Nucleic Acids Research

Survey and Summary

Get checked abstract Da Wei Huang, Brad T. Sherman, and Richard A. Lempicki

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
Nucleic Acids Research Advance Access published on November 25, 2008
Nucl. Acids Res. 2009 37: 1-13; doi:10.1093/nar/gkn923 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Computational Biology

Get checked abstract Tom Whitington, Andrew C. Perkins, and Timothy L. Bailey

High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites
Nucleic Acids Research Advance Access published on November 6, 2008
Nucl. Acids Res. 2009 37: 14-25; doi:10.1093/nar/gkn866 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Gene regulation, Chromatin and Epigenetics

Get checked abstract 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
Nucl. Acids Res. 2009 37: 78-95; doi:10.1093/nar/gkn910 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract 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
Nucl. Acids Res. 2009 37: 111-122; doi:10.1093/nar/gkn926 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Youn-Bok Lee, Ioannis Bantounas, Do-Young Lee, Leonidas Phylactou, Maeve A. Caldwell, and James B. Uney

Twist-1 regulates the miR-199a/214 cluster during development
Nucleic Acids Research Advance Access published on November 23, 2008
Nucl. Acids Res. 2009 37: 123-128; doi:10.1093/nar/gkn920 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Rainer Melzer, Wim Verelst, and Günter Theißen

The class E floral homeotic protein SEPALLATA3 is sufficient to loop DNA in ‘floral quartet’-like complexes in vitro
Nucleic Acids Research Advance Access published on November 25, 2008
Nucl. Acids Res. 2009 37: 144-157; doi:10.1093/nar/gkn900 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genome integrity, repair and replication

Get checked abstract 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
Nucl. Acids Res. 2009 37: 60-69; doi:10.1093/nar/gkn912 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Dotan Sela and Joseph Shlomai

Regulation of UMSBP activities through redox-sensitive protein domains
Nucleic Acids Research Advance Access published on November 27, 2008
Nucl. Acids Res. 2009 37: 279-288; doi:10.1093/nar/gkn927 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genomics

Get checked abstract Genis Parra, Keith Bradnam, Zemin Ning, Thomas Keane, and Ian Korf

Assessing the gene space in draft genomes
Nucleic Acids Research Advance Access published on November 28, 2008
Nucl. Acids Res. 2009 37: 289-297; doi:10.1093/nar/gkn916 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Molecular Biology

Get checked abstract 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
Nucl. Acids Res. 2009 37: 47-59; doi:10.1093/nar/gkn901 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Ram Krishna Thakur, Praveen Kumar, Kangkan Halder, Anjali Verma, Anirban Kar, Jean-Luc Parent, Richa Basundra, Akinchan Kumar, and Shantanu Chowdhury

Metastases suppressor NM23-H2 interaction with G-quadruplex DNA within c-MYC promoter nuclease hypersensitive element induces c-MYC expression
Nucleic Acids Research Advance Access published on November 25, 2008
Nucl. Acids Res. 2009 37: 172-183; doi:10.1093/nar/gkn919 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Dario Benelli, Stefano Marzi, Carmine Mancone, Tonino Alonzi, Anna la Teana, and Paola Londei

Function and ribosomal localization of aIF6, a translational regulator shared by archaea and eukarya
Nucleic Acids Research Advance Access published on November 26, 2008
Nucl. Acids Res. 2009 37: 256-267; doi:10.1093/nar/gkn959 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Sarah G. Ozanick, Xuying Wang, Michael Costanzo, Renee L. Brost, Charles Boone, and James T. Anderson

Rex1p deficiency leads to accumulation of precursor initiator tRNA^Met and polyadenylation of substrate RNAs in Saccharomyces cerevisiae
Nucleic Acids Research Advance Access published on November 28, 2008
Nucl. Acids Res. 2009 37: 298-308; doi:10.1093/nar/gkn925 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Nucleic Acid Enzymes

Get checked abstract 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
Nucl. Acids Res. 2009 37: 38-46; doi:10.1093/nar/gkn895 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract 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
Nucl. Acids Res. 2009 37: 96-110; doi:10.1093/nar/gkn913 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Xiao-Ping Zhang, Vitold E. Galkin, Xiong Yu, Edward H. Egelman, and Wolf-Dietrich Heyer

Loop 2 in Saccharomyces cerevisiae Rad51 protein regulates filament formation and ATPase activity
Nucleic Acids Research Advance Access published on November 25, 2008
Nucl. Acids Res. 2009 37: 158-171; doi:10.1093/nar/gkn914 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Irene Rodríguez, José María Lázaro, Margarita Salas, and Miguel de Vega

Involvement of the TPR2 subdomain movement in the activities of 29 DNA polymerase
Nucleic Acids Research Advance Access published on November 25, 2008
Nucl. Acids Res. 2009 37: 193-203; doi:10.1093/nar/gkn928 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Eugene Valkov, Saumya Shree Gupta, Stephen Hare, Anna Helander, Pietro Roversi, Myra McClure, and Peter Cherepanov

Functional and structural characterization of the integrase from the prototype foamy virus
Nucleic Acids Research Advance Access published on November 26, 2008
Nucl. Acids Res. 2009 37: 243-255; doi:10.1093/nar/gkn938 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

