Nucleic Acids Research

Survey and Summary

Get checked abstract Andreas Fischer and Manfred Gessler

Delta–Notch—and then? Protein interactions and proposed modes of repression by Hes and Hey bHLH factors
Nucleic Acids Research Advance Access published on June 22, 2007
Nucl. Acids Res. 2007 35: 4583-4596; doi:10.1093/nar/gkm477 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Chemistry

Get checked abstract Huachuan Cao and Yinsheng Wang

Quantification of oxidative single-base and intrastrand cross-link lesions in unmethylated and CpG-methylated DNA induced by Fenton-type reagents
Nucleic Acids Research Advance Access published on July 10, 2007
Nucl. Acids Res. 2007 35: 4833-4844; doi:10.1093/nar/gkm497 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Computational Biology

Get checked abstract Maricel G. Kann, Sergey L. Sheetlin, Yonil Park, Stephen H. Bryant, and John L. Spouge

The identification of complete domains within protein sequences using accurate E-values for semi-global alignment
Nucleic Acids Research Advance Access published on June 27, 2007
Nucl. Acids Res. 2007 35: 4678-4685; doi:10.1093/nar/gkm414 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Paulien Smits, Jan A. M. Smeitink, Lambert P. van den Heuvel, Martijn A. Huynen, and Thijs J. G. Ettema

Reconstructing the evolution of the mitochondrial ribosomal proteome
Nucleic Acids Research Advance Access published on June 29, 2007
Nucl. Acids Res. 2007 35: 4686-4703; doi:10.1093/nar/gkm441 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Debopriya Das, Tyson A. Clark, Anthony Schweitzer, Miki Yamamoto, Henry Marr, Josh Arribere, Simon Minovitsky, Alexander Poliakov, Inna Dubchak, John E. Blume, and John G. Conboy

A correlation with exon expression approach to identify cis-regulatory elements for tissue-specific alternative splicing
Nucleic Acids Research Advance Access published on July 10, 2007
Nucl. Acids Res. 2007 35: 4845-4857; doi:10.1093/nar/gkm485 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Genomics

Get checked abstract Rajeev K. Azad and Jeffrey G. Lawrence

Detecting laterally transferred genes: use of entropic clustering methods and genome position
Nucleic Acids Research Advance Access published on June 25, 2007
Nucl. Acids Res. 2007 35: 4629-4639; doi:10.1093/nar/gkm204 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Achim Fischer, Alistair Lenhard, Heike Tronecker, Yvonne Lorat, Marcel Kraenzle, Oliver Sorgenfrei, Tim Zeppenfeld, Michael Haushalter, Gerhard Vogt, Ulrich Gruene, Annette Meyer, Ulrich Handlbichler, Patrick Schweizer, and Leo Gaelweiler

iGentifier: indexing and large-scale profiling of unknown transcriptomes
Nucleic Acids Research Advance Access published on June 25, 2007
Nucl. Acids Res. 2007 35: 4640-4648; doi:10.1093/nar/gkm331 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Scott William Roy and David Penny

Intron length distributions and gene prediction
Nucleic Acids Research Advance Access published on July 7, 2007
Nucl. Acids Res. 2007 35: 4737-4742; doi:10.1093/nar/gkm281 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Zasha Weinberg, Jeffrey E. Barrick, Zizhen Yao, Adam Roth, Jane N. Kim, Jeremy Gore, Joy Xin Wang, Elaine R. Lee, Kirsten F. Block, Narasimhan Sudarsan, Shane Neph, Martin Tompa, Walter L. Ruzzo, and Ronald R. Breaker

Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline
Nucleic Acids Research Advance Access published on July 9, 2007
Nucl. Acids Res. 2007 35: 4809-4819; doi:10.1093/nar/gkm487 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Molecular Biology

Get checked abstract Urtzi Garaigorta and Juan Ortín

Mutation analysis of a recombinant NS replicon shows that influenza virus NS1 protein blocks the splicing and nucleo-cytoplasmic transport of its own viral mRNA
Nucleic Acids Research Advance Access published on May 8, 2007
Nucl. Acids Res. 2007 35: 4573-4582; doi:10.1093/nar/gkm230 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Tanguy Araud, Raphael Genolet, Pascale Jaquier-Gubler, and Joseph Curran

