| | Articles Escherichia coli K-12: a cooperatively developed annotation snapshot—2005 Monica Riley, Takashi Abe, Martha B. Arnaud, Mary K.B. Berlyn, Frederick R. Blattner, Roy R. Chaudhuri, Jeremy D. Glasner, Takashi Horiuchi, Ingrid M. Keseler, Takehide Kosuge, Hirotada Mori, Nicole T. Perna, Guy Plunkett, III, Kenneth E. Rudd, Margrethe H. Serres, Gavin H. Thomas, Nicholas R. Thomson, David Wishart, and Barry L. Wanner PMCID: PMC1325200 Ddx42p—a human DEAD box protein with RNA chaperone activities Heike Uhlmann-Schiffler, Carolin Jalal, and Hans Stahl PMCID: PMC1325199 Alternative splicing regulation at tandem 3′ splice sites Martin Akerman and Yael Mandel-Gutfreund PMCID: PMC1325015 XRCC1 is phosphorylated by DNA-dependent protein kinase in response to DNA damage Nicolas Lévy, Adeline Martz, Anne Bresson, Catherine Spenlehauer, Gilbert de Murcia, and Josiane Ménissier-de Murcia PMCID: PMC1325201 Mg2+ dependency of HIV-1 reverse transcription, inhibition by nucleoside analogues and resistance Valérie Goldschmidt, Joël Didierjean, Bernard Ehresmann, Chantal Ehresmann, Catherine Isel, and Roland Marquet PMCID: PMC1325016 MaGe: a microbial genome annotation system supported by synteny results David Vallenet, Laurent Labarre, Zoé Rouy, Valérie Barbe, Stéphanie Bocs, Stéphane Cruveiller, Aurélie Lajus, Géraldine Pascal, Claude Scarpelli, and Claudine Médigue PMCID: PMC1326237 Dispersal and regulation of an adaptive mutagenesis cassette in the bacteria domain Ivan Erill, Susana Campoy, Gerard Mazon, and Jordi Barbé PMCID: PMC1326238 Evolutionary-conserved telomere-linked helicase genes of fission yeast are repressed by silencing factors, RNAi components and the telomere-binding protein Taz1 Klavs R. Hansen, Pablo Tejero Ibarra, and Geneviève Thon PMCID: PMC1326240 APOBEC3A and APOBEC3B are potent inhibitors of LTR-retrotransposon function in human cells Hal P. Bogerd, Heather L. Wiegand, Brian P. Doehle, Kira K. Lueders, and Bryan R. Cullen PMCID: PMC1326241 High incidence of rapid telomere loss in telomerase-deficient Caenorhabditis elegans Iris Cheung, Michael Schertzer, Ann Rose, and Peter M. Lansdorp PMCID: PMC1326242 TBP flanking sequences: asymmetry of binding, long-range effects and consensus sequences Hana Faiger, Marina Ivanchenko, Ilana Cohen, and Tali E. Haran PMCID: PMC1326239 Role of LrpC from Bacillus subtilis in DNA transactions during DNA repair and recombination Gema López-Torrejón, María I. Martínez-Jiménez, and Silvia Ayora PMCID: PMC1326243 Selection of primer-template sequences that bind human immunodeficiency virus reverse transcriptase with high affinity Jeffrey J. DeStefano and Jason V. Cristofaro PMCID: PMC1325207 Linking uracil base excision repair and 5-fluorouracil toxicity in yeast Lauren Seiple, Pawel Jaruga, Miral Dizdaroglu, and James T. Stivers PMCID: PMC1326247 Fluorescence of covalently attached pyrene as a general RNA folding probe Mary K. Smalley and Scott K. Silverman PMCID: PMC1326244 Real-time observation of DNA looping dynamics of Type IIE restriction enzymes NaeI and NarI Bram van den Broek, Francesco Vanzi, Davide Normanno, Francesco S. Pavone, and Gijs J.L. Wuite PMCID: PMC1326248 Oct-2 DNA binding transcription factor: functional