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aalibes library [266 articles]

Neue Artikel in aalibes library ordered by importance.
  • Systematic identification of statistically significant network measures.
    Phys Rev E Stat Nonlin Soft Matter Phys, Vol. 71, No. 1 Pt 2. (January 2005)
    by E Ziv, R Koytcheff, M Middendorf, C Wiggins
    posted to networks by aalibes on 2005-03-25 23:10:14 as *** along with 1 person and 2 groups korakot Philosophy_of_Information Blog_and_Wiki_Research
  • Probing potential binding modes of the p53 tetramer to DNA based on the symmetries encoded in p53 response elements.
    Nucleic Acids Res (5 November 2007)
    by Buyong Ma, Arnold J J Levine
    posted to protein_dna p53 cancer by aalibes on 2008-07-25 11:34:04 as ** along with 1 person oelemento
  • Weight matrices for protein-DNA binding sites from a single co-crystal structure.
    Physical review. E, Statistical, nonlinear, and soft matter physics, Vol. 73, No. 6 Pt 1. (June 2006)
    by RG Endres, NS Wingreen
    posted to protein_dna by aalibes on 2008-07-24 16:01:11 as **
  • Protein-DNA recognition patterns and predictions.
    Annu Rev Biophys Biomol Struct, Vol. 34 (2005), pp. 379-398.
    by A Sarai, H Kono
    posted to protein_dna by aalibes on 2008-07-24 15:43:07 as ** along with 2 people ramensky medic0747
  • Ab initio prediction of transcription factor binding sites.
    Pac Symp Biocomput (2007), pp. 484-495.
    by LA Liu, JS Bader
    posted to protein_dna by aalibes on 2008-07-24 15:42:21 as ** along with 1 person idonaldson
  • Three-dimensional intricacies in protein-DNA recognition and transcriptional control
    Nature Structural & Molecular Biology, Vol. 14, No. 12., pp. 1118-1119.
    by Stephen C Harrison
    posted to protein_dna by aalibes on 2008-07-24 15:40:19 as **
  • Understanding the molecular machinery of genetics through 3D structures.
    Nat Rev Genet (27 December 2007)
    by Roman A A Laskowski, Janet M M Thornton
    posted to protein_structure by aalibes on 2008-07-24 14:02:30 as ** along with 4 people higueruelo jwm sebastien_vigneau grottenolm
  • From the first protein structures to our current knowledge of protein folding: delights and scepticisms.
    Nature reviews. Molecular cell biology (25 June 2008)
    by Alan R R Fersht
    posted to protein_structure by aalibes on 2008-07-24 13:36:52 as ** along with 2 people paulschlesinger dullhunk
  • Computational prediction of transcription-factor binding site locations.
    Genome Biol, Vol. 5, No. 1. (2003)
    by ML Bulyk
    posted to transcription_factors by aalibes on 2008-07-22 11:09:57 as ** along with 6 people and 1 group kaarsinogen lusk Stew nklee yevishere xili03 EisenLab
  • Protein-DNA binding specificity predictions with structural models
    Nucleic Acids Research, Vol. 33, No. 18. (2005), pp. 5781-5798.
    by Alexandre V Morozov, James J Havranek, David Baker, Eric D Siggia
    posted to protein_dna by aalibes on 2008-07-10 14:03:15 as ** along with 1 person medic0747
  • Context-dependent DNA recognition code for C2H2 zinc-finger transcription factors.
    Bioinformatics (Oxford, England) (27 June 2008)
    by Jiajian Liu, Gary D D Stormo
    posted to zinc_fingers by aalibes on 2008-07-07 12:10:40 as **
  • Two strategies for gene regulation by promoter nucleosomes
    Genome Res. (30 April 2008), gr.076059.108.
    by Itay Tirosh, Naama Barkai
    posted to nucleosome by aalibes on 2008-07-02 17:02:40 as ** along with 8 people inesdesantiago dchughes djkt fpattyn vega emptyhb roys nklee
  • A high-resolution map of nucleosome positioning on a fission yeast centromere
    Genome Res., Vol. 18, No. 7. (1 July 2008), pp. 1064-1072.
    by Jun S Song, Xingkun Liu, Shirley X Liu, Xiangwei He
    posted to nucleosome by aalibes on 2008-07-02 17:02:09 as **
  • Spatial effects on the speed and reliability of protein-DNA search
    Nucl. Acids Res., Vol. 36, No. 11. (1 June 2008), pp. 3570-3578.
    by Zeba Wunderlich, Leonid A Mirny
    posted to protein_dna by aalibes on 2008-06-26 10:48:26 as **
  • DNA physical properties determine nucleosome occupancy from yeast to fly
    Nucl. Acids Res. (17 May 2008), gkn262.
