-
1
-
-
0002759539
-
Unsupervised Learning of Multiple Motifs in Biopolymers Using Expectation Maximization
-
T. Bailey and C. Elkan, "Unsupervised Learning of Multiple Motifs in Biopolymers Using Expectation Maximization," Machine Learning, vol. 21, pp. 51-80, 1995.
-
(1995)
Machine Learning
, vol.21
, pp. 51-80
-
-
Bailey, T.1
Elkan, C.2
-
2
-
-
84959058940
-
A Simple HyperGeometric Approach for Discovering Putative Transcription Factor Binding Sites
-
Y. Barash, G. Bejerano, and N. Friedman, "A Simple HyperGeometric Approach for Discovering Putative Transcription Factor Binding Sites," Proc. Int'l Workshop Algorithms in Bioinformatics (WABI '01), pp. 278-293, 2001.
-
(2001)
Proc. Int'l Workshop Algorithms in Bioinformatics (WABI '01)
, pp. 278-293
-
-
Barash, Y.1
Bejerano, G.2
Friedman, N.3
-
3
-
-
0038716277
-
Modeling Dependencies in Protein-DNA Binding Sites
-
Y. Barash, G. Elidan, N. Friedman, and T. Kaplan, "Modeling Dependencies in Protein-DNA Binding Sites," Proc. Ann. Int'l Conf. Research in Computational Molecular Biology (RECOMB '03), pp. 28-37, 2003.
-
(2003)
Proc. Ann. Int'l Conf. Research in Computational Molecular Biology (RECOMB '03)
, pp. 28-37
-
-
Barash, Y.1
Elidan, G.2
Friedman, N.3
Kaplan, T.4
-
5
-
-
0036493201
-
Nucleotides of Transcription Factor Binding Sites Exert Interdependent Effects on the Binding Affinities of Transcription Factors
-
M.L. Bulyk, P.L.F. Johnson, and G.M. Church, "Nucleotides of Transcription Factor Binding Sites Exert Interdependent Effects on the Binding Affinities of Transcription Factors," Nucleic Acids Research, vol. 30, pp. 1255-1261, 2002.
-
(2002)
Nucleic Acids Research
, vol.30
, pp. 1255-1261
-
-
Bulyk, M.L.1
Johnson, P.L.F.2
Church, G.M.3
-
7
-
-
33751167615
-
An Efficient Algorithm for the Extended (l, d)-Motif Problem with Unknown Number of Binding Sites
-
F. Chin and H. Leung, "An Efficient Algorithm for the Extended (l, d)-Motif Problem with Unknown Number of Binding Sites," Proc. Int'l Symp. Bioinformatics and BioEngineering (BIBE '05), pp. 11-18, 2005.
-
(2005)
Proc. Int'l Symp. Bioinformatics and BioEngineering (BIBE '05)
, pp. 11-18
-
-
Chin, F.1
Leung, H.2
-
9
-
-
2442447220
-
Finding Motifs for Insufficient Number of Sequences with Strong Binding to Transcription Factor
-
F. Chin, H. Leung, S.M. Yiu, T.W. Lam, R. Rosenfeld, W.W. Tsang, D. Smith, and Y. Jiang, "Finding Motifs for Insufficient Number of Sequences with Strong Binding to Transcription Factor," Proc. Ann. Int'l Conf. Research in Computational Molecular Biology (RECOMB '04), pp. 125-132, 2004.
-
(2004)
Proc. Ann. Int'l Conf. Research in Computational Molecular Biology (RECOMB '04)
, pp. 125-132
-
-
Chin, F.1
Leung, H.2
Yiu, S.M.3
Lam, T.W.4
Rosenfeld, R.5
Tsang, W.W.6
Smith, D.7
Jiang, Y.8
-
10
-
-
29144484156
-
Enhanced Position Weight Matrices Using Mixture Models
-
S. Hannenhalli and L.S. Wang, "Enhanced Position Weight Matrices Using Mixture Models," Bioinformatics, vol. 21, pp. 204-212, 2005.
