Nucleic Acids Research

Editorial:

Claire Saxby

NAR launches new Advance Access publication model
Nucleic Acids Research Advance Access published on July 26, 2006
Nucl. Acids Res. 2006 34: 3833; doi:10.1093/nar/gkl523 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Computational Biology:

Sarath Chandra Janga, Warren F. Lamboy, Araceli M. Huerta, and Gabriel Moreno-Hagelsieb

The distinctive signatures of promoter regions and operon junctions across prokaryotes
Nucleic Acids Research Advance Access published on August 12, 2006
Nucl. Acids Res. 2006 34: 3980-3987; doi:10.1093/nar/gkl563 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Chun-Chi Liu, Wen-Shyen E. Chen, Chin-Chung Lin, Hsiang-Chuan Liu, Hsuan-Yu Chen, Pan-Chyr Yang, Pei-Chun Chang, and Jeremy J.W. Chen

Topology-based cancer classification and related pathway mining using microarray data
Nucleic Acids Research Advance Access published on August 16, 2006
Nucl. Acids Res. 2006 34: 4069-4080; doi:10.1093/nar/gkl583 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Genomics:

Rory Johnson, Richard J. Gamblin, Lezanne Ooi, Alexander W. Bruce, Ian J. Donaldson, David R. Westhead, Ian C. Wood, Richard M. Jackson, and Noel J. Buckley

Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication
Nucleic Acids Research Advance Access published on August 9, 2006
Nucl. Acids Res. 2006 34: 3862-3877; doi:10.1093/nar/gkl525 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Johanna Eddy and Nancy Maizels

Gene function correlates with potential for G4 DNA formation in the human genome
Nucleic Acids Research Advance Access published on August 10, 2006
Nucl. Acids Res. 2006 34: 3887-3896; doi:10.1093/nar/gkl529 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Jun-ichi Takeda, Yutaka Suzuki, Mitsuteru Nakao, Roberto A. Barrero, Kanako O. Koyanagi, Lihua Jin, Chie Motono, Hiroko Hata, Takao Isogai, Keiichi Nagai, Tetsuji Otsuki, Vladimir Kuryshev, Masafumi Shionyu, Kei Yura, Mitiko Go, Jean Thierry-Mieg, Danielle Thierry-Mieg, Stefan Wiemann, Nobuo Nomura, Sumio Sugano, Takashi Gojobori, and Tadashi Imanishi

Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56 419 completely sequenced and manually annotated full-length cDNAs
Nucleic Acids Research Advance Access published on August 12, 2006
Nucl. Acids Res. 2006 34: 3917-3928; doi:10.1093/nar/gkl507 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Nihar Sheth, Xavier Roca, Michelle L. Hastings, Ted Roeder, Adrian R. Krainer, and Ravi Sachidanandam

Comprehensive splice-site analysis using comparative genomics
Nucleic Acids Research Advance Access published on August 12, 2006
Nucl. Acids Res. 2006 34: 3955-3967; doi:10.1093/nar/gkl556 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Alexey V. Lobanov, Stephan Gromer, Gustavo Salinas, and Vadim N. Gladyshev

Selenium metabolism in Trypanosoma: characterization of selenoproteomes and identification of a Kinetoplastida-specific selenoprotein
Nucleic Acids Research Advance Access published on August 16, 2006
Nucl. Acids Res. 2006 34: 4012-4024; doi:10.1093/nar/gkl541 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Molecular Biology:

Annette Kamionka, Marius Majewski, Karin Roth, Ralph Bertram, Christine Kraft, and Wolfgang Hillen

Induction of single chain tetracycline repressor requires the binding of two inducers
Nucleic Acids Research Advance Access published on August 9, 2006
Nucl. Acids Res. 2006 34: 3834-3841; doi:10.1093/nar/gkl316 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Dong-Ju Shin, Michelina Plateroti, Jacques Samarut, and Timothy F. Osborne

Two uniquely arranged thyroid hormone response elements in the far upstream 5' flanking region confer direct thyroid hormone regulation to the murine cholesterol 7 hydroxylase gene
Nucleic Acids Research Advance Access published on August 9, 2006
Nucl. Acids Res. 2006 34: 3853-3861; doi:10.1093/nar/gkl506 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Qiliang Li, Xiangdong Fang, Ivan Olave, Hemei Han, Man Yu, Ping Xiang, and George Stamatoyannopoulos

Transcriptional potential of the -globin gene is dependent on the CACCC box in a developmental stage-specific manner
Nucleic Acids Research Advance Access published on August 12, 2006
Nucl. Acids Res. 2006 34: 3909-3916; doi:10.1093/nar/gkl474 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Xavier Le Guezennec, Michiel Vermeulen, and Hendrik G. Stunnenberg

Molecular characterization of Sin3 PAH-domain interactor specificity and identification of PAH partners
Nucleic Acids Research Advance Access published on August 12, 2006
Nucl. Acids Res. 2006 34: 3929-3937; doi:10.1093/nar/gkl537 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Vladimir A. Mitkevich, Artem V. Kononenko, Irina Yu. Petrushanko, Dmitry V. Yanvarev, Alexander A. Makarov, and Lev L. Kisselev

Termination of translation in eukaryotes is mediated by the quaternary eRF1•eRF3•GTP•Mg²⁺ complex. The biological roles of eRF3 and prokaryotic RF3 are profoundly distinct
Nucleic Acids Research Advance Access published on August 12, 2006
Nucl. Acids Res. 2006 34: 3947-3954; doi:10.1093/nar/gkl549 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Karin Leandersson, Kristian Riesbeck, and Tommy Andersson

