-
1
-
-
84934434457
-
Discovering sequence motifs
-
Bailey, T.L. (2008) Discovering sequence motifs. Methods Mol. Biol., 452, 231-251.
-
(2008)
Methods Mol. Biol.
, vol.452
, pp. 231-251
-
-
Bailey, T.L.1
-
2
-
-
0034072450
-
DNA binding sites: Representation and discovery
-
Stormo, G.D. (2000) DNA binding sites: representation and discovery. Bioinformatics, 16, 16-23.
-
(2000)
Bioinformatics
, vol.16
, pp. 16-23
-
-
Stormo, G.D.1
-
3
-
-
80053449230
-
A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites
-
Kulakovskiy, I.V., Belostotsky, A.A., Kasianov, A.S., Esipova, N.G., Medvedeva, Y.A., Eliseeva, I.A. and Makeev, V.J. (2011) A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites. Bioinformatics., 27, 2621-2624.
-
(2011)
Bioinformatics
, vol.27
, pp. 2621-2624
-
-
Kulakovskiy, I.V.1
Belostotsky, A.A.2
Kasianov, A.S.3
Esipova, N.G.4
Medvedeva, Y.A.5
Eliseeva, I.A.6
Makeev, V.J.7
-
4
-
-
84863195617
-
CORECLUST: Identification of the conserved CRM grammar together with prediction of gene regulation
-
Nikulova, A.A., Favorov, A.V., Sutormin, R.A., Makeev, V.J. and Mironov, A.A. (2012) CORECLUST: identification of the conserved CRM grammar together with prediction of gene regulation. Nucleic Acids Res., 40, e93.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Nikulova, A.A.1
Favorov, A.V.2
Sutormin, R.A.3
Makeev, V.J.4
Mironov, A.A.5
-
5
-
-
77956513142
-
Is-rSNP: A novel technique for in silico regulatory SNP detection
-
Macintyre, G., Bailey, J., Haviv, I. and Kowalczyk, A. (2010) is-rSNP: a novel technique for in silico regulatory SNP detection. Bioinformatics, 26, i524-i530.
-
(2010)
Bioinformatics
, vol.26
-
-
Macintyre, G.1
Bailey, J.2
Haviv, I.3
Kowalczyk, A.4
-
6
-
-
33845341455
-
Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques
-
Elnitski, L., Jin, V.X., Farnham, P.J. and Jones, S.J. (2006) Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques. Genome Res., 16, 1455-1464.
-
(2006)
Genome Res.
, vol.16
, pp. 1455-1464
-
-
Elnitski, L.1
Jin, V.X.2
Farnham, P.J.3
Jones, S.J.4
-
7
-
-
79955036679
-
Experimental strategies for studying transcription factor-DNA binding specificities
-
Geertz, M. and Maerkl, S.J. (2010) Experimental strategies for studying transcription factor-DNA binding specificities. Briefings Funct. Gen., 9, 362-373.
-
(2010)
Briefings Funct. Gen.
, vol.9
, pp. 362-373
-
-
Geertz, M.1
Maerkl, S.J.2
-
8
-
-
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
-
9
-
-
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, D108-D110.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
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
-
10
-
-
68949213578
-
Insights from genomic profiling of transcription factors
-
Farnham, P.J. (2009) Insights from genomic profiling of transcription factors. Nat. Rev. Genet., 10, 605-616.
-
(2009)
Nat. Rev. Genet.
, vol.10
, pp. 605-616
-
-
Farnham, P.J.1
-
11
-
-
80052401846
-
Tree-based position weight matrix approach to model transcription factor binding site profiles
-
Bi, Y., Kim, H., Gupta, R. and Davuluri, R.V. (2011) Tree-based position weight matrix approach to model transcription factor binding site profiles. PLoS One, 6, e24210.
-
(2011)
PLoS One
, vol.6
-
-
Bi, Y.1
Kim, H.2
Gupta, R.3
Davuluri, R.V.4
-
12
-
-
77951874066
-
Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers
-
Gotea, V., Visel, A., Westlund, J.M., Nobrega, M.A., Pennacchio, L.A. and Ovcharenko, I. (2010) Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers. Genome Res., 20, 565-577.
-
(2010)
Genome Res.
, vol.20
, pp. 565-577
-
-
Gotea, V.1
Visel, A.2
Westlund, J.M.3
Nobrega, M.A.4
Pennacchio, L.A.5
Ovcharenko, I.6
-
13
-
-
77957818564
-
Deep and wide digging for binding motifs in ChIP-Seq data
-
Kulakovskiy, I.V., Boeva, V.A., Favorov, A.V. and Makeev, V.J. (2010) Deep and wide digging for binding motifs in ChIP-Seq data. Bioinformatics, 26, 2622-2623.
