-
1
-
-
21144439147
-
Assessing computational tools for the discovery of transcription factor binding sites
-
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. Biotech., 23, 137-144.
-
(2005)
Nat. Biotech.
, vol.23
, pp. 137-144
-
-
Tompa, M.1
Li, N.2
Bailey, T.L.3
Church, G.M.4
Moor, B.D.5
Eskin, E.6
Favorov, A.V.7
Frith, M.C.8
Fu, Y.9
Kent, W.J.10
-
2
-
-
0018199224
-
DNAse footprinting: A simple method for the detection of protein-DNA binding specificity
-
Galas,D.J. and Schmitz,A. (1987) DNAse footprinting: a simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res., 5, 3157-3170.
-
(1987)
Nucleic Acids Res.
, vol.5
, pp. 3157-3170
-
-
Galas, D.J.1
Schmitz, A.2
-
3
-
-
0019877067
-
A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: Application to components of the Escherichia coli lactose operon regulatory system
-
Garner,M.M. and Revzin,A. (1981) A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: application to components of the Escherichia coli lactose operon regulatory system. Nucleic Acids Res., 9, 3047-3060.
-
(1981)
Nucleic Acids Res.
, vol.9
, pp. 3047-3060
-
-
Garner, M.M.1
Revzin, A.2
-
4
-
-
0034704248
-
Genome-wide location and function of DNA binding proteins
-
Ren,B., Robert,F., Wyrick,J.J., Aparicio,O., Jennings,E.G., Simon,I., Zeitlinger,J., Schreiber,J., Hannett,N., Kanin,E. et al. (2000) Genome-wide location and function of DNA binding proteins. Science, 290, 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
Kanin, E.10
-
5
-
-
34250159524
-
Genome-wide mapping of in vivo protein-DNA interactions
-
Johnson,D.S., Mortazavi,A., Myers,R.M. and Wold,B. (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science, 316, 1497-1502.
-
(2007)
Science
, vol.316
, pp. 1497-1502
-
-
Johnson, D.S.1
Mortazavi, A.2
Myers, R.M.3
Wold, B.4
-
6
-
-
0036324753
-
An algorithm for finding protein-DNA binding sites with applications to chromatinimmunoprecipitation microarray experiments
-
Aug
-
Liu,X.S., Brutlag,D.L. and Liu,J.S. (Aug, 2002) An algorithm for finding protein-DNA binding sites with applications to chromatinimmunoprecipitation microarray experiments. Nat. Biotechnol., 20, 835-839.
-
(2002)
Nat. Biotechnol.
, vol.20
, pp. 835-839
-
-
Liu, X.S.1
Brutlag, D.L.2
Liu, J.S.3
-
7
-
-
33750882505
-
Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities
-
Nov
-
Berger,M.F., Philippakis,A.A., Qureshi,A.M., He,F.S., Estep,P.W. and Bulyk,M.L. (Nov, 2006) Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat. Biotechnol., 24, 1429-1435.
-
(2006)
Nat. Biotechnol.
, vol.24
, pp. 1429-1435
-
-
Berger, M.F.1
Philippakis, A.A.2
Qureshi, A.M.3
He, F.S.4
Estep, P.W.5
Bulyk, M.L.6
-
8
-
-
77956654773
-
De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis
-
Fordyce,P.M., Gerber,D., Tran,D., Zheng,J., Li,H., DeRisi,J.L. and Quake,S.R. (2010) De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis. Nat. Biotechnol., 28, 970-975.
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 970-975
-
-
Fordyce, P.M.1
Gerber, D.2
Tran, D.3
Zheng, J.4
Li, H.5
Derisi, J.L.6
Quake, S.R.7
-
9
-
-
70350340058
-
Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling
-
Hu,S., Xie,Z., Onishi,A., Yu,X., Jiang,L., Lin,J., Rho,H.S., Woodard,C., Wang,H., Jeong,J.S. et al. (2009) Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling. Cell, 139, 610-622.
