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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6 November 2009

Abstract Database Issue: Arnaud Ceol, Andrew Chatr Aryamontri, Luana Licata, Daniele Peluso, Leonardo Briganti, Livia Perfetto, Luisa Castagnoli, and Gianni Cesareni
MINT, the molecular interaction database: 2009 update
Nucleic Acids Research Advance Access published on November 6, 2009.
doi:10.1093/nar/gkp983
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Abstract Database Issue: Michael Kuhn, Damian Szklarczyk, Andrea Franceschini, Monica Campillos, Christian von Mering, Lars Juhl Jensen, Andreas Beyer, and Peer Bork
STITCH 2: an interaction network database for small molecules and proteins
Nucleic Acids Research Advance Access published on November 6, 2009.
doi:10.1093/nar/gkp937
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Emilia Lim, Allison Pon, Yannick Djoumbou, Craig Knox, Savita Shrivastava, An Chi Guo, Vanessa Neveu, and David S. Wishart
T3DB: a comprehensively annotated database of common toxins and their targets
Nucleic Acids Research Advance Access published on November 6, 2009.
doi:10.1093/nar/gkp934
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Abstract Methods Online: Amy M. Quinn, Mark T. Bedford, Alexsandra Espejo, Astrid Spannhoff, Christopher P. Austin, Udo Oppermann, and Anton Simeonov
A homogeneous method for investigation of methylation-dependent protein–protein interactions in epigenetics
Nucleic Acids Research Advance Access published on November 6, 2009.
doi:10.1093/nar/gkp899
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5 November 2009

Abstract Database Issue: Neil D. Rawlings, Alan J. Barrett, and Alex Bateman
MEROPS: the peptidase database
Nucleic Acids Research Advance Access published on November 5, 2009.
doi:10.1093/nar/gkp971
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Abstract Database Issue: Yan Zhang, Jie Lv, Hongbo Liu, Jiang Zhu, Jianzhong Su, Qiong Wu, Yunfeng Qi, Fang Wang, and Xia Li
HHMD: the human histone modification database
Nucleic Acids Research Advance Access published on November 5, 2009.
doi:10.1093/nar/gkp968
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Agatha Schlüter, Alejandro Real-Chicharro, Toni Gabaldón, Francisca Sánchez-Jiménez, and Aurora Pujol
PeroxisomeDB 2.0: an integrative view of the global peroxisomal metabolome
Nucleic Acids Research Advance Access published on November 5, 2009.
doi:10.1093/nar/gkp935
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Abstract Database Issue: Gabriel Östlund, Thomas Schmitt, Kristoffer Forslund, Tina Köstler, David N. Messina, Sanjit Roopra, Oliver Frings, and Erik L. L. Sonnhammer
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis
Nucleic Acids Research Advance Access published on November 5, 2009.
doi:10.1093/nar/gkp931
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Abstract Database Issue: Tanja Davidsen, Erin Beck, Anuradha Ganapathy, Robert Montgomery, Nikhat Zafar, Qi Yang, Ramana Madupu, Phil Goetz, Kevin Galinsky, Owen White, and Granger Sutton
The comprehensive microbial resource
Nucleic Acids Research Advance Access published on November 5, 2009.
doi:10.1093/nar/gkp912
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Genome Integrity, Repair and Replication: Elaine M. Taylor, Sophie M. Cecillon, Antonio Bonis, J. Ross Chapman, Lawrence F. Povirk, and Howard D. Lindsay
The Mre11/Rad50/Nbs1 complex functions in resection-based DNA end joining in Xenopus laevis
Nucleic Acids Research Advance Access published on November 5, 2009.
doi:10.1093/nar/gkp905
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Abstract Genomics: Aaron R. Jex, Ross S. Hall, D. Timothy J. Littlewood, and Robin B. Gasser
An integrated pipeline for next-generation sequencing and annotation of mitochondrial genomes
Nucleic Acids Research Advance Access published on November 5, 2009.
doi:10.1093/nar/gkp883
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Abstract Genome Integrity, Repair and Replication: Kyle L. Brown, Marina Roginskaya, Yue Zou, Alvin Altamirano, Ashis K. Basu, and Michael P. Stone
Binding of the human nucleotide excision repair proteins XPA and XPC/HR23B to the 5R-thymine glycol lesion and structure of the cis-(5R,6S) thymine glycol epimer in the 5'-GTgG-3' sequence: destabilization of two base pairs at the lesion site
Nucleic Acids Research Advance Access published on November 5, 2009.
doi:10.1093/nar/gkp844
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4 November 2009

Abstract Methods Online: Roger A. Craig, Jin Lu, Jinquan Luo, Lei Shi, and Li Liao
Optimizing nucleotide sequence ensembles for combinatorial protein libraries using a genetic algorithm
Nucleic Acids Research Advance Access published on November 4, 2009.
doi:10.1093/nar/gkp906
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Abstract RNA: Maricarmen Vallejos, Pablo Ramdohr, Fernando Valiente-Echeverría, Karla Tapia, Felipe E. Rodriguez, Fernando Lowy, J. Pablo Huidobro-Toro, John A. Dangerfield, and Marcelo López-Lastra
The 5'-untranslated region of the mouse mammary tumor virus mRNA exhibits cap-independent translation initiation
Nucleic Acids Research Advance Access published on November 4, 2009.
doi:10.1093/nar/gkp890
[Abstract] [Full Text] [Print PDF] [Screen PDF]

1 November 2009

Abstract Database Issue: Weizhong Li, Hamish McWilliam, Ana Richart de la Torre, Adam Grodowski, Irina Benediktovich, Mickael Goujon, Stephane Nauche, and Rodrigo Lopez
Non-redundant patent sequence databases with value-added annotations at two levels
Nucleic Acids Research Advance Access published on November 1, 2009.
doi:10.1093/nar/gkp960
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Abstract Database Issue: Jeff B. Bowes, Kevin A. Snyder, Erik Segerdell, Chris J. Jarabek, Kenan Azam, Aaron M. Zorn, and Peter D. Vize
Xenbase: gene expression and improved integration
Nucleic Acids Research Advance Access published on November 1, 2009.
doi:10.1093/nar/gkp953
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Andreas Ruepp, Brigitte Waegele, Martin Lechner, Barbara Brauner, Irmtraud Dunger-Kaltenbach, Gisela Fobo, Goar Frishman, Corinna Montrone, and H.-Werner Mewes
CORUM: the comprehensive resource of mammalian protein complexes—2009
Nucleic Acids Research Advance Access published on November 1, 2009.
doi:10.1093/nar/gkp914
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Ulrike Pfreundt, Daniel P. James, Susan Tweedie, Derek Wilson, Sarah A. Teichmann, and Boris Adryan
FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database
Nucleic Acids Research Advance Access published on November 1, 2009.
doi:10.1093/nar/gkp910
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Pavel S. Novichkov, Olga N. Laikova, Elena S. Novichkova, Mikhail S. Gelfand, Adam P. Arkin, Inna Dubchak, and Dmitry A. Rodionov
RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes
Nucleic Acids Research Advance Access published on November 1, 2009.
doi:10.1093/nar/gkp894
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: P. J. Kersey, D. Lawson, E. Birney, P. S. Derwent, M. Haimel, J. Herrero, S. Keenan, A. Kerhornou, G. Koscielny, A. Kähäri, R. J. Kinsella, E. Kulesha, U. Maheswari, K. Megy, M. Nuhn, G. Proctor, D. Staines, F. Valentin, A. J. Vilella, and A. Yates
Ensembl genomes: Extending ensembl across the taxonomic space
Nucleic Acids Research Advance Access published on November 1, 2009.
doi:10.1093/nar/gkp871
[Abstract] [Full Text] [Print PDF] [Screen PDF]

