Nucleic Acids Research

Computational Biology

Get checked abstract Shea N. Gardner, Amy L. Hiddessen, Peter L. Williams, Christine Hara, Mark C. Wagner, and Bill W. Colston, Jr

Multiplex primer prediction software for divergent targets
Nucleic Acids Research Advance Access published on September 16, 2009
Nucl. Acids Res. 2009 37: 6291-6304; doi:10.1093/nar/gkp659 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Helge G. Roider, Boris Lenhard, Aditi Kanhere, Stefan A. Haas, and Martin Vingron

CpG-depleted promoters harbor tissue-specific transcription factor binding signals—implications for motif overrepresentation analyses
Nucleic Acids Research Advance Access published on September 6, 2009
Nucl. Acids Res. 2009 37: 6305-6315; doi:10.1093/nar/gkp682 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Julien Dorier and Andrzej Stasiak

Topological origins of chromosomal territories
Nucleic Acids Research Advance Access published on September 2, 2009
Nucl. Acids Res. 2009 37: 6316-6322; doi:10.1093/nar/gkp702 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Igor Dozmorov and Ivan Lefkovits

Internal standard-based analysis of microarray data. Part 1: analysis of differential gene expressions
Nucleic Acids Research Advance Access published on August 31, 2009
Nucl. Acids Res. 2009 37: 6323-6339; doi:10.1093/nar/gkp706 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Gene Regulation, Chromatin and Epigenetics

Get checked abstract Angéline Eymery, Béatrice Horard, Michèle El Atifi-Borel, Geneviève Fourel, François Berger, Anne-Laure Vitte, Arnaud Van den Broeck, Elisabeth Brambilla, Alexandra Fournier, Mary Callanan, Sylvie Gazzeri, Saadi Khochbin, Sophie Rousseaux, Eric Gilson, and Claire Vourc’h

A transcriptomic analysis of human centromeric and pericentric sequences in normal and tumor cells
Nucleic Acids Research Advance Access published on August 31, 2009
Nucl. Acids Res. 2009 37: 6340-6354; doi:10.1093/nar/gkp639 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Benny J. Evison, Rebecca A. Bilardi, Francis C. K. Chiu, Gabriella Pezzoni, Don R. Phillips, and Suzanne M. Cutts

CpG methylation potentiates pixantrone and doxorubicin-induced DNA damage and is a marker of drug sensitivity
Nucleic Acids Research Advance Access published on August 31, 2009
Nucl. Acids Res. 2009 37: 6355-6370; doi:10.1093/nar/gkp700 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genome Integrity, Repair and Replication

Get checked abstract Ali Entezam and Karen Usdin

ATM and ATR protect the genome against two different types of tandem repeat instability in Fragile X premutation mice
Nucleic Acids Research Advance Access published on August 26, 2009
Nucl. Acids Res. 2009 37: 6371-6377; doi:10.1093/nar/gkp666 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Yaobin Liu, Rodney S. Nairn, and Karen M. Vasquez

Targeted gene conversion induced by triplex-directed psoralen interstrand crosslinks in mammalian cells
Nucleic Acids Research Advance Access published on September 2, 2009
Nucl. Acids Res. 2009 37: 6378-6388; doi:10.1093/nar/gkp678 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Sreerupa Ray and Anne Grove

The yeast high mobility group protein HMO2, a subunit of the chromatin-remodeling complex INO80, binds DNA ends
Nucleic Acids Research Advance Access published on September 2, 2009
Nucl. Acids Res. 2009 37: 6389-6399; doi:10.1093/nar/gkp695 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Ali Z. Al-Minawi, Yin-Fai Lee, Daniel Håkansson, Fredrik Johansson, Cecilia Lundin, Nasrollah Saleh-Gohari, Niklas Schultz, Dag Jenssen, Helen E. Bryant, Mark Meuth, John M. Hinz, and Thomas Helleday

