aalibes's library [326 articles]

Recent papers added to aalibes's library.

	Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 26. (30 June 2009), pp. 10505-10510. by Prasad V. Burra, Ying Zhang, Adam Godzik, Boguslaw Stec posted to protein_structure by aalibes on 2009-07-01 11:24:27 as along with 2 people TRHvidsten zwang
	Motif-directed flexible backbone design of functional interactions [My Copy] Protein Science, Vol. 18, No. 6. (2009), pp. 1293-1305. by James J. Havranek, David Baker posted to protein_engineering protein_dna by aalibes on 2009-06-05 15:25:11 as along with 1 person anna_yershova
	The second wave of synthetic biology: from modules to systems [My Copy] Nature Reviews Molecular Cell Biology, Vol. 10, No. 6., pp. 410-422. by Priscilla E. M. Purnick, Ron Weiss posted to synthetic_biology by aalibes on 2009-05-25 09:53:59 as along with 5 people zwang Vincent_Rouilly druvus boko4ikameto phoenixzxl
	Quantitative analysis of EGR proteins binding to DNA: assessing additivity in both the binding site and the protein [My Copy] BMC Bioinformatics, Vol. 6, No. 1. (2005), 176. by Jiajian Liu, Gary Stormo posted to protein_dna by aalibes on 2009-05-20 10:30:59 as
	Experimentally based contact energies decode interactions responsible for protein-DNA affinity and the role of molecular waters at the binding interface [My Copy] Nucl. Acids Res. (8 May 2009), gkp289. by Alpay, Carlos J. Camacho posted to protein_dna by aalibes on 2009-05-18 11:10:14 as
	Diversity and Complexity in DNA Recognition by Transcription Factors [My Copy] Science, Vol. 324, No. 5935. (26 June 2009), pp. 1720-1723. by Gwenael Badis, Michael F. Berger, Anthony A. Philippakis, et al.Shaheynoor Talukder, Andrew R. Gehrke, Savina A. Jaeger, Esther T. Chan, Genita Metzler, Anastasia Vedenko, Xiaoyu Chen, Hanna Kuznetsov, Chi-Fong Wang, David Coburn, Daniel E. Newburger, Quaid Morris, Timothy R. Hughes, Martha L. Bulyk posted to transcription_factors by aalibes on 2009-05-18 10:04:47 as along with 17 people and 1 group absterga mingzhi galka8_diploma fenghezi TRHvidsten ilyashl cambray rpatward tibbitts dpollard siebert JustinCrocker burak dipenps roys emptyhb tmmurali RockmanLab
	Thermodynamic signature of GCN4-bZIP binding to DNA indicates the role of water in discriminating between the AP-1 and ATF/CREB sites. [My Copy] J Mol Biol, Vol. 343, No. 4. (29 October 2004), pp. 865-878. by A. I. Dragan, L. Frank, Y. Liu, E. N. Makeyeva, C. Crane-Robinson, P. L. Privalov posted to gcn4 bzip by aalibes on 2009-05-12 10:11:36 as along with 1 person hplatero
	Structural basis for the diversity of DNA recognition by bZIP transcription factors [My Copy] Nat Struct Mol Biol, Vol. 7, No. 10. (October 2000), pp. 889-893. by Yoshifumi Fujii, Toshiyuki Shimizu, Takashi Toda, Mitsuhiro Yanagida, Toshio Hakoshima posted to bzip by aalibes on 2009-05-11 11:32:22 as along with 1 person gwenknight
	Zinc-finger-based artificial transcription factors and their applications. [My Copy] Advanced drug delivery reviews (23 April 2009) by Takashi Sera posted to zinc_fingers by aalibes on 2009-05-04 14:43:08 as
	Assessment of the optimization of affinity and specificity at protein-DNA interfaces. [My Copy] Nucleic acids research (23 April 2009) by Justin Ashworth, David Baker posted to protein_dna by aalibes on 2009-04-28 12:15:43 as
