-
1
-
-
0003880161
-
-
fourth ed. Garland, New York
-
Alberts, B., Johnson, J., Lewis, J., Raff, M., Roberts, K., Walter, P., 2002. Molecular Biology of the Cell, fourth ed. Garland, New York.
-
(2002)
Molecular Biology of the Cell
-
-
Alberts, B.1
Johnson, J.2
Lewis, J.3
Raff, M.4
Roberts, K.5
Walter, P.6
-
3
-
-
0002759539
-
Unsupervised learning of multiple motifs in biopolymers using expectation maximization
-
T.L. Bailey, and C. Elkan Unsupervised learning of multiple motifs in biopolymers using expectation maximization Machine Learn. 21 1995 51 80
-
(1995)
Machine Learn.
, vol.21
, pp. 51-80
-
-
Bailey, T.L.1
Elkan, C.2
-
5
-
-
0023147228
-
Selection of DNA binding sites by regulatory proteins: Statistical-mechanical theory and application to operators and promoters
-
O.G. Berg, and P.H. von Hippel Selection of DNA binding sites by regulatory proteins: Statistical-mechanical theory and application to operators and promoters J. Mol. Biol. 193 1987 723 750
-
(1987)
J. Mol. Biol.
, vol.193
, pp. 723-750
-
-
Berg, O.G.1
Von Hippel, P.H.2
-
6
-
-
34248191269
-
SEAM: A stochastic EM-type algorithm for motif-finding in biopolymer sequences
-
C.-P. Bi SEAM: A stochastic EM-type algorithm for motif-finding in biopolymer sequences J. Bioinform. Comput. Biol. 5 2007 47 77
-
(2007)
J. Bioinform. Comput. Biol.
, vol.5
, pp. 47-77
-
-
Bi, C.-P.1
-
9
-
-
68649104708
-
A Monte Carlo em algorithm for de novo motif discovery in biomolecular sequences
-
C.-P. Bi A Monte Carlo EM algorithm for de novo motif discovery in biomolecular sequences IEEE Trans. Comput. Biol. Bioinform. 6 2009 370 386
-
(2009)
IEEE Trans. Comput. Biol. Bioinform.
, vol.6
, pp. 370-386
-
-
Bi, C.-P.1
-
10
-
-
60849096092
-
DNA motif alignment through evolving a population of Markov chains
-
C.-P. Bi DNA motif alignment through evolving a population of Markov chains BMC Bioinform. 10 2009 S13
-
(2009)
BMC Bioinform.
, vol.10
, pp. 13
-
-
Bi, C.-P.1
-
11
-
-
0030376179
-
Stochastic versions of the em algorithm: An experimental study in the mixture case
-
G. Celeux, and J. Diebolt Stochastic versions of the EM algorithm: An experimental study in the mixture case J. Statist. Comput. Simul. 55 1996 287 314
-
(1996)
J. Statist. Comput. Simul.
, vol.55
, pp. 287-314
-
-
Celeux, G.1
Diebolt, J.2
-
12
-
-
0033243858
-
Convergence of a stochastic approximation version of the em algorithm
-
B. Delyon, M. Lavielle, and E. Moulines Convergence of a stochastic approximation version of the EM algorithm Ann. Statist. 27 1999 94 128
-
(1999)
Ann. Statist.
, vol.27
, pp. 94-128
-
-
Delyon, B.1
Lavielle, M.2
Moulines, E.3
-
13
-
-
0002629270
-
Maximum likelihood from incomplete data via the em algorithm (with discussion)
-
A.P. Dempster, A.M. Laird, and D.B. Rubin Maximum likelihood from incomplete data via the EM algorithm (with discussion) J. Royal Statist. Soc. B 39 1977 1 38
-
(1977)
J. Royal Statist. Soc. B
, vol.39
, pp. 1-38
-
-
Dempster, A.P.1
Laird, A.M.2
Rubin, D.B.3
-
14
-
-
34250305146
-
The ENCODE project consortium: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
-
The ENCODE project consortium: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. 2007. Science 447, 799-816.
