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Previous Next 		Contents: Volume 36, Number 10, June 2008   [Index by Author] 

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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.

Chemistry Back

Georges Lahoud, Victor Timoshchuk, Alexandre Lebedev, Miguel de Vega, Margarita Salas, Khalil Arar, Ya-Ming Hou, and Howard Gamper
Enzymatic synthesis of structure-free DNA with pseudo-complementary properties
Nucleic Acids Research Advance Access published on April 29, 2008
Nucl. Acids Res. 2008 36: 3409-3419; doi:10.1093/nar/gkn209 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Computational Biology Back

Sündüz Keles, Christopher L. Warren, Clayton D. Carlson, and Aseem Z. Ansari
CSI-Tree: a regression tree approach for modeling binding properties of DNA-binding molecules based on cognate site identification (CSI) data
Nucleic Acids Research Advance Access published on April 13, 2008
Nucl. Acids Res. 2008 36: 3171-3184; doi:10.1093/nar/gkn057 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Zhihua Zhang and Jianzhi Zhang
Accuracy and application of the motif expression decomposition method in dissecting transcriptional regulation
Nucleic Acids Research Advance Access published on April 14, 2008
Nucl. Acids Res. 2008 36: 3185-3193; doi:10.1093/nar/gkn127 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Anthony P. Malanoski, Baochuan Lin, and David A. Stenger
A model of base-call resolution on broad-spectrum pathogen detection resequencing DNA microarrays
Nucleic Acids Research Advance Access published on April 15, 2008
Nucl. Acids Res. 2008 36: 3194-3201; doi:10.1093/nar/gkm1156 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Lei Li, Chenggang Wu, Haiming Huang, Kaizhong Zhang, Jacob Gan, and Shawn S.-C. Li
Prediction of phosphotyrosine signaling networks using a scoring matrix-assisted ligand identification approach
Nucleic Acids Research Advance Access published on April 19, 2008
Nucl. Acids Res. 2008 36: 3263-3273; doi:10.1093/nar/gkn161 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Christine Sinoquet, Sylvain Demey, and Frédérique Braun
Large-scale computational and statistical analyses of high transcription potentialities in 32 prokaryotic genomes
Nucleic Acids Research Advance Access published on April 25, 2008
Nucl. Acids Res. 2008 36: 3332-3340; doi:10.1093/nar/gkn135 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Stefan Götz, Juan Miguel García-Gómez, Javier Terol, Tim D. Williams, Shivashankar H. Nagaraj, María José Nueda, Montserrat Robles, Manuel Talón, Joaquín Dopazo, and Ana Conesa
High-throughput functional annotation and data mining with the Blast2GO suite
Nucleic Acids Research Advance Access published on April 29, 2008
Nucl. Acids Res. 2008 36: 3420-3435; doi:10.1093/nar/gkn176 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Meng-Ru Ho, Wen-Jung Jang, Chun-houh Chen, Lan-Yang Ch'ang, and Wen-chang Lin
Designating eukaryotic orthology via processed transcription units
Nucleic Acids Research Advance Access published on April 29, 2008
Nucl. Acids Res. 2008 36: 3436-3442; doi:10.1093/nar/gkn227 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Fangqing Zhao, Fanggeng Zhao, Tao Li, and Donald A. Bryant
A new pheromone trail-based genetic algorithm for comparative genome assembly
Nucleic Acids Research Advance Access published on April 29, 2008
Nucl. Acids Res. 2008 36: 3455-3462; doi:10.1093/nar/gkn168 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genomics Back

Aristotelis Tsirigos and Isidore Rigoutsos
Human and mouse introns are linked to the same processes and functions through each genome's most frequent non-conserved motifs
Nucleic Acids Research Advance Access published on May 1, 2008
Nucl. Acids Res. 2008 36: 3484-3493; doi:10.1093/nar/gkn155 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data 1]  

