Volume 11, Number 1, January 2010

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  Russ B. Altman: Editorial: Current progress in Bioinformatics 2010. 1-2

• 
  Adrian V. Dalca, Michael Brudno: Genome variation discovery with high-throughput sequencing data. 3-14
• 
  Teresa M. Przytycka, Mona Singh, Donna K. Slonim: Toward the dynamic interactome: it's about time. 15-29
• 
  Michael F. Ochs: Knowledge-based data analysis comes of age. 30-39
• 
  Peter D. Karp, Suzanne M. Paley, Markus Krummenacker, Mario Latendresse, Joseph M. Dale, Thomas J. Lee, Pallavi Kaipa, Fred Gilham, Aaron Spaulding, Liviu Popescu, Tomer Altman, Ian T. Paulsen, Ingrid M. Keseler, Ron Caspi: Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. 40-79
• 
  Gil Alterovitz, Taro Muso, Marco Ramoni: The challenges of informatics in synthetic biology: from biomolecular networks to artificial organisms. 80-95
• 
  Maricel G. Kann: Advances in translational bioinformatics: computational approaches for the hunting of disease genes. 96-110
• 
  Maxwell Lewis Neal, Roy Kerckhoffs: Current progress in patient-specific modeling. 111-126
• 
  Béatrice Duval, Jin-Kao Hao: Advances in metaheuristics for gene selection and classification of microarray data. 127-141
• 
  Peter M. A. Sloot, Alfons G. Hoekstra: Multi-scale modelling in computational biomedicine. 142-152
• 
  Markus Kirkilionis: Exploration of cellular reaction systems. 153-178

• 
  Dae-Won Kim, Hong-Seog Park: Modern Genome Annotation . Edited by Dmitrij Frishman and Alfonso Valencia. 179-180

Volume 11, Number 2, March 2010

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  David Stephen Horner, Giulio Pavesi, Tiziana Castrignanò, Paolo D'Onorio De Meo, Sabino Liuni, Michael Sammeth, Ernesto Picardi, Graziano Pesole: Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing. 181-197
• 
  Roberto Hirochi Herai, Michel Eduardo Beleza Yamagishi: Detection of human interchromosomal trans-splicing in sequence databanks. 198-209
• 
  Ronnie Alves, Domingo S. Rodríguez-Baena, Jesús S. Aguilar-Ruiz: Gene association analysis: a survey of frequent pattern mining from gene expression data. 210-224
• 
  Zsuzsanna Dosztányi, Bálint Mészáros, István Simon: Bioinformatical approaches to characterize intrinsically disordered/unstructured proteins. 225-243
• 
  Kellie J. Archer, Sarah E. Reese: Detection call algorithms for high-throughput gene expression microarray data. 244-252
• 
  Tero Aittokallio: Dealing with missing values in large-scale studies: microarray data imputation and beyond. 253-264

• 
  Artem Lysenko, Matthew Morritt Hindle, Jan Taubert, Mansoor Saqi, Christopher J. Rawlings: Data integration for plant genomics - exemplars from the integration of Arabidopsis thaliana databases. 265

Volume 11, Number 3, May 2010

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  Tommaso Mazza: Editorial: Accelerating systems biology. 267-269

• 
  Chen Li, Mélanie Courtot, Nicolas Le Novère, Camille Laibe: BioModels.net Web Services, a free and integrated toolkit for computational modelling software. 270-277
• 
  Yuhui Chen, Conor Lawless, Colin S. Gillespie, Jake Wu, Richard J. Boys, Darren J. Wilkinson: CaliBayes and BASIS: integrated tools for the calibration, simulation and storage of biological simulation models. 278-289
• 
  Roland Ewald, Jan Himmelspach, Matthias Jeschke, Stefan Leye, Adelinde M. Uhrmacher: Flexible experimentation in the modeling and simulation framework JAMES II - implications for computational systems biology. 290-300
• 
  Jiri Barnat, Lubos Brim, David Safránek: High-performance analysis of biological systems dynamics with the DiVinE model checker. 301-312
• 
  José M. Cecilia, José M. García, Ginés D. Guerrero, Miguel A. Martínez-del-Amor, Ignacio Pérez-Hurtado, Mario J. Pérez-Jiménez: Simulation of P systems with active membranes on CUDA. 313-322
• 
  Lorenzo Dematté, Davide Prandi: GPU computing for systems biology. 323-333
• 
  Paul Richmond, Dawn C. Walker, Simon Coakley, Daniela M. Romano: High performance cellular level agent-based simulation with FLAME for the GPU. 334-347
• 
  Laszlo Bako: Real-time classification of datasets with hardware embedded neuromorphic neural networks. 348-363
• 
  Tommaso Mazza, Alessandro Romanel, Ferenc Jordán: Estimating the divisibility of complex biological networks by sparseness indices. 364-374