-
(2007)
Science
, vol.447
, pp. 799-816
-
-
-
15
-
-
0035998835
-
Model-based clustering, discriminant analysis, and density estimation
-
C. Fraley, and A. Raftery Model-based clustering, discriminant analysis, and density estimation J. Amer. Statist. Assoc. 97 2002 611 631
-
(2002)
J. Amer. Statist. Assoc.
, vol.97
, pp. 611-631
-
-
Fraley, C.1
Raftery, A.2
-
16
-
-
1242264319
-
Finding functional sequence elements by multiple local alignment
-
M.C. Frith, U. Hansen, J.L. Spouge, and Z. Weng Finding functional sequence elements by multiple local alignment Nucl. Acids Res. 32 2004 189 200
-
(2004)
Nucl. Acids Res.
, vol.32
, pp. 189-200
-
-
Frith, M.C.1
Hansen, U.2
Spouge, J.L.3
Weng, Z.4
-
17
-
-
0021518209
-
Stochastic relaxation, Gibbs distribution and Bayesian restoration of images
-
S. Geman, and D. Geman Stochastic relaxation, Gibbs distribution and Bayesian restoration of images IEEE Trans. Pattern Anal. Machine Intell. 6 1984 721 741
-
(1984)
IEEE Trans. Pattern Anal. Machine Intell.
, vol.6
, pp. 721-741
-
-
Geman, S.1
Geman, D.2
-
18
-
-
4544352942
-
Transcriptional regulatory code of a eukaryotic genome
-
C.T. Harbison, D.B. Gordon, T.I. Lee, N.J. Rinaldi, K.D. MacIsaac, T.W. Danford, N.M. Hannett, J.-B. Tagne, D.B. Reynolds, J. Yoo, E.G. Jennings, J. Zeitlinger, D.K. Pokholok, M. Kellis, P.A. Rolfe, K.T. Takusagawa, E.S. Lander, D.K. Gifford, E. Fraenkel, and R.A. Young Transcriptional regulatory code of a eukaryotic genome Nature 431 2004 99 104
-
(2004)
Nature
, vol.431
, pp. 99-104
-
-
Harbison, C.T.1
Gordon, D.B.2
Lee, T.I.3
Rinaldi, N.J.4
MacIsaac, K.D.5
Danford, T.W.6
Hannett, N.M.7
Tagne, J.-B.8
Reynolds, D.B.9
Yoo, J.10
Jennings, E.G.11
Zeitlinger, J.12
Pokholok, D.K.13
Kellis, M.14
Rolfe, P.A.15
Takusagawa, K.T.16
Lander, E.S.17
Gifford, D.K.18
Fraenkel, E.19
Young, R.A.20
more..
-
19
-
-
77956890234
-
Monte Carlo sampling methods using Markov chains and their applications
-
W.K. Hastings Monte Carlo sampling methods using Markov chains and their applications Biometrika 57 1970 97 109
-
(1970)
Biometrika
, vol.57
, pp. 97-109
-
-
Hastings, W.K.1
-
22
-
-
0346490298
-
Computational discovery of gene regulatory binding motifs: A Bayesian perspective
-
S.T. Jensen, X.S. Liu, Q. Zhou, and J.S. Liu Computational discovery of gene regulatory binding motifs: A Bayesian perspective Statist. Sci. 19 2004 188 204
-
(2004)
Statist. Sci.
, vol.19
, pp. 188-204
-
-
Jensen, S.T.1
Liu, X.S.2
Zhou, Q.3
Liu, J.S.4
-
23
-
-
33748765218
-
Computational biology: Towards deciphering gene regulatory information in mammalian genomes
-
H. Ji, and W.W. Wong Computational biology: Towards deciphering gene regulatory information in mammalian genomes Biometrics 62 2006 645 663
-
(2006)
Biometrics
, vol.62
, pp. 645-663
-
-
Ji, H.1
Wong, W.W.2
-
24
-
-
34250159524
-
Genome-wide mapping of in vivo protein-DNA interactions
-
D.S. Johnson, A. Mortazavi, R.M. Myers, and B. Wold Genome-wide mapping of in vivo protein-DNA interactions Science 316 2007 1497 1502
-
(2007)
Science
, vol.316
, pp. 1497-1502
-
-
Johnson, D.S.1
Mortazavi, A.2
Myers, R.M.3
Wold, B.4
-
25
-
-
8844272773
-
Supervised detection of regulatory motifs in DNA sequences
-
S. Keles, M.J. van der Laan, S. Dudoit, B. Xing, and M.B. Eisen Supervised detection of regulatory motifs in DNA sequences Statist. Appl. Genet. Mol. Biol. 2 2003 5
-
(2003)
Statist. Appl. Genet. Mol. Biol.