The ERCC1/XPF endonuclease is required for completion of homologous recombination at DNA replication forks stalled by inter-strand cross-links
Nucleic Acids Research Advance Access published on August 27, 2009
Nucl. Acids Res. 2009 37: 6400-6413; doi:10.1093/nar/gkp705 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Ilaria Dalla Rosa, Steffi Goffart, Melanie Wurm, Constanze Wiek, Frank Essmann, Stefan Sobek, Peter Schroeder, Hongliang Zhang, Jean Krutmann, Helmut Hanenberg, Klaus Schulze-Osthoff, Christian Mielke, Yves Pommier, Fritz Boege, and Morten O. Christensen

Adaptation of topoisomerase I paralogs to nuclear and mitochondrial DNA
Nucleic Acids Research Advance Access published on August 31, 2009
Nucl. Acids Res. 2009 37: 6414-6428; doi:10.1093/nar/gkp708 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Destaye M. Moore, Justin Karlin, Sergio González-Barrera, Armen Mardiros, Michael Lisby, Ana Doughty, Jennifer Gilley, Rodney Rothstein, Errol C. Friedberg, and Paula L. Fischhaber

Rad10 exhibits lesion-dependent genetic requirements for recruitment to DNA double-strand breaks in Saccharomyces cerevisiae
Nucleic Acids Research Advance Access published on September 3, 2009
Nucl. Acids Res. 2009 37: 6429-6438; doi:10.1093/nar/gkp709 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Shinichi Kiyonari, Saki Tahara, Tsuyoshi Shirai, Shigenori Iwai, Sonoko Ishino, and Yoshizumi Ishino

Biochemical properties and base excision repair complex formation of apurinic/apyrimidinic endonuclease from Pyrococcus furiosus
Nucleic Acids Research Advance Access published on September 4, 2009
Nucl. Acids Res. 2009 37: 6439-6453; doi:10.1093/nar/gkp720 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genomics

Get checked abstract Yoshiyuki Shibata, Ankit Malhotra, Stefan Bekiranov, and Anindya Dutta

Yeast genome analysis identifies chromosomal translocation, gene conversion events and several sites of Ty element insertion
Nucleic Acids Research Advance Access published on August 26, 2009
Nucl. Acids Res. 2009 37: 6454-6465; doi:10.1093/nar/gkp650 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Amir B. Cohanim and Tali E. Haran

The coexistence of the nucleosome positioning code with the genetic code on eukaryotic genomes
Nucleic Acids Research Advance Access published on August 21, 2009
Nucl. Acids Res. 2009 37: 6466-6476; doi:10.1093/nar/gkp689 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Molecular Biology

Get checked abstract Yoshihiro Kino, Chika Washizu, Yoko Oma, Hayato Onishi, Yuriko Nezu, Noboru Sasagawa, Nobuyuki Nukina, and Shoichi Ishiura

MBNL and CELF proteins regulate alternative splicing of the skeletal muscle chloride channel CLCN1
Nucleic Acids Research Advance Access published on August 31, 2009
Nucl. Acids Res. 2009 37: 6477-6490; doi:10.1093/nar/gkp681 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Supplementary Data]  

Nucleic Acid Enzymes

Get checked abstract Tresa George, Qin Wen, Richard Griffiths, Anil Ganesh, Mark Meuth, and Cyril M. Sanders

Human Pif1 helicase unwinds synthetic DNA structures resembling stalled DNA replication forks
Nucleic Acids Research Advance Access published on August 21, 2009
Nucl. Acids Res. 2009 37: 6491-6502; doi:10.1093/nar/gkp671 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Lisa M. Sharpe Elles, Michael T. Sykes, James R. Williamson, and Olke C. Uhlenbeck

A dominant negative mutant of the E. coli RNA helicase DbpA blocks assembly of the 50S ribosomal subunit
Nucleic Acids Research Advance Access published on September 4, 2009
Nucl. Acids Res. 2009 37: 6503-6514; doi:10.1093/nar/gkp711 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