	Restricted spacer tolerance of a zinc finger nuclease with a six amino acid linker. [My Copy] Bioorganic & medicinal chemistry letters (3 March 2009) by Yuka Shimizu, Mital S S. Bhakta, David J J. Segal posted to zinc_fingers by aalibes on 2009-03-23 12:21:30 as
	Directed evolution of homing endonuclease I-SceI with altered sequence specificity [My Copy] Protein Engineering, Design and Selection, Vol. 22, No. 4. (1 April 2009), pp. 249-256. by Zhilei Chen, Fei Wen, Ning Sun, Huimin Zhao posted to meganucleases by aalibes on 2009-03-20 14:34:03 as
	A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. [My Copy] Molecular cell, Vol. 32, No. 6. (26 December 2008), pp. 878-887. by G. Badis, E. T. Chan, H. van Bakel, et al.L. Pena-Castillo, D. Tillo, K. Tsui, C. D. Carlson, A. J. Gossett, M. J. Hasinoff, C. L. Warren, M. Gebbia, S. Talukder, A. Yang, S. Mnaimneh, D. Terterov, D. Coburn, A. Li Yeo, Z. X. Yeo, N. D. Clarke, J. D. Lieb, A. Z. Ansari, C. Nislow, T. R. Hughes posted to transcription_factors by aalibes on 2009-03-17 11:39:36 as along with 1 person idonaldson
	Additivity in protein-DNA interactions: how good an approximation is it? [My Copy] Nucleic Acids Res, Vol. 30, No. 20. (15 October 2002), pp. 4442-4451. by P. V. Benos, M. L. Bulyk, G. D. Stormo posted to protein_dna by aalibes on 2009-03-12 12:28:56 as along with 4 people erdos medic0747 emptyhb yevishere
	Nucleosome positioning and gene regulation: advances through genomics. [My Copy] Nature reviews. Genetics (10 February 2009) by Cizhong Jiang, B Franklin F. Pugh posted to nucleosome by aalibes on 2009-02-16 12:36:45 as along with 12 people and 1 group hagechouchin443 humburg talponer fenghezi inesdesantiago rpatward timflutre nilsbecker siebert idonaldson WanderingAengus provero cube_and_beyond
	Proprietary science, open science and the role of patent disclosure: the case of zinc-finger proteins [My Copy] Nature Biotechnology, Vol. 27, No. 2., pp. 140-144. by Subhashini Chandrasekharan, Sapna Kumar, Cory M. Valley, Arti Rai posted to zinc_fingers by aalibes on 2009-02-16 12:36:21 as along with 1 person operon
	Looking into DNA recognition: zinc finger binding specificity. [My Copy] Nucleic Acids Res, Vol. 32, No. 22. (2004), pp. 6673-6682. by G. Paillard, C. Deremble, R. Lavery posted to zinc_fingers by aalibes on 2009-02-10 16:17:11 as
	An affinity-based scoring scheme for predicting DNA-binding activities of modularly assembled zinc-finger proteins [My Copy] Nucl. Acids Res., Vol. 37, No. 2. (1 February 2009), pp. 506-515. by Jeffry D. Sander, Peter Zaback, Keith J. Joung, Daniel F. Voytas, Drena Dobbs posted to zinc_fingers by aalibes on 2009-02-09 12:00:43 as along with 1 person maximilianh
	Systematic prediction of control proteins and their DNA binding sites [My Copy] Nucl. Acids Res., Vol. 37, No. 2. (1 February 2009), pp. 441-451. by Valeriy Sorokin, Konstantin Severinov, Mikhail S. Gelfand posted to protein_dna by aalibes on 2009-02-09 12:00:23 as
	STAMP: a web tool for exploring DNA-binding motif similarities. [My Copy] Nucleic Acids Res (3 May 2007) by Shaun Mahony, Panayiotis V V. Benos posted to transcription_factors by aalibes on 2009-02-06 11:18:33 as along with 2 people and 1 group raylim dpollard EisenLab