-
(2009)
Cell
, vol.139
, pp. 610-622
-
-
Hu, S.1
Xie, Z.2
Onishi, A.3
Yu, X.4
Jiang, L.5
Lin, J.6
Rho, H.S.7
Woodard, C.8
Wang, H.9
Jeong, J.S.10
-
10
-
-
33745614618
-
Linking DNA-binding proteins to their recognition sequences by using protein microarrays
-
Ho,S.W., Jona,G., Chen,C.T., Johnston,M. and Snyder,M. (2006) Linking DNA-binding proteins to their recognition sequences by using protein microarrays. Proc. Natl Acad. Sci. USA, 103, 9940-9945.
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 9940-9945
-
-
Ho, S.W.1
Jona, G.2
Chen, C.T.3
Johnston, M.4
Snyder, M.5
-
11
-
-
33644876958
-
TRANSFAC and its module TRANSCompel: Transcriptional gene regulation in eukaryotes
-
Matys,V., Kel-Margoulis,O.V., Fricke,E., Liebich,I., Land,S., Barre-Dirrie,A., Reuter,I., Chekmenev,D., Krull,M., Hornischer,K. et al. (2006) TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res., 34, 108-110.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 108-110
-
-
Matys, V.1
Kel-Margoulis, O.V.2
Fricke, E.3
Liebich, I.4
Land, S.5
Barre-Dirrie, A.6
Reuter, I.7
Chekmenev, D.8
Krull, M.9
Hornischer, K.10
-
12
-
-
75549083247
-
JASPAR 2010: The greatly expanded open-access database of transcription factor binding profiles
-
Portales-Casamar,E., Thongjuea,S., Kwon,A.T., Arenillas,D., Zhao,X., Valen,E., Yusuf,D., Lenhard,B., Wasserman,W.W. and Sandelin,A. (2010) JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res., 38, D105-D110.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Portales-Casamar, E.1
Thongjuea, S.2
Kwon, A.T.3
Arenillas, D.4
Zhao, X.5
Valen, E.6
Yusuf, D.7
Lenhard, B.8
Wasserman, W.W.9
Sandelin, A.10
-
13
-
-
9144257886
-
The Pfam protein families database
-
Bateman,A., Coin,L., Durbin,R., Finn,R.D., Hollich,V., GrifRths- Jones,S., Khanna,A., Marshall,M., Moxon,S., Sonnhammer,E.L.L. et al. (2004) The Pfam protein families database. Nucleic Acids Res., 32, D138-D141.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Bateman, A.1
Coin, L.2
Durbin, R.3
Finn, R.D.4
Hollich, V.5
Grifrths- Jones, S.6
Khanna, A.7
Marshall, M.8
Moxon, S.9
Sonnhammer, E.L.L.10
-
14
-
-
78651303899
-
UniPROBE, update 2011: Expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions
-
Robasky,K. and Bulyk,M.L. (2011) UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions. Nucleic Acids Res., 39, D124-D128.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Robasky, K.1
Bulyk, M.L.2
-
15
-
-
84862214168
-
ScerTF: A comprehensive database of benchmarked position weight matrices for Saccharomyces species
-
Spivak,A.T. and Stormo,G.D. (2012) ScerTF: a comprehensive database of benchmarked position weight matrices for Saccharomyces species. Nucleic Acids Res., 40, D162-D168.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Spivak, A.T.1
Stormo, G.D.2
-
16
-
-
75549090998
-
FlyTF: Improved annotation and enhanced functionality of the Drosophila transcription factor database
-
Pfreundt,U., James,D.P., Tweedie,S., Wilson,D., Teichmann,S.A. and Adryan,B. (2010) FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database. Nucleic Acids Res., 38, D443-D447.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Pfreundt, U.1
James, D.P.2
Tweedie, S.3
Wilson, D.4
Teichmann, S.A.5
Adryan, B.6
-
17
-
-
84862169505
-
YeTFaSCo: A database of evaluated yeast transcription factor sequence specificities
-
deBoer,C.G. and Hughes,T.R. (2012) YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities. Nucleic Acids Res., 40, D169-D179.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Deboer, C.G.1
Hughes, T.R.2
-
18
-
-
77950472891
-
HPDI: A database of experimental human protein-DNA interactions
-
Xie,Z., Hu,S., Blackshaw,S., Zhu,H. and Qian,J. (2010) hPDI: a database of experimental human protein-DNA interactions. Bioinformatics, 26, 287-289.