30 October 2009

Abstract Database Issue: Mitsuteru Nakao, Shinobu Okamoto, Mitsuyo Kohara, Tsunakazu Fujishiro, Takatomo Fujisawa, Shusei Sato, Satoshi Tabata, Takakazu Kaneko, and Yasukazu Nakamura
CyanoBase: the cyanobacteria genome database update 2010
Nucleic Acids Research Advance Access published on October 30, 2009.
doi:10.1093/nar/gkp915
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Giorgio Grillo, Antonio Turi, Flavio Licciulli, Flavio Mignone, Sabino Liuni, Sandro Banfi, Vincenzo Alessandro Gennarino, David S. Horner, Giulio Pavesi, Ernesto Picardi, and Graziano Pesole
UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs
Nucleic Acids Research Advance Access published on October 30, 2009.
doi:10.1093/nar/gkp902
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Yan Yuan Tseng, Z. Jeffrey Chen, and Wen-Hsiung Li
fPOP: footprinting functional pockets of proteins by comparative spatial patterns
Nucleic Acids Research Advance Access published on October 30, 2009.
doi:10.1093/nar/gkp900
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Minoru Kanehisa, Susumu Goto, Miho Furumichi, Mao Tanabe, and Mika Hirakawa
KEGG for representation and analysis of molecular networks involving diseases and drugs
Nucleic Acids Research Advance Access published on October 30, 2009.
doi:10.1093/nar/gkp896
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Peter Vanhee, Joke Reumers, Francois Stricher, Lies Baeten, Luis Serrano, Joost Schymkowitz, and Frederic Rousseau
PepX: a structural database of non-redundant protein–peptide complexes
Nucleic Acids Research Advance Access published on October 30, 2009.
doi:10.1093/nar/gkp893
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Douglas H. Turner and David H. Mathews
NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure
Nucleic Acids Research Advance Access published on October 30, 2009.
doi:10.1093/nar/gkp892
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Genomics: Huanying Ge, Min Wei, Paola Fabrizio, Jia Hu, Chao Cheng, Valter D. Longo, and Lei M. Li
Comparative analyses of time-course gene expression profiles of the long-lived sch9 ${Delta}$ mutant
Nucleic Acids Research Advance Access published on October 30, 2009.
doi:10.1093/nar/gkp849
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Judice L. Y. Koh, Huiming Ding, Michael Costanzo, Anastasia Baryshnikova, Kiana Toufighi, Gary D. Bader, Chad L. Myers, Brenda J. Andrews, and Charles Boone
DRYGIN: a database of quantitative genetic interaction networks in yeast
Nucleic Acids Research Advance Access published on October 30, 2009.
doi:10.1093/nar/gkp820
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Pawel Durek, Robert Schmidt, Joshua L. Heazlewood, Alexandra Jones, Daniel MacLean, Axel Nagel, Birgit Kersten, and Waltraud X. Schulze
PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update
Nucleic Acids Research Advance Access published on October 30, 2009.
doi:10.1093/nar/gkp810
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

29 October 2009

Abstract Nucleic Acid Enzymes: Aartjan J. W. te Velthuis, Jamie J. Arnold, Craig E. Cameron, Sjoerd H. E. van den Worm, and Eric J. Snijder
The RNA polymerase activity of SARS-coronavirus nsp12 is primer dependent
Nucleic Acids Research Advance Access published on October 29, 2009.
doi:10.1093/nar/gkp904
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Methods Online: Galen Hostetter, Su Young Kim, Stephanie Savage, Gerald C. Gooden, Michael Barrett, Jian Zhang, Lalitamba Alla, April Watanabe, Janine Einspahr, Anil Prasad, Brian J. Nickoloff, John Carpten, Jeffrey Trent, David Alberts, and Michael Bittner
Random DNA fragmentation allows detection of single-copy, single-exon alterations of copy number by oligonucleotide array CGH in clinical FFPE samples
Nucleic Acids Research Advance Access published on October 29, 2009.
doi:10.1093/nar/gkp881
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: James Robinson, Kavita Mistry, Hamish McWilliam, Rodrigo Lopez, and Steven G. E. Marsh
IPD—the Immuno Polymorphism Database
Nucleic Acids Research Advance Access published on October 29, 2009.
doi:10.1093/nar/gkp879
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Genome Integrity, Repair and Replication: Eeson Rajendra and Ashok R. Venkitaraman
Two modules in the BRC repeats of BRCA2 mediate structural and functional interactions with the RAD51 recombinase
Nucleic Acids Research Advance Access published on October 29, 2009.
doi:10.1093/nar/gkp873
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Genomics: Jun Takayama, Serge Faumont, Hirofumi Kunitomo, Shawn R. Lockery, and Yuichi Iino
Single-cell transcriptional analysis of taste sensory neuron pair in Caenorhabditis elegans
Nucleic Acids Research Advance Access published on October 29, 2009.
doi:10.1093/nar/gkp868
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

28 October 2009

Abstract RNA: Roman J. Szczesny, Lukasz S. Borowski, Lien K. Brzezniak, Aleksandra Dmochowska, Kamil Gewartowski, Ewa Bartnik, and Piotr P. Stepien
Human mitochondrial RNA turnover caught in flagranti: involvement of hSuv3p helicase in RNA surveillance
Nucleic Acids Research Advance Access published on October 28, 2009.
doi:10.1093/nar/gkp903
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Methods Online: D. Baddeley, V. O. Chagin, L. Schermelleh, S. Martin, A. Pombo, P. M. Carlton, A. Gahl, P. Domaing, U. Birk, H. Leonhardt, C. Cremer, and M. C. Cardoso
Measurement of replication structures at the nanometer scale using super-resolution light microscopy
Nucleic Acids Research Advance Access published on October 28, 2009.
doi:10.1093/nar/gkp901
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract RNA: Carsten A. Raabe, Cecilia P. Sanchez, Gerrit Randau, Thomas Robeck, Boris V. Skryabin, Suresh V. Chinni, Michael Kube, Richard Reinhardt, Guey Hooi Ng, Ravichandran Manickam, Vladimir Y. Kuryshev, Michael Lanzer, Juergen Brosius, Thean Hock Tang, and Timofey S. Rozhdestvensky
A global view of the nonprotein-coding transcriptome in Plasmodium falciparum
Nucleic Acids Research Advance Access published on October 28, 2009.
doi:10.1093/nar/gkp895
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Victor M. Markowitz, I-Min A. Chen, Krishna Palaniappan, Ken Chu, Ernest Szeto, Yuri Grechkin, Anna Ratner, Iain Anderson, Athanasios Lykidis, Konstantinos Mavromatis, Natalia N. Ivanova, and Nikos C. Kyrpides
The integrated microbial genomes system: an expanding comparative analysis resource
Nucleic Acids Research Advance Access published on October 28, 2009.
doi:10.1093/nar/gkp887
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract RNA: Katarzyna Dorota Raczynska, Craig G. Simpson, Adam Ciesiolka, Lukasz Szewc, Dominika Lewandowska, Jim McNicol, Zofia Szweykowska-Kulinska, John W. S. Brown, and Artur Jarmolowski
Involvement of the nuclear cap-binding protein complex in alternative splicing in Arabidopsis thaliana
Nucleic Acids Research Advance Access published on October 28, 2009.
doi:10.1093/nar/gkp869
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Gene Regulation, Chromatin and Epigenetics: Kyu-Han Kim, Jae-Yeon Jeong, Young-Joon Surh, and Kyu-Won Kim
Expression of stress-response ATF3 is mediated by Nrf2 in astrocytes
Nucleic Acids Research Advance Access published on October 28, 2009.
doi:10.1093/nar/gkp865
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

27 October 2009

Abstract Methods Online: Paul Brotherton, Juan J. Sanchez, Alan Cooper, and Phillip Endicott
Preferential access to genetic information from endogenous hominin ancient DNA and accurate quantitative SNP-typing via SPEX
Nucleic Acids Research Advance Access published on October 27, 2009.
doi:10.1093/nar/gkp897
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Carol J. Bult, James A. Kadin, Joel E. Richardson, Judith A. Blake, Janan T Eppig, and the Mouse Genome Database Group
The Mouse Genome Database: enhancements and updates
Nucleic Acids Research Advance Access published on October 27, 2009.
doi:10.1093/nar/gkp880
[Abstract] [Full Text] [Print PDF] [Screen PDF]