	High-resolution dynamic mapping of histone-DNA interactions in a nucleosome [My Copy] Nat Struct Mol Biol, Vol. 16, No. 2. (February 2009), pp. 124-129. by Michael A. Hall, Alla Shundrovsky, Lu Bai, Robert M. Fulbright, John T. Lis, Michelle D. Wang posted to nucleosome by aalibes on 2009-02-05 11:06:45 as along with 1 person RamuAnandakrishnan
	Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities [My Copy] Nat Biotech, Vol. 24, No. 11. (24 November 2006), pp. 1429-1435. by Michael F. Berger, Anthony A. Philippakis, Aaron M. Qureshi, Fangxue S. He, Preston W. Estep, Martha L. Bulyk posted to transcription_factors by aalibes on 2009-01-23 15:30:28 as along with 10 people and 1 group absterga cambray jfr dpollard stsaft maldi cthachuk olympos yevishere kristallreiner EisenLab
	Biological Systems from an Engineer's Point of View [My Copy] PLoS Biology, Vol. 7, No. 1. (1 January 2009), e21. by Gregory T. Reeves, Scott E. Fraser posted to systems_biology by aalibes on 2009-01-23 11:01:29 as along with 9 people GeeSharpMinor pansapiens nuin pablocarb pawelszczesny tswayne dswan dullhunk druvus
	High-resolution DNA binding specificity analysis of yeast transcription factors. [My Copy] Genome research (21 January 2009) by Cong Zhu, Kelsey Byers, Rachel McCord, et al.Zhenwei Shi, Michael Berger, Daniel Newburger, Katrina Saulrieta, Zachary Smith, Mita Shah, Mathangi Radhakrishnan, Anthony Philippakis, Yanhui Hu, Federico De Masi, Marcin Pacek, Andreas Rolfs, Tvs Murthy, Joshua Labaer, Martha L L. Bulyk posted to transcription_factors by aalibes on 2009-01-23 10:43:13 as along with 8 people austin_mcdonald siebert dolchan rpatward xwbcn absterga djkt kristallreiner
	Structural Basis of Restoring Sequence-Specific DNA Binding and Transactivation to Mutant p53 by Suppressor Mutations☆ [My Copy] Journal of Molecular Biology, Vol. 385, No. 1. (09 January 2009), pp. 249-265. by O. Suad, H. Rozenberg, R. Brosh, et al.Y. Diskinposner, N. Kessler, L. Shimon, F. Frolow, A. Liran, V. Rotter, Z. Shakked posted to transcription_factors cancer by aalibes on 2009-01-20 15:54:25 as
	Adaptive Evolution in Zinc Finger Transcription Factors [My Copy] PLoS Genet, Vol. 5, No. 1. (2 January 2009), e1000325. by Ryan O. Emerson, James H. Thomas posted to zinc_fingers by aalibes on 2009-01-14 11:49:59 as along with 4 people and 1 group polivares dpollard JustinCrocker djkt RockmanLab
	Kalign--an accurate and fast multiple sequence alignment algorithm. [My Copy] BMC Bioinformatics, Vol. 6 (2005) by T. Lassmann, E. L. Sonnhammer posted to tools by aalibes on 2008-12-15 10:39:17 as along with 6 people Thaverkamp BioNica johanviklund CharlesM knaseanka Haggan
	Crystal structure of I-DmoI in complex with its target DNA provides new insights into meganuclease engineering. [My Copy] Proceedings of the National Academy of Sciences of the United States of America (30 October 2008) by María, Jesús Prieto, Pilar Redondo, et al.Alejandro D. D. Nadra, Andreu Alibes, Luis Serrano, Sylvestre Grizot, Philippe Duchateau, Frédéric Pâques, Francisco J. J. Blanco, Guillermo Montoya posted to meganucleases by aalibes on 2008-12-10 12:08:36 as
	Expanding or Restricting the Target Site Repertoire of Zinc-finger Nucleases: The Inter-domain Linker as a Major Determinant of Target Site Selectivity. [My Copy] Molecular therapy : the journal of the American Society of Gene Therapy (11 November 2008) by Eva-Maria M. Händel, Stephen Alwin, Toni Cathomen posted to zinc_fingers by aalibes on 2008-11-18 09:51:26 as along with 1 person guhjy
