Nucleic Acids Research, Volume 39

Volume 39, Number 1, January 2011

Survey and Summary

• 
  Siu-Hong Chan, Barry L. Stoddard, Shuang-yong Xu:
  Natural and engineered nicking endonucleases - from cleavage mechanism to engineering of strand-specificity. 1-18

Methods Online

• 
  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

Computational Biology

• 
  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

Gene Regulation, Chromatin and Epigenetics

• 
  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

Genome Integrity, Repair and Replication

• 
  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

Genomics

• 
  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

Molecular Biology

• 
  Suman Kapoor, Gautam Das, Umesh Varshney:
  Crucial contribution of the multiple copies of the initiator tRNA genes in the fidelity of tRNA^fMet 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

Nucleic Acid Enzymes

• 
  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

Rna

• 
  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

Structural Biology

• 
  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

Synthetic Biology and Chemistry

• 
  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

Methods Online

• 
  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

Computational Biology

• 
  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

Gene Regulation, Chromatin and Epigenetics

• 
  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

Genome Integrity, Repair and Replication

• 
  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

Genomics

• 
  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

Molecular Biology

• 
  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

Nucleic Acid Enzymes

• 
  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

Rna

• 
  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

Structural Biology

• 
  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 Pt^II 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

Articles

• 
  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, Sungchul Jung, Youngjun Jang, Charny Park, Sangok Kim, Sanghyuk Lee, Wan Kyu Kim:
  miRGator v2.0 : an integrated system for functional investigation of microRNAs. 158-162
• 
  Sheng-Da Hsu, Feng-Mao Lin, Wei-Yun Wu, Chao Liang, Wei-Chih Huang, Wen-Ling Chan, Wen-Ting Tsai, Goun-Zhou Chen, Chia-Jung Lee, Chih-Min Chiu, Chia-Hung Chien, Ming-Chia Wu, Chi-Ying F. Huang, Ann-Ping Tsou, Hsien-Da Huang:
  miRTarBase: a database curates experimentally validated microRNA-target interactions. 163-169
• 
  Koray D. Kaya, Gökhan Karakülah, Cengiz M. Yakicier, Aybar C. Acar, Özlen Konu:
  mESAdb: microRNA Expression and Sequence Analysis Database. 170-180
• 
  Yijun Meng, Lingfeng Gou, Dijun Chen, Chuanzao Mao, Yongfeng Jin, Ping Wu, Ming Chen:
  PmiRKB: a plant microRNA knowledge base. 181-187
• 
  Naama Elefant, Amnon Berger, Harel Shein, Matan Hofree, Hanah Margalit, Yael Altuvia:
  RepTar: a database of predicted cellular targets of host and viral miRNAs. 188-194
• 
  William A. Cantara, Pamela F. Crain, Jef Rozenski, James A. McCloskey, Kimberly A. Harris, Xiaonong Zhang, Franck A. P. Vendeix, Daniele Fabris, Paul F. Agris:
  The RNA modification database, RNAMDB: 2011 update. 195-201
• 
  Jian-Hua Yang, Jun-Hao Li, Peng Shao, Hui Zhou, Yue-Qin Chen, Liang-Hu Qu:
  starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data. 202-209
• 
  Takashi Abe, Toshimichi Ikemura, Junichi Sugahara, Akio Kanai, Yasuo Ohara, Hiroshi Uehara, Makoto Kinouchi, Shigehiko Kanaya, Yuko Yamada, Akira Muto, Hachiro Inokuchi:
  tRNADB-CE 2011: tRNA gene database curated manually by experts. 210-213
• 
  Ongoing and future developments at the Universal Protein Resource. 214-219
• 
  Hans-Werner Mewes, Andreas Ruepp, Fabian J. Theis, Thomas Rattei, Mathias C. Walter, Dmitrij Frishman, Karsten Suhre, Manuel Spannagl, Klaus F. X. Mayer, Volker Stümpflen, Alexey V. Antonov:
  MIPS: curated databases and comprehensive secondary data resources in 2010. 220-224
• 
  Aron Marchler-Bauer, Shennan Lu, John B. Anderson, Farideh Chitsaz, Myra K. Derbyshire, Carol DeWeese-Scott, Jessica H. Fong, Lewis Y. Geer, Renata C. Geer, Noreen R. Gonzales, Marc Gwadz, David I. Hurwitz, John D. Jackson, Zhaoxi Ke, Christopher J. Lanczycki, Fu Lu, Gabriele H. Marchler, Mikhail Mullokandov, Marina V. Omelchenko, Cynthia L. Robertson, James S. Song, Narmada Thanki, Roxanne A. Yamashita, Dachuan Zhang, Naigong Zhang, Chanjuan Zheng, Stephen H. Bryant:
  CDD: a Conserved Domain Database for the functional annotation of proteins. 225-229
• 
  Shruti Rastogi, Burkhard Rost:
  LocDB: experimental annotations of localization for Homo sapiens and Arabidopsis thaliana. 230-234
• 
  Emilie Chautard, Marie Fatoux-Ardore, Lionel Ballut, Nicolas Thierry-Mieg, Sylvie Ricard-Blum:
  MatrixDB, the extracellular matrix interaction database. 235-240
• 
  Nancy Y. Yu, Matthew R. Laird, Cory Spencer, Fiona S. L. Brinkman:
  PSORTdb - an expanded, auto-updated, user-friendly protein subcellular localization database for Bacteria and Archaea. 241-244
• 
  Mohsen Khorshid, Christoph Rodak, Mihaela Zavolan:
  CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins. 245-252
• 
  Florian Gnad, Jeremy Gunawardena, Matthias Mann:
  PHOSIDA 2011: the posttranslational modification database. 253-260
• 
  Holger Dinkel, Claudia Chica, Allegra Via, Cathryn M. Gould, Lars Juhl Jensen, Toby J. Gibson, Francesca Diella:
  Phospho.ELM: a database of phosphorylation sites - update 2011. 261-267
• 
  Andreas Zanzoni, Daniel Carbajo, Francesca Diella, Pier Federico Gherardini, Anna Tramontano, Manuela Helmer-Citterich, Allegra Via:
  Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites. 268-271
• 
  Amy L. Robertson, Mark A. Bate, Steve G. Androulakis, Stephen P. Bottomley, Ashley M. Buckle:
  PolyQ: a database describing the sequence and domain context of polyglutamine repeats in proteins. 272-276
• 
  Benjamin A. Lewis, Rasna R. Walia, Michael Terribilini, Jeff Ferguson, Charles Zheng, Vasant G. Honavar, Drena Dobbs:
  PRIDB: a protein-RNA interface database. 277-282
• 
  Robert M. Waterhouse, Evgeny M. Zdobnov, Fredrik Tegenfeldt, Jia Li, Evgenia V. Kriventseva:
  OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011. 283-288
• 
  Adrian M. Altenhoff, Adrian Schneider, Gaston H. Gonnet, Christophe Dessimoz:
  OMA 2011: orthology inference among 1000 complete genomes. 289-294
• 
  Daniel Park, Rohit Singh, Michael Baym, Chung-Shou Liao, Bonnie Berger:
  IsoBase: a database of functionally related proteins across PPI networks. 295-300
• 
  Kate B. Cook, Hilal Kazan, Khalid Zuberi, Quaid Morris, Timothy R. Hughes:
  RBPDB: a database of RNA-binding specificities. 301-308
• 
  Bas Vroling, Marijn P. A. Sanders, Coos Baakman, Annika Borrmann, Stefan Verhoeven, Jan P. G. Klomp, Laerte Oliveira, Jacob de Vlieg, Gert Vriend:
  GPCRDB: information system for G protein-coupled receptors. 309-319
• 
  Daiane C. F. Golbert, Leandra Linhares-Lacerda, Luiz Gonzaga Almeida, Eliane Correa-de-Santana, Alice R. de Oliveira, Alex S. Mundstein, Wilson Savino, Ana T. R. de Vasconcelos:
  Laminin database: a tool to retrieve high-throughput and curated data for studies on laminins. 320-323
• 
  Konstantinos D. Tsirigos, Pantelis G. Bagos, Stavros J. Hamodrakas:
  OMPdb: a database of β-barrel outer membrane proteins from Gram-negative bacteria. 324-331
• 
  Laura Soito, Chris Williamson, Stacy T. Knutson, Jacquelyn S. Fetrow, Leslie B. Poole, Kimberly J. Nelson:
  PREX: PeroxiRedoxin classification indEX, a database of subfamily assignments across the diverse peroxiredoxin family. 332-337
• 
  Anja Jankowsky, Ulf-Peter Guenther, Eckhard Jankowsky:
  The RNA helicase database. 338-341
• 
  David C. Cantu, Yingfei Chen, Matthew L. Lemons, Peter J. Reilly:
  ThYme: a database for thioester-active enzymes. 342-346
• 
  Allan Lo, Cheng-Wei Cheng, Yi-Yuan Chiu, Ting-Yi Sung, Wen-Lian Hsu:
  TMPad: an integrated structural database for helix-packing folds in transmembrane proteins. 347-355
• 
  Young-Cheul Shin, Soo-Yong Shin, Insuk So, Dongseop Kwon, Ju-Hong Jeon:
  TRIP Database: a manually curated database of protein-protein interactions for mammalian TRP channels. 356-361
• 
  Warren J. Gallin, Patrick A. Boutet:
  VKCDB: voltage-gated K⁺ channel database updated and upgraded. 362-366
• 
  Olivier Taboureau, Sonny Kim Nielsen, Karine Audouze, Nils Weinhold, Daniel Edsgärd, Francisco S. Roque, Irene Kouskoumvekaki, Alina Bora, Ramona Curpan, Thomas Skøt Jensen, Søren Brunak, Tudor I. Oprea:
  ChemProt: a disease chemical biology database. 367-372
• 
  René Ranzinger, Stephan Herget, Claus-Wilhelm von der Lieth, Martin Frank:
  GlycomeDB - a unified database for carbohydrate structures. 373-376
• 
  Jessica Ahmed, Saskia Preissner, Mathias Dunkel, Catherine L. Worth, Andreas Eckert, Robert Preissner:
  SuperSweet - a resource on natural and artificial sweetening agents. 377-382
• 
  Regina Z. Cer, Kevin H. Bruce, Uma Mudunuri, Ming Yi, Natalia Volfovsky, Brian T. Luke, Albino Bacolla, Jack R. Collins, Robert M. Stephens:
  Non-B DB: a database of predicted non-B DNA-forming motifs in mammalian genomes. 383-391
• 
  Peter W. Rose, Bojan Beran, Chunxiao Bi, Wolfgang Bluhm, Dimitris Dimitropoulos, David S. Goodsell, Andreas Prlic, Martha Quesada, Greg B. Quinn, John D. Westbrook, Jasmine Young, Benjamin T. Yukich, Christine Zardecki, Helen M. Berman, Philip E. Bourne:
  The RCSB Protein Data Bank: redesigned web site and web services. 392-401
• 
  Sameer Velankar, Younes Alhroub, Anaëlle Alili, Christoph Best, Harry Boutselakis, Ségolène Caboche, Matthew J. Conroy, Jose M. Dana, Glen van Ginkel, Adel Golovin, Swanand P. Gore, Aleksandras Gutmanas, Pauline Haslam, Miriam Hirshberg, Melford John, Ingvar C. Lagerstedt, Saqib Mir, Laurence E. Newman, Thomas J. Oldfield, Christopher J. Penkett, Jorge Pineda-Castillo, Luana Rinaldi, Gaurav Sahni, Grégoire Sawka, Sanchayita Sen, Robert A. Slowley, Alan W. Sousa da Silva, Antonio Suarez-Uruena, Jawahar Swaminathan, Martyn F. Symmons, Wim F. Vranken, Michael E. Wainwright, Gerard J. Kleywegt:
  PDBe: Protein Data Bank in Europe. 402-410
• 
  Robbie P. Joosten, Tim A. H. te Beek, Elmar Krieger, Maarten L. Hekkelman, Rob W. W. Hooft, Reinhard Schneider, Chris Sander, Gert Vriend:
  A series of PDB related databases for everyday needs. 411-419
• 
  Alison L. Cuff, Ian Sillitoe, Tony E. Lewis, Andrew B. Clegg, Robert Rentzsch, Nicholas Furnham, Marialuisa Pellegrini-Calace, David T. Jones, Janet M. Thornton, Christine A. Orengo:
  Extending CATH: increasing coverage of the protein structure universe and linking structure with function. 420-426
• 
  David A. de Lima Morais, Hai Fang, Owen J. L. Rackham, Derek Wilson, Ralph Pethica, Cyrus Chothia, Julian Gough:
  SUPERFAMILY 1.75 including a domain-centric gene ontology method. 427-434
• 
  Peter Vanhee, Erik Verschueren, Lies Baeten, Francois Stricher, Luis Serrano, Frederic Rousseau, Joost Schymkowitz:
  BriX: a database of protein building blocks for structural analysis, modeling and design. 435-442
• 
  Mateusz Sikora, Joanna I. Sulkowska, Bartlomiej S. Witkowski, Marek Cieplak:
  BSDB: the biomolecule stretching database. 443-450
• 
  Do-Nyun Kim, Josiah Altschuler, Campbell Strong, Gaël McGill, Mark Bathe:
  Conformational dynamics data bank: a database for conformational dynamics of proteins and supramolecular protein assemblies. 451-455
• 
  Catherine L. Lawson, Matthew L. Baker, Christoph Best, Chunxiao Bi, Matthew T. Dougherty, Powei Feng, Glen van Ginkel, Batsal Devkota, Ingvar C. Lagerstedt, Steven J. Ludtke, Richard H. Newman, Thomas J. Oldfield, Ian Rees, Gaurav Sahni, Raul Sala, Sameer Velankar, Joe D. Warren, John D. Westbrook, Kim Henrick, Gerard J. Kleywegt, Helen M. Berman, Wah Chiu:
  EMDataBank.org: unified data resource for CryoEM. 456-464
• 
  Ursula Pieper, Benjamin M. Webb, David T. Barkan, Dina Schneidman-Duhovny, Avner Schlessinger, Hannes Braberg, Zheng Yang, Elaine C. Meng, Eric F. Pettersen, Conrad C. Huang, Ruchira S. Datta, Parthasarathy Sampathkumar, Mallur S. Madhusudhan, Kimmen Sjölander, Thomas E. Ferrin, Stephen K. Burley, Andrej Sali:
  ModBase, a database of annotated comparative protein structure models, and associated resources. 465-474
• 
  Ezequiel I. Juritz, Sebastian Fernandez Alberti, Gustavo D. Parisi:
  PCDB: a database of protein conformational diversity. 475-479
• 
  Lee Whitmore, Benjamin Woollett, Andrew J. Miles, D. P. Klose, Robert W. Janes, B. A. Wallace:
  PCDDB: the protein circular dichroism data bank, a repository for circular dichroism spectral and metadata. 480-486
• 
  Chie Motono, Junichi Nakata, Ryotaro Koike, Kana Shimizu, Matsuyuki Shirota, Takayuki Amemiya, Kentaro Tomii, Nozomi Nagano, Naofumi Sakaya, Kiyotaka Misoo, Miwa Sato, Akinori Kidera, Hidekazu Hiroaki, Tsuyoshi Shirai, Kengo Kinoshita, Tamotsu Noguchi, Motonori Ota:
  SAHG, a comprehensive database of predicted structures of all human proteins. 487-493
• 
  Kyle Ellrott, Christian M. Zmasek, Dana Weekes, S. Sri Krishna, Constantina Bakolitsa, Adam Godzik, John C. Wooley:
  TOPSAN: a dynamic web database for structural genomics. 494-496
• 
  Fiona M. McCarthy, Cathy R. Gresham, Teresia J. Buza, Philippe Chouvarine, Lakshmi R. Pillai, Ranjit Kumar, Seval Ozkan, Hui Wang, Prashanti Manda, Tony Arick, Susan M. Bridges, Shane C. Burgess:
  AgBase: supporting functional modeling in agricultural organisms. 497-506
• 
  Marion Gremse, Antje Chang, Ida Schomburg, Andreas Grote, Maurice Scheer, Christian Ebeling, Dietmar Schomburg:
  The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources. 507-513
• 
  Ruth L. Seal, Susan M. Gordon, Michael J. Lush, Mathew W. Wright, Elspeth A. Bruford:
  genenames.org: the HGNC resources in 2011. 514-519
• 
  Cheng-Kai Shiau, De-Leung Gu, Chian-Feng Chen, Chi-Hung Lin, Yuh-Shan Jou:
  IGRhCellID: integrated genomic resources of human cell lines for identification. 520-524
• 
  Edward Hemphill, Asav P. Dharia, Chih Lee, Caroline M. Jakuba, Jason D. Gibson, Frederick W. Kolling IV, Craig E. Nelson:
  SCLD: a stem cell lineage database for the annotation of cell types and developmental lineages. 525-533
• 
  Joanna L. Sharman, Chidochangu P. Mpamhanga, Michael Spedding, Pierre Germain, Bart Staels, Catherine Dacquet, Vincent Laudet, Anthony J. Harmar:
  IUPHAR-DB: new receptors and tools for easy searching and visualization of pharmacological data. 534-538
• 
  Darren A. Natale, Cecilia N. Arighi, Winona C. Barker, Judith A. Blake, Carol J. Bult, Michael Caudy, Harold J. Drabkin, Peter D'Eustachio, Alexei V. Evsikov, Hongzhan Huang, Jules Nchoutmboube, Natalia V. Roberts, Barry Smith, Jian Zhang, Cathy H. Wu:
  The Protein Ontology: a structured representation of protein forms and complexes. 539-545
• 
  Shulei Sun, Jing Chen, Weizhong Li, Ilkay Altintas, Abel W. Lin, Steven Peltier, Karen I. Stocks, Eric E. Allen, Mark H. Ellisman, Jeffrey S. Grethe, John C. Wooley:
  Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource. 546-551
• 
  Shujiro Okuda, Akiyasu C. Yoshizawa:
  ODB: a database for operon organizations, 2011 update. 552-555
• 
  Jaime Huerta-Cepas, Salvador Capella-Gutiérrez, Leszek P. Pryszcz, Ivan Andreevich Denisov, Diego Kormes, Marina Marcet-Houben, Toni Gabaldón:
  PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions. 556-560
• 
  Damian Szklarczyk, Andrea Franceschini, Michael Kuhn, Milan Simonovic, Alexander Roth, Pablo Minguez, Tobias Doerks, Manuel Stark, Jean Muller, Peer Bork, Lars Juhl Jensen, Christian von Mering:
  The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. 561-568
• 
