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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8 May 2008

Abstract Web Server Issue: Richard G. Côté, Philip Jones, Lennart Martens, Rolf Apweiler, and Henning Hermjakob
The Ontology Lookup Service: more data and better tools for controlled vocabulary queries
Nucleic Acids Research Advance Access published on May 8, 2008.
doi:10.1093/nar/gkn252
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Abstract Web Server Issue: Andreu Alibés, Andrés Cañada, and Ramón Díaz-Uriarte
PaLS: filtering common literature, biological terms and pathway information
Nucleic Acids Research Advance Access published on May 8, 2008.
doi:10.1093/nar/gkn251
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Abstract Chemistry: Jaroslav Malina, Michael J. Hannon, and Viktor Brabec
DNA binding of dinuclear iron(II) metallosupramolecular cylinders. DNA unwinding and sequence preference
Nucleic Acids Research Advance Access published on May 8, 2008.
doi:10.1093/nar/gkn244
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Abstract Web Server Issue: Alexandra Shulman-Peleg, Maxim Shatsky, Ruth Nussinov, and Haim J. Wolfson
MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions
Nucleic Acids Research Advance Access published on May 8, 2008.
doi:10.1093/nar/gkn185
[Abstract] [Full Text] [Print PDF] [Screen PDF]

7 May 2008

Abstract Molecular Biology: Keren Weidenfeld-Baranboim, Keren Bitton-Worms, and Ami Aronheim
TRE-dependent transcription activation by JDP2–CHOP10 association
Nucleic Acids Research Advance Access published on May 7, 2008.
doi:10.1093/nar/gkn268
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Web Server Issue: Brigitte Waegele, Thorsten Schmidt, H. Werner Mewes, and Andreas Ruepp
OREST: the online resource for EST analysis
Nucleic Acids Research Advance Access published on May 7, 2008.
doi:10.1093/nar/gkn253
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Web Server Issue: Christian Cole, Jonathan D. Barber, and Geoffrey J. Barton
The Jpred 3 secondary structure prediction server
Nucleic Acids Research Advance Access published on May 7, 2008.
doi:10.1093/nar/gkn238
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Web Server Issue: Bernd W. Brandt, Jaap Heringa, and Jack A. M. Leunissen
SEQATOMS: a web tool for identifying missing regions in PDB in sequence context
Nucleic Acids Research Advance Access published on May 7, 2008.
doi:10.1093/nar/gkn237
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Web Server Issue: Alexander E. Ivliev, Peter A. C. 't Hoen, Michel P. Villerius, Johan T. den Dunnen, and Bernd W. Brandt
Microarray retriever: a web-based tool for searching and large scale retrieval of public microarray data
Nucleic Acids Research Advance Access published on May 7, 2008.
doi:10.1093/nar/gkn213
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Structural Biology: C. Gondeau, L. Chaloin, P. Lallemand, B. Roy, C. Périgaud, T. Barman, A. Varga, M. Vas, C. Lionne, and S. T. Arold
Molecular basis for the lack of enantioselectivity of human 3-phosphoglycerate kinase
Nucleic Acids Research Advance Access published on May 7, 2008.
doi:10.1093/nar/gkn212
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Web Server Issue: Claus Lundegaard, Kasper Lamberth, Mikkel Harndahl, Søren Buus, Ole Lund, and Morten Nielsen
NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8–11
Nucleic Acids Research Advance Access published on May 7, 2008.
doi:10.1093/nar/gkn202
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Web Server Issue: A. E. Lobley, T. Nugent, C. A. Orengo, and D. T. Jones
FFPred: an integrated feature-based function prediction server for vertebrate proteomes
Nucleic Acids Research Advance Access published on May 7, 2008.
doi:10.1093/nar/gkn193
[Abstract] [Full Text] [Print PDF] [Screen PDF]