, vol.2
, pp. 5
-
-
Keles, S.1
Van Der Laan, M.J.2
Dudoit, S.3
Xing, B.4
Eisen, M.B.5
-
27
-
-
0027912333
-
Detecting subtle sequence signals: A gibbs sampling strategy for multiple alignment
-
C.E. Lawrence Detecting subtle sequence signals: A gibbs sampling strategy for multiple alignment Science 262 1993 208 214
-
(1993)
Science
, vol.262
, pp. 208-214
-
-
Lawrence, C.E.1
-
28
-
-
0025320805
-
An expectation maximization algorithm for the identification and characterization of common sites in unaligned biopolymer sequences
-
C.E. Lawrence, and A.A. Reilly An expectation maximization algorithm for the identification and characterization of common sites in unaligned biopolymer sequences Proteins: Struct. Funct. Genet. 7 1990 41 51
-
(1990)
Proteins: Struct. Funct. Genet.
, vol.7
, pp. 41-51
-
-
Lawrence, C.E.1
Reilly, A.A.2
-
29
-
-
0035880733
-
Evolutionary Monte Carlo for protein folding simulations
-
F. Liang, and W.H. Wong Evolutionary Monte Carlo for protein folding simulations J. Chem. Phys. 115 2001 3374 3380
-
(2001)
J. Chem. Phys.
, vol.115
, pp. 3374-3380
-
-
Liang, F.1
Wong, W.H.2
-
30
-
-
79951870792
-
The collapsed Gibbs sampler with applications to a gene regulation problem
-
J.S. Liu The collapsed Gibbs sampler with applications to a gene regulation problem J. Amer. Statist. Assoc. 89 1994 958 966
-
(1994)
J. Amer. Statist. Assoc.
, vol.89
, pp. 958-966
-
-
Liu, J.S.1
-
31
-
-
14644404134
-
Bayesian modeling and computation in bioinformatics research
-
J.S. Liu Bayesian modeling and computation in bioinformatics research T. Jiang, Y. Xu, M. Zhang, Current Topics in Computational Biology 2002 MIT Press 11 44
-
(2002)
Current Topics in Computational Biology
, pp. 11-44
-
-
Liu, J.S.1
-
33
-
-
84950424966
-
Bayesian models for multiple local sequence alignment and Gibbs sampling strategies
-
J.S. Liu, A.F. Neuwald, and C.E. Lawrence Bayesian models for multiple local sequence alignment and Gibbs sampling strategies J. Amer. Statist. Assoc. 90 1995 1156 1170
-
(1995)
J. Amer. Statist. Assoc.
, vol.90
, pp. 1156-1170
-
-
Liu, J.S.1
Neuwald, A.F.2
Lawrence, C.E.3
-
34
-
-
33646229522
-
Practical strategies for discovering regulatory DNA sequence motifs
-
K.D. MacIsaac, and E. Fraenkel Practical strategies for discovering regulatory DNA sequence motifs PLoS Comput. Biol. 2 2006 e26
-
(2006)
PLoS Comput. Biol.