Volume 11, Number 4, July 2010

• 
  Franck Valentin, Silvano Squizzato, Mickael Goujon, Hamish McWilliam, Juri Paern, Rodrigo Lopez: Fast and efficient searching of biological data resources - using EB-eye. 375-384
• 
  Shuangge Ma, Jian Huang, Mingyu Shi, Yang Li, Ben-Chang Shia: Semiparametric prognosis models in genomic studies. 385-393
• 
  Emma M. B. Weeding, Jason Houle, Yiannis N. Kaznessis: SynBioSS designer: a web-based tool for the automated generation of kinetic models for synthetic biological constructs. 394-402
• 
  Daniël B. van Schalkwijk, Kees van Bochove, Ben van Ommen, Andreas P. Freidig, Eugene P. van Someren, Jan van der Greef, Albert A. de Graaf: Developing computational model-based diagnostics to analyse clinical chemistry data. 403-416
• 
  Jing Zhao, Peng Jiang, Weidong Zhang: Molecular networks for the study of TCM Pharmacology. 417-430
• 
  Melinda R. Dwinell: Online tools for understanding rat physiology. 431-439
• 
  Maurizio Casiraghi, Massimo Labra, Emanuele Ferri, Andrea Galimberti, Fabrizio De Mattia: DNA barcoding: a six-question tour to improve users' awareness about the method. 440-453

Volume 11, Number 5, September 2010

• 
  Keith Robison: Editorial: Second-generation sequencing. 455-456

• 
  Konrad H. Paszkiewicz, David J. Studholme: De novo assembly of short sequence reads. 457-472
• 
  Heng Li, Nils Homer: A survey of sequence alignment algorithms for next-generation sequencing. 473-483
• 
  Daniel C. Koboldt, Li Ding, Elaine R. Mardis, Richard K. Wilson: Challenges of sequencing human genomes. 484-498
• 
  Thomas Werner: Next generation sequencing in functional genomics. 499-511
• 
  Mikael Huss: Introduction into the analysis of high-throughput-sequencing based epigenome data. 512-523
• 
  Keith Robison: Application of second-generation sequencing to cancer genomics. 524-534

Volume 11, Number 6, November 2010

• 
  Indra Neil Sarkar: Editorial: Bioinformatics education in the 21st century. 535-536

• 
  Michael P. Cummings, Glena G. Temple: Broader incorporation of bioinformatics in education: opportunities and challenges. 537-543
• 
  Maria Victoria Schneider, James Watson, Teresa K. Attwood, Kristian Rother, Aidan Budd, Jennifer McDowall, Allegra Via, Pedro Fernandes, Tommi H. Nyrönen, Thomas Blicher, Philip Jones, Marie-Claude Blatter, Javier De Las Rivas, David Phillip Judge, Wouter van der Gool, Catherine Brooksbank: Bioinformatics training: a review of challenges, actions and support requirements. 544-551
• 
  Victoria Ann Wright, Brendan W. Vaughan, Thomas Laurent, Rodrigo Lopez, Catherine Brooksbank, Maria Victoria Schneider: Bioinformatics training: selecting an appropriate learning content management system - an example from the European Bioinformatics Institute. 552-562
• 
  Peter S. Cooper, Dawn Lipshultz, Wayne Matten, Scott D. McGinnis, Steven Pechous, Monica L. Romiti, Tao Tao, Majda Valjavec-Gratian, Eric W. Sayers: Education resources of the National Center for Biotechnology Information. 563-569
• 
  John R. Jungck, Samuel S. Donovan, Anton E. Weisstein, Noppadon Khiripet, Stephen J. Everse: Bioinformatics education dissemination with an evolutionary problem solving perspective. 570-581
• 
  Kristian Rother, Magdalena Rother, Alexandra Pleus, Annette Upmeier zu Belzen: Multi-stage learning aids applied to hands-on software training. 582-586
• 
  Pier Luigi Buttigieg: Perspectives on presentation and pedagogy in aid of bioinformatics education. 587-597
• 
  Jennifer M. Williams, Mary E. Mangan, Cynthia Perreault-Micale, Scott Lathe, Neeraj Sirohi, Warren C. Lathe: OpenHelix: bioinformatics education outside of a different box. 598-609
• 
  Grant Yamashita, Holly Miller, Anthony Goddard, Cathy Norton: A model for Bioinformatics training: the marine biological laboratory. 610-615
• 
  Urmila Kulkarni-Kale, Sangeeta Sawant, Vishwas Chavan: Bioinformatics education in India. 616-625
• 
  Pedro L. Fernandes: The GTPB training programme in Portugal. 626-634

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