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Previous Next 		Contents: Volume 35, Number 1, January 2007   [Index by Author] 

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To see an article, click its [Full Text] or [PDF] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.

Survey and Summary Back

Keith Knapp and Yi-Ping Phoebe Chen
An evaluation of contemporary hidden Markov model genefinders with a predicted exon taxonomy
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: 317-324; doi:10.1093/nar/gkl1026 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Chemistry Back

Pascal A. Küpfer and Christian J. Leumann
The chemical stability of abasic RNA compared to abasic DNA
Nucleic Acids Research Advance Access published on December 6, 2006
Nucl. Acids Res. 2007 35: 58-68; doi:10.1093/nar/gkl948 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Sherry M. Tsai, Michelle E. Farkas, C. James Chou, Joel M. Gottesfeld, and Peter B. Dervan
Unanticipated differences between {alpha}- and {gamma}-diaminobutyric acid-linked hairpin polyamide-alkylator conjugates
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: 307-316; doi:10.1093/nar/gkl1025 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Computational Biology Back

Thao T. Tran, Phuongan Dam, Zhengchang Su, Farris L. Poole, II, Michael W. W. Adams, G. Tong Zhou, and Ying Xu
Operon prediction in Pyrococcus furiosus
Nucleic Acids Research Advance Access published on December 5, 2006
Nucl. Acids Res. 2007 35: 11-20; doi:10.1093/nar/gkl974 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Itay Mayrose, Tomer Shlomi, Nimrod D. Rubinstein, Jonathan M. Gershoni, Eytan Ruppin, Roded Sharan, and Tal Pupko
Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm
Nucleic Acids Research Advance Access published on December 6, 2006
Nucl. Acids Res. 2007 35: 69-78; doi:10.1093/nar/gkl975 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Zhenbao Yu, Zhaofeng Jian, Shi-Hsiang Shen, Enrico Purisima, and Edwin Wang
Global analysis of microRNA target gene expression reveals that miRNA targets are lower expressed in mature mouse and Drosophila tissues than in the embryos
Nucleic Acids Research Advance Access published on December 7, 2006
Nucl. Acids Res. 2007 35: 152-164; doi:10.1093/nar/gkl1032 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Donglin Liu, J. Michael Brockman, Brinda Dass, Lucie N. Hutchins, Priyam Singh, John R. McCarrey, Clinton C. MacDonald, and Joel H. Graber
Systematic variation in mRNA 3'-processing signals during mouse spermatogenesis
Nucleic Acids Research Advance Access published on December 8, 2006
Nucl. Acids Res. 2007 35: 234-246; doi:10.1093/nar/gkl919 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Tra Thi Vu and Jiri Vohradsky
Nonlinear differential equation model for quantification of transcriptional regulation applied to microarray data of Saccharomyces cerevisiae
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: 279-287; doi:10.1093/nar/gkl1001 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Phuongan Dam, Victor Olman, Kyle Harris, Zhengchang Su, and Ying Xu
Operon prediction using both genome-specific and general genomic information
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: 288-298; doi:10.1093/nar/gkl1018 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Genomics Back

M. Thomas P. Gilbert, Jonas Binladen, Webb Miller, Carsten Wiuf, Eske Willerslev, Hendrik Poinar, John E. Carlson, James H. Leebens-Mack, and Stephan C. Schuster
Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis
Nucleic Acids Research Advance Access published on August 18, 2006
Nucl. Acids Res. 2007 35: 1-10; doi:10.1093/nar/gkl483 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [supplementary data]  

Genaro Hernandez, Jr, Faramarz Valafar, and William E. Stumph
Insect small nuclear RNA gene promoters evolve rapidly yet retain conserved features involved in determining promoter activity and RNA polymerase specificity
Nucleic Acids Research Advance Access published on December 5, 2006
Nucl. Acids Res. 2007 35: 21-34; doi:10.1093/nar/gkl982 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Jonathan L. Jacobs, Ashton T. Belew, Rasa Rakauskaite, and Jonathan D. Dinman
Identification of functional, endogenous programmed –1 ribosomal frameshift signals in the genome of Saccharomyces cerevisiae
Nucleic Acids Research Advance Access published on December 7, 2006
Nucl. Acids Res. 2007 35: 165-174; doi:10.1093/nar/gkl1033 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Arunadevi Yarragudi, Laura Wegener Parfrey, and Randall H. Morse
Genome-wide analysis of transcriptional dependence and probable target sites for Abf1 and Rap1 in Saccharomyces cerevisiae
Nucleic Acids Research Advance Access published on December 7, 2006
Nucl. Acids Res. 2007 35: 193-202; doi:10.1093/nar/gkl1059 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Molecular Biology Back

