kaarsinogen's dna_binding [58 articles] Export Sort

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	Learning to translate sequence and structure to function: identifying DNA binding and membrane binding proteins. [My Copy] Annals of biomedical engineering, Vol. 35, No. 6. (June 2007), pp. 1043-1052. by R. E. Langlois, M. B. Carson, N. Bhardwaj, H. Lu posted to dna_binding machine_learning protein-dna_interaction by kaarsinogen on 2008-08-12 18:54:34 as
	Residue-level prediction of DNA-binding sites and its application on DNA-binding protein predictions [My Copy] FEBS Letters, Vol. 581, No. 5. (6 March 2007), pp. 1058-1066. by Nitin Bhardwaj, Hui Lu posted to dna_binding protein-dna_interaction by kaarsinogen on 2008-03-07 19:15:28 as
	Prediction of DNA-binding residues from sequence [My Copy] Bioinformatics, Vol. 23, No. 13. (1 July 2007), pp. i347-353. by Yanay Ofran, Venkatesh Mysore, Burkhard Rost posted to dna_binding protein-dna_interaction by kaarsinogen on 2008-03-07 19:03:24 as along with 3 people aalibes GustavoLacerda chrn
	BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences. [My Copy] Nucleic Acids Res, Vol. 34, No. Web Server issue. (1 July 2006) by L. Wang, S. J. Brown posted to dna_binding protein-dna_interaction protein-rna by kaarsinogen on 2007-06-04 18:06:47 as
	Connecting protein structure with predictions of regulatory sites [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 17. (24 April 2007), pp. 7068-7073. by Alexandre V. Morozov, Eric D. Siggia posted to dna_binding protein-dna_interaction protein_structure transcription_factor by kaarsinogen on 2007-06-01 22:37:08 as along with 7 people and 2 groups vingron nklee maximilianh ana aalibes johncumbers lusk structural_bioinformatics Bioinformatics
	How do site-specific DNA-binding proteins find their targets? [My Copy] Nucl. Acids Res., Vol. 32, No. 10. (3 June 2004), pp. 3040-3052. by Stephen E. Halford, John F. Marko posted to dna_binding protein-dna_interaction transcription_factor by kaarsinogen on 2007-06-01 21:29:15 as along with 3 people and 1 group samjlord JintuRabha chrn moernerlab
	DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces [My Copy] Nucl. Acids Res., Vol. 35, No. 5. (12 March 2007), pp. 1465-1477. by Harianto Tjong, Huan-Xiang Zhou posted to dna_binding machine_learning protein-dna_interaction protein_descriptors protein_structure transcription_factor by kaarsinogen on 2007-06-01 21:15:06 as along with 1 person medic0747
	A structure-based method for identifying DNA-binding proteins and their sites of DNA-interaction [My Copy] Journal of Structural and Functional Genomics, Vol. 5, No. 4. (January 2005), pp. 255-265. by William Mclaughlin, Daniel Kulp, Joanna Cruz, Xiang-Jun Lu, Catherine Lawson, Helen Berman posted to protein_structure protein-dna_interaction dna_binding by kaarsinogen on 2007-01-22 06:42:38 as
	Detection, Rescue, and Mapping of Mutations in the Adenovirus DNA Binding Protein Gene [My Copy] PNAS, Vol. 80, No. 6. (15 March 1983), pp. 1674-1677. by J. C. Nicolas, C. S. H. Young, F. Suarez, M. Girard, A. J. Levine posted to dna_binding protein_site_mutation voronoi_paper by kaarsinogen on 2006-11-20 18:28:06 as
	Functional analysis of the adenovirus type 5 DNA-binding protein: site-directed mutants which are defective for adeno-associated virus helper activity. [My Copy] J Virol, Vol. 60, No. 2. (November 1986), pp. 653-661. by C. O. Quinn, G. R. Kitchingman posted to dna_binding protein_site_mutation voronoi_paper by kaarsinogen on 2006-11-20 18:26:36 as