Alternatively spliced isoforms of the human elk-1 mRNA within the 5' UTR: implications for ELK-1 expression
Nucleic Acids Research Advance Access published on June 25, 2007
Nucl. Acids Res. 2007 35: 4649-4663; doi:10.1093/nar/gkm482 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Daphne Reiss, Ying Zhang, and Dixie L. Mager

Widely variable endogenous retroviral methylation levels in human placenta
Nucleic Acids Research Advance Access published on July 7, 2007
Nucl. Acids Res. 2007 35: 4743-4754; doi:10.1093/nar/gkm455 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Irina Saraiva Franco, Luís Jaime Mota, Cláudio Manuel Soares, and Isabel de Sá-Nogueira

Probing key DNA contacts in AraR-mediated transcriptional repression of the Bacillus subtilis arabinose regulon
Nucleic Acids Research Advance Access published on July 7, 2007
Nucl. Acids Res. 2007 35: 4755-4766; doi:10.1093/nar/gkm509 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Hong Jiang, Jennifer Coleman, Robin Miskimins, Rekha Srinivasan, and W. Keith Miskimins

Cap-independent translation through the p27 5'-UTR
Nucleic Acids Research Advance Access published on July 7, 2007
Nucl. Acids Res. 2007 35: 4767-4778; doi:10.1093/nar/gkm512 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Wenyi Gu, Jianmin Ding, Xiao Wang, Rachel L. de Kluyver, Nicholas A. Saunders, Ian H. Frazer, and Kong-Nan Zhao

Generalized substitution of isoencoding codons shortens the duration of papillomavirus L1 protein expression in transiently gene-transfected keratinocytes due to cell differentiation
Nucleic Acids Research Advance Access published on July 9, 2007
Nucl. Acids Res. 2007 35: 4820-4832; doi:10.1093/nar/gkm496 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Maria Nilsson, Karin Dahlman-Wright, Charlotta Karelmo, Jan-Åke Gustafsson, and Knut R. Steffensen

Elk1 and SRF transcription factors convey basal transcription and mediate glucose response via their binding sites in the human LXRB gene promoter
Nucleic Acids Research Advance Access published on July 10, 2007
Nucl. Acids Res. 2007 35: 4858-4868; doi:10.1093/nar/gkm492 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Karen Rothfels, Owen Rowland, and Jacqueline Segall

Zinc fingers 1 and 7 of yeast TFIIIA are essential for assembly of a functional transcription complex on the 5 S RNA gene
Nucleic Acids Research Advance Access published on July 10, 2007
Nucl. Acids Res. 2007 35: 4869-4881; doi:10.1093/nar/gkm517 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Akiko Kobayashi, Youko Watanabe, Koji Akasaka, and Tetsuro Kokubo

Real-time monitoring of functional interactions between upstream and core promoter sequences in living cells of sea urchin embryos
Nucleic Acids Research Advance Access published on July 10, 2007
Nucl. Acids Res. 2007 35: 4882-4894; doi:10.1093/nar/gkm519 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Nucleic Acid Enzymes

Get checked abstract Natalia Demeshkina, Go Hirokawa, Akira Kaji, and Hideko Kaji

Novel activity of eukaryotic translocase, eEF2: dissociation of the 80S ribosome into subunits with ATP but not with GTP
Nucleic Acids Research Advance Access published on June 22, 2007
Nucl. Acids Res. 2007 35: 4597-4607; doi:10.1093/nar/gkm468 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Shuang-Yong Xu, Zhenyu Zhu, Penghua Zhang, Siu-Hong Chan, James C. Samuelson, Jianping Xiao, Debra Ingalls, and Geoffrey G. Wilson

Discovery of natural nicking endonucleases Nb.BsrDI and Nb.BtsI and engineering of top-strand nicking variants from BsrDI and BtsI
Nucleic Acids Research Advance Access published on June 22, 2007
Nucl. Acids Res. 2007 35: 4608-4618; doi:10.1093/nar/gkm481 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Daniel Klaiman, Michal Amitsur, Shani Blanga-Kanfi, Michal Chai, Darrell R. Davis, and Gabriel Kaufmann

