Nucl. Acids Res. -- Nucleic Acids Research Advance Access

Nucleic Acids Research Advance Access

Nucleic Acids Research Advance Access articles are papers that have been copyedited and typeset but not yet paginated for inclusion in an issue of the journal. More information, including how to cite Advance Access papers, can be found on the Advance Access page.

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21 November 2008

Abstract Database Issue: Daniel Lawson, Peter Arensburger, Peter Atkinson, Nora J. Besansky, Robert V. Bruggner, Ryan Butler, Kathryn S. Campbell, George K. Christophides, Scott Christley, Emmanuel Dialynas, Martin Hammond, Catherine A. Hill, Nathan Konopinski, Neil F. Lobo, Robert M. MacCallum, Greg Madey, Karine Megy, Jason Meyer, Seth Redmond, David W. Severson, Eric O. Stinson, Pantelis Topalis, Ewan Birney, William M. Gelbart, Fotis C. Kafatos, Christos Louis, and Frank H. Collins
VectorBase: a data resource for invertebrate vector genomics
Nucleic Acids Research Advance Access published on November 21, 2008.
doi:10.1093/nar/gkn857
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20 November 2008

Abstract Gene regulation, chromation and genetics: Nickolai A. Tchurikov, Olga V. Kretova, Evgenia D. Moiseeva, and Dmitri V. Sosin
Evidence for RNA synthesis in the intergenic region between enhancer and promoter and its inhibition by insulators in Drosophila melanogaster
Nucleic Acids Research Advance Access published on November 20, 2008.
doi:10.1093/nar/gkn926
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Abstract Database Issue: Milton H. Saier Jr, Ming Ren Yen, Keith Noto, Dorjee G. Tamang, and Charles Elkan
The Transporter Classification Database: recent advances
Nucleic Acids Research Advance Access published on November 20, 2008.
doi:10.1093/nar/gkn862
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16 November 2008

Abstract Nucleic Acid Enzymes: Hyongi Chon, Alex Vassilev, Melvin L. DePamphilis, Yingming Zhao, Junmei Zhang, Peter M. Burgers, Robert J. Crouch, and Susana M. Cerritelli
Contributions of the two accessory subunits, RNASEH2B and RNASEH2C, to the activity and properties of the human RNase H2 complex
Nucleic Acids Research Advance Access published on November 16, 2008.
doi:10.1093/nar/gkn913
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Abstract Gene regulation, chromatin and epigenetics: Peter M. Wilson, William Fazzone, Melissa J. LaBonte, Heinz-Josef Lenz, and Robert D. Ladner
Regulation of human dUTPase gene expression and p53-mediated transcriptional repression in response to oxaliplatin-induced DNA damage
Nucleic Acids Research Advance Access published on November 16, 2008.
doi:10.1093/nar/gkn910
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Abstract Methods Online: Kalim U. Mir, Hong Qi, Oleg Salata, and Giuseppe Scozzafava
Sequencing by Cyclic Ligation and Cleavage (CycLiC) directly on a microarray captured template
Nucleic Acids Research Advance Access published on November 16, 2008.
doi:10.1093/nar/gkn906
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Abstract RNA: Scott Davis, Stephanie Propp, Susan M. Freier, Laura E. Jones, Martin J. Serra, Garth Kinberger, Balkrishen Bhat, Eric E. Swayze, C. Frank Bennett, and Christine Esau
Potent inhibition of microRNA in vivo without degradation
Nucleic Acids Research Advance Access published on November 16, 2008.
doi:10.1093/nar/gkn904
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Abstract Database issue: David J. Sherman, Tiphaine Martin, Macha Nikolski, Cyril Cayla, Jean-Luc Souciet, Pascal Durrens, and for the Génolevures Consortium
Génolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes
Nucleic Acids Research Advance Access published on November 16, 2008.
doi:10.1093/nar/gkn859
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Abstract Database Issue: Hsi-Yuan Huang, Heng-Yi Chang, Chih-Hung Chou, Ching-Ping Tseng, Shinn-Ying Ho, Chi-Dung Yang, Yih-Wei Ju, and Hsien-Da Huang
sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes
Nucleic Acids Research Advance Access published on November 16, 2008.
doi:10.1093/nar/gkn852
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14 November 2008