Lin Ma, Yuk Y. Sham, Kylie J. Walters, and Howard C. Towle
A critical role for the loop region of the basic helix–loop–helix/leucine zipper protein Mlx in DNA binding and glucose-regulated transcription
Nucleic Acids Research Advance Access published on December 5, 2006
Nucl. Acids Res. 2007 35: 35-44; doi:10.1093/nar/gkl987 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Alexandre Calon, Isabelle Gross, Irwin Davidson, Michèle Kedinger, Isabelle Duluc, Claire Domon-Dell, and Jean-Noël Freund
Functional interaction between the homeoprotein CDX1 and the transcriptional machinery containing the TATA-binding protein
Nucleic Acids Research Advance Access published on December 7, 2006
Nucl. Acids Res. 2007 35: 175-185; doi:10.1093/nar/gkl1034 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Sun-Young Kim, Sang-Gyu Kim, Youn-Sung Kim, Pil Joon Seo, Mikyoung Bae, Hye-Kyung Yoon, and Chung-Mo Park
Exploring membrane-associated NAC transcription factors in Arabidopsis: implications for membrane biology in genome regulation
Nucleic Acids Research Advance Access published on December 7, 2006
Nucl. Acids Res. 2007 35: 203-213; doi:10.1093/nar/gkl1068 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Mai A. Al-Mohanna, Huda H. Al-Khalaf, Nujoud Al-Yousef, and Abdelilah Aboussekhra
The p16INK4a tumor suppressor controls p21WAF1 induction in response to ultraviolet light
Nucleic Acids Research Advance Access published on December 7, 2006
Nucl. Acids Res. 2007 35: 223-233; doi:10.1093/nar/gkl1075 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

David C. Grainger, Hirofumi Aiba, Douglas Hurd, Douglas F. Browning, and Stephen J. W. Busby
Transcription factor distribution in Escherichia coli: studies with FNR protein
Nucleic Acids Research Advance Access published on December 12, 2006
Nucl. Acids Res. 2007 35: 269-278; doi:10.1093/nar/gkl1023 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Barbara Kedzierska, Lu-Yun Lian, and Finbarr Hayes
Toxin–antitoxin regulation: bimodal interaction of YefM–YoeB with paired DNA palindromes exerts transcriptional autorepression
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: 325-339; doi:10.1093/nar/gkl1028 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Maria Lokshin, Yingchun Li, Christian Gaiddon, and Carol Prives
p53 and p73 display common and distinct requirements for sequence specific binding to DNA
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: 340-352; doi:10.1093/nar/gkl1047 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Nucleic Acid Enzymes Back

Emmanuele Crespan, Ludmila Alexandrova, Anastasiya Khandazhinskaya, Maxim Jasko, Marina Kukhanova, Giuseppe Villani, Ulrich Hübscher, Silvio Spadari, and Giovanni Maga
Expanding the repertoire of DNA polymerase substrates: template-instructed incorporation of non-nucleoside triphosphate analogues by DNA polymerases ß and {lambda}
Nucleic Acids Research Advance Access published on December 5, 2006
Nucl. Acids Res. 2007 35: 45-57; doi:10.1093/nar/gkl1016 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Amy R. Reckinger, Kyeong Soo Jeong, Arkady B. Khodursky, and Hiroshi Hiasa
RecA can stimulate the relaxation activity of topoisomerase I: Molecular basis of topoisomerase-mediated genome-wide transcriptional responses in Escherichia coli
Nucleic Acids Research Advance Access published on December 6, 2006
Nucl. Acids Res. 2007 35: 79-86; doi:10.1093/nar/gkl981 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Fuyang Li, Monika Papworth, Michal Minczuk, Christian Rohde, Yingying Zhang, Sergei Ragozin, and Albert Jeltsch
Chimeric DNA methyltransferases target DNA methylation to specific DNA sequences and repress expression of target genes
Nucleic Acids Research Advance Access published on December 6, 2006
Nucl. Acids Res. 2007 35: 100-112; doi:10.1093/nar/gkl1035 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Peter Cherepanov
LEDGF/p75 interacts with divergent lentiviral integrases and modulates their enzymatic activity in vitro
Nucleic Acids Research Advance Access published on December 7, 2006
Nucl. Acids Res. 2007 35: 113-124; doi:10.1093/nar/gkl885 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Michael D. Hamilton, Anthony A. Nuara, Don B. Gammon, R. Mark Buller, and David H. Evans
Duplex strand joining reactions catalyzed by vaccinia virus DNA polymerase
Nucleic Acids Research Advance Access published on December 7, 2006
Nucl. Acids Res. 2007 35: 143-151; doi:10.1093/nar/gkl1015 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jason W. Rausch and Stuart F. J. Le Grice
Purine analog substitution of the HIV-1 polypurine tract primer defines regions controlling initiation of plus-strand DNA synthesis
Nucleic Acids Research Advance Access published on December 12, 2006
Nucl. Acids Res. 2007 35: 256-268; doi:10.1093/nar/gkl909 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