Parallel dimerization of a PrrC-anticodon nuclease region implicated in tRNA^Lys recognition
Nucleic Acids Research Advance Access published on June 29, 2007
Nucl. Acids Res. 2007 35: 4704-4714; doi:10.1093/nar/gkm494 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Arianna Loregian, Elisa Sinigalia, Beatrice Mercorelli, Giorgio Palù, and Donald M. Coen

Binding parameters and thermodynamics of the interaction of the human cytomegalovirus DNA polymerase accessory protein, UL44, with DNA: implications for the processivity mechanism
Nucleic Acids Research Advance Access published on July 7, 2007
Nucl. Acids Res. 2007 35: 4779-4791; doi:10.1093/nar/gkm506 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Gintautas Tamulaitis, Mindaugas Zaremba, Roman H. Szczepanowski, Matthias Bochtler, and Virginijus Siksnys

Nucleotide flipping by restriction enzymes analyzed by 2-aminopurine steady-state fluorescence
Nucleic Acids Research Advance Access published on July 7, 2007
Nucl. Acids Res. 2007 35: 4792-4799; doi:10.1093/nar/gkm513 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Julie A.C. Alexandre, Béatrice Roy, Dimitri Topalis, Sylvie Pochet, Christian Périgaud, and Dominique Deville-Bonne

Enantioselectivity of human AMP, dTMP and UMP-CMP kinases
Nucleic Acids Research Advance Access published on July 10, 2007
Nucl. Acids Res. 2007 35: 4895-4904; doi:10.1093/nar/gkm479 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

RNA

Get checked abstract Xiaowei (Sylvia) Chen, Timofey S. Rozhdestvensky, Lesley J. Collins, Jürgen Schmitz, and David Penny

Combined experimental and computational approach to identify non-protein-coding RNAs in the deep-branching eukaryote Giardia intestinalis
Nucleic Acids Research Advance Access published on June 22, 2007
Nucl. Acids Res. 2007 35: 4619-4628; doi:10.1093/nar/gkm474 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Get checked abstract Stephen D. Baird, Stephen M. Lewis, Marcel Turcotte, and Martin Holcik

A search for structurally similar cellular internal ribosome entry sites
Nucleic Acids Research Advance Access published on June 25, 2007
Nucl. Acids Res. 2007 35: 4664-4677; doi:10.1093/nar/gkm483 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract A. Serman, F. Le Roy, C. Aigueperse, M. Kress, F. Dautry, and D. Weil

GW body disassembly triggered by siRNAs independently of their silencing activity
Nucleic Acids Research Advance Access published on June 29, 2007
Nucl. Acids Res. 2007 35: 4715-4727; doi:10.1093/nar/gkm491 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Julie K. Hurt, Sureyya Olgen, and George A. Garcia

Site-specific modification of Shigella flexneri virF mRNA by tRNA-guanine transglycosylase in vitro
Nucleic Acids Research Advance Access published on July 10, 2007
Nucl. Acids Res. 2007 35: 4905-4913; doi:10.1093/nar/gkm473 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Structural Biology

Get checked abstract Scott Bailey, William K. Eliason, and Thomas A. Steitz

The crystal structure of the Thermus aquaticus DnaB helicase monomer
Nucleic Acids Research Advance Access published on July 1, 2007
Nucl. Acids Res. 2007 35: 4728-4736; doi:10.1093/nar/gkm507 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Eric Girard, Thierry Prangé, Anne-Claire Dhaussy, Evelyne Migianu-Griffoni, Marc Lecouvey, Jean-Claude Chervin, Mohamed Mezouar, Richard Kahn, and Roger Fourme

Adaptation of the base-paired double-helix molecular architecture to extreme pressure
Nucleic Acids Research Advance Access published on July 7, 2007
Nucl. Acids Res. 2007 35: 4800-4808; doi:10.1093/nar/gkm511 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Kostas Repanas, Nora Zingler, Liliana E. Layer, Gerald G. Schumann, Anastassis Perrakis, and Oliver Weichenrieder

Determinants for DNA target structure selectivity of the human LINE-1 retrotransposon endonuclease
Nucleic Acids Research Advance Access published on July 10, 2007
Nucl. Acids Res. 2007 35: 4914-4926; doi:10.1093/nar/gkm516 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

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