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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27 November 2009

Abstract Genome Integrity, Repair and Replication: Conceição A. S. A. Minetti, David P. Remeta, Rian Dickstein, and Kenneth J. Breslauer
Energetic signatures of single base bulges: thermodynamic consequences and biological implications
Nucleic Acids Research Advance Access published on November 27, 2009.
doi:10.1093/nar/gkp1036
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Abstract Structural Biology: Zhenjiang Zhang, Jixun Dai, Elizabeth Veliath, Roger A. Jones, and Danzhou Yang
Structure of a two-G-tetrad intramolecular G-quadruplex formed by a variant human telomeric sequence in K⁺ solution: insights into the interconversion of human telomeric G-quadruplex structures
Nucleic Acids Research Advance Access published on November 27, 2009.
doi:10.1093/nar/gkp1029
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26 November 2009

Abstract Molecular Biology: Jesper Sejrup Nielsen, Lisbeth Kristensen Lei, Tine Ebersbach, Anders Steno Olsen, Janne Kudsk Klitgaard, Poul Valentin-Hansen, and Birgitte Haahr Kallipolitis
Defining a role for Hfq in Gram-positive bacteria: evidence for Hfq-dependent antisense regulation in Listeria monocytogenes
Nucleic Acids Research Advance Access published on November 26, 2009.
doi:10.1093/nar/gkp1081
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Abstract Methods Online: Annette Lasham, Mike Herbert, Natacha Coppieters ‘t Wallant, Rachna Patel, Sheryl Feng, Marika Eszes, Helen Cao, and Glen Reid
A rapid and sensitive method to detect siRNA-mediated mRNA cleavage in vivo using 5' RACE and a molecular beacon probe
Nucleic Acids Research Advance Access published on November 26, 2009.
doi:10.1093/nar/gkp1076
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Abstract Survey and Summary: David Schild and Claudia Wiese
Overexpression of RAD51 suppresses recombination defects: a possible mechanism to reverse genomic instability
Nucleic Acids Research Advance Access published on November 26, 2009.
doi:10.1093/nar/gkp1063
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Abstract Genome Integrity, Repair and Replication: Stuart J. Haring, Troy D. Humphreys, and Marc S. Wold
A naturally occurring human RPA subunit homolog does not support DNA replication or cell-cycle progression
Nucleic Acids Research Advance Access published on November 26, 2009.
doi:10.1093/nar/gkp1062
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Abstract Methods Online: Joséphine Abi-Ghanem, Brahim Heddi, Nicolas Foloppe, and Brigitte Hartmann
DNA structures from phosphate chemical shifts
Nucleic Acids Research Advance Access published on November 26, 2009.
doi:10.1093/nar/gkp1061
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Abstract Structural Biology: Xianchi Dong, Minyun Zhou, Chen Zhong, Bei Yang, Ning Shen, and Jianping Ding
Crystal structure of Pyrococcus horikoshii tryptophanyl-tRNA synthetase and structure-based phylogenetic analysis suggest an archaeal origin of tryptophanyl-tRNA synthetase
Nucleic Acids Research Advance Access published on November 26, 2009.
doi:10.1093/nar/gkp1053
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Abstract Database Issue: Li Ji, Tanya Barrett, Oluwabukunmi Ayanbule, Dennis B. Troup, Dmitry Rudnev, Rolf N. Muertter, Maxim Tomashevsky, Alexandra Soboleva, and Douglas J. Slotta
NCBI Peptidome: a new repository for mass spectrometry proteomics data
Nucleic Acids Research Advance Access published on November 26, 2009.
doi:10.1093/nar/gkp1047
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Abstract RNA: Changying Zeng, Wenquan Wang, Yun Zheng, Xin Chen, Weiping Bo, Shun Song, Weixiong Zhang, and Ming Peng
Conservation and divergence of microRNAs and their functions in Euphorbiaceous plants
Nucleic Acids Research Advance Access published on November 26, 2009.
doi:10.1093/nar/gkp1035
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25 November 2009

Abstract Genome Integrity, Repair and Replication: Atsushi Katafuchi, Akira Sassa, Naoko Niimi, Petr Grúz, Hirofumi Fujimoto, Chikahide Masutani, Fumio Hanaoka, Toshihiro Ohta, and Takehiko Nohmi
Critical amino acids in human DNA polymerases ${eta}$ and ${kappa}$ involved in erroneous incorporation of oxidized nucleotides
Nucleic Acids Research Advance Access published on November 25, 2009.
doi:10.1093/nar/gkp1095
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Abstract Gene Regulation, Chromatin and Epigenetics: Toshiyuki Ueki and Derek R. Lovley
Genome-wide gene regulation of biosynthesis and energy generation by a novel transcriptional repressor in Geobacter species
Nucleic Acids Research Advance Access published on November 25, 2009.
doi:10.1093/nar/gkp1085
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Abstract Gene Regulation, Chromatin and Epigenetics: Chase T. Archer and Thomas Kodadek
The hydrophobic patch of ubiquitin is required to protect transactivator–promoter complexes from destabilization by the proteasomal ATPases
Nucleic Acids Research Advance Access published on November 25, 2009.
doi:10.1093/nar/gkp1066
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24 November 2009