-
(2010)
Bioinformatics
, vol.26
, pp. 287-289
-
-
Xie, Z.1
Hu, S.2
Blackshaw, S.3
Zhu, H.4
Qian, J.5
-
19
-
-
65249169219
-
TFCat: The curated catalog of mouse and human transcription factors
-
Fulton,D.L., Sundararajan,S., Badis,G., Hughes,T.R., Wasserman,W.W., Roach,J.C. and Sladek,R. (2009) TFCat: the curated catalog of mouse and human transcription factors. Genome Biol., 10, R29.
-
(2009)
Genome Biol.
, vol.10
-
-
Fulton, D.L.1
Sundararajan, S.2
Badis, G.3
Hughes, T.R.4
Wasserman, W.W.5
Roach, J.C.6
Sladek, R.7
-
20
-
-
0033647653
-
An overview of the structures of protein-DNA complexes
-
Luscombe,N.M., Austin,S.E., Berman,H.M. and Thornton,J.M. (2000) An overview of the structures of protein-DNA complexes. Genome Biol., 1, REVIEWS001.
-
(2000)
Genome Biol.
, vol.1
-
-
Luscombe, N.M.1
Austin, S.E.2
Berman, H.M.3
Thornton, J.M.4
-
21
-
-
0035393302
-
Amino acid-base interactions: A three-dimensional analysis of protein-DNA interactions at an atomic level
-
Luscombe,N.M., Laskowski,R.A. and Thornton,J.M. (2001) Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Res., 29, 2860-2874.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 2860-2874
-
-
Luscombe, N.M.1
Laskowski, R.A.2
Thornton, J.M.3
-
22
-
-
0037439997
-
Structural classification of zinc fingers: Survey and summary
-
Krishna,S.S., Majumdar,I. and Grishin,N.V. (2003) Structural classification of zinc fingers: survey and summary. Nucleic Acids Res., 31, 532-550.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 532-550
-
-
Krishna, S.S.1
Majumdar, I.2
Grishin, N.V.3
-
23
-
-
0036074510
-
Protein-DNA interactions: Amino acid conservation and the effects of mutations on binding specificity
-
Luscombe,N.M. and Thornton,J.M. (2002) Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity. J. Mol. Biol., 320, 991-1009.
-
(2002)
J. Mol. Biol.
, vol.320
, pp. 991-1009
-
-
Luscombe, N.M.1
Thornton, J.M.2
-
24
-
-
0033574510
-
Protein-DNA interactions: A structural analysis
-
Jones,S., van Heyningen,P., Berman,H.M. and Thornton,J.M. (1999) Protein-DNA interactions: a structural analysis. J. Mol. Biol., 287, 877-896.
-
(1999)
J. Mol. Biol.
, vol.287
, pp. 877-896
-
-
Jones, S.1
Van Heyningen, P.2
Berman, H.M.3
Thornton, J.M.4
-
25
-
-
0346258292
-
Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins
-
Jones,S., Shanahan,H.P., Berman,H.M. and Thornton,J.M. (2003) Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins. Nucleic Acids Res., 31, 7189-7198.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 7189-7198
-
-
Jones, S.1
Shanahan, H.P.2
Berman, H.M.3
Thornton, J.M.4
-
26
-
-
33745317385
-
Enhancing the prediction of transcription factor binding sites by incorporating structural properties and nucleotide covariations
-
Gunewardena,S., Jeavons,P. and Zhang,Z. (2006) Enhancing the prediction of transcription factor binding sites by incorporating structural properties and nucleotide covariations. J. Comput. Biol., 13, 929-945.