    by Vincent Miele, Cedric Vaillant, Yves D'aubenton-Carafa, Claude Thermes, Thierry Grange
    posted to nucleosome by aalibes on 2008-06-26 10:47:11 as ** along with 1 person vega
  • Inaugural Article: The direction of gut looping is established by changes in the extracellular matrix and in cell:cell adhesion
    Proceedings of the National Academy of Sciences, Vol. 105, No. 25. (24 June 2008), pp. 8499-8506.
    by Natasza A Kurpios, Marta Ibanes, Nicole M Davis, Wei Lui, Tamar Katz, James F Martin, Juan C Belmonte, Clifford J Tabin
    posted to marta by aalibes on 2008-06-25 10:22:05 as ** along with 1 person OriginalLurch
  • Statistical distributions of nucleosomes: nonrandom locations by a stochastic mechanism.
    Nucleic acids research, Vol. 16, No. 14A. (25 July 1988), pp. 6677-6690.
    by RD Kornberg, L Stryer
    posted to nucleosome by aalibes on 2008-06-20 16:20:32 as **
  • Crystal structures of I-SceI complexed to nicked DNA substrates: snapshots of intermediates along the DNA cleavage reaction pathway
    Nucl. Acids Res., Vol. 36, No. 10. (1 June 2008), pp. 3287-3296.
    by Carmen M Moure, Frederick S Gimble, Florante A Quiocho
    posted to meganucleases by aalibes on 2008-06-19 15:46:17 as **
  • Zinc-finger Nucleases: The Next Generation Emerges.
    Molecular therapy : the journal of the American Society of Gene Therapy (10 June 2008)
    by Toni Cathomen, J Keith Joung
    posted to zinc_fingers by aalibes on 2008-06-17 13:13:37 as **
  • A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome
    Genome Res. (12 June 2008), gr.078261.108.
    by Travis N Mavrich, Ilya P Ioshikhes, Bryan J Venters, Cizhong Jiang, Lynn P Tomsho, Ji Qi, Stephan C Schuster, Istvan Albert, Franklin B Pugh
    posted to nucleosome by aalibes on 2008-06-17 13:11:55 as ** along with 1 person vega
  • A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning
    Genome Res. (13 May 2008), gr.076463.108.
    by Anton Valouev, Jeffrey Ichikawa, Thaisan Tonthat, Jeremy Stuart, Swati Ranade, Heather Peckham, Kathy Zeng, Joel A Malek, Gina Costa, Kevin Mckernan, Arend Sidow, Andrew Fire, Steven M Johnson
    posted to nucleosome by aalibes on 2008-06-11 10:12:52 as ** along with 5 people and 1 group caseybrown vega Stew dpollard maximilianh RockmanLab
  • Specific DNA-binding by Apicomplexan AP2 transcription factors
    Proceedings of the National Academy of Sciences (9 June 2008), 0801993105.
    by Erandi K De Silva, Andrew R Gehrke, Kellen Olszewski, Ilsa Leon, Jasdave S Chahal, Martha L Bulyk, Manuel Llinas
    posted to transcription_factors by aalibes on 2008-06-10 13:36:35 as ** along with 1 person maximilianh
  • Cell cycle-specified fluctuation of nucleosome occupancy at gene promoters.
    PLoS genetics, Vol. 2, No. 9. (22 September 2006)
    by GJ Hogan, CK Lee, JD Lieb
    posted to nucleosome by aalibes on 2008-06-03 09:11:05 as **
  • DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions
    Nucl. Acids Res. (31 May 2008), gkn332.
    by Mu Gao, Jeffrey Skolnick
    posted to protein_dna by aalibes on 2008-06-02 11:25:11 as ** along with 1 person reyez
  • Re-cracking the nucleosome positioning code.
    Statistical applications in genetics and molecular biology, Vol. 7 (2008)
    by MR Segal
    posted to nucleosome by aalibes on 2008-05-13 16:12:23 as **
  • DNA conformations and their sequence preferences
    Nucl. Acids Res. (13 May 2008), gkn260.
    by Daniel Svozil, Jan Kalina, Marek Omelka, Bohdan Schneider
    posted to dna by aalibes on 2008-05-13 16:06:34 as ** along with 4 people and 2 groups fpattyn reyez jmrivort TOchi Neuroblastoma G-quadruplex
  • How protein stability and new functions trade off.
    PLoS computational biology, Vol. 4, No. 2. (February 2008)
    by N Tokuriki, F Stricher, L Serrano, DS Tawfik
    posted to protein_stability by aalibes on 2008-05-13 10:08:58 as **
  • Generation and analysis of mesophilic variants of the thermostable archaeal I-DmoI homing endonuclease.