Abstract Database Issue: Yukiko Yamazaki, Ryo Akashi, Yutaka Banno, Takashi Endo, Hiroshi Ezura, Kaoru Fukami-Kobayashi, Kazuo Inaba, Tadashi Isa, Katsuhiko Kamei, Fumie Kasai, Masatomo Kobayashi, Nori Kurata, Makoto Kusaba, Tetsuro Matuzawa, Shohei Mitani, Taro Nakamura, Yukio Nakamura, Norio Nakatsuji, Kiyoshi Naruse, Hironori Niki, Eiji Nitasaka, Yuichi Obata, Hitoshi Okamoto, Moriya Okuma, Kazuhiro Sato, Tadao Serikawa, Toshihiko Shiroishi, Hideaki Sugawara, Hideko Urushibara, Masatoshi Yamamoto, Yoshio Yaoita, Atsushi Yoshiki, and Yuji Kohara
NBRP databases: databases of biological resources in Japan
Nucleic Acids Research Advance Access published on November 24, 2009.
doi:10.1093/nar/gkp996
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Abstract Database Issue: Catherine Brooksbank, Graham Cameron, and Janet Thornton
The European Bioinformatics Institute’s data resources
Nucleic Acids Research Advance Access published on November 24, 2009.
doi:10.1093/nar/gkp986
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Abstract Database Issue: Saskia Preissner, Katharina Kroll, Mathias Dunkel, Christian Senger, Gady Goldsobel, Daniel Kuzman, Stefan Guenther, Rainer Winnenburg, Michael Schroeder, and Robert Preissner
SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions
Nucleic Acids Research Advance Access published on November 24, 2009.
doi:10.1093/nar/gkp970
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Abstract Gene Regulation, Chromatin and Epigenetics: Hamid Reza Rezvani, Walid Mahfouf, Nsrein Ali, Cecile Chemin, Cecile Ged, Arianna L. Kim, Hubert de Verneuil, Alain Taïeb, David R. Bickers, and Frédéric Mazurier
Hypoxia-inducible factor-1 ${alpha}$ regulates the expression of nucleotide excision repair proteins in keratinocytes
Nucleic Acids Research Advance Access published on November 24, 2009.
doi:10.1093/nar/gkp1072
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Abstract Nucleic Acid Enzymes: Chie Tomikawa, Takashi Yokogawa, Tamotsu Kanai, and Hiroyuki Hori
N⁷-Methylguanine at position 46 (m⁷G46) in tRNA from Thermus thermophilus is required for cell viability at high temperatures through a tRNA modification network
Nucleic Acids Research Advance Access published on November 24, 2009.
doi:10.1093/nar/gkp1059
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Abstract Gene Regulation, Chromatin and Epigenetics: Moo-Rim Kang, Sang-Wang Lee, Elisa Um, Hyun Tae Kang, Eun Seong Hwang, Eun-Joo Kim, and Soo-Jong Um
Reciprocal roles of SIRT1 and SKIP in the regulation of RAR activity: implication in the retinoic acid-induced neuronal differentiation of P19 cells
Nucleic Acids Research Advance Access published on November 24, 2009.
doi:10.1093/nar/gkp1056
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Abstract Nucleic Acid Enzymes: Jason A. Stewart, Judith L. Campbell, and Robert A. Bambara
Dna2 is a structure-specific nuclease, with affinity for 5'-flap intermediates
Nucleic Acids Research Advance Access published on November 24, 2009.
doi:10.1093/nar/gkp1055
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Abstract Gene Regulation, Chromatin and Epigenetics: Wenge Li, Nehal Thakor, Eugenia Y. Xu, Ying Huang, Chi Chen, Rong Yu, Martin Holcik, and Ah-Ng Kong
An internal ribosomal entry site mediates redox-sensitive translation of Nrf2
Nucleic Acids Research Advance Access published on November 24, 2009.
doi:10.1093/nar/gkp1048
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Abstract Database Issue: Nicholas Paul Gauthier, Lars Juhl Jensen, Rasmus Wernersson, Søren Brunak, and Thomas S. Jensen
Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results
Nucleic Acids Research Advance Access published on November 24, 2009.
doi:10.1093/nar/gkp1044
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Abstract Survey and Summary: Arnold Stein, Taichi E. Takasuka, and Clayton K. Collings
Are nucleosome positions in vivo primarily determined by histone–DNA sequence preferences?
Nucleic Acids Research Advance Access published on November 24, 2009.
doi:10.1093/nar/gkp1043
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Abstract Genome Integrity, Repair and Replication: Tohru Yamamori, Jeremy DeRicco, Asma Naqvi, Timothy A. Hoffman, Ilwola Mattagajasingh, Kenji Kasuno, Saet-Byel Jung, Cuk-Seong Kim, and Kaikobad Irani
SIRT1 deacetylates APE1 and regulates cellular base excision repair
Nucleic Acids Research Advance Access published on November 24, 2009.
doi:10.1093/nar/gkp1039
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Abstract Gene Regulation, Chromatin and Epigenetics: Yi-Jiun Chen, Bertrand Chin-Ming Tan, Ya-Yun Cheng, Jin-Shin Chen, and Sheng-Chung Lee
Differential regulation of CHOP translation by phosphorylated eIF4E under stress conditions
Nucleic Acids Research Advance Access published on November 24, 2009.
doi:10.1093/nar/gkp1034
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Abstract Database Issue: Aedín C. Culhane, Thomas Schwarzl, Razvan Sultana, Kermshlise C. Picard, Shaita C. Picard, Tim H. Lu, Katherine R. Franklin, Simon J. French, Gerald Papenhausen, Mick Correll, and John Quackenbush
GeneSigDB—a curated database of gene expression signatures
Nucleic Acids Research Advance Access published on November 24, 2009.
doi:10.1093/nar/gkp1015
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Abstract Molecular Biology: M. Banerjee, M. Datta, P. Majumder, D. Mukhopadhyay, and N. P. Bhattacharyya
Transcription regulation of caspase-1 by R393 of HIPPI and its molecular partner HIP-1
Nucleic Acids Research Advance Access published on November 24, 2009.
doi:10.1093/nar/gkp1011
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Abstract Database Issue: Jun Zhao, Graham Klyne, Elizabeth Benson, Elin Gudmannsdottir, Helen White-Cooper, and David Shotton
FlyTED: the Drosophila Testis Gene Expression Database
Nucleic Acids Research Advance Access published on November 24, 2009.
doi:10.1093/nar/gkp1006
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23 November 2009