Abstract Genome integrity, repair and replication: Elizabeth S. Dorn, Paul D. Chastain II, Jonathan R. Hall, and Jeanette Gowen Cook
Analysis of re-replication from deregulated origin licensing by DNA fiber spreading
Nucleic Acids Research Advance Access published on November 14, 2008.
doi:10.1093/nar/gkn912
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Abstract Molecular Biology: Jing-Yi Lin, Mei-Ling Li, and Shin-Ru Shih
Far upstream element binding protein 2 interacts with enterovirus 71 internal ribosomal entry site and negatively regulates viral translation
Nucleic Acids Research Advance Access published on November 14, 2008.
doi:10.1093/nar/gkn901
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Nucleic Acid Enzymes: Tonatiuh Romero Salas, Irina Petruseva, Olga Lavrik, and Carole Saintomé
Evidence for direct contact between the RPA3 subunit of the human replication protein A and single-stranded DNA
Nucleic Acids Research Advance Access published on November 14, 2008.
doi:10.1093/nar/gkn895
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Abstract RNA: Kyung-Chul Woo, Tae-Don Kim, Kyung-Ha Lee, Do-Yeon Kim, Wanil Kim, Kyung-Yeol Lee, and Kyong-Tai Kim
Mouse period 2 mRNA circadian oscillation is modulated by PTB–mediated rhythmic mRNA degradation
Nucleic Acids Research Advance Access published on November 14, 2008.
doi:10.1093/nar/gkn893
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Abstract Database Issue: Andrew R. Cameron, Manoj Samanta, Autumn Yuan, Dong He, and Eric Davidson
SpBase: the sea urchin genome database and web site
Nucleic Acids Research Advance Access published on November 14, 2008.
doi:10.1093/nar/gkn887
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Abstract Database Issue: Helen M. Berman, John D. Westbrook, Margaret J. Gabanyi, Wendy Tao, Raship Shah, Andrei Kouranov, Torsten Schwede, Konstantin Arnold, Florian Kiefer, Lorenza Bordoli, Jürgen Kopp, Michael Podvinec, Paul D. Adams, Lester G. Carter, Wladek Minor, Rajesh Nair, and Joshua La Baer
The protein structure initiative structural genomics knowledgebase
Nucleic Acids Research Advance Access published on November 14, 2008.
doi:10.1093/nar/gkn790
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12 November 2008

Abstract RNA: Julia P. Swiercz, Hindra, Jan Bobek, Henry J. Haiser, Christina Di Berardo, Brian Tjaden, and Marie A. Elliot
Small non-coding RNAs in Streptomyces coelicolor
Nucleic Acids Research Advance Access published on November 12, 2008.
doi:10.1093/nar/gkn898
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Abstract Methods online: Wei-li Liu, Mark Stevenson, Leonard W. Seymour, and Kerry D. Fisher
Quantification of siRNA using competitive qPCR
Nucleic Acids Research Advance Access published on November 12, 2008.
doi:10.1093/nar/gkn903
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Abstract Gene Regulation, Chromatin and Epigenetics: Jonathan D. Turner, Laetitia P. L. Pelascini, Joana A. Macedo, and Claude P. Muller
Highly individual methylation patterns of alternative glucocorticoid receptor promoters suggest individualized epigenetic regulatory mechanisms
Nucleic Acids Research Advance Access published on November 12, 2008.
doi:10.1093/nar/gkn897
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Abstract Molecular Biology: Rajita A. Karran and Katalin A. Hudak
Depurination within the intergenic region of Brome mosaic virus RNA3 inhibits viral replication in vitro and in vivo
Nucleic Acids Research Advance Access published on November 12, 2008.
doi:10.1093/nar/gkn896
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Abstract Methods online: Kazumasa Yasui, Yasunobu Kano, Kaori Tanaka, Kunitomo Watanabe, Mariko Shimizu-Kadota, Hirofumi Yoshikawa, and Tohru Suzuki
Improvement of bacterial transformation efficiency using plasmid artificial modification
Nucleic Acids Research Advance Access published on November 12, 2008.
doi:10.1093/nar/gkn884
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Abstract Database Issue: J. R. Cole, Q. Wang, E. Cardenas, J. Fish, B. Chai, R. J. Farris, A. S. Kulam-Syed-Mohideen, D. M. McGarrell, T. Marsh, G. M. Garrity, and J. M. Tiedje
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
Nucleic Acids Research Advance Access published on November 12, 2008.
doi:10.1093/nar/gkn879
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Genomics: Dawn M. Simon and Steven Zimmerly
A diversity of uncharacterized reverse transcriptases in bacteria
Nucleic Acids Research Advance Access published on November 12, 2008.
doi:10.1093/nar/gkn867
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Abstract Database Issue: Andres Leon Eduardo, Ezkurdia Iakes, García Beatriz, Valencia Alfonso, and Juan David
EcID. A database for the inference of functional interactions in E. coli
Nucleic Acids Research Advance Access published on November 12, 2008.
doi:10.1093/nar/gkn853
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Abstract Database Issue: Ulrike Schmidt, Swantje Struck, Bjoern Gruening, Julia Hossbach, Ines S. Jaeger, Roza Parol, Ulrike Lindequist, Eberhard Teuscher, and Robert Preissner
SuperToxic: a comprehensive database of toxic compounds
Nucleic Acids Research Advance Access published on November 12, 2008.
doi:10.1093/nar/gkn850
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Abstract Gene regulation, Chromatin and Epigenetics: Laura V. Papp, Junning Wang, Derek Kennedy, Didier Boucher, Yan Zhang, Vadim N. Gladyshev, Ravindra N. Singh, and Kum Kum Khanna
Functional characterization of alternatively spliced human SECISBP2 transcript variants
Nucleic Acids Research Advance Access published on November 12, 2008.
doi:10.1093/nar/gkn829
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10 November 2008