RNA

Get checked abstract Takayuki Nojima, Takako Oshiro-Ideue, Hiroto Nakanoya, Hidenobu Kawamura, Tomomi Morimoto, Yasushi Kawaguchi, Naoyuki Kataoka, and Masatoshi Hagiwara

Herpesvirus protein ICP27 switches PML isoform by altering mRNA splicing
Nucleic Acids Research Advance Access published on September 3, 2009
Nucl. Acids Res. 2009 37: 6515-6527; doi:10.1093/nar/gkp633 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Wei Huang, Joohyun Kim, Shantenu Jha, and Fareed Aboul-ela

A mechanism for S-adenosyl methionine assisted formation of a riboswitch conformation: a small molecule with a strong arm
Nucleic Acids Research Advance Access published on August 31, 2009
Nucl. Acids Res. 2009 37: 6528-6539; doi:10.1093/nar/gkp664 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Dmitrii Trubetskoy, Florence Proux, Frédéric Allemand, Marc Dreyfus, and Isabelle Iost

SrmB, a DEAD-box helicase involved in Escherichia coli ribosome assembly, is specifically targeted to 23S rRNA in vivo
Nucleic Acids Research Advance Access published on September 4, 2009
Nucl. Acids Res. 2009 37: 6540-6549; doi:10.1093/nar/gkp685 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Youheng Wei, Qianghai Xiao, Ting Zhang, Zongchun Mou, Jia You, and Wei-Jun Ma

Differential regulation of mRNA stability controls the transient expression of genes encoding Drosophila antimicrobial peptide with distinct immune response characteristics
Nucleic Acids Research Advance Access published on September 2, 2009
Nucl. Acids Res. 2009 37: 6550-6561; doi:10.1093/nar/gkp693 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Yong Zhang, Jie Wang, Shoujun Huang, Xiaopeng Zhu, Jun Liu, Ning Yang, Dandan Song, Rimao Wu, Wei Deng, Geir Skogerbø, Xiu-Jie Wang, Runsheng Chen, and Dahai Zhu

Systematic identification and characterization of chicken (Gallus gallus) ncRNAs
Nucleic Acids Research Advance Access published on August 31, 2009
Nucl. Acids Res. 2009 37: 6562-6574; doi:10.1093/nar/gkp704 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Man Lung Yeung, Yamina Bennasser, Koichi Watashi, Shu-Yun Le, Laurent Houzet, and Kuan-Teh Jeang

Pyrosequencing of small non-coding RNAs in HIV-1 infected cells: evidence for the processing of a viral-cellular double-stranded RNA hybrid
Nucleic Acids Research Advance Access published on September 3, 2009
Nucl. Acids Res. 2009 37: 6575-6586; doi:10.1093/nar/gkp707 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Rachael Kenworthy, Diana Lambert, Feng Yang, Nan Wang, Zihong Chen, Haizhen Zhu, Fanxiu Zhu, Chen Liu, Kui Li, and Hengli Tang

Short-hairpin RNAs delivered by lentiviral vector transduction trigger RIG-I-mediated IFN activation
Nucleic Acids Research Advance Access published on September 3, 2009
Nucl. Acids Res. 2009 37: 6587-6599; doi:10.1093/nar/gkp714 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Wei-Lun Chang and Woan-Yuh Tarn

A role for transportin in deposition of TTP to cytoplasmic RNA granules and mRNA decay
Nucleic Acids Research Advance Access published on September 3, 2009
Nucl. Acids Res. 2009 37: 6600-6612; doi:10.1093/nar/gkp717 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Structural Biology

Get checked abstract Dmitrij Golovenko, Elena Manakova, Giedre Tamulaitiene, Saulius Grazulis, and Virginijus Siksnys