-
(2005)
Bioinformatics
, vol.21
, pp. 204-212
-
-
Hannenhalli, S.1
Wang, L.S.2
-
11
-
-
0001811485
-
Identification of Consensus Patterns in Unaligned DNA and Protein Sequences: A Large-Deviation Statistical Basis for Penalizing Gaps
-
G.Z. Hertz and G.D. Stormo, "Identification of Consensus Patterns in Unaligned DNA and Protein Sequences: A Large-Deviation Statistical Basis for Penalizing Gaps," Proc. Third Int'l Conf. Bioinformatics and Genome Research, pp. 201-216, 1995.
-
(1995)
Proc. Third Int'l Conf. Bioinformatics and Genome Research
, pp. 201-216
-
-
Hertz, G.Z.1
Stormo, G.D.2
-
12
-
-
0034628901
-
Computational Identification of CIS-Regulatory Elements Associated with Groups of Functionally Related Genes in Saccharomyces cerevisiae
-
J.D. Hughes, P.W. Estep, S. Tavazoie, and G.M. Church, "Computational Identification of CIS-Regulatory Elements Associated with Groups of Functionally Related Genes in Saccharomyces cerevisiae," J. Molecular Biology, vol. 296, no. 5, pp. 1205-1214, 2000.
-
(2000)
J. Molecular Biology
, vol.296
, Issue.5
, pp. 1205-1214
-
-
Hughes, J.D.1
Estep, P.W.2
Tavazoie, S.3
Church, G.M.4
-
14
-
-
0035187203
-
Combining Frequency and Positional Information to Predict Transcription Factor Binding Sites
-
S. Kielbasa, J. Korbel, D. Beule, J. Schuchhardt, and H. Herzel, "Combining Frequency and Positional Information to Predict Transcription Factor Binding Sites," Bioinformatics, vol. 17, pp. 1019-1026, 2001.
-
(2001)
Bioinformatics
, vol.17
, pp. 1019-1026
-
-
Kielbasa, S.1
Korbel, J.2
Beule, D.3
Schuchhardt, J.4
Herzel, H.5
-
15
-
-
0027912333
-
Detecting Subtule Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment
-
C. Lawrence, S. Altschul, M. Boguski, J. Liu, A. Neuwald, and J. Wootton, "Detecting Subtule Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment," Science, vol. 262, pp. 208-214, 1993.
-
(1993)
Science
, vol.262
, pp. 208-214
-
-
Lawrence, C.1
Altschul, S.2
Boguski, M.3
Liu, J.4
Neuwald, A.5
Wootton, J.6
-
16
-
-
0025320805
-
An Expectation Maximization (em) Algorithm for the Identification and Characterization of Common Sites in Unaligned Biopolymer Sequences
-
C. Lawrence and A. Reilly, "An Expectation Maximization (em) Algorithm for the Identification and Characterization of Common Sites in Unaligned Biopolymer Sequences," Proteins: Structure, Function and Genetics, vol. 7, pp. 41-51, 1990.
-
(1990)
Proteins: Structure, Function and Genetics
, vol.7
, pp. 41-51
-
-
Lawrence, C.1
Reilly, A.2
-
18
-
-
38449121252
-
Discovering Motifs with Transcription Factor Domain Knowledge
-
H. Leung and F. Chin, "Discovering Motifs with Transcription Factor Domain Knowledge," Proc. Pacific Symp. Biocomputing (PSB '07), pp. 472-483, 2007.
-
(2007)
Proc. Pacific Symp. Biocomputing (PSB '07)
, pp. 472-483
-
-
Leung, H.1
Chin, F.2
-
19
-
-
27544437350
-
Finding Exact Optimal Motif in Matrix Representation by Partitioning
-
H. Leung and F. Chin, "Finding Exact Optimal Motif in Matrix Representation by Partitioning," Bioinformatics, vol. 22, pp. 86-92, 2005.
