.3    Sengupta, A.M.4
  • 6
    • 1642452665 scopus 로고    scopus 로고
    • Analyzing protein-DNA recognition mechanisms
    • 10.1016/j.str.2003.11.022, 14725771
    • Paillard G, Lavery R. Analyzing protein-DNA recognition mechanisms. Structure 2004, 12:113-122. 10.1016/j.str.2003.11.022, 14725771.
    • (2004) Structure , vol.12 , pp. 113-122
    • Paillard, G.1    Lavery, R.2
  • 7
    • 13544274449 scopus 로고    scopus 로고
    • Looking into DNA recognition: Zinc finger binding specificity
    • 10.1093/nar/gkh1003, 545445, 15613596
    • Paillard G, Deremble C, Lavery R. Looking into DNA recognition: Zinc finger binding specificity. Nucleic Acids Research 2004, 32(22):6673-6682. 10.1093/nar/gkh1003, 545445, 15613596.
    • (2004) Nucleic Acids Research , vol.32 , Issue.22 , pp. 6673-6682
    • Paillard, G.1    Deremble, C.2    Lavery, R.3
  • 8
    • 14244273151 scopus 로고    scopus 로고
    • ADAPT: A molecular mechanics approach for studying the structural properties of long DNA sequences
    • Lafontaine I, Lavery R. ADAPT: A molecular mechanics approach for studying the structural properties of long DNA sequences. Biopolymers (Nucleic Acid Science) 2001, 56:292-310.
    • (2001) Biopolymers (Nucleic Acid Science) , vol.56 , pp. 292-310
    • Lafontaine, I.1    Lavery, R.2
  • 9
    • 0035661846 scopus 로고    scopus 로고
    • High-speed molecular mechanics searches for optimal DNA interaction sites
    • Lafontaine I, Lavery R. High-speed molecular mechanics searches for optimal DNA interaction sites. Comb Chem High Throughput Screen 2001, 4(8):707-717.
    • (2001) Comb Chem High Throughput Screen , vol.4 , Issue.8 , pp. 707-717
    • Lafontaine, I.1    Lavery, R.2
  • 10
    • 0033884290 scopus 로고    scopus 로고
    • Optimization of nucleic acid sequences
    • 10.1016/S0006-3495(00)76326-0, 1300968, 10920002
    • Lafontaine I, Lavery R. Optimization of nucleic acid sequences. Biophys J 2000, 79(2):680-685. 10.1016/S0006-3495(00)76326-0, 1300968, 10920002.
    • (2000) Biophys J , vol.79 , Issue.2 , pp. 680-685
    • Lafontaine, I.1    Lavery, R.2
  • 11
    • 34547418057 scopus 로고    scopus 로고
    • Nucleosome Occupancy Information Improves de novo Motif Discovery
    • 2692033, 15531607
    • Narlikar L, Gordân R, Hartemink AJ. Nucleosome Occupancy Information Improves de novo Motif Discovery. Proc. RECOMB'07 2007, 107-121. 2692033, 15531607.
    • (2007) Proc. RECOMB'07 , pp. 107-121
    • Narlikar, L.1    Gordân, R.2    Hartemink, A.J.3
  • 12
    • 73449094886 scopus 로고    scopus 로고
    • Discovery of Regulatory Elements is Improved by a Discriminatory Approach
    • 10.1371/journal.pcbi.1000562, 2770120, 19911049
    • Valen E, Sandelin A, Winther O, Krogh A. Discovery of Regulatory Elements is Improved by a Discriminatory Approach. PLoS Comput Biol 2009, 5(11):e1000562. 10.1371/journal.pcbi.1000562, 2770120, 19911049.
    • (2009) PLoS Comput Biol , vol.5 , Issue.11
    • Valen, E.1    Sandelin, A.2    Winther, O.3    Krogh, A.4
  • 13
    • 33747879675 scopus 로고    scopus 로고
    • Informative priors based on transcription factor structural class improve de novo motif discovery
    • 29837, 11125091
    • Narlikar L, Gordân R, Ohler U, Hartemink AJ. Informative priors based on transcription factor structural class improve de novo motif discovery. Proc. ISMB'06 (Supplement of Bioinformatics) 2006, 384-392. 29837, 11125091.