6 May 2008

Abstract Molecular Biology: Xudong Wu, Yanhua Gong, Jiping Yue, Boqin Qiang, Jiangang Yuan, and Xiaozhong Peng
Cooperation between EZH2, NSPc1-mediated histone H2A ubiquitination and Dnmt1 in HOX gene silencing
Nucleic Acids Research Advance Access originally published on May 6, 2008. This version published May 6, 2008.
doi:10.1093/nar/gkn243
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Web Server Issue: Alexey V. Antonov, Thorsten Schmidt, Yu Wang, and Hans W. Mewes
ProfCom: a web tool for profiling the complex functionality of gene groups identified from high-throughput data
Nucleic Acids Research Advance Access published on May 6, 2008.
doi:10.1093/nar/gkn239
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Web Server Issue: Jüri Reimand, Laur Tooming, Hedi Peterson, Priit Adler, and Jaak Vilo
GraphWeb: mining heterogeneous biological networks for gene modules with functional significance
Nucleic Acids Research Advance Access published on May 6, 2008.
doi:10.1093/nar/gkn230
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract RNA: Shoji P. Ohuchi, Yoshiya Ikawa, and Yoshikazu Nakamura
Selection of a novel class of RNA–RNA interaction motifs based on the ligase ribozyme with defined modular architecture
Nucleic Acids Research Advance Access published on May 6, 2008.
doi:10.1093/nar/gkn206
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Abstract Web Server Issue: Roberto Mosca and Thomas R. Schneider
RAPIDO: a web server for the alignment of protein structures in the presence of conformational changes
Nucleic Acids Research Advance Access published on May 6, 2008.
doi:10.1093/nar/gkn197
[Abstract] [Full Text] [Print PDF] [Screen PDF]

3 May 2008

Abstract Structural Biology: 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.
doi:10.1093/nar/gkn245
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Structural Biology: Chia-Lung Li, Wei-Zen Yang, Yi-Ping Chen, and Hanna S. Yuan
Structural and functional insights into human Tudor-SN, a key component linking RNA interference and editing
Nucleic Acids Research Advance Access published on May 3, 2008.
doi:10.1093/nar/gkn236
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Web Server Issue: Bart Hooghe, Paco Hulpiau, Frans van Roy, and Pieter De Bleser
ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species
Nucleic Acids Research Advance Access published on May 3, 2008.
doi:10.1093/nar/gkn195
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Computational Bology: Zeba Wunderlich and Leonid A. Mirny
Spatial effects on the speed and reliability of protein–DNA search
Nucleic Acids Research Advance Access published on May 3, 2008.
doi:10.1093/nar/gkn173
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

2 May 2008

Abstract Molecular Biology: 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.
doi:10.1093/nar/gkn242
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Web Server Issue: Li-Wei Jiang, Kuang-Lun Lin, and Chin Lung Lu
OGtree: a tool for creating genome trees of prokaryotes based on overlapping genes
Nucleic Acids Research Advance Access published on May 2, 2008.
doi:10.1093/nar/gkn240
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract RNA: Takeshi Yokoyama and Tsutomu Suzuki
Ribosomal RNAs are tolerant toward genetic insertions: evolutionary origin of the expansion segments
Nucleic Acids Research Advance Access published on May 2, 2008.
doi:10.1093/nar/gkn224
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Survey and Summary: Jerzy Orlowski and Janusz M. Bujnicki
Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses
Nucleic Acids Research Advance Access published on May 2, 2008.
doi:10.1093/nar/gkn175
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

1 May 2008

Abstract Methods online: 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.
doi:10.1093/nar/gkn235
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Methods Online: 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.
doi:10.1093/nar/gkn234
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Molecular Biology: Philippe Simon, Fabio Cannata, Loïc Perrouault, Ludovic Halby, Jean-Paul Concordet, Alexandre Boutorine, Vladimir Ryabinin, Alexandre Sinyakov, and Carine Giovannangeli
Sequence-specific DNA cleavage mediated by bipyridine polyamide conjugates
Nucleic Acids Research Advance Access published on May 1, 2008.
doi:10.1093/nar/gkn231
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Methods Online: 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.
doi:10.1093/nar/gkn200
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Genomics: 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.
doi:10.1093/nar/gkn155
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

29 April 2008

Abstract Web Server Issue: Daeui Park, Byoung-Chul Kim, Seong-Woong Cho, Seong-Jin Park, Jong-Soon Choi, Seung Il Kim, Jong Bhak, and Sunghoon Lee
MassNet: a functional annotation service for protein mass spectrometry data
Nucleic Acids Research Advance Access published on April 29, 2008.
doi:10.1093/nar/gkn241
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Web Server Issue: Eitan Yaffe, Dan Fishelovitch, Haim J. Wolfson, Dan Halperin, and Ruth Nussinov
MolAxis: a server for identification of channels in macromolecules
Nucleic Acids Research Advance Access published on April 29, 2008.
doi:10.1093/nar/gkn223
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Web Server Issue: Vegeir Knudsen and Gustavo Caetano-Anollés
NOBAI: a web server for character coding of geometrical and statistical features in RNA structure
Nucleic Acids Research Advance Access published on April 29, 2008.
doi:10.1093/nar/gkn220
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Chemistry: Joel R. Morgan, Robert P. Lyon, Dean Y. Maeda, and John A. Zebala
Snap-to-it probes: chelate-constrained nucleobase oligomers with enhanced binding specificity
Nucleic Acids Research Advance Access published on April 29, 2008.
doi:10.1093/nar/gkn219
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Chemistry: 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.
doi:10.1093/nar/gkn209
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Molecular Biology: 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.
doi:10.1093/nar/gkn204
[Abstract] [Full Text] [Print PDF] [Screen PDF]

