Home >> Nucleic Acids Research, Volume 38, Number 3
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Nucleic Acids Research (NAR) is a fully Open Access journal, providing rapid publication of leading edge research into the nucleic acids under the following categories: chemistry, computational biology, genomics, molecular biology, nucleic acid enzymes, RNA and structural biology. There is a Survey and Summary section, and methods papers are published
in NAR Methods Online. Each year the first issue is devoted to biological databases, and a later issue to relevant web-based software resources.

Publisher: Oxford University Press

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Volume 38, Number 3, 25 January 2010

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Free Content Nucleic Acids Research
pp. i-i(1)

Free Content Nucleic Acids Research
pp. ii-ii(1)

Free Content Subscriptions
pp. iii-iii(1)

Free Content Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data
pp. e13-e13(1)
Authors: Blahnik, Kimberly R.; Dou, Lei; OGeen, Henriette; McPhillips, Timothy; Xu, Xiaoqin; Cao, Alina R.; Iyengar, Sushma; Nicolet, Charles M.; Ludscher, Bertram; Korf, Ian; Farnham, Peggy J.

Free Content Specific local induction of DNA strand breaks by infrared multi-photon absorption
pp. e14-e14(1)
Authors: Trutlein, D.; Deibler, M.; Leitenstorfer, A.; Ferrando-May, E.

Free Content Quantitative analysis of ribosomemRNA complexes at different translation stages
pp. e15-e15(1)
Authors: Shirokikh, Nikolay E.; Alkalaeva, Elena Z.; Vassilenko, Konstantin S.; Afonina, Zhanna A.; Alekhina, Olga M.; Kisselev, Lev L.; Spirin, Alexander S.

Free Content A single-molecule assay for telomerase structure-function analysis
pp. e16-e16(1)
Authors: Wu, John Y.; Stone, Michael D.; Zhuang, Xiaowei

Free Content A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data
pp. e17-e17(1)
Authors: Barbosa-Morais, Nuno L.; Dunning, Mark J.; Samarajiwa, Shamith A.; Darot, Jeremy F. J.; Ritchie, Matthew E.; Lynch, Andy G.; Tavar, Simon

Free Content DNA structures from phosphate chemical shifts
pp. e18-e18(1)
Authors: Abi-Ghanem, Josphine; Heddi, Brahim; Foloppe, Nicolas; Hartmann, Brigitte

Free Content A rapid and sensitive method to detect siRNA-mediated mRNA cleavage in vivo using 5 RACE and a molecular beacon probe
pp. e19-e19(1)
Authors: Lasham, Annette; Herbert, Mike; Coppieters t Wallant, Natacha; Patel, Rachna; Feng, Sheryl; Eszes, Marika; Cao, Helen; Reid, Glen

Free Content Are nucleosome positions in vivo primarily determined by histoneDNA sequence preferences?
pp. 709-719(11)
Authors: Stein, Arnold; Takasuka, Taichi E.; Collings, Clayton K.

Free Content GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains
pp. 720-737(18)
Authors: Lee, David A.; Rentzsch, Robert; Orengo, Christine

Free Content Correlated changes between regulatory cis elements and condition-specific expression in paralogous gene families
pp. 738-749(12)
Authors: Singh, Larry N.; Hannenhalli, Sridhar

Free Content Adenovirus VA RNA-derived miRNAs target cellular genes involved in cell growth, gene expression and DNA repair
pp. 750-763(14)
Authors: Aparicio, Oscar; Carnero, Elena; Abad, Xabier; Razquin, Nerea; Guruceaga, Elizabeth; Segura, Victor; Fortes, Puri

Free Content Differential regulation of CHOP translation by phosphorylated eIF4E under stress conditions
pp. 764-777(14)
Authors: Chen, Yi-Jiun; Tan, Bertrand Chin-Ming; Cheng, Ya-Yun; Chen, Jin-Shin; Lee, Sheng-Chung

Free Content An internal ribosomal entry site mediates redox-sensitive translation of Nrf2
pp. 778-788(11)
Authors: Li, Wenge; Thakor, Nehal; Xu, Eugenia Y.; Huang, Ying; Chen, Chi; Yu, Rong; Holcik, Martin; Kong, Ah-Ng

Free Content The hydrophobic patch of ubiquitin is required to protect transactivatorpromoter complexes from destabilization by the proteasomal ATPases
pp. 789-796(8)
Authors: Archer, Chase T.; Kodadek, Thomas

Free Content Hypoxia-inducible factor-1 regulates the expression of nucleotide excision repair proteins in keratinocytes
pp. 797-809(13)
Authors: Rezvani, Hamid Reza; Mahfouf, Walid; Ali, Nsrein; Chemin, Cecile; Ged, Cecile; Kim, Arianna L.; de Verneuil, Hubert; Taeb, Alain; Bickers, David R.; Mazurier, Frdric

Free Content Genome-wide gene regulation of biosynthesis and energy generation by a novel transcriptional repressor in Geobacter species
pp. 810-821(12)
Authors: Ueki, Toshiyuki; Lovley, Derek R.