-
(2005)
Bioinformatics
, vol.22
, pp. 86-92
-
-
Leung, H.1
Chin, F.2
-
21
-
-
23844526796
-
Finding Motifs with Insufficient Number of Strong Binding Sites
-
H. Leung, F. Chin, S.M. Yiu, R. Rosenfeld, and W.W. Tsang, "Finding Motifs with Insufficient Number of Strong Binding Sites," J. Computational Biology, vol. 12, no. 6, pp. 686-701, 2005.
-
(2005)
J. Computational Biology
, vol.12
, Issue.6
, pp. 686-701
-
-
Leung, H.1
Chin, F.2
Yiu, S.M.3
Rosenfeld, R.4
Tsang, W.W.5
-
22
-
-
10044245485
-
Finding Similar Regions in Many Strings
-
M. Li, B. Ma, and L. Wang, "Finding Similar Regions in Many Strings," J. Computer and System Sciences, vol. 65, pp. 73-96, 2002.
-
(2002)
J. Computer and System Sciences
, vol.65
, pp. 73-96
-
-
Li, M.1
Ma, B.2
Wang, L.3
-
23
-
-
84960356916
-
cWINNOWER Algorithm for Finding Fuzzy DNA Motifs
-
S. Liang, "cWINNOWER Algorithm for Finding Fuzzy DNA Motifs," Proc. IEEE CS Bioinformatics Conf., pp. 260-265, 2003.
-
(2003)
Proc. IEEE CS Bioinformatics Conf
, pp. 260-265
-
-
Liang, S.1
-
24
-
-
0035875327
-
Non-Independence of MNT Repressor-Operator Interaction Determined by a New Quantitative Multiple Fluorescence Relative Affinity (QuMFRA) Assay
-
T.K. Man and G.D. Stormo, "Non-Independence of MNT Repressor-Operator Interaction Determined by a New Quantitative Multiple Fluorescence Relative Affinity (QuMFRA) Assay," Nucleic Acids Research, vol. 29, pp. 2471-2478, 2001.
-
(2001)
Nucleic Acids Research
, vol.29
, pp. 2471-2478
-
-
Man, T.K.1
Stormo, G.D.2
-
25
-
-
33747829925
-
MoD Tools: Regulatory Motif Discovery in Nucleotide Sequences from Co-Regulated or Homologous Genes
-
G. Pavesi, P. Mereghetti, F. Zambelli, M. Stefani, G. Mauri, and G. Pesole, "MoD Tools: Regulatory Motif Discovery in Nucleotide Sequences from Co-Regulated or Homologous Genes," Nucleic Acids Research, vol. 34, pp. 566-570, 2006.
-
(2006)
Nucleic Acids Research
, vol.34
, pp. 566-570
-
-
Pavesi, G.1
Mereghetti, P.2
Zambelli, F.3
Stefani, M.4
Mauri, G.5
Pesole, G.6
-
26
-
-
0026729501
-
Wordup: An Efficient Algorithm for Discovering Statistically Significant Patterns in DNA Sequences
-
G. Pesole, N. Prunella, S. Liuni, M. Attimonelli, and C. Saccone, "Wordup: An Efficient Algorithm for Discovering Statistically Significant Patterns in DNA Sequences," Nucleic Acids Research, vol. 20, no. 11, pp. 2871-2875, 1992.
-
(1992)
Nucleic Acids Research
, vol.20
, Issue.11
, pp. 2871-2875
-
-
Pesole, G.1
Prunella, N.2
Liuni, S.3
Attimonelli, M.4
Saccone, C.5
-
28
-
-
84863048117
-
Exact Algorithms for Planted Motif Challenge Problem
-
S. Rajasekaran, S. Baila, and C.H. Huang, "Exact Algorithms for Planted Motif Challenge Problem," Proc. Asia-Pacific Bioinformatics Conf (APBC '05), pp. 249-259, 2005.
