-
1
-
-
70349312354
-
ChIP-seq: Advantages and challenges of a maturing technology
-
Park, P.J. (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat. Rev. Genet., 10, 669-680.
-
(2009)
Nat. Rev. Genet.
, vol.10
, pp. 669-680
-
-
Park, P.J.1
-
2
-
-
70349576551
-
ChIP-Chip: Algorithms for calling binding sites
-
Liu, X.S. and Meyer, C.A. (2009) ChIP-Chip: algorithms for calling binding sites. Methods Mol. Biol., 556, 165-175.
-
(2009)
Methods Mol. Biol.
, vol.556
, pp. 165-175
-
-
Liu, X.S.1
Meyer, C.A.2
-
4
-
-
67849122301
-
Using ChIP-chip and ChIP-seq to study the regulation of gene expression: Genome-wide localization studies reveal widespread regulation of transcription elongation
-
Gilchrist, D.A., Fargo, D.C. and Adelman, K. (2009) Using ChIP-chip and ChIP-seq to study the regulation of gene expression: genome-wide localization studies reveal widespread regulation of transcription elongation. Methods, 48, 398-408.
-
(2009)
Methods
, vol.48
, pp. 398-408
-
-
Gilchrist, D.A.1
Fargo, D.C.2
Adelman, K.3
-
5
-
-
68949162986
-
Transcriptional programs: Modelling higher order structure in transcriptional control
-
Reid, J.E., Ott, S. and Wernisch, L. (2009) Transcriptional programs: modelling higher order structure in transcriptional control. BMC Bioinformatics, 10, 218.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 218
-
-
Reid, J.E.1
Ott, S.2
Wernisch, L.3
-
6
-
-
26444584579
-
Limitations and potentials of current motif discovery algorithms
-
DOI 10.1093/nar/gki791
-
Hu, J., Li, B. and Kihara, D. (2005) Limitations and potentials of current motif discovery algorithms. Nucleic Acids Res., 33, 4899-4913. (Pubitemid 41418889)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.15
, pp. 4899-4913
-
-
Hu, J.1
Li, B.2
Kihara, D.3
-
7
-
-
33646229522
-
Practical strategies for discovering regulatory DNA sequence motifs
-
MacIsaac, K.D. and Fraenkel, E. (2006) Practical strategies for discovering regulatory DNA sequence motifs. PLoS Comput. Biol., 2, e36.
-
(2006)
PLoS Comput. Biol.
, vol.2
-
-
MacIsaac, K.D.1
Fraenkel, E.2
-
8
-
-
33747064917
-
How does DNA sequence motif discovery work?
-
D'haeseleer, P. (2006) How does DNA sequence motif discovery work? Nat. Biotechnol., 24, 959-961.
-
(2006)
Nat. Biotechnol.
, vol.24
, pp. 959-961
-
-
D'Haeseleer, P.1
-
9
-
-
38549144819
-
A survey of DNA motif finding algorithms
-
Das, M.K. and Dai, H.-K. (2007) A survey of DNA motif finding algorithms. BMC Bioinformatics, 8(Suppl. 7), S21.
-
(2007)
BMC Bioinformatics
, vol.8
, Issue.SUPPL. 7
-
-
Das, M.K.1
Dai, H.-K.2
-
10
-
-
0002629270
-
Maximum likelihood from incomplete data via the em Algorithm
-
Dempster, A.P., Laird, N.M. and Rubin, D.B. (1977) Maximum likelihood from incomplete data via the EM Algorithm. J. Roy. Stat. Soc. Ser. B, 39, 1-38.
-
(1977)
J. Roy. Stat. Soc. Ser. B
, vol.39
, pp. 1-38
-
-
Dempster, A.P.1
Laird, N.M.2
Rubin, D.B.3
-
11
-
-
0001956238
-
Stochastic relaxation, Gibbs distributions and the Bayesian restoration of images
-
Geman, S. and Geman, D. (1993) Stochastic relaxation, Gibbs distributions and the Bayesian restoration of images. J. Appl. Stat., 20, 25-62.
-
(1993)
J. Appl. Stat.
, vol.20
, pp. 25-62
-
-
Geman, S.1
Geman, D.2
-
12
-
-
0025320805
-
An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences
-
Lawrence, C.E. and Reilly, A.A. (1990) An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences. Proteins, 7, 41-51. (Pubitemid 20102601)
-
(1990)
Proteins: Structure, Function and Genetics
, vol.7
, Issue.1
, pp. 41-51
-
-
Lawrence, C.E.1
Reilly, A.A.2
-
13
-
-
0028685490
-
Fitting a mixture model by expectation maximization to discover motifs in biopolymers
-
Bailey, T.L. and Elkan, C. (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers, Proc. Int. Conf. Intell. Syst. Mol. Biol., 2, 28-36.