RNA Back

Eddo Kim, Alon Magen, and Gil Ast
Different levels of alternative splicing among eukaryotes
Nucleic Acids Research Advance Access published on December 7, 2006
Nucl. Acids Res. 2007 35: 125-131; doi:10.1093/nar/gkl924 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Supplementary Data]  

Roberto Marcucci, Francisco E. Baralle, and Maurizio Romano
Complex splicing control of the human Thrombopoietin gene by intronic G runs
Nucleic Acids Research Advance Access published on December 7, 2006
Nucl. Acids Res. 2007 35: 132-142; doi:10.1093/nar/gkl965 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Rafael Nisa-Martínez, José I. Jiménez-Zurdo, Francisco Martínez-Abarca, Estefanía Muñoz-Adelantado, and Nicolás Toro
Dispersion of the RmInt1 group II intron in the Sinorhizobium meliloti genome upon acquisition by conjugative transfer
Nucleic Acids Research Advance Access published on December 7, 2006
Nucl. Acids Res. 2007 35: 214-222; doi:10.1093/nar/gkl1072 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

R. Sajic, K. Lee, K. Asai, D. Sakac, D. R. Branch, C. Upton, and A. Cochrane
Use of modified U1 snRNAs to inhibit HIV-1 replication
Nucleic Acids Research Advance Access published on December 8, 2006
Nucl. Acids Res. 2007 35: 247-255; doi:10.1093/nar/gkl1022 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Elias Bechara, Laetitia Davidovic, Mireille Melko, Mounia Bensaid, Sandra Tremblay, Josiane Grosgeorge, Edouard W. Khandjian, Enzo Lalli, and Barbara Bardoni
Fragile X related protein 1 isoforms differentially modulate the affinity of fragile X mental retardation protein for G-quartet RNA structure
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: 299-306; doi:10.1093/nar/gkl1021 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Structural Biology Back

Christian G. Noble, Barbara Beuth, and Ian A. Taylor
Structure of a nucleotide-bound Clp1-Pcf11 polyadenylation factor
Nucleic Acids Research Advance Access published on December 6, 2006
Nucl. Acids Res. 2007 35: 87-99; doi:10.1093/nar/gkl1010 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Elisabetta Sabini, Saugata Hazra, Manfred Konrad, Stephen K. Burley, and Arnon Lavie
Structural basis for activation of the therapeutic L-nucleoside analogs 3TC and troxacitabine by human deoxycytidine kinase
Nucleic Acids Research Advance Access published on December 7, 2006
Nucl. Acids Res. 2007 35: 186-192; doi:10.1093/nar/gkl1038 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Methods Online Back

Ian J. Donaldson and Berthold Göttgens
CoMoDis: composite motif discovery in mammalian genomes
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2007 35: e1; doi:10.1093/nar/gkl839 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Honghai Gao, Jianmin Huang, Francis Barany, and Weiguo Cao
Switching base preferences of mismatch cleavage in endonuclease V: an improved method for scanning point mutations
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2007 35: e2; doi:10.1093/nar/gkl916 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Kenji Kinoshita, Kentaro Fujimoto, Toru Yakabe, Shin Saito, Yuzo Hamaguchi, Takayuki Kikuchi, Ken Nonaka, Shigenori Murata, Daisuke Masuda, Wataru Takada, Sohei Funaoka, Susumu Arai, Hisao Nakanishi, Kanehisa Yokoyama, Kazuhiko Fujiwara, and Kenichi Matsubara
Multiple primer extension by DNA polymerase on a novel plastic DNA array coated with a biocompatible polymer
Nucleic Acids Research Advance Access published on November 28, 2006
Nucl. Acids Res. 2007 35: e3; doi:10.1093/nar/gkl939 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Reimo Tetzner, Dimo Dietrich, and Juergen Distler
Control of carry-over contamination for PCR-based DNA methylation quantification using bisulfite treated DNA
Nucleic Acids Research Advance Access published on November 28, 2006
Nucl. Acids Res. 2007 35: e4; doi:10.1093/nar/gkl955 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Kavitha Madishetty, Pascal Condamine, Jan T. Svensson, Edmundo Rodriguez, and Timothy J. Close
An improved method to identify BAC clones using pooled overgos
Nucleic Acids Research Advance Access published on December 6, 2006
Nucl. Acids Res. 2007 35: e5; doi:10.1093/nar/gkl920 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Bernard A. Konfortov, Alan T. Bankier, and Paul H. Dear
An efficient method for multi-locus molecular haplotyping
Nucleic Acids Research Advance Access published on December 7, 2006
Nucl. Acids Res. 2007 35: e6; doi:10.1093/nar/gkl742 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Elhanan Borenstein, Tomer Shlomi, Eytan Ruppin, and Roded Sharan
Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes
Nucleic Acids Research Advance Access published on December 7, 2006
Nucl. Acids Res. 2007 35: e7; doi:10.1093/nar/gkl792 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

To see an article, click its [Full Text] or [PDF] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.