-
(2006)
J. Comput. Biol.
, vol.13
, pp. 929-945
-
-
Gunewardena, S.1
Jeavons, P.2
Zhang, Z.3
-
27
-
-
20544460658
-
Protein-DNA recognition patterns and predictions
-
Sarai,A. and Kono,H. (2005) Protein-DNA recognition patterns and predictions. Annu. Rev. Biophys. Biomol. Struct., 34, 379-398.
-
(2005)
Annu. Rev. Biophys. Biomol. Struct.
, vol.34
, pp. 379-398
-
-
Sarai, A.1
Kono, H.2
-
28
-
-
47249118465
-
Extracting sequence features to predict protein-DNA interactions: A comparative study
-
Zhou,Q. and Liu,J.S. (2008) Extracting sequence features to predict protein-DNA interactions: a comparative study. Nucleic Acids Res., 36, 4137-4148.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 4137-4148
-
-
Zhou, Q.1
Liu, J.S.2
-
29
-
-
1542400269
-
Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information
-
Ahmad,S., Gromiha,M.M. and Sarai,A. (2004) Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information. Bioinformatics, 20, 477-486.
-
(2004)
Bioinformatics
, vol.20
, pp. 477-486
-
-
Ahmad, S.1
Gromiha, M.M.2
Sarai, A.3
-
30
-
-
54549096025
-
Protein- DNA interactions: Structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins
-
Ahmad,S., Keskin,O., Sarai,A. and Nussinov,R. (2008) Protein- DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins. Nucleic Acids Res., 36, 5922-5932.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 5922-5932
-
-
Ahmad, S.1
Keskin, O.2
Sarai, A.3
Nussinov, R.4
-
31
-
-
27544474147
-
Computational discovery of transcriptional regulatory rules
-
Pham,T.H., Clemente,J.C., Satou,K. and Ho,T.B. (2005) Computational discovery of transcriptional regulatory rules. Bioinformatics, 21, 101-107.
-
(2005)
Bioinformatics
, vol.21
, pp. 101-107
-
-
Pham, T.H.1
Clemente, J.C.2
Satou, K.3
Ho, T.B.4
-
32
-
-
34547852238
-
Prediction of DNAbinding residues from sequence
-
Ofran,Y., Mysore,V. and Rost,B. (2007) Prediction of DNAbinding residues from sequence. Bioinformatics, 23, i347-i353.
-
(2007)
Bioinformatics
, vol.23
-
-
Ofran, Y.1
Mysore, V.2
Rost, B.3
-
33
-
-
79960092508
-
Generalizing and learning protein-DNA binding sequence representations by an evolutionary algorithm
-
Wong,K.C., Peng,C., Wong,M.H. and Leung,K.S. (2011) Generalizing and learning protein-DNA binding sequence representations by an evolutionary algorithm. Soft. Comput., 15, 1631-1642.
-
(2011)
Soft. Comput.
, vol.15
, pp. 1631-1642
-
-
Wong, K.C.1
Peng, C.2
Wong, M.H.3
Leung, K.S.4
-
34
-
-
78049408050
-
Discovering protein-DNA binding sequence patterns using association rule mining
-
Leung,K.S., Wong,K.C., Chan,T.M., Wong,M.H., Lee,K.H., Lau,C.K. and Tsui,S.K. (2010) Discovering protein-DNA binding sequence patterns using association rule mining. Nucleic Acids Res., 38, 6324-6337.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 6324-6337
-
-
Leung, K.S.1
Wong, K.C.2
Chan, T.M.3
Wong, M.H.4
Lee, K.H.5
Lau, C.K.6
Tsui, S.K.7
-
35
-
-
79951538869
-
Discovering approximateassociated sequence patterns for protein-DNA interactions
-
Chan,T.M., Wong,K.C., Lee,K.H., Wong,M.H., Lau,C.K., Tsui,S.K. and Leung,K.S. (2011) Discovering approximateassociated sequence patterns for protein-DNA interactions. Bioinformatics, 27, 471-478.