-
(1994)
Proc. Int. Conf. Intell. Syst. Mol. Biol.
, vol.2
, pp. 28-36
-
-
Bailey, T.L.1
Elkan, C.2
-
14
-
-
0037461026
-
Greedy mixture learning for multiple motif discovery in biological sequences
-
DOI 10.1093/bioinformatics/btg037
-
Blekas, K., Fotiadis, D.I. and Likas, A. (2003) Greedy mixture learning for multiple motif discovery in biological sequences. Bioinformatics, 19, 607-617. (Pubitemid 36417055)
-
(2003)
Bioinformatics
, vol.19
, Issue.5
, pp. 607-617
-
-
Blekas, K.1
Fotiadis, D.I.2
Likas, A.3
-
15
-
-
2442718022
-
Motif discovery in heterogeneous sequence data
-
Prakash, A., Blanchette, M., Sinha, S. and Tompa, M. (2004) Motif discovery in heterogeneous sequence data. Pac. Symp. Biocomput., 1, 348-359.
-
(2004)
Pac. Symp. Biocomput.
, vol.1
, pp. 348-359
-
-
Prakash, A.1
Blanchette, M.2
Sinha, S.3
Tompa, M.4
-
16
-
-
13244260826
-
PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences
-
Sinha, S., Blanchette, M. and Tompa, M. (2004) PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences. BMC Bioinformatics, 5, 170.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 170
-
-
Sinha, S.1
Blanchette, M.2
Tompa, M.3
-
17
-
-
2442693190
-
Phylogenetic Motif Detection by Expectation Maximization on Evolutionary Mixtures
-
Moses, A.M., Chiang, D.Y. and Eisen, M.B. (2004) Phylogenetic Motif Detection by Expectation Maximization on Evolutionary Mixtures. Pac. Symp. Biocomput., 324-335.
-
(2004)
Pac. Symp. Biocomput.
, pp. 324-335
-
-
Moses, A.M.1
Chiang, D.Y.2
Eisen, M.B.3
-
18
-
-
29244482771
-
Genetic interaction motif finding by expectation maximization-a novel statistical model for inferring gene modules from synthetic lethality
-
Qi, Y., Ye, P. and Bader, J.S. (2005) Genetic interaction motif finding by expectation maximization-a novel statistical model for inferring gene modules from synthetic lethality. BMC Bioinformatics, 6, 288.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 288
-
-
Qi, Y.1
Ye, P.2
Bader, J.S.3
-
19
-
-
32544434809
-
A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data
-
DOI 10.1093/bioinformatics/bti815
-
MacIsaac, K.D., Gordon, D.B., Nekludova, L., Odom, D.T., Schreiber, J., Gifford, D.K., Young, R.A. and Fraenkel, E. (2006) A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data. Bioinformatics, 22, 423-429. (Pubitemid 43231416)
-
(2006)
Bioinformatics
, vol.22
, Issue.4
, pp. 423-429
-
-
MacIsaac, K.D.1
Gordon, D.B.2
Nekludova, L.3
Odom, D.T.4
Schreiber, J.5
Gifford, D.K.6
Young, R.A.7
Fraenkel, E.8
-
20
-
-
59649113226
-
GADEM: A genetic algorithm guided formation of spaced dyads coupled with an em algorithm for motif discovery
-
Li, L. (2009) GADEM: a genetic algorithm guided formation of spaced dyads coupled with an EM algorithm for motif discovery. J. Comput. Biol., 16, 317-329.
-
(2009)
J. Comput. Biol.
, vol.16
, pp. 317-329
-
-
Li, L.1
-
21
-
-
21144439147
-
Assessing computational tools for the discovery of transcription factor binding sites
-
DOI 10.1038/nbt1053
-
Tompa, M., Li, N., Bailey, T.L., Church, G.M., Moor, B.D., Eskin, E., Favorov, A.V., Frith, M.C., Fu, Y., Kent, W.J. et al. (2005) Assessing computational tools for the discovery of transcription factor binding sites. Nat. Biotechnol., 23, 137-144. (Pubitemid 41724640)
-
(2005)
Nature Biotechnology
, vol.23
, Issue.1
, pp. 137-144
-
-
Tompa, M.1
Li, N.2
Bailey, T.L.3
Church, G.M.4
De Moor, B.5
Eskin, E.6
Favorov, A.V.7
Frith, M.C.8
Fu, Y.9
Kent, W.J.10
Makeev, V.J.11
Mironov, A.A.12
Noble, W.S.13
Pavesi, G.14
Pesole, G.15
Regnier, M.16
Simonis, N.17
Sinha, S.18
Thijs, G.19
Van Helden, J.20
Vandenbogaert, M.21
Weng, Z.22
Workman, C.23
Ye, C.24
Zhu, Z.25
more..