25 October 2009

Abstract Database Issue: Renzo Kottmann, Ivalyo Kostadinov, Melissa Beth Duhaime, Pier Luigi Buttigieg, Pelin Yilmaz, Wolfgang Hankeln, Jost Waldmann, and Frank Oliver Glöckner
Megx.net: integrated database resource for marine ecological genomics
Nucleic Acids Research Advance Access published on October 25, 2009.
doi:10.1093/nar/gkp918
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: S. Velankar, C. Best, B. Beuth, C. H. Boutselakis, N. Cobley, A. W. Sousa Da Silva, D. Dimitropoulos, A. Golovin, M. Hirshberg, M. John, E. B. Krissinel, R. Newman, T. Oldfield, A. Pajon, C. J. Penkett, J. Pineda-Castillo, G. Sahni, S. Sen, R. Slowley, A. Suarez-Uruena, J. Swaminathan, G. van Ginkel, W. F. Vranken, K. Henrick, and G. J. Kleywegt
PDBe: Protein Data Bank in Europe
Nucleic Acids Research Advance Access published on October 25, 2009.
doi:10.1093/nar/gkp916
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Structural Biology: Ke-wei Zheng, Zhao Chen, Yu-hua Hao, and Zheng Tan
Molecular crowding creates an essential environment for the formation of stable G-quadruplexes in long double-stranded DNA
Nucleic Acids Research Advance Access published on October 25, 2009.
doi:10.1093/nar/gkp898
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Nucleic Acid Enzymes: Corentin Claeys Bouuaert and Ronald Chalmers
Transposition of the human Hsmar1 transposon: rate-limiting steps and the importance of the flanking TA dinucleotide in second strand cleavage
Nucleic Acids Research Advance Access published on October 25, 2009.
doi:10.1093/nar/gkp891
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Christian J. A. Sigrist, Lorenzo Cerutti, Edouard de Castro, Petra S. Langendijk-Genevaux, Virginie Bulliard, Amos Bairoch, and Nicolas Hulo
PROSITE, a protein domain database for functional characterization and annotation
Nucleic Acids Research Advance Access published on October 25, 2009.
doi:10.1093/nar/gkp885
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Computational Biology: Theodoros G. Soldatos, Seán I. O’Donoghue, Venkata P. Satagopam, Lars J. Jensen, Nigel P. Brown, Adriano Barbosa-Silva, and Reinhard Schneider
Martini: using literature keywords to compare gene sets
Nucleic Acids Research Advance Access published on October 25, 2009.
doi:10.1093/nar/gkp876
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Molecular Biology: Evelina Y. Basenko, Anthony J. Cesare, Shilpa Iyer, Jack D. Griffith, and Michael J. McEachern
Telomeric circles are abundant in the stn1-M1 mutant that maintains its telomeres through recombination
Nucleic Acids Research Advance Access published on October 25, 2009.
doi:10.1093/nar/gkp814
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Paulino Pérez-Rodríguez, Diego Mauricio Riaño-Pachón, Luiz Gustavo Guedes Corrêa, Stefan A. Rensing, Birgit Kersten, and Bernd Mueller-Roeber
PlnTFDB: updated content and new features of the plant transcription factor database
Nucleic Acids Research Advance Access published on October 25, 2009.
doi:10.1093/nar/gkp805
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

23 October 2009

Abstract Database Issue: Ron Milo, Paul Jorgensen, Uri Moran, Griffin Weber, and Michael Springer
BioNumbers—the database of key numbers in molecular and cell biology
Nucleic Acids Research Advance Access published on October 23, 2009.
doi:10.1093/nar/gkp889
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Paula de Matos, Rafael Alcántara, Adriano Dekker, Marcus Ennis, Janna Hastings, Kenneth Haug, Inmaculada Spiteri, Steve Turner, and Christoph Steinbeck
Chemical Entities of Biological Interest: an update
Nucleic Acids Research Advance Access published on October 23, 2009.
doi:10.1093/nar/gkp886
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Molecular Biology: Karthik S. Harve, Ricky Lareu, Raj Rajagopalan, and Michael Raghunath
Understanding how the crowded interior of cells stabilizes DNA/DNA and DNA/RNA hybrids–in silico predictions and in vitro evidence
Nucleic Acids Research Advance Access published on October 23, 2009.
doi:10.1093/nar/gkp884
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Methods Online: Jianzhong Su, Yan Zhang, Jie Lv, Hongbo Liu, Xiaoyan Tang, Fang Wang, Yunfeng Qi, Yujia Feng, and Xia Li
CpG_MI: a novel approach for identifying functional CpG islands in mammalian genomes
Nucleic Acids Research Advance Access published on October 23, 2009.
doi:10.1093/nar/gkp882
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Gene Regulation, Chromatin and Epigenetics: Margarita Silicheva, Anton Golovnin, Ekaterina Pomerantseva, Aleksander Parshikov, Pavel Georgiev, and Oksana Maksimenko
Drosophila mini-white model system: new insights into positive position effects and the role of transcriptional terminators and gypsy insulator in transgene shielding
Nucleic Acids Research Advance Access published on October 23, 2009.
doi:10.1093/nar/gkp877
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Methods Online: Yaniv Lustig, Chaim Wachtel, Mark Safro, Li Liu, and Shulamit Michaeli
‘RNA walk’ a novel approach to study RNA–RNA interactions between a small RNA and its target
Nucleic Acids Research Advance Access published on October 23, 2009.
doi:10.1093/nar/gkp872
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Andrew Blake, Karen Pickford, Simon Greenaway, Steve Thomas, Amanda Pickard, Christine M. Williamson, Niels C. Adams, Alison Walling, Tim Beck, Martin Fray, Jo Peters, Tom Weaver, Steve D. M. Brown, John M. Hancock, and Ann-Marie Mallon
MouseBook: an integrated portal of mouse resources
Nucleic Acids Research Advance Access published on October 23, 2009.
doi:10.1093/nar/gkp867
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Lewis Y. Geer, Aron Marchler-Bauer, Renata C. Geer, Lianyi Han, Jane He, Siqian He, Chunlei Liu, Wenyao Shi, and Stephen H. Bryant
The NCBI BioSystems database
Nucleic Acids Research Advance Access published on October 23, 2009.
doi:10.1093/nar/gkp858
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Methods Online: Ernest Turro, Alex Lewin, Anna Rose, Margaret J. Dallman, and Sylvia Richardson
MMBGX: a method for estimating expression at the isoform level and detecting differential splicing using whole-transcript Affymetrix arrays
Nucleic Acids Research Advance Access published on October 23, 2009.
doi:10.1093/nar/gkp853
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Genome Integrity, Repair and Replication: James E. Graham, Viknesh Sivanathan, David J. Sherratt, and Lidia K. Arciszewska
FtsK translocation on DNA stops at XerCD-dif
Nucleic Acids Research Advance Access published on October 23, 2009.
doi:10.1093/nar/gkp843
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Methods Online: C. A. Stein, J. Bo Hansen, Johnathan Lai, SiJian Wu, Anatoliy Voskresenskiy, Anja Høg, Jesper Worm, Maj Hedtjärn, Naira Souleimanian, Paul Miller, Harris S. Soifer, Daniella Castanotto, Luba Benimetskaya, Henrik Ørum, and Troels Koch
Efficient gene silencing by delivery of locked nucleic acid antisense oligonucleotides, unassisted by transfection reagents
Nucleic Acids Research Advance Access published on October 23, 2009.
doi:10.1093/nar/gkp841
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Motohiro Mihara, Takeshi Itoh, and Takeshi Izawa
SALAD database: a motif-based database of protein annotations for plant comparative genomics
Nucleic Acids Research Advance Access published on October 23, 2009.
doi:10.1093/nar/gkp831
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Methods Online: Joohoon Kim and Milan Mrksich
Profiling the selectivity of DNA ligases in an array format with mass spectrometry
Nucleic Acids Research Advance Access published on October 23, 2009.
doi:10.1093/nar/gkp827
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Methods Online: Tao Zeng and Jinyan Li
Maximization of negative correlations in time-course gene expression data for enhancing understanding of molecular pathways
Nucleic Acids Research Advance Access published on October 23, 2009.
doi:10.1093/nar/gkp822
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Molecular Biology: Laura Baranello, Davide Bertozzi, Maria Vittoria Fogli, Yves Pommier, and Giovanni Capranico
DNA topoisomerase I inhibition by camptothecin induces escape of RNA polymerase II from promoter-proximal pause site, antisense transcription and histone acetylation at the 5 human HIF-1 ${alpha}$ gene locus
Nucleic Acids Research Advance Access published on October 23, 2009.
doi:10.1093/nar/gkp817
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Synthetic Biology and Chemistry: Sivaprasad Attaluri, Radha R. Bonala, In-Young Yang, Mark A. Lukin, Yujing Wen, Arthur P. Grollman, Masaaki Moriya, Charles R. Iden, and Francis Johnson
DNA adducts of aristolochic acid II: total synthesis and site-specific mutagenesis studies in mammalian cells
Nucleic Acids Research Advance Access published on October 23, 2009.
doi:10.1093/nar/gkp815
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract RNA: Victoria A. Barron, Hui Zhu, Melissa N. Hinman, Andrea N. Ladd, and Hua Lou
The neurofibromatosis type I pre-mRNA is a novel target of CELF protein-mediated splicing regulation
Nucleic Acids Research Advance Access published on October 23, 2009.
doi:10.1093/nar/gkp766
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Genome Integrity, Repair and Replication: Carmen Bertoni, Arjun Rustagi, and Thomas A. Rando
Enhanced gene repair mediated by methyl-CpG-modified single-stranded oligonucleotides
Nucleic Acids Research Advance Access published on October 23, 2009.
doi:10.1093/nar/gkp757
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Structural Biology: Björn M. Burmann, Xiao Luo, Paul Rösch, Markus C. Wahl, and Max E. Gottesman
Fine tuning of the E. coli NusB:NusE complex affinity to BoxA RNA is required for processive antitermination
Nucleic Acids Research Advance Access published on October 23, 2009.
doi:10.1093/nar/gkp736
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Gene Regulation, Chromatin and Epigenetics: Daniela Zychlinski, Steffen Erkelenz, Vanessa Melhorn, Christopher Baum, Heiner Schaal, and Jens Bohne
Limited complementarity between U1 snRNA and a retroviral 5' splice site permits its attenuation via RNA secondary structure
Nucleic Acids Research Advance Access published on October 23, 2009.
doi:10.1093/nar/gkp694
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

