| 547 | -- | 548 | Paolo Romano, Rosalba Giugno, Alfredo Pulvirenti. Editorial |
| 549 | -- | 561 | Paolo Romano, Rosalba Giugno, Alfredo Pulvirenti. Tools and collaborative environments for bioinformatics research |
| 562 | -- | 575 | Andrea Splendiani, Michaela Gündel, Jonathan M. Austyn, Duccio Cavalieri, Ciro Scognamiglio, Marco Brandizi. Knowledge sharing and collaboration in translational research, and the DC-THERA Directory |
| 576 | -- | 587 | Ismael Navas Delgado, Alejandro Real-Chicharro, Miguel Angel Medina, Francisca Sánchez-Jiménez, José Francisco Aldana Montes. Social pathway annotation: extensions of the systems biology metabolic modelling assistant |
| 588 | -- | 600 | Dario Corrada, Federica Viti, Ivan Merelli, Cristina Battaglia, Luciano Milanesi. myMIR: a genome-wide microRNA targets identification and annotation tool |
| 601 | -- | 613 | Magdalena Rother, Kristian Rother, Tomasz Puton, Janusz M. Bujnicki. RNA tertiary structure prediction with ModeRNA |
| 614 | -- | 625 | Paolo Ribeca, Gabriel Valiente. Computational challenges of sequence classification in microbiomic data |
| 626 | -- | 633 | Adam M. Szalkowski, Christoph D. Schmid. Rapid innovation in ChIP-seq peak-calling algorithms is outdistancing benchmarking efforts |
| 634 | -- | 644 | Helen E. Lockstone. Exon array data analysis using Affymetrix power tools and R statistical software |
| 645 | -- | 659 | Yijun Meng, Chaogang Shao, Ming Chen 0005. Toward microRNA-mediated gene regulatory networks in plants |
| 660 | -- | 671 | Shannon L. N. Mayne, Hugh-George Patterton. Bioinformatics tools for the structural elucidation of multi-subunit protein complexes by mass spectrometric analysis of protein-protein cross-links |
| 672 | -- | 688 | Hua Zhang, Tuo Zhang, Ke Chen 0003, Kanaka Durga Kedarisetti, Marcin J. Mizianty, Qingbo Bao, Wojciech Stach, Lukasz A. Kurgan. Critical assessment of high-throughput standalone methods for secondary structure prediction |
| 689 | -- | 701 | Matthieu Chavent, Bruno Lévy, Michael Krone, Katrin Bidmon, Jean-Philippe Nomine, Thomas Ertl, Marc Baaden. GPU-powered tools boost molecular visualization |
| 702 | -- | 713 | Tomas Klingström, Dariusz Plewczynski. Protein-protein interaction and pathway databases, a graphical review |
| 714 | -- | 722 | Shuangge Ma, Ying Dai. Principal component analysis based methods in bioinformatics studies |
| 723 | -- | 735 | Louis du Plessis, Nives Skunca, Christophe Dessimoz. The what, where, how and why of gene ontology - a primer for bioinformaticians |