-
22
-
-
0029962489
-
ParaMEME: A parallel implementation and a web interface for a DNA and protein motif discovery tool
-
Grundy, W.N., Bailey, T.L. and Elkan, C.P. (1996) ParaMEME: a parallel implementation and a web interface for a DNA and protein motif discovery tool. Comput. Appl. Biosci., 12, 303-310.
-
(1996)
Comput. Appl. Biosci.
, vol.12
, pp. 303-310
-
-
Grundy, W.N.1
Bailey, T.L.2
Elkan, C.P.3
-
23
-
-
33750387399
-
-
Sandve, G.K., Nedland, M., Syrstad, Ø.B., Eidsheim, L.A., Abul, O. and Drabløs, F. (2006) Workshop on Algorithms in Bioinformatics (WABI)'06, pp. 197-206.
-
(2006)
Workshop on Algorithms in Bioinformatics (WABI)'06
, pp. 197-206
-
-
Sandve, G.K.1
Nedland, M.2
Syrstad, ØB.3
Eidsheim, L.A.4
Abul, O.5
Drabløs, F.6
-
24
-
-
57049178944
-
GPU-MEME: Using graphics hardware to accelerate motif finding in DNA sequences
-
Chetty, M., Ngom, A., and Ahmad, S., (eds) Pattern Recognition in Bioinformatics Springer, Berlin/Heidelberg
-
Chen, C., Schmidt, B., Weiguo, L., and Müller-Wittig, W. (2008) GPU-MEME: Using Graphics Hardware to Accelerate Motif Finding in DNA Sequences. In Chetty, M., Ngom, A., and Ahmad, S., (eds), Pattern Recognition in Bioinformatics, Lecture Notes in Computer Science. Springer, Berlin/Heidelberg, pp. 448-459.
-
(2008)
Lecture Notes in Computer Science
, pp. 448-459
-
-
Chen, C.1
Schmidt, B.2
Weiguo, L.3
Müller-Wittig, W.4
-
26
-
-
38849131252
-
High-throughput sequence alignment using Graphics Processing Units
-
Schatz, M., Trapnell, C., Delcher, A. and Varshney, A. (2007) High-throughput sequence alignment using Graphics Processing Units. BMC Bioinformatics, 8, 474.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 474
-
-
Schatz, M.1
Trapnell, C.2
Delcher, A.3
Varshney, A.4
-
28
-
-
78650487811
-
Unified view of backward backtracking in short read mapping
-
Elomaa, T., Mannila, H., and Orponen, P. (eds) Algorithms and Applications Springer, Berlin/Heidelberg
-
Mäkinen, V., Välimäki, N., Laaksonen, A., and Katainen, R. (2010) Unified view of backward backtracking in short read mapping. In Elomaa, T., Mannila, H., and Orponen, P. (eds), Algorithms and Applications, Lecture Notes in Computer Science. Springer, Berlin/Heidelberg, pp. 182-195.
-
(2010)
Lecture Notes in Computer Science
, pp. 182-195
-
-
Mäkinen, V.1
Välimäki, N.2
Laaksonen, A.3
Katainen, R.4
-
29
-
-
69849083725
-
Suffix tree characterization of maximal motifs in biological sequences
-
Federico, M. and Pisanti, N. (2009) Suffix tree characterization of maximal motifs in biological sequences. Theor. Comput. Sci., 410, 4391-4401.
-
(2009)
Theor. Comput. Sci.
, vol.410
, pp. 4391-4401
-
-
Federico, M.1
Pisanti, N.2
-
30
-
-
0033677426
-
Algorithms for extracting structured motifs using a suffix tree with an application to promoter and regulatory site consensus identification
-
Marsan, L. and Sagot, M.F. (2000) Algorithms for extracting structured motifs using a suffix tree with an application to promoter and regulatory site consensus identification. J. Comput. Biol., 7, 345-362.