22 October 2009

Abstract Database Issue: Panagiotis Alexiou, Thanasis Vergoulis, Martin Gleditzsch, George Prekas, Theodore Dalamagas, Molly Megraw, Ivo Grosse, Timos Sellis, and Artemis G. Hatzigeorgiou
miRGen 2.0: a database of microRNA genomic information and regulation
Nucleic Acids Research Advance Access published on October 22, 2009.
doi:10.1093/nar/gkp888
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: B. Aranda, P. Achuthan, Y. Alam-Faruque, I. Armean, A. Bridge, C. Derow, M. Feuermann, A. T. Ghanbarian, S. Kerrien, J. Khadake, J. Kerssemakers, C. Leroy, M. Menden, M. Michaut, L. Montecchi-Palazzi, S. N. Neuhauser, S. Orchard, V. Perreau, B. Roechert, K. van Eijk, and H. Hermjakob
The IntAct molecular interaction database in 2010
Nucleic Acids Research Advance Access published on October 22, 2009.
doi:10.1093/nar/gkp878
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Ron Caspi, Tomer Altman, Joseph M. Dale, Kate Dreher, Carol A. Fulcher, Fred Gilham, Pallavi Kaipa, Athikkattuvalasu S. Karthikeyan, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Lukas A. Mueller, Suzanne Paley, Liviu Popescu, Anuradha Pujar, Alexander G. Shearer, Peifen Zhang, and Peter D. Karp
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
Nucleic Acids Research Advance Access published on October 22, 2009.
doi:10.1093/nar/gkp875
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract RNA: Guihua Sun, Haitang Li, and John J. Rossi
Sequence context outside the target region influences the effectiveness of miR-223 target sites in the RhoB 3'UTR
Nucleic Acids Research Advance Access published on October 22, 2009.
doi:10.1093/nar/gkp870
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Computational Biology: Alexis Vandenbon and Kenta Nakai
Modeling tissue-specific structural patterns in human and mouse promoters
Nucleic Acids Research Advance Access published on October 22, 2009.
doi:10.1093/nar/gkp866
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract RNA: Yuki Kuwano, Rudolf Pullmann Jr., Bernard S. Marasa, Kotb Abdelmohsen, Eun Kyung Lee, Xiaoling Yang, Jennifer L. Martindale, Ming Zhan, and Myriam Gorospe
NF90 selectively represses the translation of target mRNAs bearing an AU-rich signature motif
Nucleic Acids Research Advance Access published on October 22, 2009.
doi:10.1093/nar/gkp861
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract RNA: Tian Sheng Chen, Ruenn Chai Lai, May May Lee, Andre Boon Hwa Choo, Chuen Neng Lee, and Sai Kiang Lim
Mesenchymal stem cell secretes microparticles enriched in pre-microRNAs
Nucleic Acids Research Advance Access published on October 22, 2009.
doi:10.1093/nar/gkp857
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Genome Integrity, Repair and Replication: Sofia L. Vidal-Cardenas and Carol W. Greider
Comparing effects of mTR and mTERT deletion on gene expression and DNA damage response: a critical examination of telomere length maintenance-independent roles of telomerase
Nucleic Acids Research Advance Access published on October 22, 2009.
doi:10.1093/nar/gkp855
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Eli Kaminuma, Jun Mashima, Yuichi Kodama, Takashi Gojobori, Osamu Ogasawara, Kousaku Okubo, Toshihisa Takagi, and Yasukazu Nakamura
DDBJ launches a new archive database with analytical tools for next-generation sequence data
Nucleic Acids Research Advance Access published on October 22, 2009.
doi:10.1093/nar/gkp847
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Structural Biology: Richard Lavery, Krystyna Zakrzewska, David Beveridge, Thomas C. Bishop, David A. Case, Thomas Cheatham III, Surjit Dixit, B. Jayaram, Filip Lankas, Charles Laughton, John H. Maddocks, Alexis Michon, Roman Osman, Modesto Orozco, Alberto Perez, Tanya Singh, Nada Spackova, and Jiri Sponer
A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA
Nucleic Acids Research Advance Access originally published on October 22, 2009. This version published November 6, 2009.
doi:10.1093/nar/gkp834
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Lynn M. Schriml, Cesar Arze, Suvarna Nadendla, Anu Ganapathy, Victor Felix, Anup Mahurkar, Katherine Phillippy, Aaron Gussman, Sam Angiuoli, Elodie Ghedin, Owen White, and Neil Hall
GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database
Nucleic Acids Research Advance Access published on October 22, 2009.
doi:10.1093/nar/gkp832
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Structural Biology: In Suk Joung, Özgül Persil Çetinkol, Nicholas V. Hud, and Thomas E. Cheatham III
Molecular dynamics simulations and coupled nucleotide substitution experiments indicate the nature of A·A base pairing and a putative structure of the coralyne-induced homo-adenine duplex
Nucleic Acids Research Advance Access published on October 22, 2009.
doi:10.1093/nar/gkp730
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data] [Supplementary Data]