Molecular Biology Back

Jennifer V. Ditlevson, Silvia Tornaletti, Boris P. Belotserkovskii, Virginia Teijeiro, Guliang Wang, Karen M. Vasquez, and Philip C. Hanawalt
Inhibitory effect of a short Z-DNA forming sequence on transcription elongation by T7 RNA polymerase
Nucleic Acids Research Advance Access published on April 9, 2008
Nucl. Acids Res. 2008 36: 3163-3170; doi:10.1093/nar/gkn136 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Markus A. Kleinschmidt, Gundula Streubel, Birgit Samans, Michael Krause, and Uta-Maria Bauer
The protein arginine methyltransferases CARM1 and PRMT1 cooperate in gene regulation
Nucleic Acids Research Advance Access published on April 15, 2008
Nucl. Acids Res. 2008 36: 3202-3213; doi:10.1093/nar/gkn166 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Xavier Lampe, Omar Abdel Samad, Allan Guiguen, Christelle Matis, Sophie Remacle, Jacques J. Picard, Filippo M. Rijli, and René Rezsohazy
An ultraconserved Hox–Pbx responsive element resides in the coding sequence of Hoxa2 and is active in rhombomere 4
Nucleic Acids Research Advance Access published on April 16, 2008
Nucl. Acids Res. 2008 36: 3214-3225; doi:10.1093/nar/gkn148 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Jung-Young Park, Han-Wook Yoo, Bok-Ryang Kim, Raekil Park, Sang-Yun Choi, and Youngho Kim
Identification of a novel human Rad51 variant that promotes DNA strand exchange
Nucleic Acids Research Advance Access published on April 16, 2008
Nucl. Acids Res. 2008 36: 3226-3234; doi:10.1093/nar/gkn171 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Ariane Gratias, Gersende Lepère, Olivier Garnier, Sarah Rosa, Sandra Duharcourt, Sophie Malinsky, Eric Meyer, and Mireille Bétermier
Developmentally programmed DNA splicing in Paramecium reveals short-distance crosstalk between DNA cleavage sites
Nucleic Acids Research Advance Access published on April 17, 2008
Nucl. Acids Res. 2008 36: 3244-3251; doi:10.1093/nar/gkn154 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Martine Roovers, Katarzyna H. Kaminska, Karolina L. Tkaczuk, Daniel Gigot, Louis Droogmans, and Janusz M. Bujnicki
The YqfN protein of Bacillus subtilis is the tRNA: m1A22 methyltransferase (TrmK)
Nucleic Acids Research Advance Access published on April 17, 2008
Nucl. Acids Res. 2008 36: 3252-3262; doi:10.1093/nar/gkn169 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Li Liang, Li Deng, Son C. Nguyen, Xin Zhao, Christopher D. Maulion, Changshun Shao, and Jay A. Tischfield
Human DNA ligases I and III, but not ligase IV, are required for microhomology-mediated end joining of DNA double-strand breaks
Nucleic Acids Research Advance Access published on April 24, 2008
Nucl. Acids Res. 2008 36: 3297-3310; doi:10.1093/nar/gkn184 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Tatsuki Kunoh, Toshiyuki Habu, and Tomohiro Matsumoto
Involvement of fission yeast Clr6-HDAC in regulation of the checkpoint kinase Cds1
Nucleic Acids Research Advance Access published on April 24, 2008
Nucl. Acids Res. 2008 36: 3311-3319; doi:10.1093/nar/gkn203 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Paul Peixoto, Yang Liu, Sabine Depauw, Marie-Paule Hildebrand, David W. Boykin, Christian Bailly, W. David Wilson, and Marie-Hélène David-Cordonnier
Direct inhibition of the DNA-binding activity of POU transcription factors Pit-1 and Brn-3 by selective binding of a phenyl-furan-benzimidazole dication
Nucleic Acids Research Advance Access published on April 25, 2008
Nucl. Acids Res. 2008 36: 3341-3353; doi:10.1093/nar/gkn208 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Cameron N. Gundry, Steven F. Dobrowolski, Y. Ranae Martin, Thomas C. Robbins, Lyle M. Nay, Nathan Boyd, Thomas Coyne, Mikeal D. Wall, Carl T. Wittwer, and David H.-F. Teng
Base-pair neutral homozygotes can be discriminated by calibrated high-resolution melting of small amplicons
Nucleic Acids Research Advance Access published on April 29, 2008
Nucl. Acids Res. 2008 36: 3401-3408; doi:10.1093/nar/gkn204 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Misato Nakanishi, Yasuhiro Tomaru, Hisashi Miura, Yoshihide Hayashizaki, and Masanori Suzuki
Identification of transcriptional regulatory cascades in retinoic acid-induced growth arrest of HepG2 cells
Nucleic Acids Research Advance Access published on April 29, 2008
Nucl. Acids Res. 2008 36: 3443-3454; doi:10.1093/nar/gkn066 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Manikandan Paramasivam, Susanna Cogoi, Vyacheslav V. Filichev, Niels Bomholt, Erik B. Pedersen, and Luigi E. Xodo
Purine twisted-intercalating nucleic acids: a new class of anti-gene molecules resistant to potassium-induced aggregation
Nucleic Acids Research Advance Access published on May 2, 2008
Nucl. Acids Res. 2008 36: 3494-3507; doi:10.1093/nar/gkn242 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Nucleic Acid Enzymes Back