Structural mechanisms for the 5'-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII
Nucleic Acids Research Advance Access published on September 3, 2009
Nucl. Acids Res. 2009 37: 6613-6624; doi:10.1093/nar/gkp699 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract D. Renciuk, I. Kejnovská, P. Skoláková, K. Bednárová, J. Motlová, and M. Vorlícková

Arrangements of human telomere DNA quadruplex in physiologically relevant K⁺ solutions
Nucleic Acids Research Advance Access published on August 28, 2009
Nucl. Acids Res. 2009 37: 6625-6634; doi:10.1093/nar/gkp701 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Synthetic Biology and Chemistry

Get checked abstract Huachuan Cao, Yong Jiang, and Yinsheng Wang

Kinetics of deamination and Cu(II)/H₂O₂/Ascorbate-induced formation of 5-methylcytosine glycol at CpG sites in duplex DNA
Nucleic Acids Research Advance Access published on August 25, 2009
Nucl. Acids Res. 2009 37: 6635-6643; doi:10.1093/nar/gkp615 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Methods Online

Get checked abstract Agnès Méreau, Vincent Anquetil, Marie Cibois, Maud Noiret, Aline Primot, Audrey Vallée, and Luc Paillard

Analysis of splicing patterns by pyrosequencing
Nucleic Acids Research Advance Access published on August 11, 2009
Nucl. Acids Res. 2009 37: e126; doi:10.1093/nar/gkp626 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Lindsey L. Snyder, Iqbal Ahmed, and Laura F. Steel

RNA polymerase III can drive polycistronic expression of functional interfering RNAs designed to resemble microRNAs
Nucleic Acids Research Advance Access published on August 13, 2009
Nucl. Acids Res. 2009 37: e127; doi:10.1093/nar/gkp657 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Dorjbal Dorjsuren, David M. Wilson, III, William A. Beard, John P. McDonald, Christopher P. Austin, Roger Woodgate, Samuel H. Wilson, and Anton Simeonov

A real-time fluorescence method for enzymatic characterization of specialized human DNA polymerases
Nucleic Acids Research Advance Access published on August 14, 2009
Nucl. Acids Res. 2009 37: e128; doi:10.1093/nar/gkp641 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Anestis Tsakiridis, Elena Tzouanacou, Afifah Rahman, Douglas Colby, Richard Axton, Ian Chambers, Valerie Wilson, Lesley Forrester, and Joshua M. Brickman

Expression-independent gene trap vectors for random and targeted mutagenesis in embryonic stem cells
Nucleic Acids Research Advance Access published on August 19, 2009
Nucl. Acids Res. 2009 37: e129; doi:10.1093/nar/gkp640 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Valérie Moreau, Emilie Voirin, Clément Paris, Mitsuharu Kotera, Marc Nothisen, Jean-Serge Rémy, Jean-Paul Behr, Patrick Erbacher, and Nathalie Lenne-Samuel

Zip Nucleic Acids: new high affinity oligonucleotides as potent primers for PCR and reverse transcription
Nucleic Acids Research Advance Access published on August 20, 2009
Nucl. Acids Res. 2009 37: e130; doi:10.1093/nar/gkp661 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Chunquan Li, Xia Li, Yingbo Miao, Qianghu Wang, Wei Jiang, Chun Xu, Jing Li, Junwei Han, Fan Zhang, Binsheng Gong, and Liangde Xu

SubpathwayMiner: a software package for flexible identification of pathways
Nucleic Acids Research Advance Access published on August 25, 2009
Nucl. Acids Res. 2009 37: e131; doi:10.1093/nar/gkp667 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Front-Matter/Back-Matter

Nucleic Acids Research: VOLUME 37 ISSUE 19 2009
Nucl. Acids Res. 2009 37: i; doi:10.1093/nar/gkp1051 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nucleic Acids Research
Nucl. Acids Res. 2009 37: ii; doi:10.1093/nar/gkp1050 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Subscriptions
Nucl. Acids Res. 2009 37: iii; doi:10.1093/nar/gkp1052 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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