-
(2011)
Bioinformatics
, vol.27
, pp. 471-478
-
-
Chan, T.M.1
Wong, K.C.2
Lee, K.H.3
Wong, M.H.4
Lau, C.K.5
Tsui, S.K.6
Leung, K.S.7
-
36
-
-
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
-
37
-
-
0041853625
-
MATCH: A tool for searching transcription factor binding sites in DNA sequences
-
Kel,A.E., Goessling,E., Reuter,I., Cheremushkin,E., Kel- Margoulis,O.V. and Wingender,E. (2003) MATCH: a tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res., 31, 3576-3579.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3576-3579
-
-
Kel, A.E.1
Goessling, E.2
Reuter, I.3
Cheremushkin, E.4
Kel- Margoulis, O.V.5
Wingender, E.6
-
38
-
-
0023678091
-
Computer methods for analyzing sequence recognition of nucleic acids
-
Stormo,G.D. (1988) Computer methods for analyzing sequence recognition of nucleic acids. Annu. Rev. BioChem., 17, 241-263.
-
(1988)
Annu. Rev. BioChem.
, vol.17
, pp. 241-263
-
-
Stormo, G.D.1
-
39
-
-
0346490298
-
Computational discovery of gene regulatory binding motifs: A Bayesian perspective
-
Jensen,S.T., Liu,X.S., Zhou,Q. and Liu,J.S. (2004) Computational discovery of gene regulatory binding motifs: a Bayesian perspective. Stat. Sci., 19, 188-204.
-
(2004)
Stat. Sci.
, vol.19
, pp. 188-204
-
-
Jensen, S.T.1
Liu, X.S.2
Zhou, Q.3
Liu, J.S.4
-
40
-
-
34347339593
-
Improved benchmarks for computational motif discovery
-
Sandve,G.K., Abul,O., Walseng,V. and Drablos,F. (2007) Improved benchmarks for computational motif discovery. BMC Bioinformatics, 8, 193.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 193
-
-
Sandve, G.K.1
Abul, O.2
Walseng, V.3
Drablos, F.4
-
41
-
-
0034628901
-
Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae
-
Hughes,J.D., Estep,P.W., Tavazoie,S. and Church,G.M. (2000) Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J. Mol. Biol., 296, 1205-1214.
-
(2000)
J. Mol. Biol.
, vol.296
, pp. 1205-1214
-
-
Hughes, J.D.1
Estep, P.W.2
Tavazoie, S.3
Church, G.M.4
-
42
-
-
0036137323
-
A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling
-
Thijs,G., Lescot,M., Marchal,K., Rombauts,S., DeMoor,B., Rouze,P. and Moreau,Y. (2001) A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling. Bioinformatics, 17, 1113-1122.
-
(2001)
Bioinformatics
, vol.17
, pp. 1113-1122
-
-
Thijs, G.1
Lescot, M.2
Marchal, K.3
Rombauts, S.4
Demoor, B.5
Rouze, P.6
Moreau, Y.7
-
43
-
-
4544295425
-
Environmentally induced foregut remodeling by PHA-4/FoxA and DAF-12/NHR
-
Ao,W., Gaudet,J., Kent,W.J., Muttumu,S. and Mango,S.E. (2004) Environmentally induced foregut remodeling by PHA-4/FoxA and DAF-12/NHR. Science, 305, 1743-1746.
-
(2004)
Science
, vol.305
, pp. 1743-1746
-
-
Ao, W.1
Gaudet, J.2
Kent, W.J.3
Muttumu, S.4
Mango, S.E.5
-
45
-
-
0033655171
-
ANN-Spec: A method for discovering transcription factor binding sites with improved specificity
-
Workman,C.T. and Stormo,G.D. (2000) ANN-Spec: a method for discovering transcription factor binding sites with improved specificity. Pac. Symp. Biocomput., 467-478.
-
(2000)
Pac. Symp. Biocomput.
, pp. 467-478
-
-
Workman, C.T.1
Stormo, G.D.2
-
46
-
-
19544379737
-
A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length
-
Favorov,A.V., Gelfand,M.S., Gerasimova,A.V., Ravcheev,D.A., Mironov,A.A. and Makeev,V.J. (2005) A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length. Bioinformatics, 21, 2240-2245.
