메뉴 건너뛰기




Volumn 10, Issue SUPPL. 1, 2009, Pages

DNA motif alignment by evolving a population of Markov chains

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM DESIGN; CIS-REGULATORY ELEMENTS; INFORMATION EXCHANGES; MARKOV CHAIN MONTE CARLO METHOD; METROPOLIS-HASTINGS; PROPOSAL DISTRIBUTION; SITE DISTRIBUTION; STOCHASTIC SAMPLING;

EID: 60849096092     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-S1-S13     Document Type: Article
Times cited : (7)

References (37)
  • 2
    • 33646229522 scopus 로고    scopus 로고
    • Practical strategies for discovering regulatory DNA sequence motifs
    • 10.1371/journal.pcbi.0020026
    • MacIsaac KD Fraenkel E Practical strategies for discovering regulatory DNA sequence motifs PLoS Computat Biol 2006, 2:e36 10.1371/ journal.pcbi.0020026
    • (2006) PLoS Computat Biol , vol.2
    • MacIsaac, K.D.1    Fraenkel, E.2
  • 3
    • 33748765218 scopus 로고    scopus 로고
    • Computational biology: Towards deciphering gene regulatory information in mammalian genomes
    • 10.1111/j.1541-0420.2006.00625.x 16984301
    • Ji H Wong WW Computational biology: Towards deciphering gene regulatory information in mammalian genomes Biometrics 2006, 62:645-663 10.1111/ j.1541-0420.2006.00625.x 16984301
    • (2006) Biometrics , vol.62 , pp. 645-663
    • Ji, H.1    Wong, W.W.2
  • 4
    • 0028679709 scopus 로고
    • On the complexity of multiple sequence alignment
    • 8790475
    • Wang L Jiang T On the complexity of multiple sequence alignment J Comput Biol 1994, 1:337-348 8790475
    • (1994) J Comput Biol , vol.1 , pp. 337-348
    • Wang, L.1    Jiang, T.2
  • 5
    • 0025320805 scopus 로고
    • An expectation maximization algorithm for the identification and characterization of common sites in unaligned biopolymer sequences
    • 10.1002/prot.340070105
    • Lawrence CE Reilly AA An expectation maximization algorithm for the identification and characterization of common sites in unaligned biopolymer sequences Proteins: Structure, Function and Genetics 1990, 7:41-51 10.1002/prot.340070105
    • (1990) Proteins: Structure, Function and Genetics , vol.7 , pp. 41-51
    • Lawrence, C.E.1    Reilly, A.A.2
  • 6
    • 0002629270 scopus 로고
    • Maximum likelihood from incomplete data via the EM algorithm (with discussion)
    • Dempster AP Laird AM Rubin DB Maximum likelihood from incomplete data via the EM algorithm (with discussion) J Roy Statist Soc Ser B 1977, 39:1-38
    • (1977) J Roy Statist Soc Ser B , vol.39 , pp. 1-38
    • Dempster, A.P.1    Laird, A.M.2    Rubin, D.B.3
  • 7
    • 18244387717 scopus 로고    scopus 로고
    • The EM algorithm - An old folk-song sung to a fast new tune
    • 10.1111/1467-9868.00082
    • Meng XL Dyk D The EM algorithm - an old folk-song sung to a fast new tune J Roy Statist Soc Ser B 1997, 59:511-567 10.1111/1467-9868.00082
    • (1997) J Roy Statist Soc Ser B , vol.59 , pp. 511-567
    • Meng, X.L.1    Dyk, D.2
  • 8
    • 34248191269 scopus 로고    scopus 로고
    • SEAM: A stochastic EM-type algorithm for motif-finding in biopolymer sequences
    • 10.1142/S0219720007002527 17477491
    • Bi CP SEAM: A stochastic EM-type algorithm for motif-finding in biopolymer sequences J Bioinform Comput Biol 2007, 5:47-77 10.1142/ S0219720007002527 17477491
    • (2007) J Bioinform Comput Biol , vol.5 , pp. 47-77
    • Bi, C.P.1
  • 9
    • 0002759539 scopus 로고
    • Unsupervised learning of multiple motifs in biopolymers using expectation maximization
