Nucleic Acids Research

Survey and Summary:

Emanuele Buratti, Marco Baralle, and Francisco E. Baralle

Defective splicing, disease and therapy: searching for master checkpoints in exon definition
Nucl. Acids Res. 2006 34: 3494-3510; doi:10.1093/nar/gkl498 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Debraj GuhaThakurta

Computational identification of transcriptional regulatory elements in DNA sequence
Nucl. Acids Res. 2006 34: 3585-3598; doi:10.1093/nar/gkl372 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Articles:

Francesco Vanzi, Chiara Broggio, Leonardo Sacconi, and Francesco Saverio Pavone

Lac repressor hinge flexibility and DNA looping: single molecule kinetics by tethered particle motion
Nucl. Acids Res. 2006 34: 3409-3420; doi:10.1093/nar/gkl393 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Eyal Kamhi, Galit Yahalom, Gideon Kass, Yael Hacham, Ruth Sperling, and Joseph Sperling

AUG sequences are required to sustain nonsense-codon-mediated suppression of splicing
Nucl. Acids Res. 2006 34: 3421-3433; doi:10.1093/nar/gkl390 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Irma Lozada-Chávez, Sarath Chandra Janga, and Julio Collado-Vides

Bacterial regulatory networks are extremely flexible in evolution
Nucl. Acids Res. 2006 34: 3434-3445; doi:10.1093/nar/gkl423 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Laura M. Patterson-Fortin, Kimberley R. Colvin, and George W. Owttrim

A LexA-related protein regulates redox-sensitive expression of the cyanobacterial RNA helicase, crhR
Nucl. Acids Res. 2006 34: 3446-3454; doi:10.1093/nar/gkl426 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Catalina Hernández-Sánchez, Óscar Bártulos, Ana I. Valenciano, Alicia Mansilla, and Flora de Pablo

The regulated expression of chimeric tyrosine hydroxylase–insulin transcripts during early development
Nucl. Acids Res. 2006 34: 3455-3464; doi:10.1093/nar/gkl436 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Yong Zhang, X. Shirley Liu, Qing-Rong Liu, and Liping Wei

Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species
Nucl. Acids Res. 2006 34: 3465-3475; doi:10.1093/nar/gkl473 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Naonori Inoue, Noriaki Minakawa, and Akira Matsuda

Synthesis and properties of 4'-ThioDNA: unexpected RNA-like behavior of 4'-ThioDNA
Nucl. Acids Res. 2006 34: 3476-3483; doi:10.1093/nar/gkl491 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Jonathan Livny, Anja Brencic, Stephen Lory, and Matthew K. Waldor

Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool sRNAPredict2
Nucl. Acids Res. 2006 34: 3484-3493; doi:10.1093/nar/gkl453 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Mahima Kaushik and Shrikant Kukreti

Structural polymorphism exhibited by a quasipalindrome present in the locus control region (LCR) of the human ß-globin gene cluster
Nucl. Acids Res. 2006 34: 3511-3522; doi:10.1093/nar/gkl456 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Oliver Mortusewicz, Ulrich Rothbauer, M. Cristina Cardoso, and Heinrich Leonhardt

Differential recruitment of DNA Ligase I and III to DNA repair sites
Nucl. Acids Res. 2006 34: 3523-3532; doi:10.1093/nar/gkl492 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

K. Bryson, V. Loux, R. Bossy, P. Nicolas, S. Chaillou, M. van de Guchte, S. Penaud, E. Maguin, M. Hoebeke, P. Bessières, and J-F Gibrat

AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system
Nucl. Acids Res. 2006 34: 3533-3545; doi:10.1093/nar/gkl471 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Norman E. Davey, Denis C. Shields, and Richard J. Edwards

SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent
Nucl. Acids Res. 2006 34: 3546-3554; doi:10.1093/nar/gkl486 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Noriyuki Suka, Emiko Nakashima, Kaori Shinmyozu, Masumi Hidaka, and Hisato Jingami