-
(2005)
Bioinformatics
, vol.21
, pp. 2240-2245
-
-
Favorov, A.V.1
Gelfand, M.S.2
Gerasimova, A.V.3
Ravcheev, D.A.4
Mironov, A.A.5
Makeev, V.J.6
-
47
-
-
38849109559
-
TFBS identification based on genetic algorithm with combined representations and adaptive post-processing
-
Chan,T.M., Leung,K.S. and Lee,K.H. (2008) TFBS identification based on genetic algorithm with combined representations and adaptive post-processing. Bioinformatics, 24, 341-349.
-
(2008)
Bioinformatics
, vol.24
, pp. 341-349
-
-
Chan, T.M.1
Leung, K.S.2
Lee, K.H.3
-
48
-
-
0032826179
-
Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
-
Hertz,G.Z. and Stormo,G.D. (1999) Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics, 15, 563-577.
-
(1999)
Bioinformatics
, vol.15
, pp. 563-577
-
-
Hertz, G.Z.1
Stormo, G.D.2
-
49
-
-
1242264319
-
Finding functional sequence elements by multiple local alignment
-
Frith,M.C., Hansen,U., Spouge,J.L. and Weng,Z. (2004) Finding functional sequence elements by multiple local alignment. Nucleic Acids Res., 32, 189-200.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 189-200
-
-
Frith, M.C.1
Hansen, U.2
Spouge, J.L.3
Weng, Z.4
-
50
-
-
0344376570
-
Finding composite regulatory patterns in DNA sequences
-
Eskin,E. and Pevzner,P.A. (2002) Finding composite regulatory patterns in DNA sequences. Bioinformatics, 18(Suppl. 1), S354-S363.
-
(2002)
Bioinformatics
, vol.18 SUPPL. 1
-
-
Eskin, E.1
Pevzner, P.A.2
-
51
-
-
0032483307
-
Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies
-
van Helden,J., Andre,B. and Collado-Vides,J. (1998) Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J. Mol. Biol., 281, 827-842.
-
(1998)
J. Mol. Biol.
, vol.281
, pp. 827-842
-
-
Van Helden, J.1
Andre, B.2
Collado-Vides, J.3
-
52
-
-
39149128313
-
A hybrid model for robust detection of transcription factor binding sites
-
Gunewardena,S. and Zhang,Z. (2008) A hybrid model for robust detection of transcription factor binding sites. Bioinformatics, 24, 484-491.
-
(2008)
Bioinformatics
, vol.24
, pp. 484-491
-
-
Gunewardena, S.1
Zhang, Z.2
-
53
-
-
28444456845
-
Rare events and conditional events on random strings
-
Régnier,M. and Denise,A. (2004) Rare events and conditional events on random strings. Discrete Math., 6, 191-214.
-
(2004)
Discrete Math.
, vol.6
, pp. 191-214
-
-
Régnier, M.1
Denise, A.2
-
54
-
-
3242884167
-
Weeder Web: Discovery of transcription factor binding sites in a set of sequences from co-regulated genes
-
Pavesi,G., Mereghetti,P., Mauri,G. and Pesole,G. (2004) Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes. Nucleic Acids Res., 32, 199-203.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 199-203
-
-
Pavesi, G.1
Mereghetti, P.2
Mauri, G.3
Pesole, G.4
-
55
-
-
0042905768
-
YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation
-
Sinha,S. and Tompa,M. (2003) YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation. Nucleic Acids Res., 31, 3586-3588.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3586-3588
-
-
Sinha, S.1
Tompa, M.2
-
56
-
-
67649982744
-
Diversity and complexity in DNA recognition by transcription factors
-
Badis,G., Berger,M.F., Philippakis,A.A., Talukder,S., Gehrke,A.R., Jaeger,S.A., Chan,T., Metzler,G., Vedenko,A., Chen,X. et al. (2009) Diversity and complexity in DNA recognition by transcription factors. Science, 324, 1720-1723.