21 October 2009

Abstract Database Issue: Richard J. Roberts, Tamas Vincze, Janos Posfai, and Dana Macelis
REBASE—a database for DNA restriction and modification: enzymes, genes and genomes
Nucleic Acids Research Advance Access published on October 21, 2009.
doi:10.1093/nar/gkp874
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Methods Online: Xiaowei Wang, Xiaohui Wang, Rajeev K. Varma, Lesslie Beauchamp, Susan Magdaleno, and Timothy J. Sendera
Selection of hyperfunctional siRNAs with improved potency and specificity
Nucleic Acids Research Advance Access published on October 21, 2009.
doi:10.1093/nar/gkp864
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Genomics: Federico Bolognani, Tania Contente-Cuomo, and Nora I. Perrone-Bizzozero
Novel recognition motifs and biological functions of the RNA-binding protein HuD revealed by genome-wide identification of its targets
Nucleic Acids Research Advance Access published on October 21, 2009.
doi:10.1093/nar/gkp863
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Molecular Biology: Zhe-Xian Tian, Emilie Fargier, Micheál Mac Aogáin, Claire Adams, Yi-Ping Wang, and Fergal O’Gara
Transcriptome profiling defines a novel regulon modulated by the LysR-type transcriptional regulator MexT in Pseudomonas aeruginosa
Nucleic Acids Research Advance Access published on October 21, 2009.
doi:10.1093/nar/gkp828
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

20 October 2009

Abstract Synthetic Biology and Chemistry: Barbara Puffer, Christoph Kreutz, Ulrike Rieder, Marc-Olivier Ebert, Robert Konrat, and Ronald Micura
5-Fluoro pyrimidines: labels to probe DNA and RNA secondary structures by 1D ¹⁹F NMR spectroscopy
Nucleic Acids Research Advance Access published on October 20, 2009.
doi:10.1093/nar/gkp862
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Gene Regulation, Chromatin and Epigenetics: Yuji Goto and Hiroshi Kimura
Inactive X chromosome-specific histone H3 modifications and CpG hypomethylation flank a chromatin boundary between an X-inactivated and an escape gene
Nucleic Acids Research Advance Access published on October 20, 2009.
doi:10.1093/nar/gkp860
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Gene Regulation, Chromatin and Epigenetics: Vincenzo Cavalieri, Raffaella Melfi, and Giovanni Spinelli
Promoter activity of the sea urchin (Paracentrotus lividus) nucleosomal H3 and H2A and linker H1 ${alpha}$ -histone genes is modulated by enhancer and chromatin insulator
Nucleic Acids Research Advance Access published on October 20, 2009.
doi:10.1093/nar/gkp859
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Genomics: Tatiana Teixeira Torres, Marlies Dolezal, Christian Schlötterer, and Birgit Ottenwälder
Expression profiling of Drosophila mitochondrial genes via deep mRNA sequencing
Nucleic Acids Research Advance Access published on October 20, 2009.
doi:10.1093/nar/gkp856
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Martin Aslett, Cristina Aurrecoechea, Matthew Berriman, John Brestelli, Brian P. Brunk, Mark Carrington, Daniel P. Depledge, Steve Fischer, Bindu Gajria, Xin Gao, Malcolm J. Gardner, Alan Gingle, Greg Grant, Omar S. Harb, Mark Heiges, Christiane Hertz-Fowler, Robin Houston, Frank Innamorato, John Iodice, Jessica C. Kissinger, Eileen Kraemer, Wei Li, Flora J. Logan, John A. Miller, Siddhartha Mitra, Peter J. Myler, Vishal Nayak, Cary Pennington, Isabelle Phan, Deborah F. Pinney, Gowthaman Ramasamy, Matthew B. Rogers, David S. Roos, Chris Ross, Dhileep Sivam, Deborah F. Smith, Ganesh Srinivasamoorthy, Christian J. Stoeckert Jr, Sandhya Subramanian, Ryan Thibodeau, Adrian Tivey, Charles Treatman, Giles Velarde, and Haiming Wang
TriTrypDB: a functional genomic resource for the Trypanosomatidae
Nucleic Acids Research Advance Access published on October 20, 2009.
doi:10.1093/nar/gkp851
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Lauren M. Brinkac, Tanja Davidsen, Erin Beck, Anuradha Ganapathy, Elisabet Caler, Robert J. Dodson, A. Scott Durkin, Derek M. Harkins, Hernan Lorenzi, Ramana Madupu, Yinong Sebastian, Susmita Shrivastava, Mathangi Thiagarajan, Joshua Orvis, Jaideep P. Sundaram, Jonathon Crabtree, Kevin Galens, Yongmei Zhao, Jason M. Inman, Robert Montgomery, Seth Schobel, Kevin Galinsky, David M. Tanenbaum, Adam Resnick, Nikhat Zafar, Owen White, and Granger Sutton
Pathema: a clade-specific bioinformatics resource center for pathogen research
Nucleic Acids Research Advance Access published on October 20, 2009.
doi:10.1093/nar/gkp850
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: The UniProt Consortium
The Universal Protein Resource (UniProt) in 2010
Nucleic Acids Research Advance Access published on October 20, 2009.
doi:10.1093/nar/gkp846
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Benjamin A. Shoemaker, Dachuan Zhang, Ratna R. Thangudu, Manoj Tyagi, Jessica H. Fong, Aron Marchler-Bauer, Stephen H. Bryant, Thomas Madej, and Anna R. Panchenko
Inferred Biomolecular Interaction Server—a web server to analyze and predict protein interacting partners and binding sites
Nucleic Acids Research Advance Access published on October 20, 2009.
doi:10.1093/nar/gkp842
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Survey and Summary: Marta Olejniczak, Paulina Galka, and Wlodzimierz J. Krzyzosiak
Sequence-non-specific effects of RNA interference triggers and microRNA regulators
Nucleic Acids Research Advance Access published on October 20, 2009.
doi:10.1093/nar/gkp829
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Methods Online: Artem Zykovich, Ian Korf, and David J. Segal
Bind-n-Seq: high-throughput analysis of in vitro protein–DNA interactions using massively parallel sequencing
Nucleic Acids Research Advance Access published on October 20, 2009.
doi:10.1093/nar/gkp802
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Nucleic Acid Enzymes: Mohamed Labazi, Lahcen Jaafar, and Hernan Flores-Rozas
Modulation of the DNA-binding activity of Saccharomyces cerevisiae MSH2–MSH6 complex by the high-mobility group protein NHP6A, in vitro
Nucleic Acids Research Advance Access published on October 20, 2009.
doi:10.1093/nar/gkp649
[Abstract] [Full Text] [Print PDF] [Screen PDF]

15 October 2009

Abstract Structural Biology: Krzysztof Kuchta, Lukasz Knizewski, Lucjan S. Wyrwicz, Leszek Rychlewski, and Krzysztof Ginalski
Comprehensive classification of nucleotidyltransferase fold proteins: identification of novel families and their representatives in human
Nucleic Acids Research Advance Access published on October 15, 2009.
doi:10.1093/nar/gkp854
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

14 October 2009

Abstract Methods Online: Murizal Zainol, Julia Stoute, Gabriela M. Almeida, Alexander Rapp, Karen J. Bowman, George D. D. Jones, and ECVAG
Introducing a true internal standard for the Comet assay to minimize intra- and inter-experiment variability in measures of DNA damage and repair
Nucleic Acids Research Advance Access published on October 14, 2009.
doi:10.1093/nar/gkp826
[Abstract] [Full Text] [Print PDF] [Screen PDF]

13 October 2009

Abstract RNA: Renata Moreno, Stefano Marzi, Pascale Romby, and Fernando Rojo
The Crc global regulator binds to an unpaired A-rich motif at the Pseudomonas putida alkS mRNA coding sequence and inhibits translation initiation
Nucleic Acids Research Advance Access published on October 13, 2009.
doi:10.1093/nar/gkp825
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Genomics: Wan-Jen Hong, Robert Tibshirani, and Gilbert Chu
Local false discovery rate facilitates comparison of different microarray experiments
Nucleic Acids Research Advance Access published on October 13, 2009.
doi:10.1093/nar/gkp813
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract RNA: Xian Zhang, Tongtong Zou, Jaladanki N. Rao, Lan Liu, Lan Xiao, Peng-Yuan Wang, Yu-Hong Cui, Myriam Gorospe, and Jian-Ying Wang
Stabilization of XIAP mRNA through the RNA binding protein HuR regulated by cellular polyamines
Nucleic Acids Research Advance Access published on October 13, 2009.
doi:10.1093/nar/gkp755
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