The WD40-repeat protein Pwp1p associates in vivo with 25S ribosomal chromatin in a histone H4 tail-dependent manner
Nucl. Acids Res. 2006 34: 3555-3567; doi:10.1093/nar/gkl487 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

J. H. A. Nagel, C. Flamm, I. L. Hofacker, K. Franke, M. H. de Smit, P. Schuster, and C. W. A. Pleij

Structural parameters affecting the kinetics of RNA hairpin formation
Nucl. Acids Res. 2006 34: 3568-3576; doi:10.1093/nar/gkl445 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jing Mi, Xiuwu Zhang, Zahid N Rabbani, Yingmiao Liu, Zhen Su, Zeljko Vujaskovic, Christopher D. Kontos, Bruce A. Sullenger, and Bryan M. Clary

H1 RNA polymerase III promoter-driven expression of an RNA aptamer leads to high-level inhibition of intracellular protein activity
Nucl. Acids Res. 2006 34: 3577-3584; doi:10.1093/nar/gkl482 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Devanathan Raghunathan, Víctor M. Sánchez-Pedregal, Jochen Junker, Claudia Schwiegk, Markus Kalesse, Andreas Kirschning, and Teresa Carlomagno

TAR-RNA recognition by a novel cyclic aminoglycoside analogue
Nucl. Acids Res. 2006 34: 3599-3608; doi:10.1093/nar/gkl494 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Methods Online:

Asim S. Siddiqui, Allen D. Delaney, Angelique Schnerch, Obi L. Griffith, Steven J. M. Jones, and Marco A. Marra

Sequence biases in large scale gene expression profiling data
Nucl. Acids Res. 2006 34: e83; doi:10.1093/nar/gkl404 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Patrick Ng, Jack J.S. Tan, Hong Sain Ooi, Yen Ling Lee, Kuo Ping Chiu, Melissa J. Fullwood, Kandhadayar G. Srinivasan, Clotilde Perbost, Lei Du, Wing-Kin Sung, Chia-Lin Wei, and Yijun Ruan

Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes
Nucl. Acids Res. 2006 34: e84; doi:10.1093/nar/gkl444 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

James J. Yun, Lawrence E. Heisler, Irene I. L. Hwang, Olivia Wilkins, Suzanne K. Lau, Martin Hyrcza, Bamini Jayabalasingham, Jing Jin, JoAnne McLaurin, Ming-Sound Tsao, and Sandy D. Der

Genomic DNA functions as a universal external standard in quantitative real-time PCR
Nucl. Acids Res. 2006 34: e85; doi:10.1093/nar/gkl400 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Florian Jarosch, Klaus Buchner, and Sven Klussmann

In vitro selection using a dual RNA library that allows primerless selection
Nucl. Acids Res. 2006 34: e86; doi:10.1093/nar/gkl463 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Kévin Le Brigand, Roslin Russell, Chimène Moreilhon, Jean-Marie Rouillard, Bernard Jost, Franck Amiot, Virginie Magnone, Christine Bole-Feysot, Philippe Rostagno, Virginie Virolle, Virginie Defamie, Philippe Dessen, Gary Williams, Paul Lyons, Géraldine Rios, Bernard Mari, Erdogan Gulari, Philippe Kastner, Xavier Gidrol, Tom C. Freeman, and Pascal Barbry

An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomes
Nucl. Acids Res. 2006 34: e87; doi:10.1093/nar/gkl485 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Reiner Schulz, Trevelyan R. Menheniott, Kathryn Woodfine, Andrew J. Wood, Jonathan D. Choi, and Rebecca J. Oakey

Chromosome-wide identification of novel imprinted genes using microarrays and uniparental disomies
Nucl. Acids Res. 2006 34: e88; doi:10.1093/nar/gkl461 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Rong Tan, Chunhua Li, Sijing Jiang, and Lixin Ma

A novel and simple method for construction of recombinant adenoviruses
Nucl. Acids Res. 2006 34: e89; doi:10.1093/nar/gkl449 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

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