-
(2009)
Science
, vol.324
, pp. 1720-1723
-
-
Badis, G.1
Berger, M.F.2
Philippakis, A.A.3
Talukder, S.4
Gehrke, A.R.5
Jaeger, S.A.6
Chan, T.7
Metzler, G.8
Vedenko, A.9
Chen, X.10
-
57
-
-
34547844155
-
RankMotif++: A motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors
-
Chen,X., Hughes,T.R. and Morris,Q. (2007) RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors. Bioinformatics, 23, i72-i79.
-
(2007)
Bioinformatics
, vol.23
-
-
Chen, X.1
Hughes, T.R.2
Morris, Q.3
-
58
-
-
29144500327
-
Profiling condition-specific, genome-wide regulation of mRNA stability in yeast
-
Foat,B.C., Houshmandi,S.S., Olivas,W.M. and Bussemaker,H.J. (2005) Profiling condition-specific, genome-wide regulation of mRNA stability in yeast. Proc. Natl Acad. Sci. USA, 102, 17675-17680.
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 17675-17680
-
-
Foat, B.C.1
Houshmandi, S.S.2
Olivas, W.M.3
Bussemaker, H.J.4
-
59
-
-
33746691336
-
Extensive low-affinity transcriptional interactions in the yeast genome
-
Tanay,A. (2006) Extensive low-affinity transcriptional interactions in the yeast genome. Genome Res., 16, 962-972.
-
(2006)
Genome Res.
, vol.16
, pp. 962-972
-
-
Tanay, A.1
-
60
-
-
79958115193
-
Quantitative analysis demonstrates most transcription factors require only simple models of specificity
-
Zhao,Y. and Stormo,G.D. (2011) Quantitative analysis demonstrates most transcription factors require only simple models of specificity. Nat. Biotechnol., 29, 480-483.
-
(2011)
Nat. Biotechnol.
, vol.29
, pp. 480-483
-
-
Zhao, Y.1
Stormo, G.D.2
-
61
-
-
84873594686
-
Evaluation of methods for modeling transcription factor sequence specificity
-
Weirauch,M.T., Cote,A., Norel,R., Annala,M., Zhao,Y., Riley,T.R., Saez-Rodriguez,J., Cokelaer,T., Vedenko,A., Talukder,S. et al. (2013) Evaluation of methods for modeling transcription factor sequence specificity. Nat. Biotechnol., 31, 126-134.
-
(2013)
Nat. Biotechnol.
, vol.31
, pp. 126-134
-
-
Weirauch, M.T.1
Cote, A.2
Norel, R.3
Annala, M.4
Zhao, Y.5
Riley, T.R.6
Saez-Rodriguez, J.7
Cokelaer, T.8
Vedenko, A.9
Talukder, S.10
-
62
-
-
0023147228
-
Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters
-
Berg,O.G. and von Hippel,P.H. (1987) Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J. Mol. Biol., 193, 723-750.
-
(1987)
J. Mol. Biol.
, vol.193
, pp. 723-750
-
-
Berg, O.G.1
Von Hippel, P.H.2
-
63
-
-
79955372696
-
Maximally efficient modeling of DNA sequence motifs at all levels of complexity
-
Stormo,G.D. (2011) Maximally efficient modeling of DNA sequence motifs at all levels of complexity. Genetics, 187, 1219-1224.
-
(2011)
Genetics
, vol.187
, pp. 1219-1224
-
-
Stormo, G.D.1
-
64
-
-
0003516147
-
-
Cambridge University Press
-
Durbin,R., Eddy,S.R., Krogh,A. and Mitchison,G. (1998) Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press.
-
(1998)
Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids
-
-
Durbin, R.1
Eddy, S.R.2
Krogh, A.3
Mitchison, G.4
-
65
-
-
80052477053
-
-
Morgan Kaufmann Publishers Inc, San Francisco, CA, USA
-
Rabiner,L.R. (1990) Readings in Speech Recognition. Chapter A Tutorial on Hidden Markov Models and Selected Applications in Speech Recognition. Morgan Kaufmann Publishers Inc, San Francisco, CA, USA, pp. 267-296.