Siying Chen, Maria Magdalena Coman, Miho Sakato, Michael O’Donnell, and Manju M. Hingorani
Conserved residues in the {delta} subunit help the E. coli clamp loader, {gamma} complex, target primer-template DNA for clamp assembly
Nucleic Acids Research Advance Access published on April 19, 2008
Nucl. Acids Res. 2008 36: 3274-3286; doi:10.1093/nar/gkn157 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Steven M. Yannone, Imran S. Khan, Rui-Zhe Zhou, Tong Zhou, Kristoffer Valerie, and Lawrence F. Povirk
Coordinate 5' and 3' endonucleolytic trimming of terminally blocked blunt DNA double-strand break ends by Artemis nuclease and DNA-dependent protein kinase
Nucleic Acids Research Advance Access published on April 25, 2008
Nucl. Acids Res. 2008 36: 3354-3365; doi:10.1093/nar/gkn205 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Alok Dhar and Robert S. Lahue
Rapid unwinding of triplet repeat hairpins by Srs2 helicase of Saccharomyces cerevisiae
Nucleic Acids Research Advance Access published on April 25, 2008
Nucl. Acids Res. 2008 36: 3366-3373; doi:10.1093/nar/gkn225 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

RNA Back

Yan Hai, Wenguang Cao, Guodong Liu, Say-Pham Hong, Sherif Abou Elela, Roscoe Klinck, Jiayou Chu, and Jiuyong Xie
A G-tract element in apoptotic agents-induced alternative splicing
Nucleic Acids Research Advance Access published on April 24, 2008
Nucl. Acids Res. 2008 36: 3320-3331; doi:10.1093/nar/gkn207 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Angela Schwede, Louise Ellis, Julia Luther, Mark Carrington, Georg Stoecklin, and Christine Clayton
A role for Caf1 in mRNA deadenylation and decay in trypanosomes and human cells
Nucleic Acids Research Advance Access published on April 27, 2008
Nucl. Acids Res. 2008 36: 3374-3388; doi:10.1093/nar/gkn108 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Monika Kuciak, Caroline Gabus, Roland Ivanyi-Nagy, Katharina Semrad, Roman Storchak, Olivier Chaloin, Sylviane Muller, Yves Mély, and Jean-Luc Darlix
The HIV-1 transcriptional activator Tat has potent nucleic acid chaperoning activities in vitro
Nucleic Acids Research Advance Access published on April 28, 2008
Nucl. Acids Res. 2008 36: 3389-3400; doi:10.1093/nar/gkn177 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Subash C. B. Gopinath, Dhakshnamoorthy Balasundaresan, Thirumananseri Kumarevel, Tomoko S. Misono, Hiroshi Mizuno, and Penmetcha K. R. Kumar
Insights into anti-termination regulation of the hut operon in Bacillus subtilis: importance of the dual RNA-binding surfaces of HutP
Nucleic Acids Research Advance Access published on April 29, 2008
Nucl. Acids Res. 2008 36: 3463-3473; doi:10.1093/nar/gkn199 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Structural Biology Back

