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	Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates [My Copy] Nature Nanotechnology, Vol. advance online publication (08 November 2009) by Hareem T. Maune, Si-ping Han, Robert D. Barish, et al.Marc Bockrath, IIIWilliam A. Goddard, W. K. RothemundPaul, Erik Winfree posted to origami dna_binding by BjoernAlbrecht on 2009-12-09 10:41:17 as along with 1 person and 1 group Pedersen DNA nanotechnology
	The transcription unit architecture of the Escherichia coli genome [My Copy] Nature Biotechnology In Nat Biotech, Vol. 27, No. 11. (01 November 2009), pp. 1043-1049. by Byung-Kwan Cho, Karsten Zengler, Yu Qiu, et al.Young S. Park, Eric M. Knight, Christian L. Barrett, Yuan Gao, Bernhard O. Palsson posted to transcription mrna genome gene_regulation e_coli dna_binding chromosome_organization bacteria by jjray on 2009-11-09 03:49:20 as along with 6 people pinney karthikraman venancio JeremyZucker dbikard rsaito
	Prevalence of Temperature-Dependent Heat Capacity Changes in Protein-DNA Interactions☆ [My Copy] Biophysical Journal, Vol. 94, No. 8. (15 April 2008), pp. 3258-3265. by C. Liu, A. Richard, K. Datta, V. Licata posted to dna_binding by kasta on 2009-11-05 18:38:30 as
	Thermodynamic characterization of non-sequence-specific DNA-binding by the Sso7d protein from Sulfolobus solfataricus1 [My Copy] Journal of Molecular Biology, Vol. 276, No. 4. (March 1998), pp. 775-786. by T. Lundback posted to dna_binding by kasta on 2009-11-05 18:37:59 as
	Thermodynamics of the binding of Thermus aquaticus DNA polymerase to primed-template DNA [My Copy] Nucl. Acids Res., Vol. 31, No. 19. (1 October 2003), pp. 5590-5597. by Kausiki Datta, Vince J. LiCata posted to dna_binding by kasta on 2009-11-05 18:37:33 as
	Physical constraints and functional characteristics of transcription factorâDNA interaction [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 19. (17 September 2002), pp. 12015-12020. by Ulrich Gerland, J. David Moroz, Terence Hwa posted to protein_dna_interactions dna_binding biophysics by emptyhb on 2009-11-04 18:53:31 as along with 2 people and 1 group jstajic dquest TranscriptionalRegulationWithThermodynamicModels
	Kinetics of Protein-DNA Interaction: Facilitated Target Location in Sequence-Dependent Potential [My Copy] Biophysical Journal, Vol. 87, No. 6. (1 December 2004), pp. 4021-4035. by M. Slutsky posted to protein_dna_interactions dna_binding by emptyhb on 2009-11-04 18:50:50 as along with 1 person and 1 group blobbybirdman Myxo group
	Spatial and Mechanical Properties of Dilute DNA Monolayers on Gold Imaged by AFM [My Copy] The Journal of Physical Chemistry B, Vol. 107, No. 15. (1 April 2003), pp. 3591-3597. by Donats Erts, Boris Polyakov, Hakan Olin, Eimer Tuite posted to dna_binding by BjoernAlbrecht on 2009-10-14 14:08:17 as along with 1 person hakanolin
	Self-assembled DNA nanostructures for distance-dependent multivalent ligand\|[ndash]\|protein binding [My Copy] Nature Nanotechnology, Vol. 3, No. 7. (22 June 2008), pp. 418-422. by Sherri Rinker, Yonggang Ke, Yan Liu, Rahul Chhabra, Hao Yan posted to dna_binding by BjoernAlbrecht on 2009-10-14 13:29:59 as along with 3 people metemadi dna Ynubiis
	Mutational analysis of the preferential binding of human topoisomerase I to supercoiled DNA [My Copy] FEBS Journal, Vol. 9999, No. 9999. (2009) by Zheng Yang, James F. Carey, James J. Champoux posted to topoisomerase supercoiled_dna dna_binding dna by A_Coletta_Thesis to the group Structural Biology Group TorVergata on 2009-09-15 13:55:46 as
	The Consequences of Base Pair Composition Biases for Regulatory Network Organization in Prokaryotes [My Copy] Mol Biol Evol, Vol. 26, No. 10. (1 October 2009), pp. 2171-2173. by Otto X. Cordero, Paulien Hogeweg posted to prokaryote network gene_regulation evolution dna_binding dna by jjray on 2009-09-07 16:28:22 as along with 3 people operon emptyhb maximilianh