	Why are proteins so robust to site mutations? [My Copy] J Mol Biol, Vol. 315, No. 3. (18 January 2002), pp. 479-484. by D. M. Taverna, R. A. Goldstein posted to dna_binding protein_site_mutation voronoi_paper by kaarsinogen on 2006-11-20 18:22:26 as along with 3 people eckart_bindewald cdeane bpcusack
	DNA-binding specificity of Mcm1: operator mutations that alter DNA-bending and transcriptional activities by a MADS box protein. [My Copy] Mol Cell Biol, Vol. 17, No. 4. (April 1997), pp. 1881-1889. by T. B. Acton, H. Zhong, A. K. Vershon posted to dna_binding protein_site_mutation voronoi_paper by kaarsinogen on 2006-11-20 18:13:45 as
	PSSM-based prediction of DNA binding sites in proteins. [My Copy] BMC Bioinformatics, Vol. 6 (2005) by S. Ahmad, A. Sarai posted to 2005_2006_dnabp dna_binding protein-dna_interaction pssm by kaarsinogen on 2006-11-03 23:08:37 as
	Predicting DNA-binding sites of proteins from amino acid sequence. [My Copy] BMC Bioinformatics, Vol. 7 (2006) by C. Yan, M. Terribilini, F. Wu, R. L. Jernigan, D. Dobbs, V. Honavar posted to 2005_2006_dnabp dna_binding protein-dna_interaction protein_descriptors by kaarsinogen on 2006-11-03 20:47:02 as along with 3 people ameetsoni ezralanglois dandaman
	Conservation of DNA curvature signals in regulatory regions of prokaryotic genes. [My Copy] Nucleic Acids Res, Vol. 31, No. 23. (1 December 2003), pp. 6770-6777. by R. Jáuregui, C. Abreu-Goodger, G. Moreno-Hagelsieb, J. Collado-Vides, E. Merino posted to dna_binding protein_structure signaling_pathways transcription transcription_factor by kaarsinogen on 2006-10-02 21:19:13 as
	Using evolutionary and structural information to predict DNA-binding sites on DNA-binding proteins. [My Copy] Proteins, Vol. 64, No. 1. (1 July 2006), pp. 19-27. by I. B. Kuznetsov, Z. Gou, R. Li, S. Hwang posted to 2005_2006_dnabp dna_binding evolution protein-dna_interaction svm by kaarsinogen on 2006-07-29 00:36:37 as along with 1 person hplatero
	Whole-genome discovery of transcription factor binding sites by network-level conservation. [My Copy] Genome research, Vol. 14, No. 1. (1 January 2004), pp. 99-108. by M. Pritsker, Y. C. Liu, M. A. Beer, S. Tavazoie posted to dna_binding e_coli gene_regulation genome protein-dna_interaction transcription_factor by kaarsinogen on 2006-07-17 22:47:37 as along with 5 people alhufton Dulce aprasad koller xili03
	Discovery of novel transcription factor binding sites by statistical overrepresentation. [My Copy] Nucleic Acids Res, Vol. 30, No. 24. (15 December 2002), pp. 5549-5560. by S. Sinha, M. Tompa posted to dna_binding e_coli transcription_factor by kaarsinogen on 2006-07-17 22:44:59 as along with 11 people wowalz GustavoLacerda dquest xiaobeizhao smiddha GeeSharpMinor xi03 xili03 ep161302 wenhan pradiptaray
	A motif co-occurrence approach for genome-wide prediction of transcription-factor-binding sites in Escherichia coli. [My Copy] Genome Res, Vol. 14, No. 2. (February 2004), pp. 201-208. by M. L. Bulyk, A. M. McGuire, N. Masuda, G. M. Church posted to dna_binding e_coli gene_regulation genome protein-dna_interaction transcription_factor by kaarsinogen on 2006-07-17 22:24:10 as along with 3 people wowalz LeightonP sconlan
	Adaptive evolution of transcription factor binding sites. [My Copy] BMC Evol Biol, Vol. 4, No. 1. (28 October 2004) by J. Berg, S. Willmann, M. Lässig posted to dna_binding e_coli protein-dna_interaction transcription_factor by kaarsinogen on 2006-07-17 19:07:37 as along with 4 people and 1 group bmajoros jjray discreteonyxorb cisevol cis-regulatory-evolution
	Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis. [My Copy] Genome Res, Vol. 11, No. 7. (July 2001), pp. 1175-1186. by P. F. Cliften, L. W. Hillier, L. Fulton, et al.T. Graves, T. Miner, W. R. Gish, R. H. Waterston, M. Johnston posted to dna_binding genome protein-dna_interaction transcription_factor by kaarsinogen on 2006-06-28 23:05:19 as along with 2 people evaf nklee