-
(2010)
Bioinformatics
, vol.26
, pp. 2622-2623
-
-
Kulakovskiy, I.V.1
Boeva, V.A.2
Favorov, A.V.3
Makeev, V.J.4
-
14
-
-
79951974373
-
CompleteMOTIFs: Dna motif discovery platform for transcription factor binding experiments
-
Kuttippurathu, L., Hsing, M., Liu, Y., Schmidt, B., Maskell, D.L., Lee, K., He, A., Pu, W.T. and Kong, S.W. (2011) CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments. Bioinformatics, 27, 715-717.
-
(2011)
Bioinformatics
, vol.27
, pp. 715-717
-
-
Kuttippurathu, L.1
Hsing, M.2
Liu, Y.3
Schmidt, B.4
Maskell, D.L.5
Lee, K.6
He, A.7
Pu, W.T.8
Kong, S.W.9
-
15
-
-
84860115916
-
A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information
-
Ma, X., Kulkarni, A., Zhang, Z., Xuan, Z., Serfling, R. and Zhang, M.Q. (2012) A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information. Nucleic Acids Res., 40, e50.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Ma, X.1
Kulkarni, A.2
Zhang, Z.3
Xuan, Z.4
Serfling, R.5
Zhang, M.Q.6
-
16
-
-
79955550445
-
A user's guide to the encyclopedia of DNA elements (ENCODE)
-
ENCODE Project Consortium
-
ENCODE Project Consortium. (2011) A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol., 9, e1001046.
-
(2011)
PLoS Biol.
, vol.9
-
-
-
17
-
-
84860833500
-
Reorganizing the protein space at the Universal Protein Resource (UniProt)
-
UniProt Consortium
-
UniProt Consortium. (2012) Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res., 40, D71-D75.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
-
18
-
-
77952043585
-
Discovery of DNA motifs recognized by transcription factors through integration of different experimental sources
-
Kulakovskiy, I.V. and Makeev, V.J. (2010) Discovery of DNA motifs recognized by transcription factors through integration of different experimental sources. Biophysics, 54, 667-674.
-
(2010)
Biophysics
, vol.54
, pp. 667-674
-
-
Kulakovskiy, I.V.1
Makeev, V.J.2
-
19
-
-
84859865967
-
The UCSC Genome Browser database: Extensions and updates 2011
-
(Database issue)
-
Dreszer, T.R., Karolchik, D., Zweig, A.S., Hinrichs, A.S., Raney, B.J., Kuhn, R.M., Meyer, L.R., Wong, M., Sloan, C.A., Rosenbloom, K.R. et al. (2012) The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Res., 40(Database issue), D918-D923.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Dreszer, T.R.1
Karolchik, D.2
Zweig, A.S.3
Hinrichs, A.S.4
Raney, B.J.5
Kuhn, R.M.6
Meyer, L.R.7
Wong, M.8
Sloan, C.A.9
Rosenbloom, K.R.10
-
20
-
-
77953006022
-
Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities
-
Jolma, A., Kivioja, T., Toivonen, J., Cheng, L., Wei, G., Enge, M., Taipale, M., Vaquerizas, J.M., Yan, J., Sillanpaa, M.J. et al. (2010) Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. Genome Res., 20, 861-873.
-
(2010)
Genome Res.
, vol.20
, pp. 861-873
-
-
Jolma, A.1
Kivioja, T.2
Toivonen, J.3
Cheng, L.4
Wei, G.5
Enge, M.6
Taipale, M.7
Vaquerizas, J.M.8
Yan, J.9
Sillanpaa, M.J.10
-
21
-
-
27744480577
-
Dragon plant biology explorer. A text-mining tool for integrating associations between genetic and biochemical entities with genome annotation and biochemical terms lists
-
Bajic, V.B., Veronika, M., Veladandi, P.S., Meka, A., Heng, M.W., Rajaraman, K., Pan, H. and Swarup, S. (2005) Dragon plant biology explorer. A text-mining tool for integrating associations between genetic and biochemical entities with genome annotation and biochemical terms lists. Plant Physiol., 138, 1914-1925.
-
(2005)
Plant Physiol.