	Predicting DNA recognition by Cys2His2 zinc finger proteins. [My Copy] Bioinformatics (Oxford, England) (13 November 2008) by Anton V V. Persikov, Robert Osada, Mona Singh posted to zinc_fingers by aalibes on 2008-11-17 09:58:59 as along with 5 people and 1 group lptolik maximilianh wilbur hugowill kgutwin KeatingJClub
	Investigation of transcription factor Ndt80 affinity differences for wild type and mutant DNA: A molecular dynamics study [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 73, No. 2. (2008), pp. 325-337. by Katarina Hart, Lennart Nilsson posted to transcription_factors protein_dna by aalibes on 2008-11-07 16:13:10 as
	Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases [My Copy] Nature, Vol. 456, No. 7218. (6 November 2008), pp. 107-111. by Pilar Redondo, Jesus Prieto, Ines G. Munoz, et al.Andreu Alibes, Francois Stricher, Luis Serrano, Jean-Pierre Cabaniols, Fayza Daboussi, Sylvain Arnould, Christophe Perez, Philippe Duchateau, Frederic Paques, Francisco J. Blanco, Guillermo Montoya posted to meganucleases by aalibes on 2008-11-06 08:19:49 as along with 1 person jbhiatt
	SysZNF: the C2H2 zinc finger gene database. [My Copy] Nucleic acids research (30 October 2008) by Guohui Ding, Peter Lorenz, Michael Kreutzer, Yixue Li, Hans-Juergen J. Thiesen posted to zinc_fingers by aalibes on 2008-11-03 13:40:25 as along with 1 person guhjy
	Prediction of TF target sites based on atomistic models of protein-DNA complexes [My Copy] BMC Bioinformatics, Vol. 9 (16 October 2008), 436. by Vladimir E. Angarica, Abel G. Perez, Ana T. Vasconcelos, Julio Collado-Vides, Bruno Contreras-Moreira posted to transcription_factors protein_dna by aalibes on 2008-10-22 09:16:34 as along with 2 people emptyhb lptolik
	You Bastard: A Narrative Exploration of the Experience of Indignation within Organizations [My Copy] Organization Studies, Vol. 26, No. 11. (1 November 2005), pp. 1625-1640. by David Sims posted to ignobel by aalibes on 2008-10-20 15:07:38 as along with 5 people rschulz01 kevinemamy neils shasha_s ajaymalik
	DNA-binding specificity of NGFI-A and related zinc finger transcription factors [My Copy] Mol. Cell. Biol., Vol. 15, No. 4. (1 April 1995), pp. 2275-2287. by A. H. Swirnoff, J. Milbrandt posted to zinc_fingers paper by aalibes on 2008-10-17 11:12:57 as along with 1 person kristallreiner
	Analysis of zinc fingers optimized via phage display: evaluating the utility of a recognition code [My Copy] Journal of Molecular Biology, Vol. 285, No. 5. (05 February 1999), pp. 1917-1934. by S. Wolfe posted to zinc_fingers paper by aalibes on 2008-10-17 11:12:05 as
	A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors [My Copy] Nature Biotechnology, Vol. 23, No. 8. (24 July 2005), pp. 988-994. by Xiangdong Meng, Michael H. Brodsky, Scot A. Wolfe posted to transcription_factors protein_dna paper by aalibes on 2008-10-17 11:11:02 as along with 3 people and 1 group austin_mcdonald jbhiatt ajarman Jarman Lab
	Protein-DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins [My Copy] Nucl. Acids Res. (18 September 2008), gkn573. by Shandar Ahmad, Ozlem Keskin, Akinori Sarai, Ruth Nussinov posted to protein_dna by aalibes on 2008-10-13 12:08:59 as along with 2 people TOchi maximilianh
	UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. [My Copy] Nucleic acids research (8 October 2008) by Daniel E E. Newburger, Martha L L. Bulyk posted to protein_dna by aalibes on 2008-10-13 08:54:31 as along with 2 people lptolik guhjy