    • (2006) Proc. ISMB'06 (Supplement of Bioinformatics) , pp. 384-392
    • Narlikar, L.1    Gordân, R.2    Ohler, U.3    Hartemink, A.J.4
  • 14
    • 47249120085 scopus 로고    scopus 로고
    • A Fast, Alignment-Free, Conservation-Based Method for Transcription Factor Binding Site Discovery
    • 2692033, 15531607
    • Gordân R, Narlikar L, Hartemink AJ. A Fast, Alignment-Free, Conservation-Based Method for Transcription Factor Binding Site Discovery. Proc. RECOMB'08 2008, 98-111. 2692033, 15531607.
    • (2008) Proc. RECOMB'08 , pp. 98-111
    • Gordân, R.1    Narlikar, L.2    Hartemink, A.J.3
  • 15
    • 40549105160 scopus 로고    scopus 로고
    • Using DNA Duplex Stability Information for Transcription Factor Binding Site Discovery
    • Gordân R, Hartemink AJ. Using DNA Duplex Stability Information for Transcription Factor Binding Site Discovery. Pacific Symposium on Biocomputing 2008, 453-464.
    • (2008) Pacific Symposium on Biocomputing , pp. 453-464
    • Gordân, R.1    Hartemink, A.J.2
  • 16
    • 77951266764 scopus 로고    scopus 로고
    • Finding regulatory DNA motifs using alignment-free evolutionary conservation information
    • Gordân R, Narlikar L, Hartemink AJ. Finding regulatory DNA motifs using alignment-free evolutionary conservation information. Nuc Ac Res 2010, 38(6):e90.
    • (2010) Nuc Ac Res , vol.38 , Issue.6
    • Gordân, R.1    Narlikar, L.2    Hartemink, A.J.3
  • 17
    • 77950640390 scopus 로고    scopus 로고
    • The value of position-specific priors in motif discovery using MEME
    • 10.1186/1471-2105-11-179, 2868008, 20380693
    • Bailey TL, Bodén M, Whitington T, Machanick P. The value of position-specific priors in motif discovery using MEME. BMC Bioinformatics 2010, 11:179. 10.1186/1471-2105-11-179, 2868008, 20380693.
    • (2010) BMC Bioinformatics , vol.11 , pp. 179
    • Bailey, T.L.1    Bodén, M.2    Whitington, T.3    Machanick, P.4
  • 18
    • 66349101154 scopus 로고    scopus 로고
    • Predicting functionality of protein-DNA interactions by integrating diverse evidence
    • Ucar D, Beyer A, Parthasarathy S, Workman CT. Predicting functionality of protein-DNA interactions by integrating diverse evidence. 2009, 25(12):i137-i144.
    • (2009) , vol.25 , Issue.12
    • Ucar, D.1    Beyer, A.2    Parthasarathy, S.3    Workman, C.T.4
  • 19
    • 50849090969 scopus 로고    scopus 로고
    • Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data
    • 10.1038/nmeth.1246, 2917543, 19160518, Serafim Batzoglo and RMM
    • Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, Sidow A. Serafim Batzoglo and RMM Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nature Methods 2008, 5:829-834. 10.1038/nmeth.1246, 2917543, 19160518, Serafim Batzoglo and RMM.
    • (2008) Nature Methods , vol.5 , pp. 829-834
    • Valouev, A.1    Johnson, D.S.2    Sundquist, A.3    Medina, C.4    Anton, E.5    Sidow, A.6
  • 20
    • 48249140621 scopus 로고    scopus 로고
    • FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology
    • 10.1093/bioinformatics/btn305, 2638869, 18599518
    • Fejes AP, Robertson G, Bilenky M, Varhol R, Bainbridge M, Jones SJM. FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics 2008, 24(15):1729-1730. 10.1093/bioinformatics/btn305, 2638869, 18599518.
