-
1
-
-
1842433988
-
Computational detection of cis-regulatory modules
-
Aerts S, van Loo P, Thijs G, Moreau Y, De Moor B (2003) Computational detection of cis-regulatory modules. Bioinformatics 19(Suppl 2): 5-14.
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL. 2
, pp. 5-14
-
-
Aerts, S.1
van Loo, P.2
Thijs, G.3
Moreau, Y.4
de Moor, B.5
-
3
-
-
1542400269
-
Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information
-
doi: 10. 1093/bioinformatics/btg432
-
Ahmad S, Gromiha MM, Sarai A (2004) Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information. Bioinformatics 20(4): 477-486. doi: 10. 1093/bioinformatics/btg432.
-
(2004)
Bioinformatics
, vol.20
, Issue.4
, pp. 477-486
-
-
Ahmad, S.1
Gromiha, M.M.2
Sarai, A.3
-
4
-
-
54549096025
-
Protein-DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins
-
Ahmad S, Keskin O, Sarai A, 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
-
6
-
-
4043156577
-
Searching for statistically significant regulatory modules
-
Bailey TL, Noble WS (2003) Searching for statistically significant regulatory modules. Bioinformatics 19(Suppl 2): 16-25.
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL. 2
, pp. 16-25
-
-
Bailey, T.L.1
Noble, W.S.2
-
8
-
-
9144257886
-
The pfam protein families database
-
Bateman A, Coin L, Durbin R, Finn RD, Hollich V, GrifRths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer ELL, Studholme DJ, Yeats C, Eddy SR (2004) The pfam protein families database. Nucleic Acids Res 32: D138-D141.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 138-141
-
-
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
Studholme, D.J.11
Yeats, C.12
Eddy, S.R.13
-
9
-
-
0033954256
-
The protein data bank
-
doi: 10. 1093/nar/28. 1. 235
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The protein data bank. Nucleic Acids Res 28(1): 235-242. doi: 10. 1093/nar/28. 1. 235.
-
(2000)
Nucleic Acids Res
, vol.28
, Issue.1
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
10
-
-
33745152719
-
Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression
-
Blanchette M, Bataille AR, Chen X, Poitras C, Laganiere J, Lefebvre C, Deblois G, Giguere V, Ferretti V, Bergeron D, Coulombe B, Robert F (2006) Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. Genome Res 16: 656-668.
-
(2006)
Genome Res
, vol.16
, pp. 656-668
-
-
Blanchette, M.1
Bataille, A.R.2
Chen, X.3
Poitras, C.4
Laganiere, J.5
Lefebvre, C.6
Deblois, G.7
Giguere, V.8
Ferretti, V.9
Bergeron, D.10
Coulombe, B.11
Robert, F.12
-
11
-
-
0031162961
-
Dynamic itemset counting and implication rules for market basket data
-
doi: 10. 1145/253262. 253325
-
Brin S, Motwani R, Ullman JD, Tsur S (1997) Dynamic itemset counting and implication rules for market basket data. SIGMOD Rec 26(2): 255-264. doi: 10. 1145/253262. 253325.
-
(1997)
SIGMOD Rec
, vol.26
, Issue.2
, pp. 255-264
-
-
Brin, S.1
Motwani, R.2
Ullman, J.D.3
Tsur, S.4
-
12
-
-
0037446851
-
Enhanced protein domain discovery by using language modeling techniques from speech recognition
-
Coin L, Bateman A, Durbin R (2003) Enhanced protein domain discovery by using language modeling techniques from speech recognition. Proc Natl Acad Sci USA 100: 4516-4520.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 4516-4520
-
-
Coin, L.1
Bateman, A.2
Durbin, R.3
-
13
-
-
0018199224
-
DNAse footprinting: a simple method for the detection of protein-DNA binding specificity
-
Galas DJ, Schmitz A (1987) DNAse footprinting: a simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res 5(9): 3157-3170.
-
(1987)
Nucleic Acids Res
, vol.5
, Issue.9
, pp. 3157-3170
-
-
Galas, D.J.1
Schmitz, A.2
-
14
-
-
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 MM, 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(13): 3047-3060.
-
(1981)
Nucleic Acids Res
, vol.9
, Issue.13
, pp. 3047-3060
-
-
Garner, M.M.1
Revzin, A.2
-
19
-
-
38549107891
-
The 20 years of prosite
-
Hulo N, Bairoch A, Bulliard V, Cerutti L, Cuche BA, de Castro E, Lachaize C, Langendijk-Genevaux PS, Sigrist CJA (2008) The 20 years of prosite. Nucl Acids Res 36(Suppl 1): D245-D249.