, vol.2
, pp. 26
-
-
MacIsaac, K.D.1
Fraenkel, E.2
-
36
-
-
0000251971
-
Maximum likelihood estimation via the ECM algorithm: A general framework
-
X.L. Meng, and D. Rubin Maximum likelihood estimation via the ECM algorithm: A general framework Biometrika 80 1993 267 278
-
(1993)
Biometrika
, vol.80
, pp. 267-278
-
-
Meng, X.L.1
Rubin, D.2
-
37
-
-
5744249209
-
Equations of statecalculations by fast computing machines
-
N. Metropolis, A.W. Rosenbluth, M.N. Rosenbluth, A. Teller, and H. Teller Equations of statecalculations by fast computing machines J. Chem. Phys. 21 1953 1087 1091
-
(1953)
J. Chem. Phys.
, vol.21
, pp. 1087-1091
-
-
Metropolis, N.1
Rosenbluth, A.W.2
Rosenbluth, M.N.3
Teller, A.4
Teller, H.5
-
38
-
-
0037154247
-
Deciphering genetic regulatory codes: A challenge for functional genomics
-
A.M. Michelson Deciphering genetic regulatory codes: A challenge for functional genomics Proc. Natl. Acad. Sci. USA 99 2002 546 548
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 546-548
-
-
Michelson, A.M.1
-
39
-
-
0002788893
-
A view of the em algorithm that justifies incremental, sparse, and other variants
-
R.M. Neal, and G.E. Hinton A view of the EM algorithm that justifies incremental, sparse, and other variants M. Jordan, Learning in Graphical Models 1998 NATO Science Series Kluwer 355 368
-
(1998)
Learning in Graphical Models
, pp. 355-368
-
-
Neal, R.M.1
Hinton, G.E.2
-
40
-
-
0035224579
-
An algorithm for finding signals of unknown length in DNA sequenes
-
G. Pavesi, G. Mauri, and G. Pesole An algorithm for finding signals of unknown length in DNA sequenes Bioinformatics 17 suppl. 1 2001 S207 S214
-
(2001)
Bioinformatics
, vol.17
, Issue.SUPPL. 1
-
-
Pavesi, G.1
Mauri, G.2
Pesole, G.3
-
41
-
-
0034565285
-
Combinatorial approaches to finding subtle signals in DNA sequences
-
Pevzner, P., Sze, S.H., 2000. Combinatorial approaches to finding subtle signals in DNA sequences. In: Proc. First ISMB Conference, vol. 1, pp. 269-278.
-
(2000)
Proc. First ISMB Conference
, vol.1
, pp. 269-278
-
-
Pevzner, P.1
Sze, S.H.2
-
42
-
-
33745248430
-
MicroRNA target predictions in animals
-
N. Rajewsky MicroRNA target predictions in animals Nat. Genet. 38 2006 S8 S13
-
(2006)
Nat. Genet.
, vol.38
-
-
Rajewsky, N.1
-
43
-
-
0034704248
-
Genome-wide location and function of DNA binding proteins
-
B. Ren, F. Robert, J.J. Wyrick, O. Aparicio, E.G. Jennings, I. Simon, J. Zeitlinger, J. Schreiber, N. Hannett, E. Kannin, T.L. Volkert, C.J. Wilson, S.P. Bell, and R.A. Young Genome-wide location and function of DNA binding proteins Science 290 2000 2306 2309
-
(2000)
Science
, vol.290
, pp. 2306-2309
-
-
Ren, B.1
Robert, F.2
Wyrick, J.J.3
Aparicio, O.4
Jennings, E.G.5
Simon, I.6
Zeitlinger, J.7
Schreiber, J.8
Hannett, N.9
Kannin, E.10
Volkert, T.L.11
Wilson, C.J.12
Bell, S.P.13
Young, R.A.14
-
44
-
-
0347125328
-
JASPAR: An open-access database for eukaryotic transcription factor binding profiles
-
A. Sandelin, W. Alkema, P. Engstrom, W.W. Wasserman, and B. Lenhard JASPAR: An open-access database for eukaryotic transcription factor binding profiles Nucl. Acids Res. 32 2004 D91 D94
-
(2004)
Nucl. Acids Res.