	DNA binding sites: representation and discovery [My Copy] Bioinformatics, Vol. 16, No. 1. (1 January 2000), pp. 16-23. by Gary D. Stormo posted to dna_binding protein-dna_interaction by kaarsinogen on 2006-06-28 23:00:52 as along with 6 people stharward Dulce austin_mcdonald ajbattle erdos emptyhb
	Genome-Wide Location and Function of DNA Binding Proteins [My Copy] Science, Vol. 290, No. 5500. (22 December 2000), pp. 2306-2309. by Bing Ren, Francois Robert, John J. Wyrick, et al.Oscar Aparicio, Ezra G. Jennings, Itamar Simon, Julia Zeitlinger, Jorg Schreiber, Nancy Hannett, Elenita Kanin, Thomas L. Volkert, Christopher J. Wilson, Stephen P. Bell, Richard A. Young posted to dna_binding genome protein-dna_interaction transcription_factor by kaarsinogen on 2006-06-28 22:54:05 as along with 10 people frohike TorstenWaldminghaus aprasad miguel johncumbers tvdbulck epigenetics yevishere kristallreiner dquest
	Computational prediction of transcription-factor binding site locations [My Copy] Genome Biology, Vol. 5, No. 1. (2003), 201. by Martha Bulyk posted to dna_binding genome protein-dna_interaction transcription_factor by kaarsinogen on 2006-06-26 20:41:26 as along with 10 people and 1 group xubeisi Baschl marti tkmaia lusk Stew nklee yevishere xili03 aalibes EisenLab
	Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations. [My Copy] Science, Vol. 265, No. 5170. (15 July 1994), pp. 346-355. by Y. Cho, S. Gorina, P. D. Jeffrey, N. P. Pavletich posted to dna_binding p53 protein-dna_interaction by kaarsinogen on 2006-03-08 17:49:17 as
	Definition of a consensus binding site for p53. [My Copy] Nat Genet, Vol. 1, No. 1. (April 1992), pp. 45-49. by W. S. el-Deiry, S. E. Kern, J. A. Pietenpol, K. W. Kinzler, B. Vogelstein posted to dna_binding p53 protein-dna_interaction by kaarsinogen on 2006-03-08 17:47:28 as
	Genome-wide Prediction of Mammalian Enhancers Based on Analysis of Transcription-Factor Binding Affinity [My Copy] Cell, Vol. 124, No. 1. (13 January 2006), pp. 47-59. by O. Hallikas, K. Palin, N. Sinjushina, et al.R. Rautiainen, J. Partanen, E. Ukkonen, J. Taipale posted to 2005_2006_dnabp dna_binding genome protein-dna_interaction transcription_factor by kaarsinogen on 2006-01-30 19:48:04 as along with 16 people and 5 groups absterga xingxu cisstem Terkko tuck brant xwbcn dchughes nickluscombe olympos cabbagezs karfunkel maximilianh heliopais oelemento emptyhb Bioinformatics EisenLab G4ID EBI-regulation Genetics-of-Gambling
	A global map of p53 transcription-factor binding sites in the human genome. [My Copy] Cell, Vol. 124, No. 1. (13 January 2006), pp. 207-219. by C. L. Wei, Q. Wu, V. B. Vega, et al.K. P. Chiu, P. Ng, T. Zhang, A. Shahab, H. C. Yong, Y. Fu, Z. Weng, J. Liu, X. D. Zhao, J. L. Chew, Y. L. Lee, V. A. Kuznetsov, W. K. Sung, L. D. Miller, B. Lim, E. T. Liu, Q. Yu, H. H. Ng, Y. Ruan posted to 2005_2006_dnabp dna_binding genome p53 protein-dna_interaction transcription_factor by kaarsinogen on 2006-01-30 19:46:35 as along with 12 people and 1 group pick600 drestion jfr balajis tabu vega kengg jackjackjjj jtomasch karfunkel maralena bozdagd Plantandetc
	Structural features of protein-nucleic acid recognition sites. [My Copy] Biochemistry, Vol. 38, No. 7. (16 February 1999), pp. 1999-2017. by K. Nadassy, S. J. Wodak, J. Janin posted to dna_binding docking protein-dna_interaction protein_structure by kaarsinogen on 2006-01-25 23:39:26 as along with 2 people svozil medic0747
	Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity. [My Copy] J Mol Biol, Vol. 320, No. 5. (26 July 2002), pp. 991-1009. by N. M. Luscombe, J. M. Thornton posted to dna_binding protein-dna_interaction by kaarsinogen on 2006-01-25 23:33:55 as along with 1 person medic0747
	Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code for recognition? [My Copy] J Mol Biol, Vol. 301, No. 3. (18 August 2000), pp. 597-624. by C. O. Pabo, L. Nekludova posted to dna_binding docking protein-dna_interaction protein_structure by kaarsinogen on 2006-01-25 23:30:10 as along with 2 people yoonk medic0747
	Protein-DNA interactions: a structural analysis [My Copy] Journal of Molecular Biology, Vol. 287, No. 5. (16 April 1999), pp. 877-896. by S. Jones posted to dna_binding protein-dna_interaction protein_structure by kaarsinogen on 2006-01-25 22:49:03 as along with 3 people vingron semin medic0747
	Structure-based prediction of DNA target sites by regulatory proteins. [My Copy] Proteins, Vol. 35, No. 1. (1 April 1999), pp. 114-131. by H. Kono, A. Sarai posted to dna_binding protein-dna_interaction protein_structure transcription_factor by kaarsinogen on 2006-01-25 22:44:19 as along with 1 person medic0747
	A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. [My Copy] J Mol Biol, Vol. 284, No. 2. (27 November 1998), pp. 241-254. by K. Robison, A. M. McGuire, G. M. Church posted to dna_binding e_coli protein-dna_interaction by kaarsinogen on 2006-01-25 22:38:11 as along with 2 people medic0747 nklee
	Quantitative parameters for amino acid-base interaction: implications for prediction of protein-DNA binding sites. [My Copy] Nucleic Acids Res, Vol. 26, No. 10. (15 May 1998), pp. 2306-2312. by Y. Mandel-Gutfreund, H. Margalit posted to dna_binding protein-dna_interaction protein_structure by kaarsinogen on 2006-01-25 22:35:43 as along with 2 people medic0747 roys
	Consistencies of individual DNA base-amino acid interactions in structures and sequences. [My Copy] Nucleic Acids Res, Vol. 23, No. 22. (25 November 1995), pp. 4707-4711. by B. Lustig, R. L. Jernigan posted to dna_binding protein-dna_interaction protein_descriptors protein_structure by kaarsinogen on 2006-01-25 22:32:32 as
	A simple physical model for the prediction and design of protein-DNA interactions. [My Copy] J Mol Biol, Vol. 344, No. 1. (12 November 2004), pp. 59-70. by J. J. Havranek, C. M. Duarte, D. Baker posted to dna_binding protein-dna_interaction by kaarsinogen on 2006-01-25 22:25:52 as along with 2 people aalibes medic0747
	Support vector machines for predicting rRNA-, RNA-, and DNA-binding proteins from amino acid sequence. [My Copy] Biochim Biophys Acta, Vol. 1648, No. 1-2. (30 May 2003), pp. 127-133. by Y. D. Cai, S. L. Lin posted to dna_binding protein_descriptors svm by kaarsinogen on 2006-01-25 19:13:32 as
	Global analysis of protein activities using proteome chips. [My Copy] Science (New York, N.Y.), Vol. 293, No. 5537. (14 September 2001), pp. 2101-2105. by H. Zhu, M. Bilgin, R. Bangham, et al.D. Hall, A. Casamayor, P. Bertone, N. Lan, R. Jansen, S. Bidlingmaier, T. Houfek, T. Mitchell, P. Miller, R. A. Dean, M. Gerstein, M. Snyder posted to dna_binding protein-dna_interaction protein_chips by kaarsinogen on 2006-01-23 19:46:22 as along with 2 people Buntworthy selrac
	Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites. [My Copy] Nat Biotechnol, Vol. 21, No. 4. (April 2003), pp. 435-439. by Z. S. Qin, L. A. McCue, W. Thompson, L. Mayerhofer, C. E. Lawrence, J. S. Liu posted to bayesian_network dna_binding protein-dna_interaction by kaarsinogen on 2005-11-11 20:05:51 as along with 3 people balajis nklee wenhan