12 October 2009

Abstract Genomics: Ola Wallerman, Mehdi Motallebipour, Stefan Enroth, Kalicharan Patra, Madhu Sudhan Reddy Bysani, Jan Komorowski, and Claes Wadelius
Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing
Nucleic Acids Research Advance Access published on October 12, 2009.
doi:10.1093/nar/gkp823
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Survey and Summary: Bouke A. de Boer, Jan M. Ruijter, Frans P. J. M. Voorbraak, and Antoon F. M. Moorman
More than a decade of developmental gene expression atlases: where are we now?
Nucleic Acids Research Advance Access published on October 12, 2009.
doi:10.1093/nar/gkp819
[Abstract] [Full Text] [Print PDF] [Screen PDF]

9 October 2009

Abstract Nucleic Acid Enzymes: Hana Macícková-Cahová and Michal Hocek
Cleavage of adenine-modified functionalized DNA by type II restriction endonucleases
Nucleic Acids Research Advance Access published on October 9, 2009.
doi:10.1093/nar/gkp845
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Molecular Biology: Mykola I. Onyshchenko, Timur I. Gaynutdinov, Ethan A. Englund, Daniel H. Appella, Ronald D. Neumann, and Igor G. Panyutin
Stabilization of G-quadruplex in the BCL2 promoter region in double-stranded DNA by invading short PNAs
Nucleic Acids Research Advance Access published on October 9, 2009.
doi:10.1093/nar/gkp840
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Stefan M. Woerner, Yan P. Yuan, Axel Benner, Sebastian Korff, Magnus von Knebel Doeberitz, and Peer Bork
SelTarbase, a database of human mononucleotide-microsatellite mutations and their potential impact to tumorigenesis and immunology
Nucleic Acids Research Advance Access published on October 9, 2009.
doi:10.1093/nar/gkp839
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Gene Regulation, Chromatin and Epigenetics: Elena S. Philonenko, Denis B. Klochkov, Victoria V. Borunova, Alexey A. Gavrilov, Sergey V. Razin, and Olga V. Iarovaia
TMEM8 – a non-globin gene entrapped in the globin web
Nucleic Acids Research Advance Access published on October 9, 2009.
doi:10.1093/nar/gkp838
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Methods Online: Antony K. Chen, Mark A. Behlke, and Andrew Tsourkas
Sub-cellular trafficking and functionality of 2'-O-methyl and 2'-O-methyl-phosphorothioate molecular beacons
Nucleic Acids Research Advance Access published on October 9, 2009.
doi:10.1093/nar/gkp837
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Gene Regulation, Chromatin and Epigenetics: Xueqing Xu, Koji Tsumagari, Janet Sowden, Rabi Tawil, Alan P. Boyle, Lingyun Song, Terrence S. Furey, Gregory E. Crawford, and Melanie Ehrlich
DNaseI hypersensitivity at gene-poor, FSH dystrophy-linked 4q35.2
Nucleic Acids Research Advance Access published on October 9, 2009.
doi:10.1093/nar/gkp833
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Hifzur Rahman Ansari, Darren R. Flower, and G. P. S. Raghava
AntigenDB: an immunoinformatics database of pathogen antigens
Nucleic Acids Research Advance Access published on October 9, 2009.
doi:10.1093/nar/gkp830
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Computational Biology: David G. Dineen, Andreas Wilm, Pádraig Cunningham, and Desmond G. Higgins
High DNA melting temperature predicts transcription start site location in human and mouse
Nucleic Acids Research Advance Access published on October 9, 2009.
doi:10.1093/nar/gkp821
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract RNA: Agnès Baudin-Baillieu, Céline Fabret, Xue-hai Liang, Dorota Piekna-Przybylska, Maurille J. Fournier, and Jean-Pierre Rousset
Nucleotide modifications in three functionally important regions of the Saccharomyces cerevisiae ribosome affect translation accuracy
Nucleic Acids Research Advance Access published on October 9, 2009.
doi:10.1093/nar/gkp816
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Milana Frenkel-Morgenstern, Ariel A. Cohen, Naama Geva-Zatorsky, Eran Eden, Jaime Prilusky, Irina Issaeva, Alex Sigal, Cellina Cohen-Saidon, Yuvalal Liron, Lydia Cohen, Tamar Danon, Natalie Perzov, and Uri Alon
Dynamic Proteomics: a database for dynamics and localizations of endogenous fluorescently-tagged proteins in living human cells
Nucleic Acids Research Advance Access published on October 9, 2009.
doi:10.1093/nar/gkp808
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Hee Shin Kim, Terence Murphy, Jing Xia, Doina Caragea, Yoonseong Park, Richard W. Beeman, Marcé D. Lorenzen, Stephen Butcher, J. Robert Manak, and Susan J. Brown
BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum
Nucleic Acids Research Advance Access published on October 9, 2009.
doi:10.1093/nar/gkp807
[Abstract] [Full Text] [Print PDF] [Screen PDF]

8 October 2009

Abstract Molecular Biology: Huang Huang, Renping Qiao, Deyao Zhao, Tong Zhang, Youxian Li, Fan Yi, Fangfang Lai, Junmei Hong, Xianfeng Ding, Zhenjun Yang, Lihe Zhang, Quan Du, and Zicai Liang
Profiling of mismatch discrimination in RNAi enabled rational design of allele-specific siRNAs
Nucleic Acids Research Advance Access published on October 8, 2009.
doi:10.1093/nar/gkp835
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Methods Online: Nicholas J. Croucher, Maria C. Fookes, Timothy T. Perkins, Daniel J. Turner, Samuel B. Marguerat, Thomas Keane, Michael A. Quail, Miao He, Sammey Assefa, Jürg Bähler, Robert A. Kingsley, Julian Parkhill, Stephen D. Bentley, Gordon Dougan, and Nicholas R. Thomson
A simple method for directional transcriptome sequencing using Illumina technology
Nucleic Acids Research Advance Access published on October 8, 2009.
doi:10.1093/nar/gkp811
[Abstract] [Full Text] [Print PDF] [Screen PDF]

7 October 2009

Abstract RNA: Marie-Hélène Mazauric, Yeonee Seol, Satoko Yoshizawa, Koen Visscher, and Dominique Fourmy
Interaction of the HIV-1 frameshift signal with the ribosome
Nucleic Acids Research Advance Access published on October 7, 2009.
doi:10.1093/nar/gkp779
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

6 October 2009

Abstract Database Issue: Marek S. Skrzypek, Martha B. Arnaud, Maria C. Costanzo, Diane O. Inglis, Prachi Shah, Gail Binkley, Stuart R. Miyasato, and Gavin Sherlock
New tools at the Candida Genome Database: biochemical pathways and full-text literature search
Nucleic Acids Research Advance Access published on October 6, 2009.
doi:10.1093/nar/gkp836
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Structural Biology: Zeina Hobaika, Loussine Zargarian, Yves Boulard, Richard G. Maroun, Olivier Mauffret, and Serge Fermandjian
Specificity of LTR DNA recognition by a peptide mimicking the HIV-1 integrase ${alpha}$ 4 helix
Nucleic Acids Research Advance Access published on October 6, 2009.
doi:10.1093/nar/gkp824
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Zhenhai Zhang, Jingyin Yu, Daofeng Li, Zuyong Zhang, Fengxia Liu, Xin Zhou, Tao Wang, Yi Ling, and Zhen Su
PMRD: plant microRNA database
Nucleic Acids Research Advance Access published on October 6, 2009.
doi:10.1093/nar/gkp818
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Molecular Biology: Grace S. Tan, Barry G. Garchow, Xuhang Liu, Jennifer Yeung, John P. Morris IV, Trinna L. Cuellar, Michael T. McManus, and Marianthi Kiriakidou
Expanded RNA-binding activities of mammalian Argonaute 2
Nucleic Acids Research Advance Access published on October 6, 2009.
doi:10.1093/nar/gkp812
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Nucleic Acid Enzymes: Rachel M. Smith, Fiona M. Diffin, Nigel J. Savery, Jytte Josephsen, and Mark D. Szczelkun
DNA cleavage and methylation specificity of the single polypeptide restriction–modification enzyme LlaGI
Nucleic Acids Research Advance Access published on October 6, 2009.
doi:10.1093/nar/gkp790
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Genome Integrity, Repair and Replication: Shuang Liu, Hongyan Wang, Xiang Wang, Lin Lu, Ning Gao, Peter S. N. Rowe, Baocheng Hu, and Ya Wang
MEPE/OF45 protects cells from DNA damage induced killing via stabilizing CHK1
Nucleic Acids Research Advance Access published on October 6, 2009.
doi:10.1093/nar/gkp768
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