    • Bailey T Elkan C Unsupervised learning of multiple motifs in biopolymers using expectation maximization Machine Learning 1995, 21:51-80
    • (1995) Machine Learning , vol.21 , pp. 51-80
    • Bailey, T.1    Elkan, C.2
  • 12
    • 77956890234 scopus 로고
    • Monte Carlo sampling methods using Markov chains and their applications
    • 10.1093/biomet/57.1.97
    • Hastings WK Monte Carlo sampling methods using Markov chains and their applications Biometrika 1970, 57:97-109 10.1093/biomet/57.1.97
    • (1970) Biometrika , vol.57 , pp. 97-109
    • Hastings, W.K.1
  • 13
    • 0027912333 scopus 로고
    • Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment
    • 10.1126/science.8211139 8211139
    • 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, 262:208-214 10.1126/science.8211139 8211139
    • (1993) Science , vol.262 , pp. 208-214
    • Lawrence, C.E.1    Altschul, S.F.2    Boguski, M.S.3    Liu, J.S.4    Neuwald, A.F.5    Wootton, J.C.6
  • 14
    • 0035228215 scopus 로고    scopus 로고
    • BioProspector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes
    • Liu X Brutlag DL Liu JS BioProspector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes Proc. Pacific Symposium on Biocomputing (PSB) 2001, 127-138
    • (2001) Proc. Pacific Symposium on Biocomputing (PSB) , pp. 127-138
    • Liu, X.1    Brutlag, D.L.2    Liu, J.S.3
  • 16
    • 0002696801 scopus 로고    scopus 로고
    • The art of data augmentation
    • 10.1198/10618600152418584
    • van Dyk DA Meng XL The art of data augmentation J Comput Graph Stat 2001, 10:1-50 10.1198/10618600152418584
    • (2001) J Comput Graph Stat , vol.10 , pp. 1-50
    • van Dyk, D.A.1    Meng, X.L.2
  • 17
    • 38649088564 scopus 로고    scopus 로고
    • Data augmentation algorithms for detecting conserved domains in protein sequences: A comparative study
    • 10.1021/pr070475q 18081244
    • Bi CP Data augmentation algorithms for detecting conserved domains in protein sequences: A comparative study J Proteome Res 2008, 7:192-201 10.1021/pr070475q 18081244
    • (2008) J Proteome Res , vol.7 , pp. 192-201
    • Bi, C.P.1
  • 20
    • 0034403006 scopus 로고    scopus 로고
    • Evolutionary Monte Carlo: Applications to Cp model sampling and change point problem
    • Liang F Wong WH Evolutionary Monte Carlo: Applications to Cp model sampling and change point problem Statistica Sinica 2000, 10:317-342
    • (2000) Statistica Sinica , vol.10 , pp. 317-342
    • Liang, F.1    Wong, W.H.2
  • 21
    • 0037266164 scopus 로고    scopus 로고
    • Population Markov chain Monte Carlo
    • 10.1023/A:1020206129842
    • Laskey KB Myers J Population Markov chain Monte Carlo Machine Learning 2003, 50:175-196 10.1023/A:1020206129842
    • (2003) Machine Learning , vol.50 , pp. 175-196
    • Laskey, K.B.1    Myers, J.2
  • 22
    • 0001927585 scopus 로고
    • On information and sufficiency
    • 10.1214/aoms/1177729694
    • Kullback S Leibler RA On information and sufficiency Ann Math Statist 1951, 22:79-86 10.1214/aoms/1177729694
    • (1951) Ann Math Statist , vol.22 , pp. 79-86
    • Kullback, S.1    Leibler, R.A.2
  • 23
    • 0023147228 scopus 로고
    • Selection of DNA binding sites by regulatory proteins: Statistical-mechanical theory and application to operators and promoters
    • 10.1016/0022-2836(87)90354-8 3612791
    • Berg O von Hippel PH Selection of DNA binding sites by regulatory proteins: Statistical-mechanical theory and application to operators and promoters Journal of Molecular Biology 1987, 193:723-750 10.1016/ 0022-2836(87)90354-8 3612791