, vol.138
, pp. 1914-1925
-
-
Bajic, V.B.1
Veronika, M.2
Veladandi, P.S.3
Meka, A.4
Heng, M.W.5
Rajaraman, K.6
Pan, H.7
Swarup, S.8
-
22
-
-
3242889751
-
Dragon TF association miner: A system for exploring transcription factor associations through text-mining
-
Pan, H., Zuo, L., Choudhary, V., Zhang, Z., Leow, S.H., Chong, F.T., Huang, Y., Ong, V.W., Mohanty, B., Tan, S.L. et al. (2004) Dragon TF association miner: a system for exploring transcription factor associations through text-mining. Nucleic Acids Res., 32, W230-W234.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Pan, H.1
Zuo, L.2
Choudhary, V.3
Zhang, Z.4
Leow, S.H.5
Chong, F.T.6
Huang, Y.7
Ong, V.W.8
Mohanty, B.9
Tan, S.L.10
-
23
-
-
0027519338
-
Information analysis of sequences that bind the replication initiator RepA
-
Papp, P.P., Chattoraj, D.K. and Schneider, T.D. (1993) Information analysis of sequences that bind the replication initiator RepA. J. Mol. Biol., 233, 219-230.
-
(1993)
J. Mol. Biol.
, vol.233
, pp. 219-230
-
-
Papp, P.P.1
Chattoraj, D.K.2
Schneider, T.D.3
-
24
-
-
0344906914
-
Consensus sequence Zen
-
Schneider, T.D. (2002) Consensus sequence Zen. Appl. Bioinformatics, 1, 111-119.
-
(2002)
Appl. Bioinformatics
, vol.1
, pp. 111-119
-
-
Schneider, T.D.1
-
25
-
-
0021196998
-
Protein-DNA recognition
-
Pabo, C. and Sauer, R. (1984) Protein-DNA recognition. Annu. Rev. Biochem., 53, 293-321.
-
(1984)
Annu. Rev. Biochem.
, vol.53
, pp. 293-321
-
-
Pabo, C.1
Sauer, R.2
-
26
-
-
38849086841
-
HeliCis: A DNA motif discovery tool for colocalized motif pairs with periodic spacing
-
Larsson, E., Lindahl, P. and Mostad, P. (2007) HeliCis: a DNA motif discovery tool for colocalized motif pairs with periodic spacing. BMC Bioinformatics, 8, 418.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 418
-
-
Larsson, E.1
Lindahl, P.2
Mostad, P.3
-
27
-
-
78651294477
-
TcoF-DB: Dragon database for human transcription co-factors and transcription factor interacting proteins
-
Schaefer, U., Schmeier, S. and Bajic, V.B. (2011) TcoF-DB: dragon database for human transcription co-factors and transcription factor interacting proteins. Nucleic Acids Res., 39, D106-D10.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Schaefer, U.1
Schmeier, S.2
Bajic, V.B.3
-
28
-
-
39049165160
-
Efficient and accurate P-value computation for position weight matrices
-
Touzet, H. and Varre, J.S. (2007) Efficient and accurate P-value computation for position weight matrices. Algorithms Mol Biol., 2, 15.
-
(2007)
Algorithms Mol Biol.
, vol.2
, pp. 15
-
-
Touzet, H.1
Varre, J.S.2
-
29
-
-
69849099700
-
Motif discovery and motif finding from genome-mapped DNase footprint data
-
Kulakovskiy, I.V., Favorov, A.V. and Makeev, V.J. (2009) Motif discovery and motif finding from genome-mapped DNase footprint data. Bioinformatics, 25, 2318-2325.
-
(2009)
Bioinformatics
, vol.25
, pp. 2318-2325
-
-
Kulakovskiy, I.V.1
Favorov, A.V.2
Makeev, V.J.3
-
30
-
-
0000825481
-
A statistical method for evaluating systematic relationships
-
Sokal, R. and Michener, C. (1958) A statistical method for evaluating systematic relationships. Univ. Kans. Sci. Bull., 38, 1409-1438.
-
(1958)
Univ. Kans. Sci. Bull.
, vol.38
, pp. 1409-1438
-
-
Sokal, R.1
Michener, C.2
-
32
-
-
0037398319
-
Homotypic regulatory clusters in Drosophila
-
Lifanov, A.P., Makeev, V.J., Nazina, A.G. and Papatsenko, D.A. (2003) Homotypic regulatory clusters in Drosophila. Genome Res., 13, 579-588.
-
(2003)
Genome Res.
, vol.13
, pp. 579-588
-
-
Lifanov, A.P.1
Makeev, V.J.2
Nazina, A.G.3
Papatsenko, D.A.4
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