Free Content Reciprocal roles of SIRT1 and SKIP in the regulation of RAR activity: implication in the retinoic acid-induced neuronal differentiation of P19 cells
pp. 822-831(10)
Authors: Kang, Moo-Rim; Lee, Sang-Wang; Um, Elisa; Kang, Hyun Tae; Hwang, Eun Seong; Kim, Eun-Joo; Um, Soo-Jong

Free Content SIRT1 deacetylates APE1 and regulates cellular base excision repair
pp. 832-845(14)
Authors: Yamamori, Tohru; DeRicco, Jeremy; Naqvi, Asma; Hoffman, Timothy A.; Mattagajasingh, Ilwola; Kasuno, Kenji; Jung, Saet-Byel; Kim, Cuk-Seong; Irani, Kaikobad

Free Content A naturally occurring human RPA subunit homolog does not support DNA replication or cell-cycle progression
pp. 846-858(13)
Authors: Haring, Stuart J.; Humphreys, Troy D.; Wold, Marc S.

Free Content Critical amino acids in human DNA polymerases and involved in erroneous incorporation of oxidized nucleotides
pp. 859-867(9)
Authors: Katafuchi, Atsushi; Sassa, Akira; Niimi, Naoko; Grz, Petr; Fujimoto, Hirofumi; Masutani, Chikahide; Hanaoka, Fumio; Ohta, Toshihiro; Nohmi, Takehiko

Free Content Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome
pp. 868-877(10)
Authors: Albrecht, Marco; Sharma, Cynthia M.; Reinhardt, Richard; Vogel, Jrg; Rudel, Thomas

Free Content Transcription regulation of caspase-1 by R393 of HIPPI and its molecular partner HIP-1
pp. 878-892(15)
Authors: Banerjee, M.; Datta, M.; Majumder, P.; Mukhopadhyay, D.; Bhattacharyya, N. P.

Free Content Mechanistic differences in the transcriptional activation of p53 by 14-3-3 isoforms
pp. 893-906(14)
Authors: Rajagopalan, Sridharan; Sade, Robert S.; Townsley, Fiona M.; Fersht, Alan R.

Free Content Defining a role for Hfq in Gram-positive bacteria: evidence for Hfq-dependent antisense regulation in Listeria monocytogenes
pp. 907-919(13)
Authors: Nielsen, Jesper Sejrup; Lei, Lisbeth Kristensen; Ebersbach, Tine; Olsen, Anders Steno; Klitgaard, Janne Kudsk; Valentin-Hansen, Poul; Kallipolitis, Birgitte Haahr

Free Content Dna2 is a structure-specific nuclease, with affinity for 5-flap intermediates
pp. 920-930(11)
Authors: Stewart, Jason A.; Campbell, Judith L.; Bambara, Robert A.

Free Content The helicase XPD unwinds bubble structures and is not stalled by DNA lesions removed by the nucleotide excision repair pathway
pp. 931-941(11)
Authors: Rudolf, Jana; Rouillon, Christophe; Schwarz-Linek, Ulrich; White, Malcolm F.

Free Content N7-Methylguanine at position 46 (m7G46) in tRNA from Thermus thermophilus is required for cell viability at high temperatures through a tRNA modification network
pp. 942-957(16)
Authors: Tomikawa, Chie; Yokogawa, Takashi; Kanai, Tamotsu; Hori, Hiroyuki

Free Content Homology-dependent interactions determine the order of strand exchange by IntDOT recombinase
pp. 958-969(12)
Authors: Laprise, Jennifer; Yoneji, Sumiko; Gardner, Jeffrey F.

Free Content Sequencestructure relationships in RNA loops: establishing the basis for loop homology modeling
pp. 970-980(11)
Authors: Schudoma, Christian; May, Patrick; Nikiforova, Viktoria; Walther, Dirk

Free Content Conservation and divergence of microRNAs and their functions in Euphorbiaceous plants
pp. 981-995(15)
Authors: Zeng, Changying; Wang, Wenquan; Zheng, Yun; Chen, Xin; Bo, Weiping; Song, Shun; Zhang, Weixiong; Peng, Ming

Free Content Extensive mis-splicing of a bi-partite plant mitochondrial group II intron
pp. 996-1008(13)
Authors: Elina, Helen; Brown, Gregory G.

Free Content 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
pp. 1009-1021(13)
Authors: Zhang, Zhenjiang; Dai, Jixun; Veliath, Elizabeth; Jones, Roger A.; Yang, Danzhou

Free Content 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
pp. 1022-1033(12)
Authors: Yang, Qianfan; Xiang, Junfeng; Yang, Shu; Li, Qian; Zhou, Qiuju; Guan, Aijiao; Zhang, Xiufeng; Zhang, Hong; Tang, Yalin; Xu, Guangzhi

Free Content Intrinsic flexibility of B-DNA: the experimental TRX scale
pp. 1034-1047(14)
Authors: Heddi, Brahim; Oguey, Christophe; Lavelle, Christophe; Foloppe, Nicolas; Hartmann, Brigitte

Free Content A single-label phenylpyrrolocytidine provides a molecular beacon-like response reporting HIV-1 RT RNase H activity
pp. 1048-1056(9)
Authors: Wahba, Alexander S.; Esmaeili, Abbasali; Damha, Masad J.; Hudson, Robert H. E.

Free Content Obituary
pp. 1057-1058(2)
Authors: Gardner, Jeffrey F.; Uhlenbeck, Olke C.

Free Content jpHMM: improving the reliability of recombination prediction in HIV-1
pp. 1059-1059(1)
Authors: Schultz, Anne-Kathrin; Zhang, Ming; Bulla, Ingo; Leitner, Thomas; Korber, Bette; Morgenstern, Burkhard; Stanke, Mario

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