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ORCIDNucleic Acids Research, Volume 39
Volume 39, Number 1, January 2011
- Siu-Hong Chan
, Barry L. Stoddard, Shuang-yong Xu:
Natural and engineered nicking endonucleases - from cleavage mechanism to engineering of strand-specificity. 1-18
- Uday Sandhu, Marcin Cebula, Sara Behme, Pamela Riemer, Claas Wodarczyk, Daniel Metzger, J. Reimann, Reinhold Schirmbeck, Hansjörg Hauser, Dagmar Wirth:
Strict control of transgene expression in a mouse model for sensitive biological applications based on RMCE compatible ES cells. 1 - Coren A. Milbury, Jin Li, G. Mike Makrigiorgos:
Ice-COLD-PCR enables rapid amplification and robust enrichment for low-abundance unknown DNA mutations. 2 - Bo Chen, Ping Ji:
Visualization of the protein-coding regions with a self adaptive spectral rotation approach. 3 - Lars Steinbrück, Alice Carolyn McHardy:
Allele dynamics plots for the study of evolutionary dynamics in viral populations. 4 - Carolina E. Pardo, Ian M. Carr, Christopher J. Hoffman, Russell P. Darst, Alexander F. Markham, David T. Bonthron, Michael P. Kladde:
MethylViewer: computational analysis and editing for bisulfite sequencing and methyltransferase accessibility protocol for individual templates (MAPit) projects. 5
- Ray M. Marín, Jirí Vanícek:
Efficient use of accessibility in microRNA target prediction. 19-29 - Laurent-Philippe Albou, Olivier Poch, Dino Moras:
M-ORBIS: Mapping of mOleculaR Binding sItes and Surfaces. 30-43 - Wenyi Wang, Peidong Shen, Sreedevi Thiyagarajan, Shengrong Lin, Curtis J. Palm, Rita Horvath, Thomas Klopstock, David Cutler, Lynn Pique, Iris Schrijver, Ronald W. Davis, Michael Mindrinos, Terence P. Speed, Curt Scharfe:
Identification of rare DNA variants in mitochondrial disorders with improved array-based sequencing. 44-58
- Fuminori Sugihara, Koji Kasahara, Tetsuro Kokubo:
Highly redundant function of multiple AT-rich sequences as core promoter elements in the TATA-less RPS5 promoter of Saccharomyces cerevisiae. 59-75 - Manabu Taura, Mary Ann Suico, Ryosuke Fukuda, Tomoaki Koga, Tsuyoshi Shuto, Takashi Sato, Saori Morino-Koga, Seiji Okada, Hirofumi Kai:
MEF/ELF4 transactivation by E2F1 is inhibited by p53. 76-88 - Mayra Furlan-Magaril, Eria Rebollar, Georgina Guerrero, Almudena Fernández, Eduardo Moltó, Edgar González-Buendía, Marta Cantero, Lluis Montoliu, Félix Recillas-Targa:
An insulator embedded in the chicken α-globin locus regulates chromatin domain configuration and differential gene expression. 89-103 - Si Ho Choi, Kyu Heo, Hyang-Min Byun, Woojin An, Wange Lu, Allen S. Yang:
Identification of preferential target sites for human DNA methyltransferases. 104-118 - Josefine Stockert, Till Adhikary, Kerstin Kaddatz, Florian Finkernagel, Wolfgang Meissner, Sabine Müller-Brüsselbach, Rolf Müller:
Reverse crosstalk of TGFβ and PPARβ/δ signaling identified by transcriptional profiling. 119-131
- Changanamkandath Rajesh, Dustin K. Baker, Andrew J. Pierce, Douglas L. Pittman:
The splicing-factor related protein SFPQ/PSF interacts with RAD51D and is necessary for homology-directed repair and sister chromatid cohesion. 132-145 - Astrid S. Block-Schmidt, Stefanie Dukowic-Schulze, Kristina Wanieck, Wim Reidt, Holger Puchta:
BRCC36A is epistatic to BRCA1 in DNA crosslink repair and homologous recombination in Arabidopsis thaliana. 146-154 - Dejan Ristic, Roland Kanaar, Claire Wyman:
Visualizing RAD51-mediated joint molecules: implications for recombination mechanism and the effect of sequence heterology. 155-167 - Anna Szambowska, Marcin Pierechod, Grzegorz Wegrzyn, Monika Glinkowska:
Coupling of transcription and replication machineries in λ DNA replication initiation: evidence for direct interaction of Escherichia coli RNA polymerase and the λO protein. 168-177
- Omari J. Bandele, Xuting Wang, Michelle R. Campbell, Gary S. Pittman, Douglas A. Bell:
Human single-nucleotide polymorphisms alter p53 sequence-specific binding at gene regulatory elements. 178-189 - Hao Sun, Jiejun Wu, Priyankara Wikramasinghe, Sharmistha Pal, Ravi Gupta, Anirban Bhattacharyya, Francisco J. Agosto-Perez, Louise C. Showe, Tim Hui-Ming Huang, Ramana V. Davuluri:
Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq. 190-201
- Suman Kapoor, Gautam Das, Umesh Varshney:
Crucial contribution of the multiple copies of the initiator tRNA genes in the fidelity of tRNAfMet selection on the ribosomal P-site in Escherichia coli. 202-212 - Ariane Scoumanne, Seong Jun Cho, Jin Zhang, Xinbin Chen:
The cyclin-dependent kinase inhibitor p21 is regulated by RNA-binding protein PCBP4 via mRNA stability. 213-224 - Ester Perales-Clemente, Patricio Fernández-Silva, Rebeca Acín-Pérez, Acisclo Pérez-Martos, Jose Antonio Enríquez:
Allotopic expression of mitochondrial-encoded genes in mammals: achieved goal, undemonstrated mechanism or impossible task? 225-234
- Xin Chen, Jing-Jing Ma, Min Tan, Peng Yao, Qing-Hua Hu, Gilbert Eriani, En-Duo Wang:
Modular pathways for editing non-cognate amino acids by human cytoplasmic leucyl-tRNA synthetase. 235-247
- Amy Davidson, Krystyna Patora-Komisarska, John A. Robinson, Gabriele Varani:
Essential structural requirements for specific recognition of HIV TAR RNA by peptide mimetics of Tat protein. 248-256 - Julia Starega-Roslan, Jacek Krol, Edyta Koscianska, Piotr Kozlowski, Wojciech J. Szlachcic, Krzysztof Sobczak, Wlodzimierz J. Krzyzosiak:
Structural basis of microRNA length variety. 257-268 - Christine S. Lee, Timothy P. Mui, Scott K. Silverman:
Improved deoxyribozymes for synthesis of covalently branched DNA and RNA. 269-279 - Coralie Carron, Marie-Françoise O'Donohue, Valérie Choesmel, Marlène Faubladier, Pierre-Emmanuel Gleizes:
Analysis of two human pre-ribosomal factors, bystin and hTsr1, highlights differences in evolution of ribosome biogenesis between yeast and mammals. 280-291 - Aron M. Yoffe, Peter Prinsen, William M. Gelbart, Avinoam Ben-Shaul:
The ends of a large RNA molecule are necessarily close. 292-299 - Pei-Yu Liao, Yong Seok Choi, Jonathan D. Dinman, Kelvin H. Lee:
The many paths to frameshifting: kinetic modelling and analysis of the effects of different elongation steps on programmed -1 ribosomal frameshifting. 300-312
- Mathieu Rappas, Antony W. Oliver, Laurence H. Pearl:
Structure and function of the Rad9-binding region of the DNA-damage checkpoint adaptor TopBP1. 313-324 - Seiji Komeda, Tinoush Moulaei, Masahiko Chikuma, Akira Odani, Ralph Kipping, Nicholas P. Farrell, Loren Dean Williams:
The phosphate clamp: a small and independent motif for nucleic acid backbone recognition. 325-336 - Bradley M. Lunde, Maximilian Hörner, Anton Meinhart:
Structural insights into cis element recognition of non-polyadenylated RNAs by the Nab3-RRM. 337-346 - Israel S. Fernández, Akio Yamashita, Ernesto Arias-Palomo, Yumi Bamba, Ruben A. Bartolomé, M. Angeles Canales, Joaquín Teixidó, Shigeo Ohno, Oscar Llorca:
Characterization of SMG-9, an essential component of the nonsense-mediated mRNA decay SMG1C complex. 347-358
- Ting Li, Sheng Huang, Wen Zhi Jiang, David Wright, Martin H. Spalding, Donald P. Weeks, Bing Yang:
TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain. 359-372 - Damian Ittig, Anna-Barbara Gerber, Christian J. Leumann:
Position-dependent effects on stability in tricyclo-DNA modified oligonucleotide duplexes. 373-380 - Ankit Gupta, Xiangdong Meng, Lihua Julie Zhu, Nathan D. Lawson, Scot A. Wolfe:
Zinc finger protein-dependent and -independent contributions to the in vivo off-target activity of zinc finger nucleases. 381-392
Volume 39, Number 2, January 2011
- Pieter Meysman, Thanh Hai Dang, Kris Laukens, Riet De Smet, Yan Wu, Kathleen Marchal, Kristof Engelen:
Use of structural DNA properties for the prediction of transcription-factor binding sites in Escherichia coli. 6 - Yumi Kanegae, Miho Terashima, Saki Kondo, Hiromitsu Fukuda, Aya Maekawa, Zheng Pei, Izumu Saito:
High-level expression by tissue/cancer-specific promoter with strict specificity using a single-adenoviral vector. 7 - Henrik Johansson, Magnus Isaksson, Elin Falk Sörqvist, F. Roos, Johan Stenberg, Tobias Sjöblom, Johan Botling, Patrick Micke, Karolina Edlund, S. Fredriksson, Hanna Göransson Kultima, Olle Ericsson, Mats Nilsson:
Targeted resequencing of candidate genes using selector probes. 8 - Soohyun Lee, Chae Hwa Seo, Byungho Lim, Jin Ok Yang, Jeongsu Oh, Minjin Kim, Sooncheol Lee, Byungwook Lee, Changwon Kang, Sanghyuk Lee:
Accurate quantification of transcriptome from RNA-Seq data by effective length normalization. 9 - Yumin Teng, Mark Bennett, Katie E. Evans, Huayun Zhuang-Jackson, Andy Higgs, Simon H. Reed, Raymond Waters:
A novel method for the genome-wide high resolution analysis of DNA damage. 10 - Dorjbal Dorjsuren, Daemyung Kim, David J. Maloney, David M. Wilson III, Anton Simeonov:
Complementary non-radioactive assays for investigation of human flap endonuclease 1 activity. 11
- Michiaki Hamada, Kengo Sato, Kiyoshi Asai:
Improving the accuracy of predicting secondary structure for aligned RNA sequences. 393-402 - Dong Dong, Xiaojian Shao, Naiyang Deng, Zhaolei Zhang:
Gene expression variations are predictive for stochastic noise. 403-413
- Onuma Chumsakul, Hiroki Takahashi, Taku Oshima, Takahiro Hishimoto, Shigehiko Kanaya, Naotake Ogasawara, Shu Ishikawa:
Genome-wide binding profiles of the Bacillus subtilis transition state regulator AbrB and its homolog Abh reveals their interactive role in transcriptional regulation. 414-428 - Qiao Jing Lew, Kai Ling Chu, Jialing Lee, Poh Ling Koh, Vikneswari Rajasegaran, Jin Yuan Teo, Sheng-Hao Chao:
PCAF interacts with XBP-1S and mediates XBP-1S-dependent transcription. 429-439 - Levin Böhlig, Maik Friedrich, Kurt Engeland:
p53 activates the PANK1/miRNA-107 gene leading to downregulation of CDK6 and p130 cell cycle proteins. 440-453 - Yan Gao, Jonathan Schug, Lindsay B. McKenna, John Le Lay, Klaus H. Kaestner, Linda E. Greenbaum:
Tissue-specific regulation of mouse MicroRNA genes in endoderm-derived tissues. 454-463 - Simone C. Wiesler, Robert O. J. Weinzierl:
The linker domain of basal transcription factor TFIIB controls distinct recruitment and transcription stimulation functions. 464-474 - Weifeng Huang, Huili Liu, Tao Wang, Tiantian Zhang, Juntao Kuang, Yu Luo, Stephen S. M. Chung, Li Yuan, James Y. Yang:
Tonicity-responsive microRNAs contribute to the maximal induction of osmoregulatory transcription factor OREBP in response to high-NaCl hypertonicity. 475-485 - Claudio Cantú, Vito Grande, Ilaria Alborelli, Letizia Cassinelli, Ileana Cantu', Maria Teresa Colzani, Rossella Ierardi, Luisa Ronzoni, Maria Domenica Cappellini, Giuliana Ferrari, Sergio Ottolenghi, Antonella Ronchi:
A highly conserved SOX6 double binding site mediates SOX6 gene downregulation in erythroid cells. 486-501 - Marjo Malinen, Jussi Ryynänen, Merja Heinäniemi, Sami Väisänen, Carsten Carlberg:
Cyclical regulation of the insulin-like growth factor binding protein 3 gene in response to 1α, 25-dihydroxyvitamin D3. 502-512 - Florent Hubé, Guillaume Velasco, Jérôme Rollin, Denis Furling, Claire Francastel:
Steroid receptor RNA activator protein binds to and counteracts SRA RNA-mediated activation of MyoD and muscle differentiation. 513-525
- Paul M. Rindler, Sanjay I. Bidichandani:
Role of transcript and interplay between transcription and replication in triplet-repeat instability in mammalian cells. 526-535 - Rongjuan Mi, Anne K. Abole, Weiguo Cao:
Dissecting endonuclease and exonuclease activities in endonuclease V from Thermotoga maritima. 536-544 - Ronald Lebofsky, Antoine M. van Oijen, Johannes C. Walter:
DNA is a co-factor for its own replication in Xenopus egg extracts. 545-555
- Peter A. C. 't Hoen, Michael Hirsch, Emile J. de Meijer, Renée X. de Menezes, Gert-Jan B. van Ommen, Johan T. den Dunnen:
mRNA degradation controls differentiation state-dependent differences in transcript and splice variant abundance. 556-566 - Georgii A. Bazykin, Alex V. Kochetov:
Alternative translation start sites are conserved in eukaryotic genomes. 567-577 - Song Liu, Lan Lin, Peng Jiang, Dan Wang, Yi Xing:
A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species. 578-588
- Ryuichi Sugiyama, Masaaki Hayafune, Yuichiro Habu, Norio Yamamoto, Hiroshi Takaku:
HIV-1 RT-dependent DNAzyme expression inhibits HIV-1 replication without the emergence of escape viruses. 589-598 - Boris Eliseev, Polina Kryuchkova, Elena Alkalaeva, Ludmila Frolova:
A single amino acid change of translation termination factor eRF1 switches between bipotent and omnipotent stop-codon specificity. 599-608
- Shanen M. Sherrer, Kevin A. Fiala, Jason D. Fowler, Sean A. Newmister, John M. Pryor, Zucai Suo:
Quantitative analysis of the efficiency and mutagenic spectra of abasic lesion bypass catalyzed by human Y-family DNA polymerases. 609-622 - Marika Midon, Patrick Schäfer, Alfred Pingoud, Mahua Ghosh, Andrea F. Moon, Matthew J. Cuneo, Robert E. London, Gregor Meiss:
Mutational and biochemical analysis of the DNA-entry nuclease EndA from Streptococcus pneumoniae. 623-634 - Antonio Totaro, Fabrizio Renzi, Giorgio La Fata, Claudia Mattioli, Monika Raabe, Henning Urlaub, Tilmann Achsel:
The human Pat1b protein: a novel mRNA deadenylation factor identified by a new immunoprecipitation technique. 635-647
- Luis G. Morello, Cédric Hesling, Patrícia P. Coltri, Beatriz A. Castilho, Ruth Rimokh, Nilson I. T. Zanchin:
The NIP7 protein is required for accurate pre-rRNA processing in human cells. 648-665 - Sergio Barberan-Soler, Pedro Medina, Jeffrey Estella, James Williams, Alan M. Zahler:
Co-regulation of alternative splicing by diverse splicing factors in Caenorhabditis elegans. 666-674 - Markus Brameier, Astrid Herwig, Richard Reinhardt, Lutz Walter, Jens Gruber:
Human box C/D snoRNAs with miRNA like functions: expanding the range of regulatory RNAs. 675-686 - Birthe Meineke, Beate Schwer, Raffael Schaffrath, Stewart Shuman:
Determinants of eukaryal cell killing by the bacterial ribotoxin PrrC. 687-700 - Kevin P. Jensen, Jonathan Covault:
Human miR-1271 is a miR-96 paralog with distinct non-conserved brain expression pattern. 701-711
- Éva Scheuring Vanamee, Hector Viadiu, Siu-Hong Chan, Ajay Ummat, Adrian M. Hartline, Shuang-yong Xu, Aneel K. Aggarwal:
Asymmetric DNA recognition by the OkrAI endonuclease, an isoschizomer of BamHI. 712-719 - Jaroslav Malina, Jana Kasparkova, Nicholas P. Farrell, Viktor Brabec:
Walking of antitumor bifunctional trinuclear PtII complex on double-helical DNA. 720-728 - Inés G. Muñoz, Jesús Prieto, Sunita Subramanian, Javier Coloma, Pilar Redondo, Maider Villate, Nekane Merino, Marco Marenchino, Marco D'Abramo, Francesco L. Gervasio, Sylvestre Grizot, Fayza Daboussi, Julianne Smith, Isabelle Chion-Sotinel, Frédéric Pâques, Philippe Duchateau, Andreu Alibés, Francois Stricher, Luis Serrano, Francisco J. Blanco, Guillermo Montoya:
Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus. 729-743 - Malgorzata Firczuk, Marek Wojciechowski, Honorata Czapinska, Matthias Bochtler:
DNA intercalation without flipping in the specific ThaI-DNA complex. 744-754 - Nicole M. Baker, Steven Weigand, Sarah Maar-Mathias, Alfonso Mondragón:
Solution structures of DNA-bound gyrase. 755-766 - Elisa Fadda, Régis Pomès:
On the molecular basis of uracil recognition in DNA: comparative study of T-A versus U-A structure, dynamics and open base pair kinetics. 767-780
Volume 39, Number Database-Issue, January 2011
- Michael Y. Galperin, Guy Cochrane:
The 2011 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection. 1-6 - Pascale Gaudet, Amos Bairoch, Dawn Field, Susanna-Assunta Sansone, Chris F. Taylor, Teresa K. Attwood, Alex Bateman, Judith A. Blake, Carol J. Bult, J. Michael Cherry, Rex L. Chisholm, Guy Cochrane, Charles E. Cook, Janan T. Eppig, Michael Y. Galperin, Robert Gentleman, Carole A. Goble, Takashi Gojobori, John M. Hancock, Douglas G. Howe, Tadashi Imanishi, Janet Kelso, David Landsman, Suzanna E. Lewis, Ilene Karsch-Mizrachi, Sandra E. Orchard, B. F. Francis Ouellette, Shoba Ranganathan, Lorna J. Richardson, Philippe Rocca-Serra, Paul N. Schofield, Damian Smedley, Christopher Southan, Tin Wee Tan, Tatiana A. Tatusova, Patricia L. Whetzel, Owen White, Chisato Yamasaki:
Towards BioDBcore: a community-defined information specification for biological databases. 7-10 - Richard J. Roberts, Yi-Chien Chang, Zhenjun Hu, John Rachlin, Brian P. Anton, Revonda M. Pokrzywa, Han-Pil Choi, Lina L. Faller, Jyotsna Guleria, Genevieve Housman, Niels Klitgord, Varun Mazumdar, Mark G. McGettrick, Lais Osmani, Rajeswari Swaminathan, Kevin R. Tao, Stanley Letovsky, Dennis Vitkup, Daniel Segrè, Steven L. Salzberg, Charles DeLisi, Martin Steffen, Simon Kasif:
COMBREX: a project to accelerate the functional annotation of prokaryotic genomes. 11-14 - Guy Cochrane, Ilene Karsch-Mizrachi, Yasukazu Nakamura:
The International Nucleotide Sequence Database Collaboration. 15-18 - Rasko Leinonen, Hideaki Sugawara, Martin Shumway:
The Sequence Read Archive. 19-21 - Eli Kaminuma, Takehide Kosuge, Yuichi Kodama, Hideo Aono, Jun Mashima, Takashi Gojobori, Hideaki Sugawara, Osamu Ogasawara, Toshihisa Takagi, Kousaku Okubo, Yasukazu Nakamura:
DDBJ progress report. 22-27 - Rasko Leinonen, Ruth Akhtar, Ewan Birney, Lawrence Bower, Ana Cerdeño-Tárraga, Ying Cheng, Iain Cleland, Nadeem Faruque, Neil Goodgame, Richard Gibson, Gemma Hoad, Mikyung Jang, Nima Pakseresht, Sheila Plaister, Rajesh Radhakrishnan, Kethi Reddy, Siamak Sobhany, Petra ten Hoopen, Robert Vaughan, Vadim Zalunin, Guy Cochrane:
The European Nucleotide Archive. 28-31 - Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, Eric W. Sayers:
GenBank. 32-37 - 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, Ian M. Fingerman, 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 R. Panchenko, Lon Phan, Kim D. Pruitt, Gregory D. Schuler, Edwin Sequeira, Stephen T. Sherry, Martin Shumway, Karl Sirotkin, Douglas J. Slotta, Alexandre Souvorov, Grigory Starchenko, Tatiana A. Tatusova, Lukas Wagner, Yanli Wang, W. John Wilbur, Eugene Yaschenko, Jian Ye:
Database resources of the National Center for Biotechnology Information. 38-51 - Donna R. Maglott, James Ostell, Kim D. Pruitt, Tatiana A. Tatusova:
Entrez Gene: gene-centered information at NCBI. 52-57 - Johanna R. McEntyre, Sophia Ananiadou, Stephen Andrews, William J. Black, Richard Boulderstone, Paula Buttery, David Chaplin, Sandeepreddy Chevuru, Norman Cobley, Lee-Ann Coleman, Paul Davey, Bharti Gupta, Lesley Haji-Gholam, Craig Hawkins, Alan Horne, Simon J. Hubbard, Jee-Hyub Kim, Ian Lewin, Vic Lyte, Ross MacIntyre, Sami Mansoor, Linda Mason, John McNaught, Elizabeth Newbold, Chikashi Nobata, Ernest Ong, Sharmila Pillai, Dietrich Rebholz-Schuhmann, Heather Rosie, Rob Rowbotham, C. J. Rupp, Peter Stoehr, Philip Vaughan:
UKPMC: a full text article resource for the life sciences. 58-65 - Andreas R. Gruber, Jörg Fallmann, Franz Kratochvill, Pavel Kovarik, Ivo L. Hofacker:
AREsite: a database for the comprehensive investigation of AU-rich elements. 66-69 - Carlos Lloréns, Ricardo Futami, Laura Covelli, Laura Domínguez-Escribá, Jose M. Viu, Daniel Tamarit, José Aguilar-Rodríguez, Miguel Vicente-Ripolles, Gonzalo Fuster, Guillermo P. Bernet, Florian Maumus, Alfonso Muñoz-Pomer Fuentes, José M. Sempere, Amparo Latorre, Andrés Moya:
The Gypsy Database (GyDB) of mobile genetic elements: release 2.0. 70-74 - Michael Hackenberg, Guillermo Barturen, José L. Oliver:
NGSmethDB: a database for next-generation sequencing single-cytosine-resolution DNA methylation data. 75-79 - Pier Luigi Martelli, Mattia D'Antonio, Paola Bonizzoni, Tiziana Castrignanò, Anna Maria D'Erchia, Paolo D'Onorio De Meo, Piero Fariselli, Michele Finelli, Flavio Licciulli, Marina Mangiulli, Flavio Mignone, Giulio Pavesi, Ernesto Picardi, Raffaella Rizzi, Ivan Rossi, Alessio Valletti, Andrea Zauli, Federico Zambelli, Rita Casadio, Graziano Pesole:
ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing. 80-85 - Emanuele Buratti, Martin Chivers, Gyulin Hwang, Igor Vorechovsky:
DBASS3 and DBASS5: databases of aberrant 3′- and 5′-splice sites. 86-91 - Ravi Gupta, Anirban Bhattacharyya, Francisco J. Agosto-Perez, Priyankara Wikramasinghe, Ramana V. Davuluri:
MPromDb update 2010: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-seq experimental data. 92-97 - Socorro Gama-Castro, Heladia Salgado, Martín Peralta-Gil, Alberto Santos-Zavaleta, Luis Muñiz-Rascado, Hilda Solano-Lira, Verónica Jiménez-Jacinto, Verena Weiss, Jair S. García-Sotelo, Alejandra López-Fuentes, Liliana Porrón-Sotelo, Shirley Alquicira-Hernández, Alejandra Medina-Rivera, Irma Martínez-Flores, Kevin Alquicira-Hernández, Ruth Martínez-Adame, César Bonavides-Martínez, Juan Miranda-Ríos, Araceli M. Huerta, Alfredo Mendoza-Vargas, Leonardo Collado-Torres, Blanca Taboada, Leticia Vega-Alvarado, Maricela Olvera, Leticia Olvera, Ricardo Grande, Enrique Morett, Julio Collado-Vides:
RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units). 98-105 - Ulf Schaefer, Sebastian Schmeier, Vladimir B. Bajic:
TcoF-DB: dragon database for human transcription co-factors and transcription factor interacting proteins. 106-110 - Lihua Julie Zhu, Ryan G. Christensen, Majid Kazemian, Christopher J. Hull, Metewo Selase Enuameh, Matthew D. Basciotta, Jessie A. Brasefield, Cong Zhu, Yuna Asriyan, David S. Lapointe, Saurabh Sinha, Scot A. Wolfe, Michael H. Brodsky:
FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system. 111-117 - Steven M. Gallo, Dave T. Gerrard, David Miner, Michael Simich, Benjamin Des Soye, Casey M. Bergman, Marc S. Halfon:
REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila. 118-123 - Kimberly Robasky, Martha L. Bulyk:
UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions. 124-128 - Anirban Mitra, Anil K. Kesarwani, Debnath Pal, Valakunja Nagaraja:
WebGeSTer DB - a transcription terminator database. 129-135 - Dário Abdulrehman, Pedro T. Monteiro, Miguel C. Teixeira, Nuno P. Mira, Artur B. Lourenço, Sandra Costa dos Santos, Tânia Rodrigues Cabrito, Alexandre P. Francisco, Sara C. Madeira, Ricardo Santos Aires, Arlindo L. Oliveira, Isabel Sá-Correia, Ana T. Freitas:
YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface. 136-140 - Paul P. Gardner, Jennifer Daub, John G. Tate, Benjamin L. Moore, Isabelle H. Osuch, Sam Griffiths-Jones, Robert D. Finn, Eric P. Nawrocki, Diana L. Kolbe, Sean R. Eddy, Alex Bateman:
Rfam: Wikipedia, clans and the "decimal" release. 141-145 - Paulo P. Amaral, Michael B. Clark, Dennis K. Gascoigne, Marcel E. Dinger, John S. Mattick:
lncRNAdb: a reference database for long noncoding RNAs. 146-151 - Ana Kozomara, Sam Griffiths-Jones:
miRBase: integrating microRNA annotation and deep-sequencing data. 152-157 - Sooyoung Cho, Yukyung Jun, Sanghyun Lee, Hyung-Seok Choi, Sungchu