Abstract Database Issue: Raphaël Leplae, Gipsi Lima-Mendez, and Ariane Toussaint
ACLAME: A CLAssification of Mobile genetic Elements, update 2010
Nucleic Acids Research Advance Access published on November 23, 2009.
doi:10.1093/nar/gkp938
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Abstract Database Issue: Chisato Yamasaki, Katsuhiko Murakami, Jun-ichi Takeda, Yoshiharu Sato, Akiko Noda, Ryuichi Sakate, Takuya Habara, Hajime Nakaoka, Fusano Todokoro, Akihiro Matsuya, Tadashi Imanishi, and Takashi Gojobori
H-InvDB in 2009: extended database and data mining resources for human genes and transcripts
Nucleic Acids Research Advance Access published on November 23, 2009.
doi:10.1093/nar/gkp1020
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Abstract Database Issue: Hugh Morgan, Tim Beck, Andrew Blake, Hilary Gates, Niels Adams, Guillaume Debouzy, Sophie Leblanc, Christoph Lengger, Holger Maier, David Melvin, Hamid Meziane, Dave Richardson, Sara Wells, Jacqui White, Joe Wood, The EUMODIC Consortium, Martin Hrabé de Angelis, Steve D. M. Brown, John M. Hancock, and Ann-Marie Mallon
EuroPhenome: a repository for high-throughput mouse phenotyping data
Nucleic Acids Research Advance Access published on November 23, 2009.
doi:10.1093/nar/gkp1007
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20 November 2009

Abstract Nucleic Acid Enzymes: Jana Rudolf, Christophe Rouillon, Ulrich Schwarz-Linek, and Malcolm F. White
The helicase XPD unwinds bubble structures and is not stalled by DNA lesions removed by the nucleotide excision repair pathway
Nucleic Acids Research Advance Access published on November 20, 2009.
doi:10.1093/nar/gkp1058
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Abstract Database Issue: Keiko Akagi, Robert M. Stephens, Jingfeng Li, Evgenji Evdokimov, Michael R. Kuehn, Natalia Volfovsky, and David E. Symer
MouseIndelDB: a database integrating genomic indel polymorphisms that distinguish mouse strains
Nucleic Acids Research Advance Access published on November 20, 2009.
doi:10.1093/nar/gkp1046
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Abstract Molecular Biology: Sridharan Rajagopalan, Robert S. Sade, Fiona M. Townsley, and Alan R. Fersht
Mechanistic differences in the transcriptional activation of p53 by 14-3-3 isoforms
Nucleic Acids Research Advance Access published on November 20, 2009.
doi:10.1093/nar/gkp1041
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Abstract Synthetic Biology and Chemistry: Alexander S. Wahba, Abbasali Esmaeili, Masad J. Damha, and Robert H. E. Hudson
A single-label phenylpyrrolocytidine provides a molecular beacon-like response reporting HIV-1 RT RNase H activity
Nucleic Acids Research Advance Access published on November 20, 2009.
doi:10.1093/nar/gkp1022
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Abstract Database Issue: Feng Zhu, BuCong Han, Pankaj Kumar, XiangHui Liu, XiaoHua Ma, XiaoNa Wei, Lu Huang, YangFan Guo, LianYi Han, ChanJuan Zheng, and YuZong Chen
Update of TTD: Therapeutic Target Database
Nucleic Acids Research Advance Access published on November 20, 2009.
doi:10.1093/nar/gkp1014
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19 November 2009

Abstract Database Issue: Yanli Wang, Evan Bolton, Svetlana Dracheva, Karen Karapetyan, Benjamin A. Shoemaker, Tugba O. Suzek, Jiyao Wang, Jewen Xiao, Jian Zhang, and Stephen H. Bryant
An overview of the PubChem BioAssay resource
Nucleic Acids Research Advance Access published on November 19, 2009.
doi:10.1093/nar/gkp965
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Abstract Gene Regulation, Chromatin and Epigenetics: Larry N. Singh and Sridhar Hannenhalli
Correlated changes between regulatory cis elements and condition-specific expression in paralogous gene families
Nucleic Acids Research Advance Access published on November 19, 2009.
doi:10.1093/nar/gkp989
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Abstract Structural Biology: Qianfan Yang, Junfeng Xiang, Shu Yang, Qian Li, Qiuju Zhou, Aijiao Guan, Xiufeng Zhang, Hong Zhang, Yalin Tang, and Guangzhi Xu
Verification of specific G-quadruplex structure by using a novel cyanine dye supramolecular assembly: II. The binding characterization with specific intramolecular G-quadruplex and the recognizing mechanism
Nucleic Acids Research Advance Access published on November 19, 2009.
doi:10.1093/nar/gkp1045
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Abstract Gene Regulation, Chromatin and Epigenetics: Oscar Aparicio, Elena Carnero, Xabier Abad, Nerea Razquin, Elizabeth Guruceaga, Victor Segura, and Puri Fortes
Adenovirus VA RNA-derived miRNAs target cellular genes involved in cell growth, gene expression and DNA repair
Nucleic Acids Research Advance Access published on November 19, 2009.
doi:10.1093/nar/gkp1028
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18 November 2009