  Leonor Palmeira, Simon Penel, Vincent Lotteau, Chantal Rabourdin-Combe, Christian Gautier:
  PhEVER: a database for the global exploration of virus-host evolutionary relationships. 569-575
• 
  Chantal Hulo, Edouard De Castro, Patrick Masson, Lydie Bougueleret, Amos Bairoch, Ioannis Xenarios, Philippe Le Mercier:
  ViralZone: a knowledge resource to understand virus diversity. 576-582
• 
  Ingrid M. Keseler, Julio Collado-Vides, Alberto Santos-Zavaleta, Martín Peralta-Gil, Socorro Gama-Castro, Luis Muñiz-Rascado, César Bonavides-Martínez, Suzanne M. Paley, Markus Krummenacker, Tomer Altman, Pallavi Kaipa, Aaron Spaulding, John Pacheco, Mario Latendresse, Carol A. Fulcher, Malabika Sarker, Alexander Glennon Shearer, Amanda Mackie, Ian T. Paulsen, Robert P. Gunsalus, Peter D. Karp:
  EcoCyc: a comprehensive database of Escherichia coli biology. 583-590
• 
  Marc-André Jehl, Roland Arnold, Thomas Rattei:
  Effective - a database of predicted secreted bacterial proteins. 591-595
• 
  Geoffrey L. Winsor, David K. W. Lam, Leanne Fleming, Raymond Lo, Matthew D. Whiteside, Nancy Y. Yu, Robert E. W. Hancock, Fiona S. L. Brinkman:
  Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes. 596-600
• 
  Pankaj Kumar, Pasumarthy S. Chaitanya, Hampapathalu A. Nagarajaram:
  PSSRdb: a relational database of polymorphic simple sequence repeats extracted from prokaryotic genomes. 601-605
• 
  Yucheng Shao, Ewan M. Harrison, Dexi Bi, Cui Tai, Xinyi He, Hong-Yu Ou, Kumar Rajakumar, Zixin Deng:
  TADB: a web-based resource for Type 2 toxin-antitoxin loci in bacteria and archaea. 606-611
• 
  Cristina Aurrecoechea, Ana Barreto, John Brestelli, Brian P. Brunk, Elisabet V. Caler, Steve Fischer, Bindu Gajria, Xin Gao, Alan R. Gingle, Gregory R. Grant, Omar S. Harb, Mark Heiges, John Iodice, Jessica C. Kissinger, Eileen T. Kraemer, Wei Li, Vishal Nayak, Cary Pennington, Deborah F. Pinney, Brian Pitts, David S. Roos, Ganesh Srinivasamoorthy, Christian J. Stoeckert Jr., Charles Treatman, Haiming Wang:
  AmoebaDB and MicrosporidiaDB: functional genomic resources for Amoebozoa and Microsporidia species. 612-619
• 
  Pascale Gaudet, Petra Fey, Siddhartha Basu, Yulia A. Bushmanova, Robert J. Dodson, Kerry A. Sheppard, Eric M. Just, Warren A. Kibbe, Rex L. Chisholm:
  dictyBase update 2011: web 2.0 functionality and the initial steps towards a genome portal for the Amoebozoa. 620-624
• 
  Josef Tuda, Arthur E. Mongan, Mohammed E. M. Tolba, Mihoko Imada, Junya Yamagishi, Xuenan Xuan, Hiroyuki Wakaguri, Sumio Sugano, Chihiro Sugimoto, Yutaka Suzuki:
  Full-parasites: database of full-length cDNAs of apicomplexa parasites, 2010 update. 625-631
• 
  Olivier Arnaiz, Linda Sperling:
  ParameciumDB in 2011: new tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia. 632-636
• 
  Philip Wong, Mathias C. Walter, Wanseon Lee, Gertrud Mannhaupt, Martin Münsterkötter, Hans-Werner Mewes, Gerhard Adam, Ulrich Güldener:
  FGDB: revisiting the genome annotation of the plant pathogen Fusarium graminearum. 637-639
• 
  Bongsoo Park, Jongsun Park, Kyeong-Chae Cheong, Jaeyoung Choi, Kyongyong Jung, Donghan Kim, Yong-Hwan Lee, Todd J. Ward, Kerry O'Donnell, David M. Geiser, Seogchan Kang:
  Cyber infrastructure for Fusarium: three integrated platforms supporting strain identification, phylogenetics, comparative genomics and knowledge sharing. 640-646
• 
  Darby Tien-Hao Chang, Cheng-Yi Huang, Chi-Yeh Wu, Wei-Sheng Wu:
  YPA: an integrated repository of promoter features in Saccharomyces cerevisiae. 647-652
• 
  Volker Herzig, David L. A. Wood, Felicity Newell, Pierre-Alain Chaumeil, Quentin Kaas, Greta J. Binford, Graham M. Nicholson, Dominique Gorse, Glenn F. King:
  ArachnoServer 2.0, an updated online resource for spider toxin sequences and structures. 653-657
• 
  Monica C. Munoz-Torres, Justin T. Reese, Christopher P. Childers, Anna K. Bennett, Jaideep P. Sundaram, Kevin L. Childs, Juan M. Anzola, Natalia Milshina, Christine G. Elsik:
  Hymenoptera Genome Database: integrated community resources for insect species of the order Hymenoptera. 658-662
• 
  Zhimin Huang, Liang Zhu, Yan Cao, Geng Wu, Xinyi Liu, Yingyi Chen, Qi Wang, Ting Shi, Yaxue Zhao, Yuefei Wang, Weihua Li, Yixue Li, Haifeng Chen, Guoqiang Chen, Jian Zhang:
  ASD: a comprehensive database of allosteric proteins and modulators. 663-669
• 
  Maurice Scheer, Andreas Grote, Antje Chang, Ida Schomburg, Cornelia Munaretto, Michael Rother, Carola Söhngen, Michael Stelzer, Juliane Thiele, Dietmar Schomburg:
  BRENDA, the enzyme information system in 2011. 670-676
• 
  Nozomu Sakurai, Takeshi Ara, Yoshiyuki Ogata, Ryosuke Sano, Takashi Ohno, Kenjiro Sugiyama, Atsushi Hiruta, Kiyoshi Yamazaki, Kentaro Yano, Koh Aoki, Asaph Aharoni, Kazuki Hamada, Koji Yokoyama, Shingo Kawamura, Hirofumi Otsuka, Toshiaki Tokimatsu, Minoru Kanehisa, Hideyuki Suzuki, Kazuki Saito, Daisuke Shibata:
  KaPPA-View4: a metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data. 677-684
• 
  Ethan G. Cerami, Benjamin E. Gross, Emek Demir, Igor V. Rodchenkov, Özgün Babur, Nadia Anwar, Nikolaus Schultz, Gary D. Bader, Chris Sander:
  Pathway Commons, a web resource for biological pathway data. 685-690
• 
  David Croft, Gavin O'Kelly, Guanming Wu, Robin Haw, Marc Gillespie, Lisa Matthews, Michael Caudy, Phani V. Garapati, Gopal Gopinath, Bijay Jassal, Steven Jupe, Irina Kalatskaya, Shahana Mahajan, Bruce May, Nelson Ndegwa, Esther Schmidt, Veronica Shamovsky, Christina K. Yung, Ewan Birney, Henning Hermjakob, Peter D'Eustachio, Lincoln Stein:
  Reactome: a database of reactions, pathways and biological processes. 691-697
• 
  Chris Stark, Bobby-Joe Breitkreutz, Andrew Chatr-aryamontri, Lorrie Boucher, Rose Oughtred, Michael S. Livstone, Julie Nixon, Kimberly Van Auken, Xiaodong Wang, Xiaoqi Shi, Teresa Reguly, Jennifer M. Rust, Andrew G. Winter, Kara Dolinski, Mike Tyers:
  The BioGRID Interaction Database: 2011 update. 698-704
• 
  Thomas Juettemann, Dietlind L. Gerloff:
  BISC: Binary SubComplexes in proteins database. 705-711
• 
  Atanas Kamburov, Konstantin Pentchev, Hanna Galicka, Christoph K. Wierling, Hans Lehrach, Ralf Herwig:
  ConsensusPathDB: toward a more complete picture of cell biology. 712-717
• 
  Amelie Stein, Arnaud Céol, Patrick Aloy:
  3did: identification and classification of domain-based interactions of known three-dimensional structure. 718-723
• 
  Qibin Luo, Philipp Pagel, Baiba Vilne, Dmitrij Frishman:
  DIMA 3.0: Domain Interaction Map. 724-729
• 
  Sailu Yellaboina, Asba Tasneem, Dmitri V. Zaykin, Balaji Raghavachari, Raja Jothi:
  DOMINE: a comprehensive collection of known and predicted domain-domain interactions. 730-735
• 
  Thilakam Murali, Svetlana Pacifico, Jingkai Yu, Stephen Guest, George G. Roberts III, Russell L. Finley Jr.:
  DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila. 736-743
• 
  Ashwini Patil, Kenta Nakai, Haruki Nakamura:
  HitPredict: a database of quality assessed protein-protein interactions in nine species. 744-749
• 
  Xue-wen Chen, Jong Cheol Jeong, Patrick Dermyer:
  KUPS: constructing datasets of interacting and non-interacting protein pairs with associated attributions. 750-754
• 
  Joan Segura, Narcis Fernandez-Fuentes:
  PCRPi-DB: a database of computationally annotated hot spots in protein interfaces. 755-760
• 
  Qifang Xu, Roland L. Dunbrack Jr.:
  The protein common interface database (ProtCID) - a comprehensive database of interactions of homologous proteins in multiple crystal forms. 761-770
• 
  Mohamed Barakat, Philippe Ortet, David E. Whitworth:
  P2CS: a database of prokaryotic two-component systems. 771-776
• 
  Tzong-Yi Lee, Justin Bo-Kai Hsu, Wen-Chi Chang, Hsien-Da Huang:
  RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans. 777-787
• 
  Kaja Milanowska, Joanna Krwawicz, Grzegorz Papaj, Jan Kosinski, Katarzyna Poleszak, Justyna Lesiak, Ewelina Osinska, Kristian Rother, Janusz M. Bujnicki:
  REPAIRtoire - a database of DNA repair pathways. 788-792
• 
  Arnon Paz, Zippora Brownstein, Yaara Ber, Shani Bialik, Eyal David, Dorit Sagir, Igor Ulitsky, Ran Elkon, Adi Kimchi, Karen B. Avraham, Yosef Shiloh, Ron Shamir:
  SPIKE: a database of highly curated human signaling pathways. 793-799
• 
  Paul Flicek, M. Ridwan Amode, Daniel Barrell, Kathryn Beal, Simon Brent, Yuan Chen, Peter Clapham, Guy Coates, Susan Fairley, Stephen Fitzgerald, Leo Gordon, Maurice Hendrix, Thibaut Hourlier, Nathan Johnson, Andreas Kähäri, Damian Keefe, Stephen Keenan, Rhoda Kinsella, Felix Kokocinski, Eugene Kulesha, Pontus Larsson, Ian Longden, William M. McLaren, Bert Overduin, Bethan Pritchard, Harpreet Singh Riat, Daniel Rios, Graham R. S. Ritchie, Magali Ruffier, Michael Schuster, Daniel Sobral, Giulietta Spudich, Y. Amy Tang, Stephen J. Trevanion, Jana Vandrovcova, Albert J. Vilella, Simon White, Steven P. Wilder, Amonida Zadissa, Jorge Zamora, Bronwen L. Aken, Ewan Birney, Fiona Cunningham, Ian Dunham, Richard Durbin, Xosé M. Fernández-Suárez, Javier Herrero, Tim J. P. Hubbard, Anne Parker, Glenn Proctor, Jan Vogel, Stephen M. J. Searle:
  Ensembl 2011. 800-806
• 
  Toshinori Endo, Keisuke Ueno, Kouki Yonezawa, Katsuhiko Mineta, Kohji Hotta, Yutaka Satou, Lixy Yamada, Michio Ogasawara, Hiroki Takahashi, Ayako Nakajima, Mia Nakachi, Mamoru Nomura, Junko Yaguchi, Yasunori Sasakura, Chisato Yamasaki, Miho Sera, Akiyasu C. Yoshizawa, Tadashi Imanishi, Hisaaki Taniguchi, Kazuo Inaba:
  CIPRO 2.5: Ciona intestinalis protein database, a unique integrated repository of large-scale omics data, bioinformatic analyses and curated annotation, with user rating and reviewing functionality. 807-814
• 
  Jianguo Lu, Eric Peatman, Qing Yang, Shaolin Wang, Zhiliang Hu, James M. Reecy, Huseyin Kucuktas, Zhanjiang Liu:
  The catfish genome database cBARBEL: an informatic platform for genome biology of ictalurid catfish. 815-821
• 
  Yvonne M. Bradford, Tom Conlin, Nathan A. Dunn, David Fashena, Ken Frazer, Douglas G. Howe, Jonathan Knight, Prita Mani, Ryan Martin, Sierra A. T. Moxon, Holly Paddock, Christian Pich, Sridhar Ramachandran, Barbara J. Ruef, Leyla Ruzicka, Holle Bauer Schaper, Kevin Schaper, Xiang Shao, Amy Singer, Judy Sprague, Brock Sprunger, Ceri E. Van Slyke, Monte Westerfield:
  ZFIN: enhancements and updates to the zebrafish model organism database. 822-829
• 
  Christopher P. Childers, Justin T. Reese, Jaideep P. Sundaram, Donald C. Vile, C. Michael Dickens, Kevin L. Childs, Hanni Salih, Anna K. Bennett, Darren E. Hagen, David L. Adelson, Christine G. Elsik:
  Bovine Genome Database: integrated tools for genome annotation and discovery. 830-834
• 
  Jacqueline H. Finger, Constance M. Smith, Terry F. Hayamizu, Ingeborg J. McCright, Janan T. Eppig, James A. Kadin, Joel E. Richardson, Martin Ringwald:
  The mouse Gene Expression Database (GXD): 2011 update. 835-841
• 
  Judith A. Blake, Carol J. Bult, James A. Kadin, Joel E. Richardson, Janan T. Eppig:
  The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics. 842-848
• 
  Martin Ringwald, Vivek Iyer, Jeremy C. Mason, Kevin R. Stone, Hamsa D. Tadepally, James A. Kadin, Carol J. Bult, Janan T. Eppig, Darren J. Oakley, Sebastien Briois, Elia Stupka, Vincenza Maselli, Damian Smedley, Songyan Liu, Jens Hansen, Richard A. Baldock, Geoffrey G. Hicks, William C. Skarnes:
  The IKMC web portal: a central point of entry to data and resources from the International Knockout Mouse Consortium. 849-855
• 
  Hideya Kawaji, Jessica Severin, Marina Lizio, Alistair R. R. Forrest, Erik van Nimwegen, Michael Rehli, Kate Schroder, Katharine M. Irvine, Harukazu Suzuki, Piero Carninci, Yoshihide Hayashizaki, Carsten O. Daub:
  Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. 856-860
• 
  Hiroshi Masuya, Yuko Makita, Norio Kobayashi, Koro Nishikata, Yuko Yoshida, Yoshiki Mochizuki, Koji Doi, Terue Takatsuki, Kazunori Waki, Nobuhiko Tanaka, Manabu Ishii, Akihiro Matsushima, Satoshi Takahashi, Atsushi Hijikata, Kouji Kozaki, Teiichi Furuichi, Hideya Kawaji, Shigeharu Wakana, Yukio Nakamura, Atsushi Yoshiki, Takehide Murata, Kaoru Fukami-Kobayashi, S. Sujatha Mohan, Osamu Ohara, Yoshihide Hayashizaki, Riichiro Mizoguchi, Yuichi Obata, Tetsuro Toyoda:
  The RIKEN integrated database of mammals. 861-870
• 
  Brian J. Raney, Melissa S. Cline, Kate R. Rosenbloom, Timothy R. Dreszer, Katrina Learned, Galt P. Barber, Laurence R. Meyer, Cricket A. Sloan, Venkat S. Malladi, Krishna M. Roskin, Bernard B. Suh, Angie S. Hinrichs, Hiram Clawson, Ann S. Zweig, Vanessa Kirkup, Pauline A. Fujita, Brooke L. Rhead, Kayla E. Smith, Andy Pohl, Robert M. Kuhn, Donna Karolchik, David Haussler, W. James Kent:
  ENCODE whole-genome data in the UCSC genome browser (2011 update). 871-875
• 
  Pauline A. Fujita, Brooke L. Rhead, Ann S. Zweig, Angie S. Hinrichs, Donna Karolchik, Melissa S. Cline, Mary Goldman, Galt P. Barber, Hiram Clawson, António Coelho, Mark Diekhans, Timothy R. Dreszer, Belinda Giardine, Rachel A. Harte, Jennifer Hillman-Jackson, Fan Hsu, Vanessa Kirkup, Robert M. Kuhn, Katrina Learned, Chin H. Li, Laurence R. Meyer, Andy Pohl, Brian J. Raney, Kate R. Rosenbloom, Kayla E. Smith, David Haussler, W. James Kent:
  The UCSC Genome Browser database: update 2011. 876-882
• 
  Dongwan Hong, Sung-Soo Park, Young Seok Ju, Sheehyun Kim, Jong-Yeon Shin, Sujung Kim, Saet-Byeol Yu, Won-Chul Lee, Seungbok Lee, Hansoo Park, Jong-Il Kim, Jeong-Sun Seo:
  TIARA: a database for accurate analysis of multiple personal genomes based on cross-technology. 883-888
• 
  Andrei L. Turinsky, Brian Turner, Rosanne C. Borja, James A. Gleeson, Michael Heath, Shuye Pu, Thomas Switzer, Dong Dong, Yunchen Gong, Tuan On, Xuejian Xiong, Andrew Emili, Jack Greenblatt, John Parkinson, Zhaolei Zhang, Shoshana J. Wodak:
  DAnCER: Disease-Annotated Chromatin Epigenetics Resource. 889-894
• 
  Fanlou Kong, Jing Zhu, Jun Wu, Jianjian Peng, Ying Wang, Qing Wang, Songbin Fu, Li-Lian Yuan, Tongbin Li:
  dbCRID: a database of chromosomal rearrangements in human diseases. 895-900
• 
  Scott F. Saccone, Jiaxi Quan, Gaurang Mehta, Raphael Bolze, Prasanth Thomas, Ewa Deelman, Jay A. Tischfield, John P. Rice:
  New tools and methods for direct programmatic access to the dbSNP relational database. 901-907
• 
  Ian M. Fingerman, Lee McDaniel, Xuan Zhang, Walter Ratzat, Tarek Hassan, Zhifang Jiang, Robert F. Cohen, Gregory D. Schuler:
  NCBI Epigenomics: a new public resource for exploring epigenomic data sets. 908-912
• 
  Faviel F. Gonzalez-Galarza, Stephen Christmas, Derek Middleton, Andrew R. Jones:
  Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations. 913-919
• 
  Meng-Ru Ho, Kuo-Wang Tsai, Chun-Houh Chen, Wen-Chang Lin:
  dbDNV: a resource of duplicated gene nucleotide variants in human genome. 920-925
• 
  Marianthi Georgitsi, Emmanouil Viennas, Dimitris Antoniou, Vassiliki Gkantouna, Sjozef van Baal, Emanuel F. Petricoin III, Konstantinos Poulas, Giannis Tzimas, George P. Patrinos:
  FINDbase: a worldwide database for genetic variation allele frequencies updated. 926-932
• 
  Sanchari Pradhan, Mainak Sengupta, Anirban Dutta, Kausik Bhattacharyya, Sumit K. Bag, Chitra Dutta, Kunal Ray:
  Indian genetic disease database. 933-938
• 
  Jin Ok Yang, Sangho Oh, Gunhwan Ko, Seong-Jin Park, Woo-Yeon Kim, Byungwook Lee, Sanghyuk Lee:
  VnD: a structure-centric database of disease-related SNPs and drugs. 939-944
• 
  Simon A. Forbes, Nidhi Bindal, Sally Bamford, Charlotte Cole, Chai Yin Kok, David Beare, Mingming Jia, Rebecca Shepherd, Kenric Leung, Andrew Menzies, Jon W. Teague, Peter J. Campbell, Michael R. Stratton, P. Andrew Futreal:
  COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. 945-950
• 
  J. Zachary Sanborn, Stephen C. Benz, Brian Craft, Christopher Szeto, Kord M. Kober, Laurence R. Meyer, Charles J. Vaske, Mary Goldman, Kayla E. Smith, Robert M. Kuhn, Donna Karolchik, W. James Kent, Joshua M. Stuart, David Haussler, Jingchun Zhu:
  The UCSC cancer genomics browser: update 2011. 951-959
• 
  Jessica Ahmed, Thomas Meinel, Mathias Dunkel, Manuela S. Murgueitio, Robert Adams, Corinna Blasse, Andreas Eckert, Saskia Preissner, Robert Preissner:
  CancerResource: a comprehensive database of cancer-relevant proteins and compound interactions supported by experimental knowledge. 960-967
• 
  Qingyi Cao, Meng Zhou, Xujun Wang, Clifford A. Meyer, Yong Zhang, Zhi Chen, Cheng Li, Xiaole Shirley Liu:
  CaSNP: a database for interrogating copy number alterations of cancer genome from SNP array data. 968-974
• 
  Subhash M. Agarwal, Dhwani Raghav, Harinder Singh, G. P. S. Raghava:
  CCDB: a curated database of genes involved in cervix cancer. 975-979
• 
  Monique Maqungo, Mandeep Kaur, Samuel K. Kwofie, Aleksandar Radovanovic, Ulf Schaefer, Sebastian Schmeier, Ekow Oppon, Alan Christoffels, Vladimir B. Bajic:
  DDPC: Dragon Database of Genes associated with Prostate Cancer. 980-985
• 
  Keiichi Homma, Koji Suzuki, Hideaki Sugawara:
  The Autophagy Database: an all-inclusive information resource on autophagy that provides nourishment for research. 986-990
• 
  Hui Liu, Wei Liu, Yifang Liao, Long Cheng, Qian Liu, Xiang Ren, Lisong Shi, Xin Tu, Qing Kenneth Wang, An-Yuan Guo:
  CADgene: a comprehensive database for coronary artery disease genes. 991-996
• 
  Oliver S. Burren, Ellen C. Adlem, Premanand Achuthan, Mikkel B. Christensen, Richard M. R. Coulson, John A. Todd:
  T1DBase: update 2011, organization and presentation of large-scale data sets for type 1 diabetes research. 997-1001
• 
  Helen E. Parkinson, Ugis Sarkans, Nikolay Kolesnikov, Niran Abeygunawardena, Tony Burdett, Miroslaw Dylag, Ibrahim Emam, Anna Farne, Emma Hastings, Ele Holloway, Natalja Kurbatova, Margus Lukk, James Malone, Roby Mani, Ekaterina Pilicheva, Gabriella Rustici, Anjan Sharma, Eleanor Williams, Tomasz Adamusiak, Marco Brandizi, Nataliya Sklyar, Alvis Brazma:
  ArrayExpress update - an archive of microarray and high-throughput sequencing-based functional genomics experiments. 1002-1004
• 
  Tanya Barrett, Dennis B. Troup, Stephen E. Wilhite, Pierre Ledoux, Carlos Evangelista, Irene F. Kim, Maxim Tomashevsky, Kimberly A. Marshall, Katherine H. Phillippy, Patti M. Sherman, Rolf N. Muertter, Michelle Holko, Oluwabukunmi Ayanbule, Andrey Yefanov, Alexandra Soboleva:
  NCBI GEO: archive for functional genomics data sets - 10 years on. 1005-1010
• 
  Matthew N. McCall, Karan Uppal, Harris A. Jaffee, Michael J. Zilliox, Rafael A. Irizarry:
  The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes. 1011-1015
• 
  Takeshi Obayashi, Kengo Kinoshita:
  COXPRESdb: a database to compare gene coexpression in seven model animals. 1016-1022
• 
  Rosalind J. Cutts, Emanuela Gadaleta, Stephan A. Hahn, Tatjana Crnogorac-Jurcevic, Nicholas R. Lemoine, Claude Chelala:
  The Pancreatic Expression database: 2011 update. 1023-1028
• 
  Zexian Liu, Jun Cao, Xinjiao Gao, Yanhong Zhou, Longping Wen, Xiangjiao Yang, Xuebiao Yao, Jian Ren, Yu Xue:
  CPLA 1.0: an integrated database of protein lysine acetylation. 1029-1034
• 
  Craig Knox, Vivian Law, Timothy Jewison, Philip Liu, Son Ly, Alex Frolkis, Allison Pon, Kelly Banco, Christine Mak, Vanessa Neveu, Yannick Djoumbou, Roman Eisner, Anchi Guo, David S. Wishart:
  DrugBank 3.0: a comprehensive resource for 'Omics' research on drugs. 1035-1041
• 
  Kun-Yi Hsin, Hugh P. Morgan, Steven R. Shave, Andrew C. Hinton, Paul Taylor, Malcolm D. Walkinshaw:
  EDULISS: a small-molecule database with data-mining and pharmacophore searching capabilities. 1042-1048
• 
  Jessica Ahmed, Catherine L. Worth, Paul Florian Thaben, Christian Matzig, Corinna Blasse, Mathias Dunkel, Robert Preissner:
  FragmentStore - a comprehensive database of fragments linking metabolites, toxic molecules and drugs. 1049-1054
• 
  Hao Ye, Li Ye, Hong Kang, Duanfeng Zhang, Lin Tao, Kailin Tang, Xueping Liu, Ruixin Zhu, Qi Liu, Yuzong Chen, Yixue Li, Zhi-Wei Cao:
  HIT: linking herbal active ingredients to targets. 1055-1059
• 
  Joachim von Eichborn, Manuela S. Murgueitio, Mathias Dunkel, Soeren Koerner, Philip E. Bourne, Robert Preissner:
  PROMISCUOUS: a database for network-based drug-repositioning. 1060-1066
• 
  Allan Peter Davis, Benjamin L. King, Susan Mockus, Cynthia G. Murphy, Cynthia A. Saraceni-Richards, Michael C. Rosenstein, Thomas C. Wiegers, Carolyn J. Mattingly:
  The Comparative Toxicogenomics Database: update 2011. 1067-1072
• 
  Brian Yang, Samantha Sayers, Zuoshuang Xiang, Yongqun He:
  Protegen: a web-based protective antigen database and analysis system. 1073-1078
• 
  Jean-Christophe Gelly, Mickael Orgeur, Claude Jacq, Gaëlle Lelandais:
  MitoGenesisDB: an expression data mining tool to explore spatio-temporal dynamics of mitochondrial biogenesis. 1079-1084
• 
  Ken Youens-Clark, Edward S. Buckler, Terry M. Casstevens, Charles Chen, Genevieve DeClerck, Paul S. Derwent, Palitha Dharmawardhana, Pankaj Jaiswal, Paul J. Kersey, A. S. Karthikeyan, Jerry Lu, Susan McCouch, Liya Ren, William Spooner, Joshua C. Stein, Jim Thomason, Sharon Wei, Doreen Ware:
  Gramene database in 2010: updates and extensions. 1085-1094
• 
  Mathieu Rouard, Valentin Guignon, Christelle Aluome, Marie-Angélique Laporte, Gaëtan Droc, Christian Walde, Christian M. Zmasek, Christophe Périn, Matthieu G. Conte:
  GreenPhylDB v2.0: comparative and functional genomics in plants. 1095-1102
• 
  Xiao-Chuan Liu, Zhonghai Li, Zhiqiang Jiang, Yi Zhao, Jinying Peng, Jinpu Jin, Hongwei Guo, Jingchu Luo:
  LSD: a leaf senescence database. 1103-1107
• 
  Masaru Takeya, Fukuhiro Yamasaki, Shihomi Uzuhashi, Takayuki Aoki, Hiroyuki Sawada, Toshirou Nagai, Keisuke Tomioka, Norihiko Tomooka, Toyozo Sato, Makoto Kawase:
  NIASGBdb: NIAS Genebank databases for genetic resources and plant disease information. 1108-1113
• 
  He Zhang, Jinpu Jin, Liang Tang, Yi Zhao, Xiaocheng Gu, Ge Gao, Jingchu Luo:
  PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database. 1114-1117
• 
  Alper Yilmaz, Maria Katherine Mejia-Guerra, Kyle Kurz, Xiaoyu Liang, Lonnie R. Welch, Erich Grotewold:
  AGRIS: the Arabidopsis Gene Regulatory Information Server, an update. 1118-1122
• 
  Zhiqiang Jiang, Xiao-Chuan Liu, Zhiyu Peng, Yinan Wan, Yusi Ji, Wenrong He, Wen Wan, Jingchu Luo, Hongwei Guo:
  AHD2.0: an update version of Arabidopsis Hormone Database for plant systematic studies. 1123-1129
• 
  Peng Li, Weidong Zang, Yuhua Li, Feng Xu, Jigang Wang, Tieliu Shi:
  AtPID: the overall hierarchical functional protein interaction network interface and analytic platform for Arabidopsis. 1130-1133
• 
  Mingzhi Lin, Xueling Shen, Xin Chen:
  PAIR: the predicted Arabidopsis interactome resource. 1134-1140
• 
  Yutaka Sato, Baltazar A. Antonio, Nobukazu Namiki, Hinako Takehisa, Hiroshi Minami, Kaori Kamatsuki, Kazuhiko Sugimoto, Yuji Shimizu, Hirohiko Hirochika, Yoshiaki Nagamura:
  RiceXPro: a platform for monitoring gene expression in japonica rice grown under natural field conditions. 1141-1148
• 
  Aureliano Bombarely, Naama Menda, Isaak Y. Tecle, Robert M. Buels, Susan Strickler, Thomas Fischer-York, Anuradha Pujar, Jonathan Leto, Joseph Gosselin, Lukas A. Mueller:
  The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl. 1149-1155
• 
  Zhangjun Fei, Je-Gun Joung, Xuemei Tang, Yi Zheng, Mingyun Huang, Je Min Lee, Ryan McQuinn, Denise M. Tieman, Rob Alba, Harry J. Klee, James J. Giovannoni:
  Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics. 1156-1163
• 
  Julia V. Ponomarenko, Nikitas Papangelopoulos, Dirk M. Zajonc, Björn Peters, Alessandro Sette, Philip E. Bourne:
  IEDB-3D: structural data within the immune epitope database. 1164-1170
• 
  James Robinson, Kavita Mistry, Hamish McWilliam, Rodrigo Lopez, Peter Parham, Steven G. E. Marsh:
  The IMGT/HLA database. 1171-1176