consequences of phosphorylation and glycosylation Ishtiaq Ahmad, Daniel C. Hoessli, Evelyne Walker-Nasir, Saleem M. Rafik, Abdul R. Shakoori, and Nasir-ud-Din PMCID: PMC1326018 A new method to remove hybridization bias for interspecies comparison of global gene expression profiles uncovers an association between mRNA sequence divergence and differential gene expression in Xenopus Maureen A. Sartor, Aaron M. Zorn, Jennifer A. Schwanekamp, Danielle Halbleib, Saikumar Karyala, Michael L. Howell, Gary E. Dean, Mario Medvedovic, and Craig R. Tomlinson PMCID: PMC1325202 Application of a superword array in genome assembly Xiaoqiu Huang, Shiaw-Pyng Yang, Asif T. Chinwalla, LaDeana W. Hillier, Patrick Minx, Elaine R. Mardis, and Richard K. Wilson PMCID: PMC1325203 Resolution of a structural competition involving dimeric G-quadruplex and its C-rich complementary strand Joaquim Jaumot, Ramon Eritja, Romà Tauler, and Raimundo Gargallo PMCID: PMC1325204 Functional role of NF-IL6β and its sumoylation and acetylation modifications in promoter activation of cyclooxygenase 2 gene Ju-Ming Wang, Chiung-Yuan Ko, Lei-Chin Chen, Wen-Lin Wang, and Wen-Chang Chang PMCID: PMC1325205 MSH2 is essential for the preservation of genome integrity and prevents homeologous recombination in the moss Physcomitrella patens Bénédicte Trouiller, Didier G. Schaefer, Florence Charlot, and Fabien Nogué PMCID: PMC1325206 Brain-specific promoter and polyadenylation sites of the β-adducin pre-mRNA generate an unusually long 3′-UTR Luisa Costessi, Giulia Devescovi, Francisco E. Baralle, and Andrés F. Muro PMCID: PMC1326019 Structural and dynamic basis of a supercoiling-responsive DNA element Sung-Hun Bae, Sang Hoon Yun, Dawei Sun, Heon M. Lim, and Byong-Seok Choi PMCID: PMC1326020 A novel multifunctional factor involved in trans-splicing of chloroplast introns in Chlamydomonas Livia Merendino, Karl Perron, Michèle Rahire, Isabelle Howald, Jean-David Rochaix, and Michel Goldschmidt-Clermont PMCID: PMC1326246 The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA Michael J. Law, Michael E. Linde, Eric J. Chambers, Chris Oubridge, Phinikoula S. Katsamba, Lennart Nilsson, Ian S. Haworth, and Ite A. Laird-Offringa PMCID: PMC1326249 Hypoxic stress suppresses RNA polymerase III recruitment and tRNA gene transcription in cardiomyocytes Isabelle Ernens, Sarah J. Goodfellow, Fiona Innes, Niall S. Kenneth, Louise E. Derblay, Robert J. White, and Pamela H. Scott PMCID: PMC1326236 Cockayne syndrome group B protein has novel strand annealing and exchange activities Meltem Muftuoglu, Sudha Sharma, Tina Thorslund, Tinna Stevnsner, Martin M. Soerensen, Robert M. Brosh, Jr, and Vilhelm A. Bohr PMCID: PMC1331990 Serine/arginine-rich splicing factors belong to a class of intrinsically disordered proteins Chad Haynes and Lilia M. Iakoucheva PMCID: PMC1326245 Preferential formation of (5S,6R)-thymine glycol for oligodeoxyribonucleotide synthesis and analysis of drug binding to thymine glycol-containing DNA Tatsuhiko Shimizu, Koichiro Manabe, Shinya Yoshikawa, Yusuke Kawasaki, and Shigenori Iwai PMCID: PMC1326250 Insights into the kinetics of siRNA-mediated gene silencing from live-cell and live-animal bioluminescent imaging Derek