Abstract Database Issue: Andreas Schlicker and Mario Albrecht
FunSimMat update: new features for exploring functional similarity
Nucleic Acids Research Advance Access published on November 18, 2009.
doi:10.1093/nar/gkp979
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Abstract Methods Online: Nuno L. Barbosa-Morais, Mark J. Dunning, Shamith A. Samarajiwa, Jeremy F. J. Darot, Matthew E. Ritchie, Andy G. Lynch, and Simon Tavaré
A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data
Nucleic Acids Research Advance Access published on November 18, 2009.
doi:10.1093/nar/gkp942
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Liwei Li, Khuchtumur Bum-Erdene, Peter H. Baenziger, Joshua J. Rosen, Jamison R. Hemmert, Joy A. Nellis, Marlon E. Pierce, and Samy O. Meroueh
BioDrugScreen: a computational drug design resource for ranking molecules docked to the human proteome
Nucleic Acids Research Advance Access published on November 18, 2009.
doi:10.1093/nar/gkp852
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Computational Biology: David A. Lee, Robert Rentzsch, and Christine Orengo
GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains
Nucleic Acids Research Advance Access published on November 18, 2009.
doi:10.1093/nar/gkp1049
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Genomics: Marco Albrecht, Cynthia M. Sharma, Richard Reinhardt, Jörg Vogel, and Thomas Rudel
Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome
Nucleic Acids Research Advance Access published on November 18, 2009.
doi:10.1093/nar/gkp1032
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Shaini Thomas, Shreyas Karnik, Ram Shankar Barai, V. K. Jayaraman, and Susan Idicula-Thomas
CAMP: a useful resource for research on antimicrobial peptides
Nucleic Acids Research Advance Access published on November 18, 2009.
doi:10.1093/nar/gkp1021
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract RNA: Christian Schudoma, Patrick May, Viktoria Nikiforova, and Dirk Walther
Sequence–structure relationships in RNA loops: establishing the basis for loop homology modeling
Nucleic Acids Research Advance Access published on November 18, 2009.
doi:10.1093/nar/gkp1010
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

17 November 2009

Abstract RNA: Helen Elina and Gregory G. Brown
Extensive mis-splicing of a bi-partite plant mitochondrial group II intron
Nucleic Acids Research Advance Access published on November 17, 2009.
doi:10.1093/nar/gkp994
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Molecular Biology: Santanu K. Ghosh, Chu-Chun Huang, Sujata Hajra, and Makkuni Jayaram
Yeast cohesin complex embraces 2 micron plasmid sisters in a tri-linked catenane complex
Nucleic Acids Research Advance Access published on November 17, 2009.
doi:10.1093/nar/gkp993
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Abstract Database Issue: Robert D. Finn, Jaina Mistry, John Tate, Penny Coggill, Andreas Heger, Joanne E. Pollington, O. Luke Gavin, Prasad Gunasekaran, Goran Ceric, Kristoffer Forslund, Liisa Holm, Erik L. L. Sonnhammer, Sean R. Eddy, and Alex Bateman
The Pfam protein families database
Nucleic Acids Research Advance Access published on November 17, 2009.
doi:10.1093/nar/gkp985
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Christian Koetschan, Frank Förster, Alexander Keller, Tina Schleicher, Benjamin Ruderisch, Roland Schwarz, Tobias Müller, Matthias Wolf, and Jörg Schultz
The ITS2 Database III—sequences and structures for phylogeny
Nucleic Acids Research Advance Access published on November 17, 2009.
doi:10.1093/nar/gkp966
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Structural Biology: Brahim Heddi, Christophe Oguey, Christophe Lavelle, Nicolas Foloppe, and Brigitte Hartmann
Intrinsic flexibility of B-DNA: the experimental TRX scale
Nucleic Acids Research Advance Access published on November 17, 2009.
doi:10.1093/nar/gkp962
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Kate R. Rosenbloom, Timothy R. Dreszer, Michael Pheasant, Galt P. Barber, Laurence R. Meyer, Andy Pohl, Brian J. Raney, Ting Wang, Angie S. Hinrichs, Ann S. Zweig, Pauline A. Fujita, Katrina Learned, Brooke Rhead, Kayla E. Smith, Robert M. Kuhn, Donna Karolchik, David Haussler, and W. James Kent
ENCODE whole-genome data in the UCSC Genome Browser
Nucleic Acids Research Advance Access published on November 17, 2009.
doi:10.1093/nar/gkp961
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Survey and Summary: Ivaylo P. Ivanov, John F. Atkins, and Antony J. Michael
A profusion of upstream open reading frame mechanisms in polyamine-responsive translational regulation
Nucleic Acids Research Advance Access published on November 17, 2009.
doi:10.1093/nar/gkp1037
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Abstract Methods Online: John Y. Wu, Michael D. Stone, and Xiaowei Zhuang
A single-molecule assay for telomerase structure-function analysis
Nucleic Acids Research Advance Access published on November 17, 2009.
doi:10.1093/nar/gkp1033
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Abstract Database Issue: Pawel Smialowski, Philipp Pagel, Philip Wong, Barbara Brauner, Irmtraud Dunger, Gisela Fobo, Goar Frishman, Corinna Montrone, Thomas Rattei, Dmitrij Frishman, and Andreas Ruepp
The Negatome database: a reference set of non-interacting protein pairs
Nucleic Acids Research Advance Access published on November 17, 2009.
doi:10.1093/nar/gkp1026
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: The Gene Ontology Consortium
The Gene Ontology in 2010: extensions and refinements
Nucleic Acids Research Advance Access published on November 17, 2009.
doi:10.1093/nar/gkp1018
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Cathryn M. Gould, Francesca Diella, Allegra Via, Pål Puntervoll, Christine Gemünd, Sophie Chabanis-Davidson, Sushama Michael, Ahmed Sayadi, Jan Christian Bryne, Claudia Chica, Markus Seiler, Norman E. Davey, Niall Haslam, Robert J. Weatheritt, Aidan Budd, Tim Hughes, Jakub Pas, Leszek Rychlewski, Gilles Travé, Rein Aasland, Manuela Helmer-Citterich, Rune Linding, and Toby J. Gibson
ELM: the status of the 2010 eukaryotic linear motif resource
Nucleic Acids Research Advance Access published on November 17, 2009.
doi:10.1093/nar/gkp1016
[Abstract] [Full Text] [Print PDF] [Screen PDF]