-
(2005)
Proc. Asia-Pacific Bioinformatics Conf (APBC '05)
, pp. 249-259
-
-
Rajasekaran, S.1
Baila, S.2
Huang, C.H.3
-
30
-
-
0028920041
-
Recombinant Rat CBF-C, the Third Subunit of CBF/NFY, Allows Formation of a Protein-DNA Complex with CBF-A and CBF-B and with Yeast HAP2 and HAP3
-
S. Sinha, S.N. Maity, J. Lu, and B. Crombrugghe, "Recombinant Rat CBF-C, the Third Subunit of CBF/NFY, Allows Formation of a Protein-DNA Complex with CBF-A and CBF-B and with Yeast HAP2 and HAP3," Proc. Nat'l Academy of Sciences, vol. 92, no. 5, pp. 1624-1628, 1995.
-
(1995)
Proc. Nat'l Academy of Sciences
, vol.92
, Issue.5
, pp. 1624-1628
-
-
Sinha, S.1
Maity, S.N.2
Lu, J.3
Crombrugghe, B.4
-
33
-
-
0033289316
-
An Exact Method for Finding Short Motifs in Sequences with Application to the Ribosome Binding Site Problem
-
M. Tompa, "An Exact Method for Finding Short Motifs in Sequences with Application to the Ribosome Binding Site Problem," Proc. Seventh Int'l Conf. Intelligent Systems for Molecular Biology, pp. 262-271, 1999.
-
(1999)
Proc. Seventh Int'l Conf. Intelligent Systems for Molecular Biology
, pp. 262-271
-
-
Tompa, M.1
-
34
-
-
0027381928
-
Mutations in Yeast HAP2 HAP3 Define a Hybrid CCAAT Box Binding Domain
-
Y. Xing, J.D. Fikes, and L. Guarente, "Mutations in Yeast HAP2 HAP3 Define a Hybrid CCAAT Box Binding Domain," EMBO J., vol. 12, pp. 4647-4655, 1993.
-
(1993)
EMBO J
, vol.12
, pp. 4647-4655
-
-
Xing, Y.1
Fikes, J.D.2
Guarente, L.3
-
35
-
-
0033524954
-
Analysis of Zinc Fingers Optimized via Phage Display: Evaluating the Utility of a Recognition Code
-
S. Wolfe, H. Greisman, E. Ramm, and C. Pabo, "Analysis of Zinc Fingers Optimized via Phage Display: Evaluating the Utility of a Recognition Code," J. Molecular Biology, vol. 285, no. 5, pp. 1917-1934, 1999.
-
(1999)
J. Molecular Biology
, vol.285
, Issue.5
, pp. 1917-1934
-
-
Wolfe, S.1
Greisman, H.2
Ramm, E.3
Pabo, C.4
-
36
-
-
2442478445
-
Finding Short DNA Motifs Using Permuted Markov Models
-
X. Zhao, H. Huang, and T.P. Speed, "Finding Short DNA Motifs Using Permuted Markov Models," Proc Ann. Int'l Conf. Research in Computational Molecular Biology (RECOMB '04), pp. 68-75, 2004.
-
(2004)
Proc Ann. Int'l Conf. Research in Computational Molecular Biology (RECOMB '04)
, pp. 68-75
-
-
Zhao, X.1
Huang, H.2
Speed, T.P.3
-
37
-
-
85142131297
-
-
J. Zhu and M. Zhang, SCPD: A Promoter Database of the Yeast Saccharomyces cerevisiae, Bioinformatics, 15, pp. 563-577, http://cgsigma.cshl.org/jian/, 1999.
-
J. Zhu and M. Zhang, "SCPD: A Promoter Database of the Yeast Saccharomyces cerevisiae," Bioinformatics, vol. 15, pp. 563-577, http://cgsigma.cshl.org/jian/, 1999.
-
-
-
-
38
-
-
38949198840
-
-
TRANSFAC Database
-
TRANSFAC Database, http://www.gene-regulation.com/pub/databases.html, 2007.
-
(2007)
-
-
|