-
(2000)
J. Comput. Biol.
, vol.7
, pp. 345-362
-
-
Marsan, L.1
Sagot, M.F.2
-
31
-
-
0035224579
-
An algorithm for finding signals of unknown length in DNA sequences
-
Pavesi, G., Mauri, G. and Pesole, G. (2001) An algorithm for finding signals of unknown length in DNA sequences. Bioinformatics, 17(Suppl. 1), S207-S214. (Pubitemid 33793512)
-
(2001)
Bioinformatics
, vol.17
, Issue.SUPPL. 1
-
-
Pavesi, G.1
Mauri, G.2
Pesole, G.3
-
32
-
-
33750959240
-
Fast index based algorithms and software for matching position specific scoring matrices
-
Beckstette, M., Homann, R., Giegerich, R. and Kurtz, S. (2006) Fast index based algorithms and software for matching position specific scoring matrices. BMC Bioinformatics, 7, 389.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 389
-
-
Beckstette, M.1
Homann, R.2
Giegerich, R.3
Kurtz, S.4
-
33
-
-
0001704377
-
On-line construction of suffix trees
-
Ukkonen, E. (1995) On-line construction of suffix trees. Algorithmica, 14, 249-260.
-
(1995)
Algorithmica
, vol.14
, pp. 249-260
-
-
Ukkonen, E.1
-
34
-
-
39549090389
-
SeqAn an efficient, generic C++library for sequence analysis
-
Döring, A., Weese, D., Rausch, T. and Reinert, K. (2008) SeqAn an efficient, generic C++library for sequence analysis. BMC Bioinformatics, 9, 11.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 11
-
-
Döring, A.1
Weese, D.2
Rausch, T.3
Reinert, K.4
-
35
-
-
77349099959
-
Variable structure motifs for transcription factor binding sites
-
Reid, J.E., Evans, K.J., Dyer, N., Wernisch, L. and Ott, S. (2010) Variable structure motifs for transcription factor binding sites. BMC Genomics, 11, 30.
-
(2010)
BMC Genomics
, vol.11
, pp. 30
-
-
Reid, J.E.1
Evans, K.J.2
Dyer, N.3
Wernisch, L.4
Ott, S.5
-
36
-
-
34250305146
-
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
-
DOI 10.1038/nature05874, PII NATURE05874
-
Birney, E., Stamatoyannopoulos, J.A., Dutta, A., Guigó , R., Gingeras, T.R., Margulies, E.H., Weng, Z., Snyder, M., Dermitzakis, E.T., Thurman, R.E. et al. (2007) Identification and analysis of functional elements in 1 the encode pilot project. Nature, 447, 799-816. (Pubitemid 46920138)
-
(2007)
Nature
, vol.447
, Issue.7146
, pp. 799-816
-
-
Birney, E.1
Stamatoyannopoulos, J.A.2
Dutta, A.3
Guigo, R.4
Gingeras, T.R.5
Margulies, E.H.6
Weng, Z.7
Snyder, M.8
Dermitzakis, E.T.9
Thurman, R.E.10
Kuehn, M.S.11
Taylor, C.M.12
Neph, S.13
Koch, C.M.14
Asthana, S.15
Malhotra, A.16
Adzhubei, I.17
Greenbaum, J.A.18
Andrews, R.M.19
Flicek, P.20
Boyle, P.J.21
Cao, H.22
Carter, N.P.23
Clelland, G.K.24
Davis, S.25
Day, N.26
Dhami, P.27
Dillon, S.C.28
Dorschner, M.O.29
Fiegler, H.30
Giresi, P.G.31
Goldy, J.32
Hawrylycz, M.33
Haydock, A.34
Humbert, R.35
James, K.D.36
Johnson, B.E.37
Johnson, E.M.38
Frum, T.T.39
Rosenzweig, E.R.40
Karnani, N.41
Lee, K.42
Lefebvre, G.C.43
Navas, P.A.44
Neri, F.45
Parker, S.C.J.46
Sabo, P.J.47
Sandstrom, R.48
Shafer, A.49
Vetrie, D.50
Weaver, M.51
Wilcox, S.52
Yu, M.53
Collins, F.S.54
Dekker, J.55
Lieb, J.D.56
Tullius, T.D.57
Crawford, G.E.58
Sunyaev, S.59
Noble, W.S.60
Dunham, I.61
Denoeud, F.62
Reymond, A.63
Kapranov, P.64
Rozowsky, J.65
Zheng, D.66
Castelo, R.67
Frankish, A.68
Harrow, J.69
Ghosh, S.70
Sandelin, A.71
Hofacker, I.L.72
Baertsch, R.73
Keefe, D.74
Dike, S.75
Cheng, J.76
Hirsch, H.A.77
Sekinger, E.A.78
Lagarde, J.79
Abril, J.F.80
Shahab, A.81
Flamm, C.82
Fried, C.83
Hackermuller, J.84
Hertel, J.85
Lindemeyer, M.86
Missal, K.87
Tanzer, A.88
Washietl, S.89
Korbel, J.90
Emanuelsson, O.91
Pedersen, J.S.92
Holroyd, N.93
Taylor, R.94
Swarbreck, D.95
Matthews, N.96
Dickson, M.C.97
more..