16 November 2009

Abstract Database Issue: Martin Mokrejs, Tomás Masek, Václav Vopálensky, Petr Hlubucek, Philippe Delbos, and Martin Pospísek
IRESite—a tool for the examination of viral and cellular internal ribosome entry sites
Nucleic Acids Research Advance Access published on November 16, 2009.
doi:10.1093/nar/gkp981
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Abstract RNA: Denise M. Kenski, Abby J. Cooper, Jenny J. Li, Aarron T. Willingham, Henry J. Haringsma, Tracy A. Young, Nelly A. Kuklin, Jeffrey J. Jones, Mark T. Cancilla, Daniel R. McMasters, Melina Mathur, Alan B. Sachs, and W. Michael Flanagan
Analysis of acyclic nucleoside modifications in siRNAs finds sensitivity at position 1 that is restored by 5'-terminal phosphorylation both in vitro and in vivo
Nucleic Acids Research Advance Access published on November 16, 2009.
doi:10.1093/nar/gkp913
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

13 November 2009

Abstract Molecular Biology: Clara Frumerie, Magaly Ducos-Galand, Deshmukh N. Gopaul, and Didier Mazel
The relaxed requirements of the integron cleavage site allow predictable changes in integron target specificity
Nucleic Acids Research Advance Access published on November 13, 2009.
doi:10.1093/nar/gkp990
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Cristina Aurrecoechea, John Brestelli, Brian P. Brunk, Steve Fischer, Bindu Gajria, Xin Gao, Alan Gingle, Greg Grant, Omar S. Harb, Mark Heiges, Frank Innamorato, John Iodice, Jessica C. Kissinger, Eileen T. Kraemer, Wei Li, John A. Miller, Vishal Nayak, Cary Pennington, Deborah F. Pinney, David S. Roos, Chris Ross, Ganesh Srinivasamoorthy, Christian J. Stoeckert Jr, Ryan Thibodeau, Charles Treatman, and Haiming Wang
EuPathDB: a portal to eukaryotic pathogen databases
Nucleic Acids Research Advance Access published on November 13, 2009.
doi:10.1093/nar/gkp941
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Konstantinos Liolios, I-Min A. Chen, Konstantinos Mavromatis, Nektarios Tavernarakis, Philip Hugenholtz, Victor M. Markowitz, and Nikos C. Kyrpides
The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata
Nucleic Acids Research Advance Access published on November 13, 2009.
doi:10.1093/nar/gkp848
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Structural Biology: Andrew Bowman, Richard Ward, Hassane El-Mkami, Tom Owen-Hughes, and David G. Norman
Probing the (H3-H4)₂ histone tetramer structure using pulsed EPR spectroscopy combined with site-directed spin labelling
Nucleic Acids Research Advance Access published on November 13, 2009.
doi:10.1093/nar/gkp1003
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

12 November 2009

Abstract Database Issue: Eric W. Sayers, Tanya Barrett, Dennis A. Benson, Evan Bolton, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Scott Federhen, Michael Feolo, Lewis Y. Geer, Wolfgang Helmberg, Yuri Kapustin, David Landsman, David J. Lipman, Zhiyong Lu, Thomas L. Madden, Tom Madej, Donna R. Maglott, Aron Marchler-Bauer, Vadim Miller, Ilene Mizrachi, James Ostell, Anna Panchenko, Kim D. Pruitt, Gregory D. Schuler, Edwin Sequeira, Stephen T. Sherry, Martin Shumway, Karl Sirotkin, Douglas Slotta, Alexandre Souvorov, Grigory Starchenko, Tatiana A. Tatusova, Lukas Wagner, Yanli Wang, W. John Wilbur, Eugene Yaschenko, and Jian Ye
Database resources of the National Center for Biotechnology Information
Nucleic Acids Research Advance Access published on November 12, 2009.
doi:10.1093/nar/gkp967
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Todd W. Harris, Igor Antoshechkin, Tamberlyn Bieri, Darin Blasiar, Juancarlos Chan, Wen J. Chen, Norie De La Cruz, Paul Davis, Margaret Duesbury, Ruihua Fang, Jolene Fernandes, Michael Han, Ranjana Kishore, Raymond Lee, Hans-Michael Müller, Cecilia Nakamura, Philip Ozersky, Andrei Petcherski, Arun Rangarajan, Anthony Rogers, Gary Schindelman, Erich M. Schwarz, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang, Xiaodong Wang, Gary Williams, Karen Yook, Richard Durbin, Lincoln D. Stein, John Spieth, and Paul W. Sternberg
WormBase: a comprehensive resource for nematode research
Nucleic Acids Research Advance Access published on November 12, 2009.
doi:10.1093/nar/gkp952
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Moritz Gilsdorf, Thomas Horn, Zeynep Arziman, Oliver Pelz, Evgeny Kiner, and Michael Boutros
GenomeRNAi: a database for cell-based RNAi phenotypes. 2009 update
Nucleic Acids Research Advance Access published on November 12, 2009.
doi:10.1093/nar/gkp1038
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, and Eric W. Sayers
GenBank
Nucleic Acids Research Advance Access published on November 12, 2009.
doi:10.1093/nar/gkp1024
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Annalisa Marsico, Kerstin Scheubert, Anne Tuukkanen, Andreas Henschel, Christof Winter, Rainer Winnenburg, and Michael Schroeder
MeMotif: a database of linear motifs in ${alpha}$ -helical transmembrane proteins
Nucleic Acids Research Advance Access published on November 12, 2009.
doi:10.1093/nar/gkp1042
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract RNA: Ariful Haque, Emanuele Buratti, and Francisco E. Baralle
Functional properties and evolutionary splicing constraints on a composite exonic regulatory element of splicing in CFTR exon 12
Nucleic Acids Research Advance Access published on November 12, 2009.
doi:10.1093/nar/gkp1040
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Gene Regulation, Chromatin and Epigenetics: Melisa S. Medrano, Paul F. Policastro, Tom G. Schwan, and Jenifer Coburn
Interaction of Borrelia burgdorferi Hbb with the p66 promoter
Nucleic Acids Research Advance Access published on November 12, 2009.
doi:10.1093/nar/gkp1027
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Methods Online: Nikolay E. Shirokikh, Elena Z. Alkalaeva, Konstantin S. Vassilenko, Zhanna A. Afonina, Olga M. Alekhina, Lev L. Kisselev, and Alexander S. Spirin
Quantitative analysis of ribosome–mRNA complexes at different translation stages
Nucleic Acids Research Advance Access published on November 12, 2009.
doi:10.1093/nar/gkp1025
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Genome Integrity, Repair and Replication: Meiling Lu, Rajam S. Mani, Feridoun Karimi-Busheri, Mesfin Fanta, Hailin Wang, David W. Litchfeld, and Michael Weinfeld
Independent mechanisms of stimulation of polynucleotide kinase/phosphatase by phosphorylated and non-phosphorylated XRCC1
Nucleic Acids Research Advance Access published on November 12, 2009.
doi:10.1093/nar/gkp1023
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Riu Yamashita, Hiroyuki Wakaguri, Sumio Sugano, Yutaka Suzuki, and Kenta Nakai
DBTSS provides a tissue specific dynamic view of Transcription Start Sites
Nucleic Acids Research Advance Access published on November 12, 2009.
doi:10.1093/nar/gkp1017
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract RNA: Gaëlle Mercenne, Serena Bernacchi, Delphine Richer, Guillaume Bec, Simon Henriet, Jean-Christophe Paillart, and Roland Marquet
HIV-1 Vif binds to APOBEC3G mRNA and inhibits its translation
Nucleic Acids Research Advance Access published on November 12, 2009.
doi:10.1093/nar/gkp1009
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