	A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factors. [My Copy] Cell, Vol. 138, No. 2. (23 July 2009), pp. 314-327. by Christian A. Grove, Federico De Masi, M. Inmaculada Barrasa, et al.Daniel E. Newburger, Mark J. Alkema, Martha L. Bulyk, Albertha J. Walhout posted to transcription_factors tfs protein_family promiscuity integrated_networks integrated_network dna_binding c_elegans by freddemasi on 2009-08-26 21:34:53 as along with 2 people roys emptyhb
	Nonspecific DNA-Protein Interaction: Why Proteins Can Diffuse along DNA [My Copy] Physical Review Letters, Vol. 102, No. 22. (2009), 228101. by Vincent Dahirel, Fabien Paillusson, Marie Jardat, Maria Barbi, Jean M. Victor posted to biophysics diffusion dna_binding gene_regulation by jjray on 2009-06-05 19:42:08 as along with 7 people zeldin kumar_physics flbarroso sobolevnrm edws spm82 scratchmandoo
	Diffusion, dimensionality, and noise in transcriptional regulation [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 79, No. 5. (2009), 051901. by Gasper Tkacik, William Bialek posted to biophysics diffusion dna_binding gene_regulation noise signaling stochastic by jjray on 2009-05-29 22:12:19 as along with 2 people cjryan kumar_physics
	Facilitated diffusion with DNA coiling [My Copy] Proceedings of the National Academy of Sciences (6 May 2009) by Michael A. Lomholt, Bram van den Broek, Svenja-Marei J. Kalisch, Gijs J. Wuite, Ralf Metzler posted to biophysics diffusion dna dna_binding by jjray on 2009-05-07 15:49:51 as along with 2 people fpattyn kshundyak
	Evolution of C2H2-zinc finger genes revisited. [My Copy] BMC evolutionary biology, Vol. 9 (04 March 2009), 51. by J. H. Thomas, R. O. Emerson posted to bioinformatics dna_binding geneexpression tf transcription zinc_finger by Jporci on 2009-04-17 04:35:27 as along with 1 person absterga
	Genome-wide analysis of protein-DNA interactions in living cells [My Copy] Genome Biology, Vol. 2, No. 4. (2001) by Franklin B. Pugh, David Gilmour posted to dna_binding dna_interaction by Jporci on 2009-04-16 04:33:04 as
	In vitro selection of DNA binding sites for ABF1 protein from Saccharomyces cerevisiae [My Copy] FEBS Letters, Vol. 579, No. 20. (15 August 2005), pp. 4535-4540. by R. Beinoraviciutekellner, G. Lipps, G. Krauss posted to dna_binding dna_interaction by Jporci on 2009-04-16 04:30:35 as
	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
	Energetics of the protein-DNA-water interaction [My Copy] BMC Structural Biology, Vol. 7 (10 January 2007), 4. by Francesca Spyrakis, Pietro Cozzini, Chiara Bertoli, Anna Marabotti, Glen E. Kellogg, Andrea Mozzarelli posted to 3-dimensional_structure dna dna_binding energy by jjray on 2008-07-15 16:35:59 as along with 3 people aalibes medic0747 Ema
	Chromatin decouples promoter threshold from dynamic range [My Copy] Nature, Vol. 453, No. 7192. (16 April 2008), pp. 246-250. by Felix H. Lam, David J. Steger, Erin K. O/'Shea posted to dna_binding dynamic_range gene_regulation promoter threshold_signal by jjray on 2008-05-07 21:30:41 as along with 4 people talponer mmcclean inesdesantiago emptyhb
	Crystal structure of the [lgr] repressor and a model for pairwise cooperative operator binding [My Copy] Nature, Vol. 452, No. 7190. (24 April 2008), pp. 1022-1025. by Steven Stayrook, Peera Jaru-Ampornpan, Jenny Ni, Ann Hochschild, Mitchell Lewis posted to 3-dimensional_structure cooperativity dna_binding gene_regulation transcription by jjray on 2008-04-23 23:37:03 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 dna_binding by hplatero on 2008-04-04 21:52:05 as along with 1 person kaarsinogen
	DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins [My Copy] Bioinformatics, Vol. 23, No. 5. (1 March 2007), pp. 634-636. by Seungwoo Hwang, Zhenkun Gou, Igor B. Kuznetsov posted to dna_binding by hplatero on 2008-04-04 21:51:20 as
	Tandem DNA Recognition by PhoB, a Two-Component Signal Transduction Transcriptional Activator [My Copy] Structure, Vol. 10, No. 5. (May 2002), pp. 701-713. by Alexandre G. Blanco, Maria Sola, Xavier F. Gomis-Ruth, Miquel Coll posted to 3-dimensional_structure dna_binding gene_regulation promoter two-component_system by jjray on 2008-04-02 21:21:22 as