-
(2008)
Nucl Acids Res
, vol.36
, Issue.SUPPL 1
, pp. 245-249
-
-
Hulo, N.1
Bairoch, A.2
Bulliard, V.3
Cerutti, L.4
Cuche, B.A.5
de Castro, E.6
Lachaize, C.7
Langendijk-Genevaux, P.S.8
Sigrist, C.J.A.9
-
20
-
-
0346490298
-
Computational discovery of gene regulatory binding motifs: a bayesian perspective
-
Jensen ST, Liu XS, Zhou Q, Liu JS (2004) Computational discovery of gene regulatory binding motifs: a bayesian perspective. Stat Sci 19(1): 188-204.
-
(2004)
Stat Sci
, vol.19
, Issue.1
, pp. 188-204
-
-
Jensen, S.T.1
Liu, X.S.2
Zhou, Q.3
Liu, J.S.4
-
23
-
-
0000718899
-
A map method for synthesis of combinational logic circuits
-
Karnaugh M (1953) A map method for synthesis of combinational logic circuits. Trans AIEE Commun Electron 72 (I): 593-599.
-
(1953)
Trans AIEE Commun Electron
, vol.72
, Issue.1
, pp. 593-599
-
-
Karnaugh, M.1
-
24
-
-
13544254744
-
Identifying combinatorial regulation of transcription factors and binding motifs
-
Kato M, Hata N, Banerjee N, Futcher B, Zhang MQ (2004) Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biol 5: R56.
-
(2004)
Genome Biol
, vol.5
-
-
Kato, M.1
Hata, N.2
Banerjee, N.3
Futcher, B.4
Zhang, M.Q.5
-
25
-
-
0035998754
-
TRANSCompel: a database on composite regulatory elements in eukaryotic genes
-
Kel-Margoulis OV, Kel AE, Reuter I, Deineko IV, Wingender E (2002) TRANSCompel: a database on composite regulatory elements in eukaryotic genes. Nucleic Acids Res 30: 332-334.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 332-334
-
-
Kel-Margoulis, O.V.1
Kel, A.E.2
Reuter, I.3
Deineko, I.V.4
Wingender, E.5
-
26
-
-
0028553359
-
The use of genetic programming to build queries for information retrieval
-
1994. IEEE World Congress on Computational Intelligence.doi: 10. 1109/ICEC. 1994. 349905
-
Kraft D, Petry F, Buckles B, Sadasivan T (1994) The use of genetic programming to build queries for information retrieval. In: Evolutionary Computation, 1994. IEEE World Congress on Computational Intelligence. Proceedings of the 1st IEEE conference, vol 1, pp 468-473. doi: 10. 1109/ICEC. 1994. 349905.
-
(1994)
Proceedings of the 1st IEEE conference
, vol.1
, pp. 468-473
-
-
Kraft, D.1
Petry, F.2
Buckles, B.3
Sadasivan, T.4
-
27
-
-
0034819935
-
A predictive model for regulatory sequences directing liver-specific transcription
-
Krivan W, Wasserman WW (2001) A predictive model for regulatory sequences directing liver-specific transcription. Genome Res 11: 1559-1566.
-
(2001)
Genome Res
, vol.11
, pp. 1559-1566
-
-
Krivan, W.1
Wasserman, W.W.2
-
28
-
-
0020475449
-
A simple method for displaying the hydropathic character of a protein
-
Kyte J, Doolittle RF (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157: 105-132.
-
(1982)
J Mol Biol
, vol.157
, pp. 105-132
-
-
Kyte, J.1
Doolittle, R.F.2
-
29
-
-
78049408050
-
-
Nucleic Acids Research (accepted)
-
Leung KS, Wong KC, Chan TM, Wong MH, Lee KH, Lau CK, Tsui SKW (2010) Discovering protein-DNA binding sequence patterns using association rule mining. Nucleic Acids Research (accepted).
-
(2010)
Discovering protein-DNA binding sequence patterns using association rule mining
-
-
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.W.7
-
30
-
-
0036715627
-
A species conserving genetic algorithm for multimodal function optimization
-
doi: 10. 1162/106365602760234081
-
Li JP, Balazs ME, Parks GT, Clarkson PJ (2002) A species conserving genetic algorithm for multimodal function optimization. Evol Comput 10(3): 207-234. doi: 10. 1162/106365602760234081.
-
(2002)
Evol Comput
, vol.10
, Issue.3
, pp. 207-234
-
-
Li, J.P.1
Balazs, M.E.2
Parks, G.T.3
Clarkson, P.J.4
-
31
-
-
0036324753
-
An algorithm for finding protein-DNA binding sites with applications to chromatinimmunoprecipitation microarray experiments
-
Liu XS, Brutlag DL, Liu JS (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
-
32
-
-
0036074510
-
Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity
-
Luscombe NM, Thornton JM (2002) Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity. J Mol Biol 320(5): 991-1009.