Volume 39, Number Web-Server-Issue, July 2011

Articles

• 
  Michelle D. Brazas, David S. Yim, Joseph Tadashi Yamada, B. F. Francis Ouellette:
  The 2011 bioinformatics links directory update: more resources, tools and databases and features to empower the bioinformatics community. 3-7
• 
  Sayed Mohammad Ebrahim Sahraeian, Byung-Jun Yoon:
  PicXAA-Web: a web-based platform for non-progressive maximum expected accuracy alignment of multiple biological sequences. 8-12
• 
  Paolo Di Tommaso, Sébastien Moretti, Ioannis Xenarios, Miquel Orobitg, Alberto Montanyola, Jia-Ming Chang, Jean-François Taly, Cédric Notredame:
  T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension. 13-17
• 
  Jean-Christophe Gelly, Agnel Praveen Joseph, Narayanaswamy Srinivasan, Alexandre G. de Brevern:
  iPBA: a tool for protein structure comparison using sequence alignment strategies. 18-23
• 
  M. N. Nguyen, Kuan Pern Tan, Mallur S. Madhusudhan:
  CLICK - topology-independent comparison of biomolecular 3D structures. 24-28
• 
  Robert D. Finn, Jody Clements, Sean R. Eddy:
  HMMER web server: interactive sequence similarity searching. 29-37
• 
  Lukasz Jaroszewski, Zhanwen Li, Xiao-hui Cai, Christoph Weber, Adam Godzik:
  FFAS server: novel features and applications. 38-44
• 
  Yun-Chen Liu, Chung-Han Yang, Kun-Tze Chen, Jyun-Rong Wang, Mei-Ling Cheng, Jen-Chun Chung, Hsien-Tai Chiu, Chin Lung Lu:
  R3D-BLAST: a search tool for similar RNA 3D substructures. 45-49
• 
  Anton I. Petrov, Craig L. Zirbel, Neocles Leontis:
  WebFR3D - a server for finding, aligning and analyzing recurrent RNA 3D motifs. 50-55
• 
  Norman E. Davey, Niall J. Haslam, Denis C. Shields, Richard J. Edwards:
  SLiMSearch 2.0: biological context for short linear motifs in proteins. 56-60
• 
  Lars Rønn Olsen, Niels Bjørn Hansen, Mads Tvillinggaard Bonde, Hans Jasper Genee, Dorte Koefoed Holm, Simon Carlsen, Bjarne Gram Hansen, Kiran Raosaheb Patil, Uffe Hasbro Mortensen, Rasmus Wernersson:
  PHUSER (Primer Help for USER): a novel tool for USER fusion primer design. 61-67
• 
  Christophe Blanchet, Marco Pasi, Krystyna Zakrzewska, Richard Lavery:
  CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures. 68-73
• 
  Stefan Broos, Paco Hulpiau, Jeroen Galle, Bart Hooghe, Frans van Roy, Pieter J. De Bleser:
  ConTra v2: a tool to identify transcription factor binding sites across species, update 2011. 74-78
• 
  Majid Kazemian, Michael H. Brodsky, Saurabh Sinha:
  Genome surveyor 2.0: cis-regulatory analysis in Drosophila. 79-85
• 
  Morgane Thomas-Chollier, Matthieu Defrance, Alejandra Medina-Rivera, Olivier Sand, Carl Herrmann, Denis Thieffry, Jacques van Helden:
  RSAT 2011: regulatory sequence analysis tools. 86-91
• 
  Alexander Churkin, Idan Gabdank, Danny Barash:
  The RNAmute web server for the mutational analysis of RNA secondary structures. 92-99
• 
  Michiaki Hamada, Koichiro Yamada, Kengo Sato, Martin C. Frith, Kiyoshi Asai:
  CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences. 100-106
• 
  Stefan E. Seemann, Peter Menzel, Rolf Backofen, Jan Gorodkin:
  The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences. 107-111
• 
  Mario Fasold, David Langenberger, Hans Binder, Peter F. Stadler, Steve Hoffmann:
  DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments. 112-117
• 
  Qi Liao, Hui Xiao, Dechao Bu, Chaoyong Xie, Ruoyu Miao, Haitao Luo, Guoguang Zhao, Kuntao Yu, Haitao Zhao, Geir Skogerbø, Runsheng Chen, Zhongdao Wu, Changning Liu, Yi Zhao:
  ncFANs: a web server for functional annotation of long non-coding RNAs. 118-124
• 
  Christopher Plaisier, J. Christopher Bare, Nitin S. Baliga:
  miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling. 125-131
• 
  Michael Hackenberg, Naiara Rodríguez-Ezpeleta, Ana M. Aransay:
  miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments. 132-138
• 
  Zhi Liang, Hong Zhou, Zongxiao He, Haoran Zheng, Jiarui Wu:
  mirAct: a web tool for evaluating microRNA activity based on gene expression data. 139-144
• 
  Manolis Maragkakis, Thanasis Vergoulis, Panagiotis Alexiou, Martin Reczko, Kyriaki Plomaritou, Mixail Gousis, Kornilios Kourtis, Nectarios Koziris, Theodore Dalamagas, Artemis G. Hatzigeorgiou:
  DIANA-microT Web server upgrade supports Fly and Worm miRNA target prediction and bibliographic miRNA to disease association. 145-148
• 
  Florian Eggenhofer, Hakim Tafer, Peter F. Stadler, Ivo L. Hofacker:
  RNApredator: fast accessibility-based prediction of sRNA targets. 149-154
• 
  Xinbin Dai, Patrick Xuechun Zhao:
  psRNATarget: a plant small RNA target analysis server. 155-159
• 
  Edmund Lam, Alfred Kam, Jérôme Waldispühl:
  corRna: a web server for predicting multiple-point deleterious mutations in structural RNAs. 160-166
• 
  Elina Tjioe, Keren Lasker, Ben M. Webb, Haim J. Wolfson, Andrej Sali:
  MultiFit: a web server for fitting multiple protein structures into their electron microscopy density map. 167-170
• 
  Daniel B. Roche, Maria T. Buenavista, Stuart J. Tetchner, Liam J. McGuffin:
  The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction. 171-176
• 
  Naomi Fox, Filip Jagodzinski, Yang Li, Ileana Streinu:
  KINARI-Web: a server for protein rigidity analysis. 177-183
• 
  Frédéric Poitevin, Henri Orland, Sebastian Doniach, Patrice Koehl, Marc Delarue:
  AquaSAXS: a web server for computation and fitting of SAXS profiles with non-uniformally hydrated atomic models. 184-189
• 
  Ian Walsh, Alberto J. M. Martin, Tomás Di Domenico, Alessandro Vullo, Gianluca Pollastri, Silvio C. E. Tosatto:
  CSpritz: accurate prediction of protein disorder segments with annotation for homology, secondary structure and linear motifs. 190-196
• 
  Damiano Piovesan, Pier Luigi Martelli, Piero Fariselli, Andrea Zauli, Ivan Rossi, Rita Casadio:
  BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences. 197-202
• 
  Leslie Regad, Adrien Saladin, Julien Maupetit, Colette Geneix, Anne-Claude Camproux:
  SA-Mot: a web server for the identification of motifs of interest extracted from protein loops. 203-209
• 
  Junsu Ko, Dongseon Lee, Hahnbeom Park, Evangelos A. Coutsias, Julian Lee, Chaok Seok:
  The FALC-Loop web server for protein loop modeling. 210-214
• 
  Catherine L. Worth, Robert Preissner, Tom L. Blundell:
  SDM - a server for predicting effects of mutations on protein stability and malfunction. 215-222
• 
  Alexander A. Kantardjiev:
  GPU.proton.DOCK: Genuine Protein Ultrafast proton equilibria consistent DOCKing. 223-228
• 
  Pralay Mitra, Debnath Pal:
  PRUNE and PROBE - two modular web services for protein-protein docking. 229-234
• 
  Gonzalo López, Paolo Maietta, Jose Manuel Rodriguez, Alfonso Valencia, Michael L. Tress:
  firestar - advances in the prediction of functionally important residues. 235-241
• 
  Kuan Pern Tan, Raghavan Varadarajan, Mallur S. Madhusudhan:
  DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins. 242-248
• 
  Nir London, Barak Raveh, Eyal Cohen, Guy Fathi, Ora Schueler-Furman:
  Rosetta FlexPepDock web server - high resolution modeling of peptide-protein interactions. 249-253
• 
  I-Hsin Liu, Yu-Shu Lo, Jinn-Moon Yang:
  PAComplex: a web server to infer peptide antigen families and binding models from TCR-pMHC complexes. 254-260
• 
  Matteo Floris, Joel Masciocchi, Marco Fanton, Stefano Moro:
  Swimming into peptidomimetic chemical space using pepMMsMIMIC. 261-269
• 
  Aurélien Grosdidier, Vincent Zoete, Olivier Michielin:
  SwissDock, a protein-small molecule docking web service based on EADock DSS. 270-277
• 
  Luca Parca, Iolanda Mangone, Pier Federico Gherardini, Gabriele Ausiello, Manuela Helmer-Citterich:
  Phosfinder: a web server for the identification of phosphate-binding sites on protein structures. 278-282
• 
  Qiangfeng Cliff Zhang, Lei Deng, Markus Fisher, Jihong Guan, Barry Honig, Donald Petrey:
  PredUs: a web server for predicting protein interfaces using structural neighbors. 283-287
• 
  Andrea Passerini, Marco Lippi, Paolo Frasconi:
  MetalDetector v2.0: predicting the geometry of metal binding sites from protein sequence. 288-292
• 
  Aleksandra Gruca, Marek Sikora, Andrzej Polanski:
  RuleGO: a logical rules-based tool for description of gene groups by means of Gene Ontology. 293-301
• 
  Sang-Mun Chi, Jin Kim, Seon-Young Kim, Dougu Nam:
  ADGO 2.0: interpreting microarray data and list of genes using composite annotations. 302-306
• 
  Jüri Reimand, Tambet Arak, Jaak Vilo:
  g: Profiler - a web server for functional interpretation of gene lists (2011 update). 307-315
• 
  Chen Xie, Xizeng Mao, Jiaju Huang, Yang Ding, Jianmin Wu, Shan Dong, Lei Kong, Ge Gao, Chuan-Yun Li, Liping Wei:
  KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. 316-322
• 
  Alexey V. Antonov:
  BioProfiling.de: analytical web portal for high-throughput cell biology. 323-327
• 
  Frédéric Lecerf, Anthony Bretaudeau, Olivier Sallou, Colette Désert, Yuna Blum, Sandrine Lagarrigue, Oliver Demeure:
  AnnotQTL: a new tool to gather functional and comparative information on a genomic region. 328-333
• 
  Daniela Nitsch, Léon-Charles Tranchevent, Joana P. Gonçalves, Josef Korbinian Vogt, Sara C. Madeira, Yves Moreau:
  PINTA: a web server for network-based gene prioritization from expression data. 334-338
• 
  Marnix H. Medema, Kai Blin, Peter Cimermancic, Victor de Jager, Piotr Zakrzewski, Michael A. Fischbach, Tilmann Weber, Eriko Takano, Rainer Breitling:
  antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. 339-346
• 
  You Zhou, Yongjie Liang, Karlene H. Lynch, Jonathan J. Dennis, David S. Wishart:
  PHAST: A Fast Phage Search Tool. 347-352
• 
  Iwan Grin, Dirk Linke:
  GCView: the genomic context viewer for protein homology searches. 353-356
• 
  Markus Fischer, Qiangfeng Cliff Zhang, Fabian Dey, Brian Y. Chen, Barry Honig, Donald Petrey:
  MarkUs: a server to navigate sequence-structure-function space. 357-361
• 
  Marc Röttig, Marnix H. Medema, Kai Blin, Tilmann Weber, Christian Rausch, Oliver Kohlbacher:
  NRPSpredictor2 - a web server for predicting NRPS adenylation domain specificity. 362-367
• 
  Casey S. Greene, Olga G. Troyanskaya:
  PILGRM: an interactive data-driven discovery platform for expert biologists. 368-374
• 
  Andrea Pierleoni, Valentina Indio, Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, Rita Casadio:
  MemPype: a pipeline for the annotation of eukaryotic membrane proteins. 375-380
• 
  Anastasia Alexandridou, Nikolas Dovrolis, George T. Tsangaris, Konstantina S. Nikita, George M. Spyrou:
  PepServe: a web server for peptide analysis, clustering and visualization. 381-384
• 
  H. B. Rao, F. Zhu, G. B. Yang, Z. R. Li, Yuzong Chen:
  Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence. 385-390
• 
  ZhiZhuo Zhang, Cheng Wei Chang, Wan Ling Goh, Wing-Kin Sung, Edwin Cheung:
  CENTDIST: discovery of co-associated factors by motif distribution. 391-399
• 
  John T. Bates, Dylan Chivian, Adam P. Arkin:
  GLAMM: Genome-Linked Application for Metabolic Maps. 400-405
• 
  Junfeng Gao, Lynda B. M. Ellis, Lawrence P. Wackett:
  The University of Minnesota Pathway Prediction System: multi-level prediction and visualization. 406-411
• 
  Takuji Yamada, Ivica Letunic, Shujiro Okuda, Minoru Kanehisa, Peer Bork:
  iPath2.0: interactive pathway explorer. 412-415
• 
  Grace T. Huang, Charalambos Athanassiou, Panayiotis V. Benos:
  mirConnX: condition-specific mRNA-microRNA network integrator. 416-423
• 
  Alex Lan, Ilan Y. Smoly, Guy Rapaport, Susan Lindquist, Ernest Fraenkel, Esti Yeger Lotem:
  ResponseNet: revealing signaling and regulatory networks linking genetic and transcriptomic screening data. 424-429
• 
  Jing Qin, Mulin Jun Li, Panwen Wang, Michael Q. Zhang, Junwen Wang:
  ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor. 430-436
• 
  Kunlin Zhang, Suhua Chang, Sijia Cui, Liyuan Guo, Liuyan Zhang, Jing Wang:
  ICSNPathway: identify candidate causal SNPs and pathways from genome-wide association study by one analytical framework. 437-443
• 
  Tomaz Curk, Gregor Rot, Blaz Zupan:
  SNPsyn: detection and exploration of SNP-SNP interactions. 444-449
• 
  Wilco W. M. Fleuren, Stefan Verhoeven, Raoul Frijters, Bart Heupers, Jan Polman, René C. van Schaik, Jacob de Vlieg, Wynand Alkema:
  CoPub update: CoPub 5.0 a text mining system to answer biological questions. 450-454
• 
  Jean-Fred Fontaine, Florian Priller, Adriano Barbosa-Silva, Miguel A. Andrade-Navarro:
  Génie: literature-based gene prioritization at multi genomic scale. 455-461
• 
  Moushumi Sen Sarma, David Arcoleo, Radhika S. Khetani, Brant W. Chee, Xu Ling, Xin He, Jing Jiang, Qiaozhu Mei, ChengXiang Zhai, Bruce R. Schatz:
  BeeSpace Navigator: exploratory analysis of gene function using semantic indexing of biological literature. 462-469
• 
  Rubén Sánchez, François Serra, Joaquín Tárraga, Ignacio Medina, José Carbonell, Luis Pulido, Alejandro de María, Salvador Capella-Gutiérrez, Jaime Huerta-Cepas, Toni Gabaldón, Joaquín Dopazo, Hernán Dopazo:
  Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. 470-474
• 
  Ivica Letunic, Peer Bork:
  Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. 475-478
• 
  Joël Busset, Cédric Cabau, Camille Meslin, Géraldine Pascal:
  PhyleasProg: a user-oriented web server for wide evolutionary analyses. 479-485
• 
  Tyler W. H. Backman, Yiqun Cao, Thomas Girke:
  ChemMine tools: an online service for analyzing and clustering small molecules. 486-491
• 
  Heng Luo, Jian Chen, Leming Shi, Mike Mikailov, Huang Zhu, Kejian Wang, Lin He, Lun Yang:
  DRAR-CPI: a server for identifying drug repositioning potential and adverse drug reactions via the chemical-protein interactome. 492-498
• 
  Mohamed Uduman, Gur Yaari, Uri Hershberg, Jacob A. Stern, Mark J. Shlomchik, Steven H. Kleinstein:
  Detecting selection in immunoglobulin sequences. 499-504
• 
  Manor Askenazi, Michal Linial:
  ARISTO: ontological classification of small molecules by electron ionization-mass spectrometry. 505-510
• 
  Enguerran Vanquelef, Sabrina Simon, Gaelle Marquant, Elodie Garcia, Geoffroy Klimerak, Jean Charles Delepine, Piotr Cieplak, François-Yves Dupradeau:
  R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments. 511-517
• 
  Thomas Lingner, Kathrin Petra Aßhauer, Fabian Schreiber, Peter Meinicke:
  CoMet - a web server for comparative functional profiling of metagenomes. 518-523
• 
  Jose M. Muiño, Marlous Hoogstraat, Roeland C. H. J. van Ham, Aalt D. J. van Dijk:
  PRI-CAT: a web-tool for the analysis, storage and visualization of plant ChIP-seq experiments. 524-527
• 
  Carol Lushbough, Douglas M. Jennewein, Volker Brendel:
  The BioExtract Server: a web-based bioinformatic workflow platform. 528-532