	On the specificity of DNA-protein interactions. [My Copy] Proc Natl Acad Sci U S A, Vol. 83, No. 6. (March 1986), pp. 1608-1612. by P. H. von Hippel, O. G. Berg posted to dna_binding gene_regulation thermodynamics by jjray on 2008-04-01 20:34:15 as along with 3 people and 2 groups cisevol lambda stsaft TranscriptionalRegulationWithThermodynamicModels cis-regulatory-evolution
	Statistical modeling of transcription factor binding affinities predicts regulatory interactions. [My Copy] PLoS Comput Biol, Vol. 4, No. 3. (March 2008) by T. Manke, H. G. Roider, M. Vingron posted to dna_binding gene_regulation statistical_model transcription by jjray on 2008-03-31 21:37:11 as along with 2 people maximilianh eskay
	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
	Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. [My Copy] Journal of molecular biology, Vol. 193, No. 4. (20 February 1987), pp. 723-750. by O. G. Berg, P. H. von Hippel posted to dna_binding gene_regulation statistical_mechanics by jjray on 2008-01-24 16:06:24 as along with 9 people and 2 groups mox emptyhb indigoviolet lusk discreteonyxorb cisevol Ema brant zambujo EisenLab cis-regulatory-evolution
	Protein-Protein Interactions Dominate the Assembly Thermodynamics of a Transcription Repression Complex [My Copy] Biochemistry (1 November 2007) by H. Zhao, E. Streaker, W. Pan, D. Beckett posted to dna_binding e_coli thermodynamics transcriptional_regulatory_complex by cwbrown to the group EisenLab on 2007-11-07 00:36:20 as
	Functional Specificity of a Hox Protein Mediated by the Recognition of Minor Groove Structure [My Copy] Cell, Vol. 131, No. 3. (02 November 2007), pp. 530-543. by Rohit Joshi, Jonathan M. Passner, Remo Rohs, et al.Rinku Jain, Alona Sosinsky, Michael A. Crickmore, Vinitha Jacob, Aneel K. Aggarwal, Barry Honig, Richard S. Mann posted to dna_binding homeobox structure by cwbrown to the group EisenLab on 2007-11-07 00:16:47 as along with 4 people vingron emptyhb blobbybirdman oelemento
	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
	Quantifying DNA-protein binding specificities by using oligonucleotide mass tags and mass spectroscopy [My Copy] PNAS, Vol. 104, No. 9. (27 February 2007), pp. 3061-3066. by Lingang Zhang, Simon Kasif, And C. Cantor posted to transcription_factor method mass_spec dna_binding by cwbrown to the group EisenLab on 2007-03-29 22:07:00 as along with 2 people guhjy zwang
	Analysis of In-Vivo LacR-Mediated Gene Repression Based on the Mechanics of DNA Looping. [My Copy] PLoS ONE, Vol. 1 (2006) by Y. Zhang, A. E. McEwen, D. M. Crothers, S. D. Levene posted to dna_binding dna_looping e_coli transcription_factor by cwbrown on 2007-03-29 20:46:46 as along with 1 group EisenLab
	DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies [My Copy] PLoS Computational Biology, Vol. preprint, No. 2007. (1 February 2007), e61.eor. by Shaun Mahony, Philip Auron, Panayiotis Benos posted to dna_binding method motifs transcription_factor by cwbrown on 2007-03-29 20:45:40 as along with 1 group EisenLab
	Reprogrammable recognition codes in bicoid homeodomain-DNA interaction. [My Copy] Mol Cell Biol, Vol. 20, No. 20. (October 2000), pp. 7673-7684. by V. Dave, C. Zhao, F. Yang, C. S. Tung, J. Ma posted to dna_binding structure transcription_factor by cwbrown on 2007-03-02 19:36:34 as along with 1 group EisenLab
	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
	HMG1 and 2, and related 'architectural' DNA-binding proteins. [My Copy] Trends Biochem Sci, Vol. 26, No. 3. (March 2001), pp. 167-174. by J. O. Thomas, A. A. Travers posted to dna_binding by jwm on 2006-11-23 14:28:45 as along with 2 groups Radiation_Damage Stressosome
	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
	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

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2005_2006_dnabp	7
transcription	6
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dynamic_range	1
energy	1
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promiscuity	1
protein-rna	1
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pssm	1
signaling	1
statistical_mechanics	1
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tf	1
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threshold_signal	1
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