11 November 2009

Abstract Nucleic Acid Enzymes: Bijoy K. Mohanty and Sidney R. Kushner
Processing of the Escherichia coli leuX tRNA transcript, encoding tRNA^Leu5, requires either the 3' $->$ 5' exoribonuclease polynucleotide phosphorylase or RNase P to remove the Rho-independent transcription terminator
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp997
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Gene Regulation, Chromatin and Epigenetics: David Serre, Byron H. Lee, and Angela H. Ting
MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp992
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Jonathan Lees, Corin Yeats, Oliver Redfern, Andrew Clegg, and Christine Orengo
Gene3D: merging structure and function for a Thousand genomes
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp987
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Walter Sanseverino, Guglielmo Roma, Marco De Simone, Luigi Faino, Sara Melito, Elia Stupka, Luigi Frusciante, and Maria Raffaella Ercolano
PRGdb: a bioinformatics platform for plant resistance gene analysis
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp978
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Paul Flicek, Bronwen L. Aken, Benoit Ballester, Kathryn Beal, Eugene Bragin, Simon Brent, Yuan Chen, Peter Clapham, Guy Coates, Susan Fairley, Stephen Fitzgerald, Julio Fernandez-Banet, Leo Gordon, Stefan Gräf, Syed Haider, Martin Hammond, Kerstin Howe, Andrew Jenkinson, Nathan Johnson, Andreas Kähäri, Damian Keefe, Stephen Keenan, Rhoda Kinsella, Felix Kokocinski, Gautier Koscielny, Eugene Kulesha, Daniel Lawson, Ian Longden, Tim Massingham, William McLaren, Karine Megy, Bert Overduin, Bethan Pritchard, Daniel Rios, Magali Ruffier, Michael Schuster, Guy Slater, Damian Smedley, Giulietta Spudich, Y. Amy Tang, Stephen Trevanion, Albert Vilella, Jan Vogel, Simon White, Steven P. Wilder, Amonida Zadissa, Ewan Birney, Fiona Cunningham, Ian Dunham, Richard Durbin, Xosé M. Fernández-Suarez, Javier Herrero, Tim J. P. Hubbard, Anne Parker, Glenn Proctor, James Smith, and Stephen M. J. Searle
Ensembl’s 10th year
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp972
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Adnan S. Syed, Matteo D’Antonio, and Francesca D. Ciccarelli
Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp957
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Pryavahiny Kichenaradja, Patricia Siguier, Jocelyne Pérochon, and Michael Chandler
ISbrowser: an extension of ISfinder for visualizing insertion sequences in prokaryotic genomes
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp947
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Paramvir S. Dehal, Marcin P. Joachimiak, Morgan N. Price, John T. Bates, Jason K. Baumohl, Dylan Chivian, Greg D. Friedland, Katherine H. Huang, Keith Keller, Pavel S. Novichkov, Inna L. Dubchak, Eric J. Alm, and Adam P. Arkin
MicrobesOnline: an integrated portal for comparative and functional genomics
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp919
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Stacia R. Engel, Rama Balakrishnan, Gail Binkley, Karen R. Christie, Maria C. Costanzo, Selina S. Dwight, Dianna G. Fisk, Jodi E. Hirschman, Benjamin C. Hitz, Eurie L. Hong, Cynthia J. Krieger, Michael S. Livstone, Stuart R. Miyasato, Robert Nash, Rose Oughtred, Julie Park, Marek S. Skrzypek, Shuai Weng, Edith D. Wong, Kara Dolinski, David Botstein, and J. Michael Cherry
Saccharomyces Genome Database provides mutant phenotype data
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp917
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Genome Integrity, Repair and Replication: Chia-Yin Lu, Cheng-Hui Tsai, Steven J. Brill, and Shu-Chun Teng
Sumoylation of the BLM ortholog, Sgs1, promotes telomere–telomere recombination in budding yeast
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp1008
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Genome Integrity, Repair and Replication: Jinlan Dong, Nicholas P. George, Katrina L. Duckett, Madeleine A. P. DeBeer, and Matthew E. Lopper
The crystal structure of Neisseria gonorrhoeae PriB reveals mechanistic differences among bacterial DNA replication restart pathways
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp1031
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Gene Regulation, Chromatin and Epigenetics: Chuong D. Pham, Xi He, and Gavin R. Schnitzler
Divergent human remodeling complexes remove nucleosomes from strong positioning sequences
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp1030
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Methods Online: Kimberly R. Blahnik, Lei Dou, Henriette O’Geen, Timothy McPhillips, Xiaoqin Xu, Alina R. Cao, Sushma Iyengar, Charles M. Nicolet, Bertram Ludäscher, Ian Korf, and Peggy J. Farnham
Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp1012
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Catherine Y. Cormier, Stephanie E. Mohr, Dongmei Zuo, Yanhui Hu, Andreas Rolfs, Jason Kramer, Elena Taycher, Fontina Kelley, Michael Fiacco, Greggory Turnbull, and Joshua LaBaer
Protein Structure Initiative Material Repository: an open shared public resource of structural genomics plasmids for the biological community
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp999
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Rasko Leinonen, Ruth Akhtar, Ewan Birney, James Bonfield, Lawrence Bower, Matt Corbett, Ying Cheng, Fehmi Demiralp, Nadeem Faruque, Neil Goodgame, Richard Gibson, Gemma Hoad, Christopher Hunter, Mikyung Jang, Steven Leonard, Quan Lin, Rodrigo Lopez, Michael Maguire, Hamish McWilliam, Sheila Plaister, Rajesh Radhakrishnan, Siamak Sobhany, Guy Slater, Petra Ten Hoopen, Franck Valentin, Robert Vaughan, Vadim Zalunin, Daniel Zerbino, and Guy Cochrane
Improvements to services at the European Nucleotide Archive
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp998
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Simon A. Forbes, Gurpreet Tang, Nidhi Bindal, Sally Bamford, Elisabeth Dawson, Charlotte Cole, Chai Yin Kok, Mingming Jia, Rebecca Ewing, Andrew Menzies, Jon W. Teague, Michael R. Stratton, and P. Andrew Futreal
COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp995
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Gene Regulation, Chromatin and Epigenetics: Yong-Jin Yang, Jeung-Whan Han, Hong-Duk Youn, and Eun-Jung Cho
The tumor suppressor, parafibromin, mediates histone H3 K9 methylation for cyclin D1 repression
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp991
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data] [Supplementary Data]