-
(2002)
J Mol Biol
, vol.320
, Issue.5
, pp. 991-1009
-
-
Luscombe, N.M.1
Thornton, J.M.2
-
33
-
-
33746748243
-
An overview of the structures of protein-DNA complexes
-
Luscombe NM, Austin SE, Berman HM, Thornton JM (2000) An overview of the structures of protein-DNA complexes. Genome Biol 1(1): 1-37.
-
(2000)
Genome Biol
, vol.1
, Issue.1
, pp. 1-37
-
-
Luscombe, N.M.1
Austin, S.E.2
Berman, H.M.3
Thornton, J.M.4
-
34
-
-
33646229522
-
Practical strategies for discovering regulatory DNA sequence motifs
-
MacIsaac KD, Fraenkel E (2006) Practical strategies for discovering regulatory DNA sequence motifs. PLoS Comput Biol 2(4): e36.
-
(2006)
PLoS Comput Biol
, vol.2
, Issue.4
-
-
Macisaac, K.D.1
Fraenkel, E.2
-
35
-
-
33644876958
-
TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes
-
Matys V, Kel-Margoulis O, Fricke E, Liebich I, Land S, Barre-Dirrie A, Reuter I, Chekmenev D, Krull M, Hornischer K, Voss N, Stegmaier P, Lewicki-Potapov B, Saxel H, Kel A, Wingender E (2006) TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res 34: D108-D110.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 108-110
-
-
Matys, V.1
Kel-Margoulis, O.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
Voss, N.11
Stegmaier, P.12
Lewicki-Potapov, B.13
Saxel, H.14
Kel, A.15
Wingender, E.16
-
36
-
-
0032938751
-
A weight matrix for binding recognition by the redox-response regulator ArcA-P of Escherichia coli
-
McGuire AM, De Wulf P, Church GM, Lin EC (1999) A weight matrix for binding recognition by the redox-response regulator ArcA-P of Escherichia coli. Mol Microbiol 32: 219-221.
-
(1999)
Mol Microbiol
, vol.32
, pp. 219-221
-
-
McGuire, A.M.1
de Wulf, P.2
Church, G.M.3
Lin, E.C.4
-
37
-
-
73449105815
-
Structure-function-folding relationships and native energy landscape of dynein light chain protein: nuclear magnetic resonance insights
-
Mohan PM, Hosur RV (2009) Structure-function-folding relationships and native energy landscape of dynein light chain protein: nuclear magnetic resonance insights. J Biosci 34: 465-479.
-
(2009)
J Biosci
, vol.34
, pp. 465-479
-
-
Mohan, P.M.1
Hosur, R.V.2
-
38
-
-
25444436686
-
The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications
-
Moreland JL, Gramada A, Buzko OV, Zhang Q, Bourne PE (2005) The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications. BMC Bioinformatics 6: 21.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 21
-
-
Moreland, J.L.1
Gramada, A.2
Buzko, O.V.3
Zhang, Q.4
Bourne, P.E.5
-
39
-
-
79960085920
-
A way to simplify truth functions
-
Nelson RJ (1953) A way to simplify truth functions. J Symb Logic 18(3): 280-282.
-
(1953)
J Symb Logic
, vol.18
, Issue.3
, pp. 280-282
-
-
Nelson, R.J.1
-
40
-
-
0003546218
-
-
Upper Saddle River: Prentice-Hall, Inc
-
Nelson VP, Nagle HT, Carroll BD, Irwin JD (1995) Digital logic circuit analysis and design. Prentice-Hall, Inc., Upper Saddle River.
-
(1995)
Digital Logic Circuit Analysis and Design
-
-
Nelson, V.P.1
Nagle, H.T.2
Carroll, B.D.3
Irwin, J.D.4
-
41
-
-
34547852238
-
Prediction of DNA-binding residues from sequence
-
doi: 10. 1093/bioinformatics/btm174
-
Ofran Y, Mysore V, Rost B (2007) Prediction of DNA-binding residues from sequence. Bioinformatics 23(13): i347-i353. doi: 10. 1093/bioinformatics/btm174.
-
(2007)
Bioinformatics
, vol.23
, Issue.13
, pp. 347-353
-
-
Ofran, Y.1
Mysore, V.2
Rost, B.3
-
42
-
-
0035221556
-
Promoter region-based classification of genes
-
Pavlidis P, Furey TS, Liberto M, Haussler D, Grundy WN (2001) Promoter region-based classification of genes. In: Pacific symposium on biocomputing, pp 151-163.
-
(2001)
Pacific symposium on biocomputing
, pp. 151-163
-
-
Pavlidis, P.1
Furey, T.S.2
Liberto, M.3
Haussler, D.4
Grundy, W.N.5
-
44
-
-
70549104182
-
Multiple-valued logic minimization for pla synthesis
-
Tech. Rep. UCB/ERL M86/65, EECS Department, University of California, Berkeley
-
Rudell RL (1986) Multiple-valued logic minimization for pla synthesis. Tech. Rep. UCB/ERL M86/65, EECS Department, University of California, Berkeley. http://www. eecs. berkeley. edu/Pubs/TechRpts/1986/734. html.