Web Services

• 
  Norio Kobayashi, Manabu Ishii, Satoshi Takahashi, Yoshiki Mochizuki, Akihiro Matsushima, Tetsuro Toyoda:
  Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases. 533-540
• 
  Patricia L. Whetzel, Natalya Fridman Noy, Nigam H. Shah, Paul R. Alexander, Csongor Nyulas, Tania Tudorache, Mark A. Musen:
  BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. 541-545
• 
  Corin Yeats, Jonathan G. Lees, Phil Carter, Ian Sillitoe, Christine A. Orengo:
  The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences. 546-550

Stand Alone Programs

• 
  Pavlo Lutsik, Lars Feuerbach, Julia Arand, Thomas Lengauer, Jörn Walter, Christoph Bock:
  BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing. 551-556
• 
  Jong Hyun Kim, Woo-Cheol Kim, Lei M. Li, Sanghyun Park:
  HapEdit: an accuracy assessment viewer for haplotype assembly using massively parallel DNA-sequencing technologies. 557-561
• 
  Hugo López-Fernández, Daniel Glez-Peña, Miguel Reboiro-Jato, Gonzalo Gómez-López, David G. Pisano, Florentino Fdez-Riverola:
  PileLineGUI: a desktop environment for handling genome position files in next-generation sequencing studies. 562-566
• 
  Ji Qi, Fangqing Zhao:
  inGAP-sv: a novel scheme to identify and visualize structural variation from paired end mapping data. 567-575