Abstract Gene Regulation, Chromatin and Epigenetics: Marie-Aline Gérard, Evelyne Myslinski, Natassia Chylak, Stéphanie Baudrey, Alain Krol, and Philippe Carbon
The scaRNA2 is produced by an independent transcription unit and its processing is directed by the encoding region
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp988
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Pora Kim, Suhyeon Yoon, Namshin Kim, Sanghyun Lee, Minjeong Ko, Haeseung Lee, Hyunjung Kang, Jaesang Kim, and Sanghyuk Lee
ChimerDB 2.0—a knowledgebase for fusion genes updated
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp982
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Patrick May, Annika Kreuchwig, Thomas Steinke, and Ina Koch
PTGL: a database for secondary structure-based protein topologies
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp980
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Gene Regulation, Chromatin and Epigenetics: Yuhua Xue, Zhiyuan Yang, Ruichuan Chen, and Qiang Zhou
A capping-independent function of MePCE in stabilizing 7SK snRNA and facilitating the assembly of 7SK snRNP
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp977
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Genome Integrity, Repair and Replication: Christina Bauerschmidt, Cecilia Arrichiello, Susanne Burdak-Rothkamm, Michael Woodcock, Mark A. Hill, David L. Stevens, and Kai Rothkamm
Cohesin promotes the repair of ionizing radiation-induced DNA double-strand breaks in replicated chromatin
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp976
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Ramil N. Nurtdinov, Mikhail O. Vasiliev, Anna S. Ershova, Ilia S. Lossev, and Anna S. Karyagina
PLANdbAffy: probe-level annotation database for Affymetrix expression microarrays
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp969
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Juan Antonio Vizcaíno, Richard Côté, Florian Reisinger, Harald Barsnes, Joseph M. Foster, Jonathan Rameseder, Henning Hermjakob, and Lennart Martens
The Proteomics Identifications database: 2010 update
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp964
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Michail Yu. Lobanov, Benjamin A. Shoemaker, Sergiy O. Garbuzynskiy, Jessica H. Fong, Anna R. Panchenko, and Oxana V. Galzitskaya
ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp963
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Guohui Zheng, Andrew V. Colasanti, Xiang-Jun Lu, and Wilma K. Olson
3DNALandscapes: a database for exploring the conformational features of DNA
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp959
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Structural Biology: Senada Nozinovic, Boris Fürtig, Hendrik R. A. Jonker, Christian Richter, and Harald Schwalbe
High-resolution NMR structure of an RNA model system: the 14-mer cUUCGg tetraloop hairpin RNA
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp956
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Structural Biology: Akiyoshi Nakamura, Kelly Sheppard, Junji Yamane, Min Yao, Dieter Söll, and Isao Tanaka
Two distinct regions in Staphylococcus aureus GatCAB guarantee accurate tRNA recognition
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp955
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Genomics: Oleg V. Grinchuk, Piroon Jenjaroenpun, Yuriy L. Orlov, Jiangtao Zhou, and Vladimir A. Kuznetsov
Integrative analysis of the human cis-antisense gene pairs, miRNAs and their transcription regulation patterns
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp954
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Elodie Portales-Casamar, Supat Thongjuea, Andrew T. Kwon, David Arenillas, Xiaobei Zhao, Eivind Valen, Dimas Yusuf, Boris Lenhard, Wyeth W. Wasserman, and Albin Sandelin
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp950
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Thomas Rattei, Patrick Tischler, Stefan Götz, Marc-André Jehl, Jonathan Hoser, Roland Arnold, Ana Conesa, and Hans-Werner Mewes
SIMAP—a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp949
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Donald S. Berkholz, Peter B. Krenesky, John R. Davidson, and P. Andrew Karplus
Protein Geometry Database: a flexible engine to explore backbone conformations and their relationships to covalent geometry
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp1013
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Athanasia Spandidos, Xiaowei Wang, Huajun Wang, and Brian Seed
PrimerBank: a resource of human and mouse PCR primer pairs for gene expression detection and quantification
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp1005
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Randi Vita, Laura Zarebski, Jason A. Greenbaum, Hussein Emami, Ilka Hoof, Nima Salimi, Rohini Damle, Alessandro Sette, and Bjoern Peters
The Immune Epitope Database 2.0
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp1004
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Vineet K. Sharma, Naveen Kumar, Tulika Prakash, and Todd D. Taylor
MetaBioME: a database to explore commercially useful enzymes in metagenomic datasets
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp1001
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Ikuo Uchiyama, Toshio Higuchi, and Mikihiko Kawai
MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp948
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Brooke Rhead, Donna Karolchik, Robert M. Kuhn, Angie S. Hinrichs, Ann S. Zweig, Pauline A. Fujita, Mark Diekhans, Kayla E. Smith, Kate R. Rosenbloom, Brian J. Raney, Andy Pohl, Michael Pheasant, Laurence R. Meyer, Katrina Learned, Fan Hsu, Jennifer Hillman-Jackson, Rachel A. Harte, Belinda Giardine, Timothy R. Dreszer, Hiram Clawson, Galt P. Barber, David Haussler, and W. James Kent
The UCSC genome browser database: update 2010
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp939
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Misha Kapushesky, Ibrahim Emam, Ele Holloway, Pavel Kurnosov, Andrey Zorin, James Malone, Gabriella Rustici, Eleanor Williams, Helen Parkinson, and Alvis Brazma
Gene Expression Atlas at the European Bioinformatics Institute
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp936
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Methods Online: D. Träutlein, M. Deibler, A. Leitenstorfer, and E. Ferrando-May
Specific local induction of DNA strand breaks by infrared multi-photon absorption
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp932
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Genome Integrity, Repair and Replication: Isabel Kurth and Jean Gautier
Origin-dependent initiation of DNA replication within telomeric sequences
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp929
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Nucleic Acid Enzymes: Angela Hirtreiter, Dina Grohmann, and Finn Werner
Molecular mechanisms of RNA polymerase—the F/E (RPB4/7) complex is required for high processivity in vitro
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp928
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Samuel Hiard, Carole Charlier, Wouter Coppieters, Michel Georges, and Denis Baurain
Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp926
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Genome Integrity, Repair and Replication: Mahalakshmi Krishnamurthy, Serkalem Tadesse, Katharina Rothmaier, and Peter L. Graumann
A novel SMC-like protein, SbcE (YhaN), is involved in DNA double-strand break repair and competence in Bacillus subtilis
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp909
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Molecular Biology: Artem V. Kononenko, Vladimir A. Mitkevich, Gemma C. Atkinson, Tanel Tenson, Vera I. Dubovaya, Ludmila Yu. Frolova, Alexander A. Makarov, and Vasili Hauryliuk
GTP-dependent structural rearrangement of the eRF1:eRF3 complex and eRF3 sequence motifs essential for PABP binding
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp908
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Methods Online: Guojun Li, Bingqiang Liu, and Ying Xu
Accurate recognition of cis-regulatory motifs with the correct lengths in prokaryotic genomes
Nucleic Acids Research Advance Access published on November 11, 2009.
doi:10.1093/nar/gkp907
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