RNA

Get checked abstract 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
Nucl. Acids Res. 2009 37: 26-37; doi:10.1093/nar/gkn893 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract 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
Nucl. Acids Res. 2009 37: 70-77; doi:10.1093/nar/gkn904 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Sean A. Lynch and Justin P. Gallivan

A flow cytometry-based screen for synthetic riboswitches
Nucleic Acids Research Advance Access published on November 25, 2008
Nucl. Acids Res. 2009 37: 184-192; doi:10.1093/nar/gkn924 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Krystyna Mazan-Mamczarz, Yuki Kuwano, Ming Zhan, Elizabeth J. White, Jennifer L. Martindale, Ashish Lal, and Myriam Gorospe

Identification of a signature motif in target mRNAs of RNA-binding protein AUF1
Nucleic Acids Research Advance Access published on November 25, 2008
Nucl. Acids Res. 2009 37: 204-214; doi:10.1093/nar/gkn929 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Luc Jaeger, Erik J. Verzemnieks, and Cody Geary

The UA_handle: a versatile submotif in stable RNA architectures
Nucleic Acids Research Advance Access published on November 26, 2008
Nucl. Acids Res. 2009 37: 215-230; doi:10.1093/nar/gkn911 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Dan Li, Dagmar K. Willkomm, and Roland K. Hartmann

Minor changes largely restore catalytic activity of archaeal RNase P RNA from Methanothermobacter thermoautotrophicus
Nucleic Acids Research Advance Access published on November 26, 2008
Nucl. Acids Res. 2009 37: 231-242; doi:10.1093/nar/gkn915 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Sergey Shpiz, Dmitry Kwon, Yakov Rozovsky, and Alla Kalmykova

rasiRNA pathway controls antisense expression of Drosophila telomeric retrotransposons in the nucleus
Nucleic Acids Research Advance Access published on November 26, 2008
Nucl. Acids Res. 2009 37: 268-278; doi:10.1093/nar/gkn960 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Structural Biology

Get checked abstract Mark A. Brooks, Andrzej Dziembowski, Sophie Quevillon-Cheruel, Véronique Henriot, Céline Faux, Herman van Tilbeurgh, and Bertrand Séraphin

Structure of the yeast Pml1 splicing factor and its integration into the RES complex
Nucleic Acids Research Advance Access published on November 25, 2008
Nucl. Acids Res. 2009 37: 129-143; doi:10.1093/nar/gkn894 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Methods Online

Get checked abstract Yu Zheng, Janos Posfai, Richard D. Morgan, Tamas Vincze, and Richard J. Roberts

Using shotgun sequence data to find active restriction enzyme genes
Nucleic Acids Research Advance Access published on November 6, 2008
Nucl. Acids Res. 2009 37: e1; doi:10.1093/nar/gkn883 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Fuchun Zhou, Qiuhua Li, and Shou-Jiang Gao

A sequence-independent in vitro transposon-based strategy for efficient cloning of genomes of large DNA viruses as bacterial artificial chromosomes
Nucleic Acids Research Advance Access published on November 6, 2008
Nucl. Acids Res. 2009 37: e2; doi:10.1093/nar/gkn890 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract 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
Nucl. Acids Res. 2009 37: e3; doi:10.1093/nar/gkn884 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract 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
Nucl. Acids Res. 2009 37: e4; doi:10.1093/nar/gkn903 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract 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
Nucl. Acids Res. 2009 37: e5; doi:10.1093/nar/gkn906 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Christopher G. Knight, Mark Platt, William Rowe, David C. Wedge, Farid Khan, Philip J. R. Day, Andy McShea, Joshua Knowles, and Douglas B. Kell

Array-based evolution of DNA aptamers allows modelling of an explicit sequence-fitness landscape
Nucleic Acids Research Advance Access published on November 23, 2008
Nucl. Acids Res. 2009 37: e6; doi:10.1093/nar/gkn899 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Jenny Göransson, Carolina Wählby, Magnus Isaksson, W. Mathias Howell, Jonas Jarvius, and Mats Nilsson

A single molecule array for digital targeted molecular analyses
Nucleic Acids Research Advance Access published on November 25, 2008
Nucl. Acids Res. 2009 37: e7; doi:10.1093/nar/gkn921 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Zhen Li, Yves Fortin, and Shi-Hsiang Shen

Forward and robust selection of the most potent and noncellular toxic siRNAs from RNAi libraries
Nucleic Acids Research Advance Access published on November 29, 2008
Nucl. Acids Res. 2009 37: e8; doi:10.1093/nar/gkn953 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Nikhil U. Nair and Huimin Zhao

Mutagenic inverted repeat assisted genome engineering (MIRAGE)
Nucleic Acids Research Advance Access published on December 2, 2008
Nucl. Acids Res. 2009 37: e9; doi:10.1093/nar/gkn943 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Front-Matter/Back-Matter

Nucleic Acids Research: VOLUME 37 ISSUE 1 2009
Nucl. Acids Res. 2009 37: i; doi:10.1093/nar/gkp008 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nucleic Acids Research
Nucl. Acids Res. 2009 37: ii; doi:10.1093/nar/gkp007 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Subscriptions
Nucl. Acids Res. 2009 37: iii; doi:10.1093/nar/gkp009 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

To see an article, click its [Full Text] or [PDF] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.