1 October 2009

Abstract Genome Integrity, Repair and Replication: Nick M. Makridakis, Troy Phipps, Sudesh Srivastav, and Juergen K. V. Reichardt
PCR-free method detects high frequency of genomic instability in prostate cancer
Nucleic Acids Research Advance Access published on October 1, 2009.
doi:10.1093/nar/gkp761
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data] [Supplementary Data]

30 September 2009

Abstract Database Issue: Jun Duan, Ruiqiang Li, Daojun Cheng, Wei Fan, Xingfu Zha, Tingcai Cheng, Yuqian Wu, Jun Wang, Kazuei Mita, Zhonghuai Xiang, and Qingyou Xia
SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology
Nucleic Acids Research Advance Access published on September 30, 2009.
doi:10.1093/nar/gkp801
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Nucleic acid Enzymes: Rachel M. Smith, Jytte Josephsen, and Mark D. Szczelkun
An Mrr-family nuclease motif in the single polypeptide restriction–modification enzyme LlaGI
Nucleic Acids Research Advance Access published on September 30, 2009.
doi:10.1093/nar/gkp795
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract RNA: Simona Cuzic-Feltens, Michael H. W. Weber, and Roland K. Hartmann
Investigation of catalysis by bacterial RNase P via LNA and other modifications at the scissile phosphodiester
Nucleic Acids Research Advance Access published on September 30, 2009.
doi:10.1093/nar/gkp775
[Abstract] [Full Text] [Print PDF] [Screen PDF]

29 September 2009

Abstract Molecular Biology: María Rodríguez-Mateos, Juan J. García-Gómez, Rosario Francisco-Velilla, Miguel Remacha, Jesús de la Cruz, and Juan P. G. Ballesta
Role and dynamics of the ribosomal protein P0 and its related trans-acting factor Mrt4 during ribosome assembly in Saccharomyces cerevisiae
Nucleic Acids Research Advance Access published on September 29, 2009.
doi:10.1093/nar/gkp806
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Gene Regulation, Chromatin and Epigenetics: Joanna Boros, Amanda O’Donnell, Ian J. Donaldson, Aneta Kasza, Leo Zeef, and Andrew D. Sharrocks
Overlapping promoter targeting by Elk-1 and other divergent ETS-domain transcription factor family members
Nucleic Acids Research Advance Access published on September 29, 2009.
doi:10.1093/nar/gkp804
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Nucleic Acid Enzymes: Femi J. Olorunniji and W. Marshall Stark
The catalytic residues of Tn3 resolvase
Nucleic Acids Research Advance Access published on September 29, 2009.
doi:10.1093/nar/gkp797
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Methods Online: Takeshi Sumida, Nobuhide Doi, and Hiroshi Yanagawa
Bicistronic DNA display for in vitro selection of Fab fragments
Nucleic Acids Research Advance Access published on September 29, 2009.
doi:10.1093/nar/gkp776
[Abstract] [Full Text] [Print PDF] [Screen PDF]

28 September 2009

Abstract Database Issue: Juan Wang, Ming Lu, Chengxiang Qiu, and Qinghua Cui
TransmiR: a transcription factor–microRNA regulation database
Nucleic Acids Research Advance Access published on September 28, 2009.
doi:10.1093/nar/gkp803
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Abstract Methods Online: Kirsti Laurila, Olli Yli-Harja, and Harri Lähdesmäki
A protein–protein interaction guided method for competitive transcription factor binding improves target predictions
Nucleic Acids Research Advance Access published on September 28, 2009.
doi:10.1093/nar/gkp789
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Abstract Structural Biology: Vladimir Sychrovsky, Silvie Foldynova-Trantirkova, Nada Spackova, Koen Robeyns, Luc Van Meervelt, Wulf Blankenfeldt, Zuzana Vokacova, Jiri Sponer, and Lukas Trantirek
Revisiting the planarity of nucleic acid bases: Pyramidilization at glycosidic nitrogen in purine bases is modulated by orientation of glycosidic torsion
Nucleic Acids Research Advance Access published on September 28, 2009.
doi:10.1093/nar/gkp783
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Abstract Molecular Biology: Andrei S. Zolotukhin, Hiroaki Uranishi, Susan Lindtner, Jenifer Bear, George N. Pavlakis, and Barbara K. Felber
Nuclear export factor RBM15 facilitates the access of DBP5 to mRNA
Nucleic Acids Research Advance Access published on September 28, 2009.
doi:10.1093/nar/gkp782
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Abstract Genome Integrity, Repair and Replication: Erwin van den Born, Anders Bekkelund, Marivi N. Moen, Marina V. Omelchenko, Arne Klungland, and Pål Ø. Falnes
Bioinformatics and functional analysis define four distinct groups of AlkB DNA-dioxygenases in bacteria
Nucleic Acids Research Advance Access published on September 28, 2009.
doi:10.1093/nar/gkp774
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Abstract Computational Biology: Sascha Steinbiss, Ute Willhoeft, Gordon Gremme, and Stefan Kurtz
Fine-grained annotation and classification of de novo predicted LTR retrotransposons
Nucleic Acids Research Advance Access published on September 28, 2009.
doi:10.1093/nar/gkp759
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Abstract RNA: Thomas Geissmann, Clément Chevalier, Marie-Josée Cros, Sandrine Boisset, Pierre Fechter, Céline Noirot, Jacques Schrenzel, Patrice François, François Vandenesch, Christine Gaspin, and Pascale Romby
A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation
Nucleic Acids Research Advance Access published on September 28, 2009.
doi:10.1093/nar/gkp668
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26 September 2009

Abstract Nucleic Acid Enzymes: Henry J. Russell, Tomas T. Richardson, Kieran Emptage, and Bernard A. Connolly
The 3'–5' proofreading exonuclease of archaeal family-B DNA polymerase hinders the copying of template strand deaminated bases
Nucleic Acids Research Advance Access published on September 26, 2009.
doi:10.1093/nar/gkp800
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Abstract Database Issue: Phil Wilkinson, Jitka Sengerova, Raffaele Matteoni, Chao-Kung Chen, Gaetan Soulat, Abel Ureta-Vidal, Sabine Fessele, Michael Hagn, Marzia Massimi, Karen Pickford, Richard H. Butler, Susan Marschall, Ann-Marie Mallon, Amanda Pickard, Marcello Raspa, Ferdinando Scavizzi, Martin Fray, Vanessa Larrigaldie, Johan Leyritz, Ewan Birney, Glauco P. Tocchini-Valentini, Steve Brown, Yann Herault, Lluis Montoliu, Martin Hrabé de Angelis, and Damian Smedley
EMMA—mouse mutant resources for the international scientific community
Nucleic Acids Research Advance Access published on September 26, 2009.
doi:10.1093/nar/gkp799
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Abstract RNA: Pei-Yu Liao, Yong Seok Choi, and Kelvin H. Lee
FSscan: a mechanism-based program to identify +1 ribosomal frameshift hotspots
Nucleic Acids Research Advance Access published on September 26, 2009.
doi:10.1093/nar/gkp796
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Abstract Nucleic Acid Enzymes: Rachel M. Smith, Jytte Josephsen, and Mark D. Szczelkun
The single polypeptide restriction–modification enzyme LlaGI is a self-contained molecular motor that translocates DNA loops
Nucleic Acids Research Advance Access published on September 26, 2009.
doi:10.1093/nar/gkp794
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Abstract RNA: Kara A. Corbin-Lickfett, I-Hsiung Brandon Chen, Melanie J. Cocco, and Rozanne M. Sandri-Goldin
The HSV-1 ICP27 RGG box specifically binds flexible, GC-rich sequences but not G-quartet structures
Nucleic Acids Research Advance Access published on September 26, 2009.
doi:10.1093/nar/gkp793
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Abstract RNA: Kersten T. Schroeder and David M. J. Lilley
Ion-induced folding of a kink turn that departs from the conventional sequence
Nucleic Acids Research Advance Access published on September 26, 2009.
doi:10.1093/nar/gkp791
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25 September 2009