9 November 2009

Abstract Database Issue: J. Muller, D. Szklarczyk, P. Julien, I. Letunic, A. Roth, M. Kuhn, S. Powell, C. von Mering, T. Doerks, L. J. Jensen, and P. Bork
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations
Nucleic Acids Research Advance Access published on November 9, 2009.
doi:10.1093/nar/gkp951
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: François Ehrenmann, Quentin Kaas, and Marie-Paule Lefranc
IMGT/3Dstructure-DB and IMGT/DomainGapAlign: a database and a tool for immunoglobulins or antibodies, T cell receptors, MHC, IgSF and MhcSF
Nucleic Acids Research Advance Access originally published on November 9, 2009. This version published November 17, 2009.
doi:10.1093/nar/gkp946
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Lishan Wang, Yuanyuan Xiong, Yihua Sun, Zhaoyuan Fang, Li Li, Hongbin Ji, and Tieliu Shi
HLungDB: an integrated database of human lung cancer research
Nucleic Acids Research Advance Access published on November 9, 2009.
doi:10.1093/nar/gkp945
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Petras J. Kundrotas, Zhengwei Zhu, and Ilya A. Vakser
GWIDD: Genome-wide protein docking database
Nucleic Acids Research Advance Access published on November 9, 2009.
doi:10.1093/nar/gkp944
[Abstract] [Full Text] [Print PDF] [Screen PDF]

Abstract Database Issue: Luke E. Ulrich and Igor B. Zhulin
The MiST2 database: a comprehensive genomics resource on microbial signal transduction
Nucleic Acids Research Advance Access published on November 9, 2009.
doi:10.1093/nar/gkp940
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Hong Li, Ying He, Guohui Ding, Chuan Wang, Lu Xie, and Yixue Li
dbDEPC: a database of Differentially Expressed Proteins in human Cancers
Nucleic Acids Research Advance Access published on November 9, 2009.
doi:10.1093/nar/gkp933
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

Abstract Database Issue: Lubos Klucar, Matej Stano, and Matus Hajduk
phiSITE: database of gene regulation in bacteriophages
Nucleic Acids Research Advance Access published on November 9, 2009.
doi:10.1093/nar/gkp911
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

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
[Abstract] [Full Text] [Print PDF] [Screen PDF]

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
[Abstract] [Full Text] [Print PDF] [Screen PDF]

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
[Abstract] [Full Text] [Print PDF] [Screen PDF]

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
[Abstract] [Full Text] [Print PDF] [Screen PDF]

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
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

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
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

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
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

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
[Abstract] [Full Text] [Print PDF] [Screen PDF]

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
[Abstract] [Full Text] [Print PDF] [Screen PDF]

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
[Abstract] [Full Text] [Print PDF] [Screen PDF] [Supplementary Data]

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] [Supplementary Data]

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]