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

Abstract Computational Genomics: 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.
doi:10.1093/nar/gkn227
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract RNA: 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.
doi:10.1093/nar/gkn199
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Computational Biology: 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.
doi:10.1093/nar/gkn176
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Computational Biology: 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.
doi:10.1093/nar/gkn168
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Molecular Biology: 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.
doi:10.1093/nar/gkn066
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

28 April 2008

Abstract Web Server Issue: Ibtissem Grissa, Gilles Vergnaud, and Christine Pourcel
CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats
Nucleic Acids Research Advance Access published on April 28, 2008.
doi:10.1093/nar/gkn228
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Web Server Issue: Andrew E. Firth and Wayne M. Patrick
GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized libraries
Nucleic Acids Research Advance Access published on April 28, 2008.
doi:10.1093/nar/gkn226
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Web Server Issue: Naoshi Fukuhara and Takeshi Kawabata
HOMCOS: a server to predict interacting protein pairs and interacting sites by homology modeling of complex structures
Nucleic Acids Research Advance Access published on April 28, 2008.
doi:10.1093/nar/gkn218
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Web Server Issue: Sergey Lyskov and Jeffrey J. Gray
The RosettaDock server for local protein–protein docking
Nucleic Acids Research Advance Access published on April 28, 2008.
doi:10.1093/nar/gkn216
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Web Server Issue: Raoul Frijters, Bart Heupers, Pieter van Beek, Maurice Bouwhuis, René van Schaik, Jacob de Vlieg, Jan Polman, and Wynand Alkema
CoPub: a literature-based keyword enrichment tool for microarray data analysis
Nucleic Acids Research Advance Access published on April 28, 2008.
doi:10.1093/nar/gkn215
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Web Server Issue: Karsten Suhre and Philippe Schmitt-Kopplin
MassTRIX: mass translator into pathways
Nucleic Acids Research Advance Access published on April 28, 2008.
doi:10.1093/nar/gkn194
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract RNA: 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.
doi:10.1093/nar/gkn177
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

27 April 2008

Abstract Web Server: Maria Garcia-Boronat, Carmen M. Diez-Rivero, Ellis L. Reinherz, and Pedro A. Reche
PVS: a web server for protein sequence variability analysis tuned to facilitate conserved epitope discovery
Nucleic Acids Research Advance Access published on April 27, 2008.
doi:10.1093/nar/gkn211
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract RNA: 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.
doi:10.1093/nar/gkn108
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

25 April 2008

Abstract Nucleic Acid Enzymes: 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.
doi:10.1093/nar/gkn225
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Web Server: Kiyoshi Asai, Hisanori Kiryu, Michiaki Hamada, Yasuo Tabei, Kengo Sato, Hiroshi Matsui, Yasubumi Sakakibara, Goro Terai, and Toutai Mituyama
Software.ncrna.org: web servers for analyses of RNA sequences
Nucleic Acids Research Advance Access published on April 25, 2008.
doi:10.1093/nar/gkn222
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Web Server: Olivier Croce, François Chevenet, and Richard Christen
OligoHeatMap (OHM): an online tool to estimate and display hybridizations of oligonucleotides onto DNA sequences
Nucleic Acids Research Advance Access published on April 25, 2008.
doi:10.1093/nar/gkn221
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Web Server: Johannes Klein, Stefan Leupold, Richard Münch, Claudia Pommerenke, Thorsten Johl, Uwe Kärst, Lothar Jänsch, Dieter Jahn, and Ida Retter
ProdoNet: identification and visualization of prokaryotic gene regulatory and metabolic networks
Nucleic Acids Research Advance Access published on April 25, 2008.
doi:10.1093/nar/gkn217
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Molecular Biology