, vol.32
-
-
Sandelin, A.1
Alkema, W.2
Engstrom, P.3
Wasserman, W.W.4
Lenhard, B.5
-
45
-
-
0034072450
-
DNA binding sites: Representation and discovery
-
G.D. Stormo DNA binding sites: Representation and discovery Bioinformatics 16 2000 16 23
-
(2000)
Bioinformatics
, vol.16
, pp. 16-23
-
-
Stormo, G.D.1
-
46
-
-
0000133199
-
Identifying protein-binding sites from unaligned DNA fragments
-
G.D. Stormo, and G.W. Hartzell Identifying protein-binding sites from unaligned DNA fragments Proc. Natl. Acad. Sci. USA 86 1989 1183 1187
-
(1989)
Proc. Natl. Acad. Sci. USA
, vol.86
, pp. 1183-1187
-
-
Stormo, G.D.1
Hartzell, G.W.2
-
47
-
-
33747349191
-
Nonuniversal critical dynamics in Monte Carlo simulations
-
R.H. Swendsen, and J.S. Wang Nonuniversal critical dynamics in Monte Carlo simulations Phys. Rev. Lett. 58 1987 86 88
-
(1987)
Phys. Rev. Lett.
, vol.58
, pp. 86-88
-
-
Swendsen, R.H.1
Wang, J.S.2
-
48
-
-
84950758368
-
The calculation of posterior distributions by data augmentation
-
M.A. Tanner, and W.H. Wong The calculation of posterior distributions by data augmentation J. Amer. Statist. Assoc. 82 1987 528 550
-
(1987)
J. Amer. Statist. Assoc.
, vol.82
, pp. 528-550
-
-
Tanner, M.A.1
Wong, W.H.2
-
49
-
-
21144439147
-
Assessing computational tools for the discovery of transcription factor binding sites
-
M. Tompa, N. Li, T.L. Bailey, G.M. Church, B. De Moor, E. Eskin, A.V. Favorov, M.C. Frith, Y. Fu, W.J. Kent, V.J. Makeev, A.A. Mironov, W.S. Noble, G. Pavesi, G. Pesole, M. Regnier, N. Simonis, S. Sinha, G. Thijs, J. van Helden, M. Vandenbogaert, Z. Weng, C. Workman, C. Ye, and Z. Zhu Assessing computational tools for the discovery of transcription factor binding sites Nat. Biotechnol. 23 2005 137 144
-
(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
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..
-
50
-
-
0025194307
-
Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase
-
C. Tuerk, and L. Gold Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase Science 249 1990 505 510
-
(1990)
Science
, vol.249
, pp. 505-510
-
-
Tuerk, C.1
Gold, L.2
-
52
-
-
0028679709
-
On the complexity of multiple sequence alignment
-
L. Wang, and T. Jiang On the complexity of multiple sequence alignment J. Comput. Biol. 1 1994 337 348
-
(1994)
J. Comput. Biol.
, vol.1
, pp. 337-348
-
-
Wang, L.1
Jiang, T.2
-
53
-
-
84950432017
-
A Monte Carlo Implementation of the em algorithm and the Poor Man's Data Augmentation Algorithms
-
G.C.G. Wei, and M.A. Tanner A Monte Carlo Implementation of the EM algorithm and the Poor Man's Data Augmentation Algorithms J. Amer. Statist. Assoc. 85 1990 699 704
-
(1990)
J. Amer. Statist. Assoc.
, vol.85
, pp. 699-704
-
-
Wei, G.C.G.1
Tanner, M.A.2
-
54
-
-
0002210265
-
On the convergence properties of the em algorithm
-
C.F.J. Wu On the convergence properties of the EM algorithm Ann. Statist. 11 1983 95 103
-
(1983)
Ann. Statist.
, vol.11
, pp. 95-103
-
-
Wu, C.F.J.1
-
55
-
-
4344607122
-
CisModule: De novo discovery of cis-regulatory modules by hierarchical mixture modeling
-
Q. Zhou, and W.H. Wong CisModule: De novo discovery of cis-regulatory modules by hierarchical mixture modeling Proc. Natl. Acad. Sci. USA 101 2004 12114 12119
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 12114-12119
-
-
Zhou, Q.1
Wong, W.H.2
-
56
-
-
47249131263
-
Coupling hidden Markov models for the discovery of cis-regulatory modules in multiple species
-
Q. Zhou, and W.H. Wong Coupling hidden Markov models for the discovery of cis-regulatory modules in multiple species Ann. Appl. Statist. 1 2007 36 37
-
(2007)
Ann. Appl. Statist.
, vol.1
, pp. 36-37
-
-
Zhou, Q.1
Wong, W.H.2
|