Wei Liu, Biagio Pucci, Mosè Rossi, Francesca M. Pisani, and Rudolf Ladenstein
Structural analysis of the Sulfolobus solfataricus MCM protein N-terminal domain
Nucleic Acids Research Advance Access published on April 16, 2008
Nucl. Acids Res. 2008 36: 3235-3243; doi:10.1093/nar/gkn183 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Carmen M. Moure, Frederick S. Gimble, and Florante A. Quiocho
Crystal structures of I-SceI complexed to nicked DNA substrates: snapshots of intermediates along the DNA cleavage reaction pathway
Nucleic Acids Research Advance Access published on April 19, 2008
Nucl. Acids Res. 2008 36: 3287-3296; doi:10.1093/nar/gkn178 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Molly Coseno, Georges Martin, Christopher Berger, Gregory Gilmartin, Walter Keller, and Sylvie Doublié
Crystal structure of the 25 kDa subunit of human cleavage factor Im
Nucleic Acids Research Advance Access published on April 29, 2008
Nucl. Acids Res. 2008 36: 3474-3483; doi:10.1093/nar/gkn079 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Roland Pfoh, Hartmut Laatsch, and George M. Sheldrick
Crystal structure of trioxacarcin A covalently bound to DNA
Nucleic Acids Research Advance Access published on May 3, 2008
Nucl. Acids Res. 2008 36: 3508-3514; doi:10.1093/nar/gkn245 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Methods Online Back

Christoph Bock, Jörn Walter, Martina Paulsen, and Thomas Lengauer
Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping
Nucleic Acids Research Advance Access published on April 15, 2008
Nucl. Acids Res. 2008 36: e55; doi:10.1093/nar/gkn122 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Michaël Bekaert and Emma C. Teeling
UniPrime: a workflow-based platform for improved universal primer design
Nucleic Acids Research Advance Access published on April 19, 2008
Nucl. Acids Res. 2008 36: e56; doi:10.1093/nar/gkn191 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Dalia Daujotyte, Zita Liutkeviciute, Gintautas Tamulaitis, and Saulius Klimasauskas
Chemical mapping of cytosines enzymatically flipped out of the DNA helix
Nucleic Acids Research Advance Access published on May 1, 2008
Nucl. Acids Res. 2008 36: e57; doi:10.1093/nar/gkn200 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Liang-Hao Ding, Yang Xie, Seongmi Park, Guanghua Xiao, and Michael D. Story
Enhanced identification and biological validation of differential gene expression via Illumina whole-genome expression arrays through the use of the model-based background correction methodology
Nucleic Acids Research Advance Access published on May 1, 2008
Nucl. Acids Res. 2008 36: e58; doi:10.1093/nar/gkn234 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Takashi Takabatake, Hiroshi Ishihara, Yasushi Ohmachi, Izumi Tanaka, Masako M. Nakamura, Katsuyoshi Fujikawa, Tokuhisa Hirouchi, Shizuko Kakinuma, Yoshiya Shimada, Yoichi Oghiso, and Kimio Tanaka
Microarray-based global mapping of integration sites for the retrotransposon, intracisternal A-particle, in the mouse genome
Nucleic Acids Research Advance Access published on May 1, 2008
Nucl. Acids Res. 2008 36: e59; doi:10.1093/nar/gkn235 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Rosa Ana Risques, Gaelle Rondeau, Martin Judex, Michael McClelland, and John Welsh
Assessment of gene expression in many samples using vertical arrays
Nucleic Acids Research Advance Access published on May 12, 2008
Nucl. Acids Res. 2008 36: e60; doi:10.1093/nar/gkn263 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Olga A. Zasedateleva, Andrey L. Mikheikin, Alexander Y. Turygin, Dmitry V. Prokopenko, Alexander V. Chudinov, Elena E. Belobritskaya, Vladimir R. Chechetkin, and Alexander S. Zasedatelev
Gel-based oligonucleotide microarray approach to analyze protein–ssDNA binding specificity
Nucleic Acids Research Advance Access published on May 12, 2008
Nucl. Acids Res. 2008 36: e61; doi:10.1093/nar/gkn246 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Hsiu-Hui Tsai, Chih-Hung Huang, Alan M. Lin, and Carton W. Chen
Terminal proteins of Streptomyces chromosome can target DNA into eukaryotic nuclei
Nucleic Acids Research Advance Access published on May 14, 2008
Nucl. Acids Res. 2008 36: e62; doi:10.1093/nar/gkm1170 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

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.