Wnt-5a mRNA translation is suppressed by the Elav-like protein HuR in human breast epithelial cells
Nucleic Acids Research Advance Access published on August 12, 2006
Nucl. Acids Res. 2006 34: 3988-3999; doi:10.1093/nar/gkl571 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Mahmud K. K. Shivji, Owen R. Davies, Jane M. Savill, Debbie L. Bates, Luca Pellegrini, and Ashok R. Venkitaraman

A region of human BRCA2 containing multiple BRC repeats promotes RAD51-mediated strand exchange
Nucleic Acids Research Advance Access published on August 16, 2006
Nucl. Acids Res. 2006 34: 4000-4011; doi:10.1093/nar/gkl505 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Fiona A. Myers, Pascal Lefevre, Evangelia Mantouvalou, Kimberley Bruce, Claire Lacroix, Constanze Bonifer, Alan W. Thorne, and Colyn Crane-Robinson

Developmental activation of the lysozyme gene in chicken macrophage cells is linked to core histone acetylation at its enhancer elements
Nucleic Acids Research Advance Access published on August 16, 2006
Nucl. Acids Res. 2006 34: 4025-4035; doi:10.1093/nar/gkl543 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Christopher D. Bayliss, Martin J. Callaghan, and E. Richard Moxon

High allelic diversity in the methyltransferase gene of a phase variable type III restriction-modification system has implications for the fitness of Haemophilus influenzae
Nucleic Acids Research Advance Access published on August 16, 2006
Nucl. Acids Res. 2006 34: 4046-4059; doi:10.1093/nar/gkl568 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Balla Venkata Kranthi, Natarajan Balasubramanian, and Pundi N. Rangarajan

Isolation of a single-stranded DNA-binding protein from the methylotrophic yeast, Pichia pastoris and its identification as zeta crystallin
Nucleic Acids Research Advance Access published on August 16, 2006
Nucl. Acids Res. 2006 34: 4060-4068; doi:10.1093/nar/gkl577 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nucleic Acid Enzymes:

Tuuli Välineva, Jie Yang, and Olli Silvennoinen

Characterization of RNA helicase A as component of STAT6-dependent enhanceosome
Nucleic Acids Research Advance Access published on August 12, 2006
Nucl. Acids Res. 2006 34: 3938-3946; doi:10.1093/nar/gkl539 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ekaterina Kashkina, Michael Anikin, Tahir H. Tahirov, Sergei N. Kochetkov, Dmitry G. Vassylyev, and Dmitry Temiakov

Elongation complexes of Thermus thermophilus RNA polymerase that possess distinct translocation conformations
Nucleic Acids Research Advance Access published on August 16, 2006
Nucl. Acids Res. 2006 34: 4036-4045; doi:10.1093/nar/gkl559 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

RNA:

Birgit Lung, Anja Zemann, Monika J. Madej, Markus Schuelke, Sandra Techritz, Stephanie Ruf, Ralph Bock, and Alexander Hüttenhofer

Identification of small non-coding RNAs from mitochondria and chloroplasts
Nucleic Acids Research Advance Access published on August 9, 2006
Nucl. Acids Res. 2006 34: 3842-3852; doi:10.1093/nar/gkl448 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Structural Biology:

Cheng-Yang Huang, Che-Hsiung Hsu, Yuh-Ju Sun, Huey-Nan Wu, and Chwan-Deng Hsiao

Complexed crystal structure of replication restart primosome protein PriB reveals a novel single-stranded DNA-binding mode
Nucleic Acids Research Advance Access published on August 9, 2006
Nucl. Acids Res. 2006 34: 3878-3886; doi:10.1093/nar/gkl536 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Elizabeth Hooley, Victoria Fairweather, Anthony R. Clarke, Kevin Gaston, and R. Leo Brady

The recognition of local DNA conformation by the human papillomavirus type 6 E2 protein
Nucleic Acids Research Advance Access published on August 12, 2006
Nucl. Acids Res. 2006 34: 3897-3908; doi:10.1093/nar/gkl466 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Hannes Simader, Michael Hothorn, Christine Köhler, Jerome Basquin, George Simos, and Dietrich Suck

Structural basis of yeast aminoacyl-tRNA synthetase complex formation revealed by crystal structures of two binary sub-complexes
Nucleic Acids Research Advance Access published on August 12, 2006
Nucl. Acids Res. 2006 34: 3968-3979; doi:10.1093/nar/gkl560 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Methods Online:

Philippe Lamy, Claus L. Andersen, Friedrik P. Wikman, and Carsten Wiuf

Genotyping and annotation of Affymetrix SNP arrays
Nucleic Acids Research Advance Access published on August 9, 2006
Nucl. Acids Res. 2006 34: e100; doi:10.1093/nar/gkl475 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Kavitha Bhasi, Li Zhang, Daniel Brazeau, Aidong Zhang, and Murali Ramanathan

Information-theoretic identification of predictive SNPs and supervised visualization of genome-wide association studies
Nucleic Acids Research Advance Access published on August 9, 2006
Nucl. Acids Res. 2006 34: e101; doi:10.1093/nar/gkl520 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Rieko Oyama, Hideaki Takashima, Masato Yonezawa, Nobuhide Doi, Etsuko Miyamoto-Sato, Masataka Kinjo, and Hiroshi Yanagawa

Protein–protein interaction analysis by C-terminally specific fluorescence labeling and fluorescence cross-correlation spectroscopy
Nucleic Acids Research Advance Access published on August 16, 2006
Nucl. Acids Res. 2006 34: e102; doi:10.1093/nar/gkl477 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

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