	Identification of a Pax paired domain recognition sequence and evidence for DNA-dependent conformational changes. [My Copy] The Journal of biological chemistry, Vol. 269, No. 11. (18 March 1994), pp. 8355-8361. by J. Epstein, J. Cai, T. Glaser, L. Jepeal, R. Maas posted to tf_exp by aalibes on 2008-10-07 11:15:26 as
	The DNA-binding specificity of the hepatocyte nuclear factor 3/forkhead domain is influenced by amino-acid residues adjacent to the recognition helix. [My Copy] Molecular and cellular biology, Vol. 14, No. 4. (April 1994), pp. 2755-2766. by D. G. Overdier, A. Porcella, R. H. Costa posted to tf_exp by aalibes on 2008-10-07 11:14:49 as along with 1 person and 1 group Auger Dead 60's
	An analysis of genes regulated by the multi-functional transcriptional regulator Yin Yang-1. [My Copy] Nucleic acids research, Vol. 22, No. 24. (11 December 1994), pp. 5151-5155. by A. Shrivastava, K. Calame posted to tf_exp by aalibes on 2008-10-07 11:11:45 as
	A consensus DNA-binding site for the androgen receptor. [My Copy] Molecular endocrinology (Baltimore, Md.), Vol. 6, No. 12. (December 1992), pp. 2229-2235. by P. J. Roche, S. A. Hoare, M. G. Parker posted to tf_exp by aalibes on 2008-10-07 11:10:57 as
	Identification of DNA sequences that bind retinoid X receptor-1,25(OH)2D3-receptor heterodimers with high affinity. [My Copy] Molecular and cellular endocrinology, Vol. 113, No. 1. (30 August 1995), pp. 89-98. by S. Colnot, M. Lambert, C. Blin, M. Thomasset, C. Perret posted to tf_exp by aalibes on 2008-10-07 11:10:12 as
	Identification of AML-1 and the (8;21) translocation protein (AML-1/ETO) as sequence-specific DNA-binding proteins: the runt homology domain is required for DNA binding and protein-protein interactions. [My Copy] Molecular and cellular biology, Vol. 13, No. 10. (October 1993), pp. 6336-6345. by S. Meyers, J. R. Downing, S. W. Hiebert posted to tf_exp by aalibes on 2008-10-07 11:09:29 as
	Base preferences for DNA binding by the bHLH-Zip protein USF: effects of MgCl2 on specificity and comparison with binding of Myc family members. [My Copy] Nucleic acids research, Vol. 22, No. 14. (25 July 1994), pp. 2801-2810. by A. J. Bendall, P. L. Molloy posted to tf_exp by aalibes on 2008-10-07 11:05:51 as
	A novel DNA sequence periodicity decodes nucleosome positioning. [My Copy] Nucleic acids research (1 October 2008) by Kaifu Chen, Qingshu Meng, Lina Ma, et al.Qingyou Liu, Petrus Tang, Chungshung Chiu, Songnian Hu, Jun Yu posted to nucleosome by aalibes on 2008-10-06 09:38:29 as along with 4 people Scis0000002 polivares idonaldson lptolik
	Predicting transcription factor specificity with all-atom models. [My Copy] Nucleic acids research (1 October 2008) by Sahand Jamal J. Rahi, Peter Virnau, Leonid A A. Mirny, Mehran Kardar posted to transcription_factors by aalibes on 2008-10-06 09:38:12 as along with 6 people Jporci chrn reyez maximilianh lptolik zwang
	Nucleosome positioning in human HOX gene clusters. [My Copy] Genome research (22 August 2008) by Peter V V. Kharchenko, Caroline J J. Woo, Michael Y Y. Tolstorukov, Robert E E. Kingston, Peter J J. Park posted to nucleosome by aalibes on 2008-10-03 09:47:01 as along with 1 person inesdesantiago

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