    The Journal of biological chemistry, Vol. 283, No. 7. (15 February 2008), pp. 4364-4374.
    by J Prieto, JC Epinat, P Redondo, E Ramos, D Padró, F Cédrone, G Montoya, F Pâques, FJ Blanco
    posted to meganucleases by aalibes on 2008-05-13 09:43:07 as **
  • coliSNP database server mapping nsSNPs on protein structures.
    Nucleic acids research, Vol. 36, No. Database issue. (January 2008)
    by H Kono, T Yuasa, S Nishiue, K Yura
    posted to snp by aalibes on 2008-05-08 14:40:43 as **
  • nuScore: a web-interface for nucleosome positioning predictions
    Bioinformatics (29 April 2008), btn212.
    by Michael Y Tolstorukov, Vidhu Choudhary, Wilma K Olson, Victor B Zhurkin, Peter J Park
    posted to nucleosome by aalibes on 2008-05-05 11:29:09 as **
  • Evolvability and hierarchy in rewired bacterial gene networks
    Nature, Vol. 452, No. 7189. (17 April 2008), pp. 840-845.
    by Mark Isalan, Caroline Lemerle, Konstantinos Michalodimitrakis, Carsten Horn, Pedro Beltrao, Emanuele Raineri, Mireia Garriga-Canut, Luis Serrano
    posted to networks by aalibes on 2008-04-17 13:25:33 as ** along with 17 people and 4 groups aheilbut chad_davis michaelbarton austin AbnerCYH hryk margaritis cactus dbikard Garamonfok caseybrown biehl tmmurali dullhunk neils cmzmasek josedavid BergmanLab SynBioSys Centre de Recherches Interdisciplinaires GEB
  • FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes
    Bioinformatics, Vol. 20, No. 4. (1 March 2004), pp. 578-580.
    by Fatima Al-Shahrour, Ramon Diaz-Uriarte, Joaquin Dopazo
    posted to tools by aalibes on 2008-03-28 20:44:18 as ** along with 5 people ellakat sgoetz RMGraze macavity1g Garamonfok
  • Theoretical and experimental approaches to understand morphogen gradients
    Mol Syst Biol, Vol. 4 (25 March 2008)
    by Marta Ibanes, Juan C Belmonte
    posted to marta by aalibes on 2008-03-26 20:12:39 as ** along with 1 person bootsy
  • Dynamic Regulation of Nucleosome Positioning in the Human Genome
    Cell, Vol. 132, No. 5. (7 March 2008), pp. 887-898.
    by Dustin E Schones, Kairong Cui, Suresh Cuddapah, Tae-Young Roh, Artem Barski, Zhibin Wang, Gang Wei, Keji Zhao
    posted to nucleosome by aalibes on 2008-03-25 11:49:11 as ** along with 7 people mikaelhuss vega sameetmehta dchughes sleepingcell idonaldson oelemento
  • Structure-based prediction of transcription factor binding sites using a protein-DNA docking approach
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by Zhijie Liu, Jun-Tao Guo, Ting Li, Ying Xu
    posted to transcription_factors by aalibes on 2008-03-11 09:20:24 as ** along with 1 person neils
  • De Novo Computational Design of Retro-Aldol Enzymes
    Science, Vol. 319, No. 5868. (7 March 2008), pp. 1387-1391.
    by Lin Jiang, Eric A Althoff, Fernando R Clemente, Lindsey Doyle, Daniela Rothlisberger, Alexandre Zanghellini, Jasmine L Gallaher, Jamie L Betker, Fujie Tanaka, Carlos F Barbas, Donald Hilvert, Kendall N Houk, Barry L Stoddard, David Baker
    posted to protein_mutation by aalibes on 2008-03-07 15:09:03 as ** along with 11 people and 3 groups joseph_x_zhou ucbcjbm barry jwm aprasad dgront zwang sobolevnrm davidlott msuarezdiez scienbox McCammon structural_bioinformatics baker-group
  • GroEL stimulates protein folding through forced unfolding
    Nature Structural & Molecular Biology, Vol. 15, No. 3. (02 March 2008), pp. 303-311.
    by Zong Lin, Damian Madan, Hays S Rye
    posted to groel by aalibes on 2008-03-06 11:13:04 as ** along with 4 people hsekiguc choonpeng zwang cactus
  • Functional protein divergence in the evolution of Homo sapiens
    Genome Biology, Vol. 9 (15 February 2008), R33.
    by Nuria Lopez-Bigas, Subhajyoti De, Sarah A Teichmann
    posted to bioinformatics_general by aalibes on 2008-02-27 10:19:39 as ** along with 4 people djkt grahamc biomcgary zhanglab
  • Meganucleases and DNA double-strand break-induced recombination: perspectives for gene therapy.