-
(1986)
-
-
Rudell, R.L.1
-
45
-
-
84860506529
-
Mining ChIP-chip data for transcription factor and cofactor binding sites
-
Smith AD, Sumazin P, Das D, Zhang MQ (2005) Mining ChIP-chip data for transcription factor and cofactor binding sites. Bioinformatics Suppl 1(20): i403-i412.
-
(2005)
Bioinformatics Suppl
, vol.1
, Issue.20
-
-
Smith, A.D.1
Sumazin, P.2
Das, D.3
Zhang, M.Q.4
-
46
-
-
0033984726
-
X-ray crystallography
-
Smyth MS, Martin JH (2000) X-ray crystallography. Mol Pathol 53(1): 8-14.
-
(2000)
Mol Pathol
, vol.53
, Issue.1
, pp. 8-14
-
-
Smyth, M.S.1
Martin, J.H.2
-
47
-
-
0023678091
-
Computer methods for analyzing sequence recognition of nucleic acids
-
Stormo GD (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
-
48
-
-
40149098862
-
The evolution of combinatorial gene regulation in fungi
-
Tuch BB, Galgoczy DJ, Hernday AD, Li H, Johnson AD (2008) The evolution of combinatorial gene regulation in fungi. PLoS Biol 6: e38.
-
(2008)
PLoS Biol
, vol.6
-
-
Tuch, B.B.1
Galgoczy, D.J.2
Hernday, A.D.3
Li, H.4
Johnson, A.D.5
-
49
-
-
84983191537
-
A chart method for simplifying truth functions
-
Pittsburgh. ACM, New York.,doi: 10. 1145/609784. 609801
-
Veitch EW (1952) A chart method for simplifying truth functions. In: Proceedings of the 1952 ACM national meeting, Pittsburgh. ACM, New York, pp 127-133. doi: 10. 1145/609784. 609801.
-
(1952)
Proceedings of the 1952 ACM national meeting
, pp. 127-133
-
-
Veitch, E.W.1
-
50
-
-
0033559518
-
From head to toes: the multiple facets of Sox proteins
-
Wegner M (1999) From head to toes: the multiple facets of Sox proteins. Nucleic Acids Res 27: 1409-1420.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 1409-1420
-
-
Wegner, M.1
-
52
-
-
0032190610
-
Combinatorial transcription factors
-
Wolberger C (1998) Combinatorial transcription factors. Curr Opin Genet Dev 8: 552-559.
-
(1998)
Curr Opin Genet Dev
, vol.8
, pp. 552-559
-
-
Wolberger, C.1
-
54
-
-
77952402048
-
Effect of spatial locality on an evolutionary algorithm for multimodal optimization
-
EvoApplications 2010 Part I. Lecture notes in computer science.,Springer, Berlindoi: 10. 1007/978-3-642-12239-2_50
-
Wong KC, Leung KS, Wong MH (2010a) Effect of spatial locality on an evolutionary algorithm for multimodal optimization. In: Applications of Evolutionary Computation, EvoApplications 2010 Part I. Lecture notes in computer science, vol 6024. Springer, Berlin, pp 481-490. doi: 10. 1007/978-3-642-12239-2_50.
-
(2010)
Applications of Evolutionary Computation
, vol.6024
, pp. 481-490
-
-
Wong, K.C.1
Leung, K.S.2
Wong, M.H.3
-
55
-
-
77955912478
-
Protein structure prediction on a lattice model via multimodal optimization techniques
-
ACM, New York, doi: 10. 1145/1830483. 1830513
-
Wong KC, Leung KS, Wong MH (2010b) Protein structure prediction on a lattice model via multimodal optimization techniques. In: Proceedings of the 12th annual conference on genetic and evolutionary computation. ACM, New York, pp 155-162. doi: 10. 1145/1830483. 1830513.
-
(2010)
Proceedings of the 12th annual conference on genetic and evolutionary computation
, pp. 155-162
-
-
Wong, K.C.1
Leung, K.S.2
Wong, M.H.3
-
56
-
-
47249118465
-
Extracting sequence features to predict protein-DNA interactions: A comparative study
-
doi: 10. 1093/nar/gkn361
-
Zhou Q, Liu JS (2008) Extracting sequence features to predict protein-DNA interactions: a comparative study. Nucleic Acids Res 36(12): 4137-4148. doi: 10. 1093/nar/gkn361.
-
(2008)
Nucleic Acids Res
, vol.36
, Issue.12
, pp. 4137-4148
-
-
Zhou, Q.1
Liu, J.S.2
|