-
(1990)
Readings in Speech Recognition. Chapter A Tutorial on Hidden Markov Models and Selected Applications in Speech Recognition
, pp. 267-296
-
-
Rabiner, L.R.1
-
66
-
-
25144450883
-
Genome-wide analysis of mouse transcripts using exon microarrays and factor graphs
-
Frey,B.J., Mohammad,N., Morris,Q.D., Zhang,W., Robinson,M.D., Mnaimneh,S., Chang,R., Pan,Q., Sat,E., Rossant,J. et al. (2005) Genome-wide analysis of mouse transcripts using exon microarrays and factor graphs. Nat. Genet., 37, 991-996.
-
(2005)
Nat. Genet.
, vol.37
, pp. 991-996
-
-
Frey, B.J.1
Mohammad, N.2
Morris, Q.D.3
Zhang, W.4
Robinson, M.D.5
Mnaimneh, S.6
Chang, R.7
Pan, Q.8
Sat, E.9
Rossant, J.10
-
67
-
-
33847172327
-
Clustering by passing messages between data points
-
Frey,B.J. and Dueck,D. (2007) Clustering by passing messages between data points. Science, 315, 972-976.
-
(2007)
Science
, vol.315
, pp. 972-976
-
-
Frey, B.J.1
Dueck, D.2
-
68
-
-
77952029221
-
Deciphering the splicing code
-
Barash,Y., Calarco,J.A., Gao,W., Pan,Q., Wang,X., Shai,O., Blencowe,B.J. and Frey,B.J. (2010) Deciphering the splicing code. Nature, 465, 53-59.
-
(2010)
Nature
, vol.465
, pp. 53-59
-
-
Barash, Y.1
Calarco, J.A.2
Gao, W.3
Pan, Q.4
Wang, X.5
Shai, O.6
Blencowe, B.J.7
Frey, B.J.8
-
69
-
-
0035246323
-
On the optimality of solutions of the max-product belief-propagation algorithm in arbitrary graphs
-
Weiss,Y. and Freeman,W.T. (2001) On the optimality of solutions of the max-product belief-propagation algorithm in arbitrary graphs. IEEE Trans. Inf. Theory., 47, 736-744.
-
(2001)
IEEE Trans. Inf. Theory.
, vol.47
, pp. 736-744
-
-
Weiss, Y.1
Freeman, W.T.2
-
71
-
-
34547569191
-
STAMP: A web tool for exploring DNA-binding motif similarities
-
Mahony,S. and Benos,P.V. (2007) STAMP: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Res., 35, W253-W258.
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Mahony, S.1
Benos, P.V.2
-
72
-
-
0027092288
-
The DNA binding specificity of the bipartite POU domain and its subdomains
-
Verrijzer,C.P., Alkema,M.J., van Weperen,W.W., VanLeeuwen,H.C., Strating,M.J. and vander Vliet,P.C. (1992) The DNA binding specificity of the bipartite POU domain and its subdomains. EMBO J., 11, 4993-5003.
-
(1992)
EMBO J.
, vol.11
, pp. 4993-5003
-
-
Verrijzer, C.P.1
Alkema, M.J.2
Van Weperen, W.W.3
Vanleeuwen, H.C.4
Strating, M.J.5
Vander Vliet, P.C.6
-
73
-
-
83755196322
-
Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights
-
Gordan,R., Murphy,K.F., McCord,R.P., Zhu,C., Vedenko,A. and Bulyk,M.L. (2011) Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights. Genome Biol., 12, R125.
-
(2011)
Genome Biol.
, vol.12
-
-
Gordan, R.1
Murphy, K.F.2
McCord, R.P.3
Zhu, C.4
Vedenko, A.5
Bulyk, M.L.6
-
74
-
-
79958153978
-
Jury remains out on simple models of transcription factor specificity
-
Morris,Q., Bulyk,M.L. and Hughes,T.R. (2011) Jury remains out on simple models of transcription factor specificity. Nat. Biotechnol., 29, 483-484.
-
(2011)
Nat. Biotechnol.
, vol.29
, pp. 483-484
-
-
Morris, Q.1
Bulyk, M.L.2
Hughes, T.R.3
|