    • (1987) Journal of Molecular Biology , vol.193 , pp. 723-750
    • Berg, O.1    von Hippel, P.H.2
  • 24
    • 0034072450 scopus 로고    scopus 로고
    • DNA binding sites: Representation and discovery
    • 10.1093/bioinformatics/16.1.16 10812473
    • Stormo GD DNA binding sites: Representation and discovery Bioinformatics 2000, 16:16-23 10.1093/bioinformatics/16.1.16 10812473
    • (2000) Bioinformatics , vol.16 , pp. 16-23
    • Stormo, G.D.1
  • 25
    • 0000900670 scopus 로고    scopus 로고
    • Spelling approximate repeated or common motifs using a suffix tree
    • Lucchesi C, Moura A
    • Sagot MF Spelling approximate repeated or common motifs using a suffix tree Theoretical informatics, 1380 Lucchesi C, Moura A 1998, 111-127
    • (1998) Theoretical Informatics, 1380 , pp. 111-127
    • Sagot, M.F.1
  • 26
    • 0034565285 scopus 로고    scopus 로고
    • Combinatorial approaches to finding subtle signals in DNA sequences
    • Pevzner P Sze SH Combinatorial approaches to finding subtle signals in DNA sequences Proc. First ISMB Conference 2000, 1:269-278
    • (2000) Proc. First ISMB Conference , vol.1 , pp. 269-278
    • Pevzner, P.1    Sze, S.H.2
  • 27
    • 0036110853 scopus 로고    scopus 로고
    • Finding motifs using random projection
    • 10.1089/10665270252935430 12015879
    • Buhler J Tompa M Finding motifs using random projection Journal of Computational Biology 2002, 9:225-242 10.1089/10665270252935430 12015879
    • (2002) Journal of Computational Biology , vol.9 , pp. 225-242
    • Buhler, J.1    Tompa, M.2
  • 28
    • 0035224579 scopus 로고    scopus 로고
    • An algorithm for finding signals of unknown length in DNA sequences
    • 11473011
    • Pavesi G Mauri G Pesole G An algorithm for finding signals of unknown length in DNA sequences Bioinformatics 2001, 17(suppl 1):S207-S214 11473011
    • (2001) Bioinformatics , vol.17 , Issue.SUPPL. 1
    • Pavesi, G.1    Mauri, G.2    Pesole, G.3
  • 29
    • 21144439147 scopus 로고    scopus 로고
    • Assessing computational tools for the discovery of transcription factor binding sites
    • 10.1038/nbt1053 15637633
    • Tompa M Li N Bailey TL Church GM De Moor B et al Assessing computational tools for the discovery of transcription factor binding sites Nat Biotechnol 2005, 23:137-144 10.1038/nbt1053 15637633
    • (2005) Nat Biotechnol , vol.23 , pp. 137-144
    • Tompa, M.1    Li, N.2    Bailey, T.L.3    Church, G.M.4    De Moor, B.5
  • 33
    • 1242264319 scopus 로고    scopus 로고
    • Finding functional sequence elements by multiple local alignment
    • 373279 14704356 10.1093/nar/gkh169
    • Frith MC Hansen U Spouge JL Weng Z Finding functional sequence elements by multiple local alignment Nucleic Acids Res 2004, 32:189-200 373279 14704356 10.1093/nar/gkh169
    • (2004) Nucleic Acids Res , vol.32 , pp. 189-200
    • Frith, M.C.1    Hansen, U.2    Spouge, J.L.3    Weng, Z.4
  • 37
    • 0347125328 scopus 로고    scopus 로고
    • JASPAR: An open-access database for eukaryotic transcription factor binding profiles
    • 308747 14681366 10.1093/nar/gkh012
    • Sandelin A Alkema W Engstrom P Wasserman WW Lenhard B JASPAR: An open-access database for eukaryotic transcription factor binding profiles Nucleic Acids Res 2004, 32:D91-D94 308747 14681366 10.1093/nar/ gkh012
    • (2004) Nucleic Acids Res , vol.32
    • Sandelin, A.1    Alkema, W.2    Engstrom, P.3    Wasserman, W.W.4    Lenhard, B.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.