	Annotating nucleic acid-binding function based on protein structure. [My Copy] J Mol Biol, Vol. 326, No. 4. (28 February 2003), pp. 1065-1079. by E. W. Stawiski, L. M. Gregoret, Y. Mandel-Gutfreund posted to dna_binding protein-dna_interaction by kaarsinogen on 2005-11-11 19:30:49 as along with 1 person marti
	Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces. [My Copy] Proteins, Vol. 55, No. 4. (1 June 2004), pp. 885-894. by Y. Tsuchiya, K. Kinoshita, H. Nakamura posted to dna_binding electrostatic_potential by kaarsinogen on 2005-11-11 19:25:46 as
	Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins. [My Copy] Nucleic Acids Res, Vol. 31, No. 24. (15 December 2003), pp. 7189-7198. by S. Jones, H. P. Shanahan, H. M. Berman, J. M. Thornton posted to dna_binding electrostatic_potential by kaarsinogen on 2005-11-11 19:20:45 as along with 2 people medic0747 carlescorbi
	Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. [My Copy] Nature, Vol. 409, No. 6819. (25 January 2001), pp. 533-538. by V. R. Iyer, C. E. Horak, C. S. Scafe, D. Botstein, M. Snyder, P. O. Brown posted to dna_binding genome transcription_factor by kaarsinogen on 2005-11-04 20:43:00 as along with 1 person dquest
	Factors influencing the identification of transcription factor binding sites by cross-species comparison. [My Copy] Genome Res, Vol. 12, No. 10. (October 2002), pp. 1523-1532. by L. A. McCue, W. Thompson, C. S. Carmack, C. E. Lawrence posted to dna_binding e_coli transcription_factor by kaarsinogen on 2005-11-04 20:39:29 as along with 2 people dquest nklee
	DNA binding sites: representation and discovery. [My Copy] Bioinformatics (Oxford, England), Vol. 16, No. 1. (January 2000), pp. 16-23. by G. D. Stormo posted to dna_binding by kaarsinogen on 2005-11-04 20:37:37 as along with 9 people and 1 group yylin Stew emptyhb isimpson mbj dquest lusk ezralanglois xili03 Bioinformatics - CRUK
	Exploring potential target genes of signaling pathways by predicting conserved transcription factor binding sites. [My Copy] Bioinformatics, Vol. 19 Suppl 2 (October 2003) by C. Dieterich, R. Herwig, M. Vingron posted to signaling_pathways transcription_factor dna_binding gene by kaarsinogen on 2005-11-04 20:33:20 as
	Predicting binding sites of hydrolase-inhibitor complexes by combining several methods. [My Copy] BMC Bioinformatics, Vol. 5, No. 1. (17 December 2004) by T. Z. Sen, A. Kloczkowski, R. L. Jernigan, et al.C. Yan, V. Honavar, K. M. Ho, C. Z. Wang, Y. Ihm, H. Cao, X. Gu, D. Dobbs posted to dna_binding by kaarsinogen on 2005-11-04 20:00:06 as along with 1 person cjeans
	Evolutionary population genetics of promoters: Predicting binding sites and functional phylogenies. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 44. (1 November 2005), pp. 15936-15941. by V. Mustonen, M. Lässig posted to 2005_2006_dnabp dna_binding evolution population_genetics promoter by kaarsinogen on 2005-11-04 19:57:32 as along with 4 people and 2 groups dpollard lusk cisevol emptyhb EisenLab cis-regulatory-evolution
	rSNP_Guide, a database system for analysis of transcription factor binding to DNA with variations: application to genome annotation. [My Copy] Nucleic Acids Res, Vol. 31, No. 1. (1 January 2003), pp. 118-121. by J. V. Ponomarenko, T. I. Merkulova, G. V. Orlova, et al.O. N. Fokin, E. V. Gorshkova, A. S. Frolov, V. P. Valuev, M. P. Ponomarenko posted to dna_binding protein-dna_interaction transcription transcription_factor by kaarsinogen on 2005-10-14 20:57:18 as

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machine_learning	17
genome	17
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population_genetics	1
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kaarsinogen's dna_binding [58 articles] Export Sort

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