    • (2008) Bioinformatics , vol.24 , Issue.15 , pp. 1729-1730
    • Fejes, A.P.1    Robertson, G.2    Bilenky, M.3    Varhol, R.4    Bainbridge, M.5    Jones, S.J.M.6
  • 22
    • 77957818564 scopus 로고    scopus 로고
    • Deep and wide digging for binding motifs in ChIP-Seq data
    • 10.1093/bioinformatics/btq488, 20736340
    • Kulakovskiy IV, Boeva VA, Favorov AV, Makeev VJ. Deep and wide digging for binding motifs in ChIP-Seq data. Bioinformatics 2010, 26(20):2622-2623. 10.1093/bioinformatics/btq488, 20736340.
    • (2010) Bioinformatics , vol.26 , Issue.20 , pp. 2622-2623
    • Kulakovskiy, I.V.1    Boeva, V.A.2    Favorov, A.V.3    Makeev, V.J.4
  • 23
    • 77949916244 scopus 로고    scopus 로고
    • On the detection and refinement of transcription factor binding sites using ChIP-Seq data
    • 10.1093/nar/gkp1180, 2853110, 20056654
    • Hu M, Yu J, Taylor JM, Chinnaiyan AM, Qin ZS. On the detection and refinement of transcription factor binding sites using ChIP-Seq data. Nucleic Acids Research 2010, 38(7):2154-2167. 10.1093/nar/gkp1180, 2853110, 20056654.
    • (2010) Nucleic Acids Research , vol.38 , Issue.7 , pp. 2154-2167
    • Hu, M.1    Yu, J.2    Taylor, J.M.3    Chinnaiyan, A.M.4    Qin, Z.S.5
  • 26
    • 0033677426 scopus 로고    scopus 로고
    • Algorithms for extracting structured motifs using a suffix tree with an application to promoter and regulatory site consensus identification
    • Marsan L, Sagot MF. Algorithms for extracting structured motifs using a suffix tree with an application to promoter and regulatory site consensus identification. J Comp Bio 2000, 7(3-4):345-362.
    • (2000) J Comp Bio , vol.7 , Issue.3-4 , pp. 345-362
    • Marsan, L.1    Sagot, M.F.2
  • 29
    • 0344906814 scopus 로고    scopus 로고
    • Combining phylogenetic data with co-regulated genes to identify regulatory motifs
    • 10.1093/bioinformatics/btg329, 14668220
    • Wang T, Stormo GD. Combining phylogenetic data with co-regulated genes to identify regulatory motifs. Bioinformatics 2003, 19(18):2369-2380. 10.1093/bioinformatics/btg329, 14668220.
    • (2003) Bioinformatics , vol.19 , Issue.18 , pp. 2369-2380
    • Wang, T.1    Stormo, G.D.2
  • 30
    • 13244260826 scopus 로고    scopus 로고
    • PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences
    • 10.1186/1471-2105-5-170, 534098, 15511292
    • Sinha S, Blanchette M, Tompa M. PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences. BMC Bioinformatics 2004, 5:170. 10.1186/1471-2105-5-170, 534098, 15511292.
    • (2004) BMC Bioinformatics , vol.5 , pp. 170
    • Sinha, S.1    Blanchette, M.2    Tompa, M.3
  • 31
    • 0029197507 scopus 로고
    • The value of prior knowledge in discovering motifs with MEME
    • 29837, 11125091
    • Bailey TL, Elkan C. The value of prior knowledge in discovering motifs with MEME. Proc. ISMB'95 1995, 21-29. 29837, 11125091.
    • (1995) Proc. ISMB'95 , pp. 21-29
    • Bailey, T.L.1    Elkan, C.2
  • 32
    • 33750218960 scopus 로고    scopus 로고
    • PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny
    • 10.1371/journal.pcbi.0010067, 1309704, 16477324
    • Siddharthan R, Siggia ED, van Nimwegen E. PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny. PLoS Comput Biol 2005, 1(7):e67. 10.1371/journal.pcbi.0010067, 1309704, 16477324.
    • (2005) PLoS Comput Biol , vol.1 , Issue.7
    • Siddharthan, R.1    Siggia, E.D.2    van Nimwegen, E.3
  • 33
    • 0038349948 scopus 로고    scopus 로고
    • Sequencing and comparison of yeast species to identify genes and regulatory elements
    • 10.1038/nature01644, 12748633
    • Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 2003, 423:241-254. 10.1038/nature01644, 12748633.