Abstract Molecular Biology: Matteo Rossi, Oleg N. Demidov, Carl W. Anderson, Ettore Appella, and Sharlyn J. Mazur
Induction of PPM1D following DNA-damaging treatments through a conserved p53 response element coincides with a shift in the use of transcription initiation sites
Nucleic Acids Research Advance Access published on November 10, 2008.
doi:10.1093/nar/gkn888
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Abstract Database Issue: Saumyendra N. Basu, Ravi Kollu, and Sharmila Banerjee-Basu
AutDB: a gene reference resource for autism research
Nucleic Acids Research Advance Access published on November 10, 2008.
doi:10.1093/nar/gkn835
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Abstract Molecular Biology: Mingang Xu, John R. McCarrey, and Norman B. Hecht
A cytoplasmic variant of the KH-type splicing regulatory protein serves as a decay-promoting factor for phosphoglycerate kinase 2 mRNA in murine male germ cells
Nucleic Acids Research Advance Access published on November 10, 2008.
doi:10.1093/nar/gkn800
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Abstract Database Issue: Helen Parkinson, Misha Kapushesky, Nikolay Kolesnikov, Gabriella Rustici, Mohammad Shojatalab, Niran Abeygunawardena, Hugo Berube, Miroslaw Dylag, Ibrahim Emam, Anna Farne, Ele Holloway, Margus Lukk, James Malone, Roby Mani, Ekaterina Pilicheva, Tim F. Rayner, Faisal Rezwan, Anjan Sharma, Eleanor Williams, Xiangqun Zheng Bradley, Tomasz Adamusiak, Marco Brandizi, Tony Burdett, Richard Coulson, Maria Krestyaninova, Pavel Kurnosov, Eamonn Maguire, Sudeshna Guha Neogi, Philippe Rocca-Serra, Susanna-Assunta Sansone, Nataliya Sklyar, Mengyao Zhao, Ugis Sarkans, and Alvis Brazma
ArrayExpress update—from an archive of functional genomics experiments to the atlas of gene expression
Nucleic Acids Research Advance Access published on November 10, 2008.
doi:10.1093/nar/gkn889
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Abstract Nucleic Acid Enzymes: Femi J. Olorunniji, Jiuya He, Sandra V.C.T. Wenwieser, Martin R. Boocock, and W. Marshall Stark
Synapsis and catalysis by activated Tn3 resolvase mutants
Nucleic Acids Research Advance Access published on November 10, 2008.
doi:10.1093/nar/gkn885
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Abstract Database Issue: Zhi-yu Peng, Xin Zhou, Linchuan Li, Xiangchun Yu, Hongjiang Li, Zhiqiang Jiang, Guangyu Cao, Mingyi Bai, Xingchun Wang, Caifu Jiang, Haibin Lu, Xianhui Hou, Lijia Qu, Zhiyong Wang, Jianru Zuo, Xiangdong Fu, Zhen Su, Songgang Li, and Hongwei Guo
Arabidopsis Hormone Database: a comprehensive genetic and phenotypic information database for plant hormone research in Arabidopsis
Nucleic Acids Research Advance Access published on November 10, 2008.
doi:10.1093/nar/gkn873
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Abstract Database Issue: Masafumi Shionyu, Akihiro Yamaguchi, Kazuki Shinoda, Ken-ichi Takahashi, and Mitiko Go
AS-ALPS: a database for analyzing the effects of alternative splicing on protein structure, interaction and network in human and mouse
Nucleic Acids Research Advance Access published on November 10, 2008.
doi:10.1093/nar/gkn869
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9 November 2008

Abstract Database Issue: Seok Yang, Joo-Yeon Lee, Joon Seung Lee, Wayne P. Mitchell, Hee-Bok Oh, Chun Kang, and Kyung Hyun Kim
Influenza sequence and epitope database
Nucleic Acids Research Advance Access published on November 9, 2008.
doi:10.1093/nar/gkn881
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