-
37
-
-
54549103162
-
Priming for T helper type 2 differentiation by interleukin 2-mediated induction of interleukin 4 receptor alpha-chain expression
-
Liao, W., Schones, D.E., Oh, J., Cui, Y., Cui, K., Roh, T.-Y., Zhao, K. and Leonard, W.J. (2008) Priming for T helper type 2 differentiation by interleukin 2-mediated induction of interleukin 4 receptor alpha-chain expression. Nat. Immunol., 9, 1288-1296.
-
(2008)
Nat. Immunol.
, vol.9
, pp. 1288-1296
-
-
Liao, W.1
Schones, D.E.2
Oh, J.3
Cui, Y.4
Cui, K.5
Roh, T.-Y.6
Zhao, K.7
Leonard, W.J.8
-
38
-
-
10744226888
-
Unbiased Mapping of Transcription Factor Binding Sites along Human Chromosomes 21 and 22 Points to Widespread Regulation of Noncoding RNAs
-
DOI 10.1016/S0092-8674(04)00127-8
-
Cawley, S., Bekiranov, S., Ng, H.H., Kapranov, P., Sekinger, E.A., Kampa, D., Piccolboni, A., Sementchenko, V., Cheng, J., Williams, A.J. et al. (2004) Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell, 116, 499-509. (Pubitemid 38264428)
-
(2004)
Cell
, vol.116
, Issue.4
, pp. 499-509
-
-
Cawley, S.1
Bekiranov, S.2
Ng, H.H.3
Kapranov, P.4
Sekinger, E.A.5
Kampa, D.6
Piccolboni, A.7
Sementchenko, V.8
Cheng, J.9
Williams, A.J.10
Wheeler, R.11
Wong, B.12
Drenkow, J.13
Yamanaka, M.14
Patel, S.15
Brubaker, S.16
Tammana, H.17
Helt, G.18
Struhl, K.19
Gingeras, T.R.20
more..
-
39
-
-
50849090969
-
Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data
-
Valouev, A., Johnson, D.S., Sundquist, A., Medina, C., Anton, E., Batzoglou, S., Myers, R.M. and Sidow, A. (2008) Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat. Methods, 5, 829-834.
-
(2008)
Nat. Methods
, vol.5
, pp. 829-834
-
-
Valouev, A.1
Johnson, D.S.2
Sundquist, A.3
Medina, C.4
Anton, E.5
Batzoglou, S.6
Myers, R.M.7
Sidow, A.8
-
40
-
-
34547633677
-
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
-
DOI 10.1038/nmeth1068, PII NMETH1068
-
Robertson, G., Hirst, M., Bainbridge, M., Bilenky, M., Zhao, Y., Zeng, T., Euskirchen, G., Bernier, B., Varhol, R., Delaney, A. et al. (2007) Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods, 4, 651-657. (Pubitemid 47202477)
-
(2007)
Nature Methods
, vol.4
, Issue.8
, pp. 651-657
-
-
Robertson, G.1
Hirst, M.2
Bainbridge, M.3
Bilenky, M.4
Zhao, Y.5
Zeng, T.6
Euskirchen, G.7
Bernier, B.8
Varhol, R.9
Delaney, A.10
Thiessen, N.11
Griffith, O.L.12
He, A.13
Marra, M.14
Snyder, M.15
Jones, S.16
-
41
-
-
55749094855
-
An integrated software system for analyzing ChIP-chip and ChIP-seq data
-
Nov
-
Ji, H., Jiang, H., Ma, W., Johnson, D.S., Myers, R.M. and Wong, W.H. (2008) An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat. Biotechnol., 26, 1293-1300, Nov.
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 1293-1300
-
-
Ji, H.1
Jiang, H.2
Ma, W.3
Johnson, D.S.4
Myers, R.M.5
Wong, W.H.6
-
42
-
-
0002759539
-
Unsupervised Learning of Multiple Motifs in Biopolymers Using em
-
Bailey, T.L. and Elkan, C. (1995) Unsupervised Learning of Multiple Motifs In Biopolymers Using EM. Mach. Learn., 51-80.
-
(1995)
Mach. Learn.
, pp. 51-80
-
-
Bailey, T.L.1
Elkan, C.2
|