    • (2003) Nature , vol.423 , pp. 241-254
    • Kellis, M.1    Patterson, N.2    Endrizzi, M.3    Birren, B.4    Lander, E.S.5
  • 34
    • 1542376789 scopus 로고    scopus 로고
    • Eukaryotic Regulatory Element Conservation Analysis and Identification Using Comparative Genomics
    • 10.1101/gr.1327604, 353232, 14993210
    • Liu Y, Liu S, Wei L, Altman RB, Batzoglou S. Eukaryotic Regulatory Element Conservation Analysis and Identification Using Comparative Genomics. Genome Res 2004, 14:451-458. 10.1101/gr.1327604, 353232, 14993210.
    • (2004) Genome Res , vol.14 , pp. 451-458
    • Liu, Y.1    Liu, S.2    Wei, L.3    Altman, R.B.4    Batzoglou, S.5
  • 35
    • 33645769260 scopus 로고    scopus 로고
    • An improved map of conserved regulatory sites for Saccharomyces cerevisiae
    • 10.1186/1471-2105-7-113, 1435934, 16522208
    • 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, 1435934, 16522208.
    • (2006) BMC Bioinformatics , vol.7 , pp. 113
    • MacIsaac, K.D.1    Wang, T.2    Gordon, D.B.3    Gifford, D.K.4    Stormo, G.D.5    Fraenkel, E.6
  • 36
    • 3543023310 scopus 로고    scopus 로고
    • Evidence for nucleosome depletion at active regulatory regions genome-wide
    • Lee C, Shibata Y, Rao B, Strahl B, Lieb J. Evidence for nucleosome depletion at active regulatory regions genome-wide. Nature Genetics 2004, 36(8).
    • (2004) Nature Genetics , vol.36 , Issue.8
    • Lee, C.1    Shibata, Y.2    Rao, B.3    Strahl, B.4    Lieb, J.5
  • 37
    • 22744432660 scopus 로고    scopus 로고
    • Genome-scale identification of nucleosome positions in S cerevisiae
    • 10.1126/science.1112178, 15961632
    • Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, Altschuler SJ, Rando OJ. Genome-scale identification of nucleosome positions in S cerevisiae. Science 2005, 309(5734):626-630. 10.1126/science.1112178, 15961632.
    • (2005) Science , vol.309 , Issue.5734 , pp. 626-630
    • Yuan, G.C.1    Liu, Y.J.2    Dion, M.F.3    Slack, M.D.4    Wu, L.F.5    Altschuler, S.J.6    Rando, O.J.7
  • 39
    • 3242884167 scopus 로고    scopus 로고
    • Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes
    • Pavesi G, Mereghetti P, Mauri G, Pesole G. Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes. Nucleic Acids Research 2004, (32 Web-Server):199-203.
    • (2004) Nucleic Acids Research , pp. 199-203
    • Pavesi, G.1    Mereghetti, P.2    Mauri, G.3    Pesole, G.4
  • 41
    • 1842584947 scopus 로고    scopus 로고
    • Applied bioinformatics for the identification of regulatory elements
    • 10.1038/nrg1315, 15131651
    • Wasserman WW, Sandelin A. Applied bioinformatics for the identification of regulatory elements. Nature reviews 2004, 5(4):276-287. 10.1038/nrg1315, 15131651.
    • (2004) Nature reviews , vol.5 , Issue.4 , pp. 276-287
    • Wasserman, W.W.1    Sandelin, A.2
  • 42
    • 48249102239 scopus 로고    scopus 로고
    • Low nucleosome occupancy is encoded around functional human transcription factor binding sites
    • Daenen F, van Roy F, Bleser PJD. Low nucleosome occupancy is encoded around functional human transcription factor binding sites. BMC Genomics 2008, 9(332).
    • (2008) BMC Genomics , vol.9 , Issue.332
    • Daenen, F.1    van Roy, F.2    Bleser, P.J.D.3


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