    Curr Gene Ther, Vol. 7, No. 1. (February 2007), pp. 49-66.
    by F Pâques, P Duchateau
    posted to meganucleases by aalibes on 2008-02-22 16:03:38 as **
  • Protein-nucleic acid complexes: large, small, old, and new
    Current Opinion in Structural Biology, Vol. 18, No. 1. (February 2008), pp. 67-69.
    by Gregory D Van Duyne, Wei Yang
    posted to protein_dna by aalibes on 2008-02-20 15:13:46 as **
  • Computer design of obligate heterodimer meganucleases allows efficient cutting of custom DNA sequences
    Nucl. Acids Res. (14 February 2008), gkn059.
    by Emmanuel Fajardo-Sanchez, Francois Stricher, Frederic Paques, Mark Isalan, Luis Serrano
    posted to meganucleases by aalibes on 2008-02-18 11:54:20 as **
  • Genomic Sequence Is Highly Predictive of Local Nucleosome Depletion
    PLoS Computational Biology, Vol. 4, No. 1. (1 January 2008), e13.
    by Guo-Cheng Yuan, Jun S Liu
    posted to nucleosome by aalibes on 2008-01-29 15:14:22 as ** along with 1 person and 1 group stajich Berkeley Mycology
  • dbSNP: the NCBI database of genetic variation.
    Nucleic Acids Res, Vol. 29, No. 1. (1 January 2001), pp. 308-311.
    by ST Sherry, MH Ward, M Kholodov, J Baker, L Phan, EM Smigielski, K Sirotkin
    posted to snp by aalibes on 2008-01-25 16:13:53 as ** along with 3 people chad_davis fisherp massivemayhem
  • High-throughput mapping of the chromatin structure of human promoters
    Nat Biotech, Vol. 25, No. 2. (February 2007), pp. 244-248.
    by Fatih Ozsolak, Jun S Song, Shirley X Liu, David E Fisher
    posted to nucleosome by aalibes on 2008-01-24 14:44:04 as ** along with 5 people and 2 groups jyuh jfr dchughes vega ccr G4ID Genetics-of-Gambling
  • The Histone Database: a comprehensive resource for histones and histone fold-containing proteins.
    Proteins, Vol. 62, No. 4. (1 March 2006), pp. 838-842.
    by L Mariño-Ramírez, B Hsu, AD Baxevanis, D Landsman
    posted to nucleosome by aalibes on 2008-01-24 11:24:59 as **
  • A high-resolution atlas of nucleosome occupancy in yeast
    Nature Genetics, Vol. 39, No. 10. (16 September 2007), pp. 1235-1244.
    by William Lee, Desiree Tillo, Nicolas Bray, Randall H Morse, Ronald W Davis, Timothy R Hughes, Corey Nislow
    posted to nucleosome by aalibes on 2008-01-23 11:51:27 as ** along with 2 people siebert epigenetics
  • GeneLibrarian: an effective gene-information summarization and visualization system
    BMC Bioinformatics, Vol. 7 (29 August 2006), 392.
    by Jung-Hsien Chiang, Jyh-Wei Shin, Heng-Hui Liu, Chong-Liang Chin
    posted to tools by aalibes on 2008-01-22 15:46:41 as ** along with 2 people and 1 group yas rdiaz T_lab
  • GeneTools - Application for functional annotation and statistical hypothesis testing
    BMC Bioinformatics, Vol. 7 (24 October 2006), 470.
    by Vidar Beisvag, Frode KR Junge, Hallgeir Bergum, Lars Jolsum, Stian Lydersen, Clara-Cecilie Gunther, Heri Ramampiaro, Mette Langaas, Arne K Sandvik, Astrid Laegreid
    posted to tools by aalibes on 2008-01-22 15:46:29 as ** along with 2 people jyuh rdiaz
  • DAVID Gene Functional Classification Tool: A novel biological module-centric algorithm to functionally analyze large gene list
    Genome Biology, Vol. 8 (04 September 2007), R183.
    by Da W Huang, Brad T Sherman, Qina Tan, Jack R Collins, Gregory W Alvord, Jean Roayaei, Robert Stephens, Michael W Baseler, Clifford H Lane, Richard A Lempicki
    posted to tools by aalibes on 2008-01-22 15:39:34 as ** along with 6 people heliopais jyuh dragonrez jfr rdiaz mellabee
  • SignS: a parallelized, open-source, freely available, web-based tool for gene selection and molecular signatures for survival and censored data
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Ramon Diaz-Uriarte
    posted to tools by aalibes on 2008-01-22 09:43:20 as ** along with 4 people jfr jyuh chad_davis frohike
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