Abstract Database Issue: Michaël Bekaert, Andrew E. Firth, Yan Zhang, Vadim N. Gladyshev, John F. Atkins, and Pavel V. Baranov
Recode-2: new design, new search tools, and many more genes
Nucleic Acids Research Advance Access published on September 25, 2009.
doi:10.1093/nar/gkp788
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Abstract RNA: Mariana Pavon-Eternod, Suzanna Gomes, Renaud Geslain, Qing Dai, Marsha Rich Rosner, and Tao Pan
tRNA over-expression in breast cancer and functional consequences
Nucleic Acids Research Advance Access published on September 25, 2009.
doi:10.1093/nar/gkp787
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Abstract Database Issue: Sven Griep and Uwe Hobohm
PDBselect 1992–2009 and PDBfilter-select
Nucleic Acids Research Advance Access published on September 25, 2009.
doi:10.1093/nar/gkp786
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Abstract Genome Integrity, Repair and Replication: Eugene V. Shakirov, Xiangyu Song, Jessica A. Joseph, and Dorothy E. Shippen
POT1 proteins in green algae and land plants: DNA-binding properties and evidence of co-evolution with telomeric DNA
Nucleic Acids Research Advance Access published on September 25, 2009.
doi:10.1093/nar/gkp785
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Abstract Database Issue: Jian Ren, Zexian Liu, Xinjiao Gao, Changjiang Jin, Mingliang Ye, Hanfa Zou, Longping Wen, Zhaolei Zhang, Yu Xue, and Xuebiao Yao
MiCroKit 3.0: an integrated database of midbody, centrosome and kinetochore
Nucleic Acids Research Advance Access published on September 25, 2009.
doi:10.1093/nar/gkp784
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Abstract Gene Regulation, Chromatin and Epigenetics: Dali Li, Zhiyv Niu, Weishi Yu, Yu Qian, Qian Wang, Qiang Li, Zhengfang Yi, Jian Luo, Xiushan Wu, Yuequn Wang, Robert J. Schwartz, and Mingyao Liu
SMYD1, the myogenic activator, is a direct target of serum response factor and myogenin
Nucleic Acids Research Advance Access published on September 25, 2009.
doi:10.1093/nar/gkp773
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Abstract Nucleic Acid Enzymes: Ruta Gerasimaite, Giedrius Vilkaitis, and Saulius Klimasauskas
A directed evolution design of a GCG-specific DNA hemimethylase
Nucleic Acids Research Advance Access originally published on September 25, 2009. This version published October 8, 2009.
doi:10.1093/nar/gkp772
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Abstract Structural Biology: Bernhard Loll, Maike Gebhardt, Elmar Wahle, and Anton Meinhart
Crystal structure of the EndoG/EndoGI complex: mechanism of EndoG inhibition
Nucleic Acids Research Advance Access published on September 25, 2009.
doi:10.1093/nar/gkp770
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Abstract Methods Online: Sungmun Lee, Stephen C. Yang, Chen-Yu Kao, Robert H. Pierce, and Niren Murthy
Solid polymeric microparticles enhance the delivery of siRNA to macrophages in vivo
Nucleic Acids Research Advance Access published on September 25, 2009.
doi:10.1093/nar/gkp758
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23 September 2009

Abstract Gene Regulation, Chromatin and Epigenetics: Sung Wook Park, Wei-Hong Huang, Shawna D. Persaud, and Li-Na Wei
RIP140 in thyroid hormone-repression and chromatin remodeling of Crabp1 gene during adipocyte differentiation
Nucleic Acids Research Advance Access published on September 23, 2009.
doi:10.1093/nar/gkp780
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Abstract Gene Regulation, Chromatin and Epigenetics: Floor Frederiks, Guus J. J. E. Heynen, Sjoerd J. van Deventer, Hans Janssen, and Fred van Leeuwen
Two Dot1 isoforms in Saccharomyces cerevisiae as a result of leaky scanning by the ribosome
Nucleic Acids Research Advance Access published on September 23, 2009.
doi:10.1093/nar/gkp765
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22 September 2009

Abstract Computational Biology: Hamed Shateri Najafabadi, Hani Goodarzi, and Reza Salavati
Universal function-specificity of codon usage
Nucleic Acids Research Advance Access published on September 22, 2009.
doi:10.1093/nar/gkp792
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Abstract RNA: Tibor Pastor, Gabriele Talotti, Marzena Anna Lewandowska, and Franco Pagani
An Alu-derived intronic splicing enhancer facilitates intronic processing and modulates aberrant splicing in ATM
Nucleic Acids Research Advance Access published on September 22, 2009.
doi:10.1093/nar/gkp778
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Abstract Gene Regulation, Chromatin and Epigenetics: Francesca Mateo, Miriam Vidal-Laliena, Núria Canela, Annalisa Zecchin, Marian Martínez-Balbás, Neus Agell, Mauro Giacca, María Jesús Pujol, and Oriol Bachs
The transcriptional co-activator PCAF regulates cdk2 activity
Nucleic Acids Research Advance Access published on September 22, 2009.
doi:10.1093/nar/gkp777
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Abstract Genome Integrity, Repair and Replication: Gavin W. Wilson and David R. Edgell
Phage T4 mobE promotes trans homing of the defunct homing endonuclease I-TevIII
Nucleic Acids Research Advance Access originally published on September 22, 2009. This version published September 30, 2009.
doi:10.1093/nar/gkp769
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Abstract Nucleic Acid Enzymes: Andrey L. Mikheikin, Hsiang-Kai Lin, Preeti Mehta, Linda Jen-Jacobson, and Michael A. Trakselis
A trimeric DNA polymerase complex increases the native replication processivity
Nucleic Acids Research Advance Access published on September 22, 2009.
doi:10.1093/nar/gkp767
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Abstract Database Issue: Martha B. Arnaud, Marcus C. Chibucos, Maria C. Costanzo, Jonathan Crabtree, Diane O. Inglis, Adil Lotia, Joshua Orvis, Prachi Shah, Marek S. Skrzypek, Gail Binkley, Stuart R. Miyasato, Jennifer R. Wortman, and Gavin Sherlock
The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community
Nucleic Acids Research Advance Access published on September 22, 2009.
doi:10.1093/nar/gkp751
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Abstract Database Issue: Brian A. Kennedy, Wenqing Gao, Tim H.-M. Huang, and Victor X. Jin
HRTBLDb: an informative data resource for hormone receptors target binding loci
Nucleic Acids Research Advance Access published on September 22, 2009.
doi:10.1093/nar/gkp734
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Abstract Molecular Biology: Nikolay Korolev, Nikolay V. Berezhnoy, Khee Dong Eom, James P. Tam, and Lars Nordenskiöld
A universal description for the experimental behavior of salt-(in)dependent oligocation-induced DNA condensation
Nucleic Acids Research Advance Access published on September 22, 2009.
doi:10.1093/nar/gkp683
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18 September 2009