W. Bartlett and Mark E. Davis PMCID: PMC1331994 Stabilities of HIV-1 DIS type RNA loop–loop interactions in vitro and in vivo Christina Lorenz, Nicolas Piganeau, and Renée Schroeder PMCID: PMC1331993 A new NMR solution structure of the SL1 HIV-1Lai loop–loop dimer Fabien Kieken, Françoise Paquet, Fabienne Brulé, Jacques Paoletti, and Gérard Lancelot PMCID: PMC1331991 The hepatitis B virus PRE contains a splicing regulatory element Tilman Heise, Gunhild Sommer, Kerstin Reumann, Imke Meyer, Hans Will, and Heiner Schaal PMCID: PMC1331995 TACC3 mediates the association of MBD2 with histone acetyltransferases and relieves transcriptional repression of methylated promoters Tiziana Angrisano, Francesca Lembo, Raffaela Pero, Francesco Natale, Alfredo Fusco, Vittorio E. Avvedimento, Carmelo B. Bruni, and Lorenzo Chiariotti PMCID: PMC1331987 Characterization of sequences and mechanisms through which ISE/ISS-3 regulates FGFR2 splicing Ruben H. Hovhannisyan, Claude C. Warzecha, and Russ P. Carstens PMCID: PMC1331989 Translation of chloroplast psbD mRNA in Chlamydomonas is controlled by a secondary RNA structure blocking the AUG start codon Birgit Klinkert, Ingolf Elles, and Jörg Nickelsen PMCID: PMC1331992 Methods Online Inducible model for β-six-mediated site-specific recombination in mammalian cells Pilar Servert, Javier Garcia-Castro, Vicente Díaz, Daniel Lucas, Manuel A. Gonzalez, Carlos Martínez-A, and Antonio Bernad PMCID: PMC1325017 Fast chromatin immunoprecipitation assay Joel D. Nelson, Oleg Denisenko, Pavel Sova, and Karol Bomsztyk PMCID: PMC1325209 A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria Hong-Yu Ou, Ling-Ling Chen, James Lonnen, Roy R. Chaudhuri, Ali Bin Thani, Rebecca Smith, Natalie J. Garton, Jay Hinton, Mark Pallen, Michael R. Barer, and Kumar Rajakumar PMCID: PMC1326021 TaqMan probe array for quantitative detection of DNA targets Heping Liu, Hong Wang, Zhiyang Shi, Hua Wang, Chaoyong Yang, Spering Silke, Weihong Tan, and Zuhong Lu PMCID: PMC1326252 Rapid quantitative profiling of complex microbial populations Chana Palmer, Elisabeth M. Bik, Michael B. Eisen, Paul B. Eckburg, Theodore R. Sana, Paul K. Wolber, David A. Relman, and Patrick O. Brown PMCID: PMC1326253 A systematic approach to infer biological relevance and biases of gene network structures Alexey V. Antonov, Igor V. Tetko, and Hans W. Mewes PMCID: PMC1326251 Four-base codon mediated mRNA display to construct peptide libraries that contain multiple nonnatural amino acids Norihito Muranaka, Takahiro Hohsaka, and Masahiko Sisido PMCID: PMC1325208 Corrigenda Position of the fluorescent label is a crucial factor determining signal intensity in microarray hybridizations Lei Zhang, Thomas Hurek, and Barbara Reinhold-Hurek PMCID: PMC1331988 Corrects: Lei Zhang, et al. Position of the fluorescent label is a crucial factor determining signal intensity in microarray hybridizations. Nucleic Acids Res. 2005; 33(19): e166. Enhancing the efficiency of a polymerase chain reaction using gold nanoparticles Min Li, Yu-Cheng Lin, Chao-Chin Wu, and Hsiao-Sheng Liu PMCID: PMC1331996 Corrects: Min Li, et al. Enhancing the efficiency of a PCR using gold nanoparticles. Nucleic Acids Res. 2005; 33(21): e184. |
