| 375 | -- | 376 | Christophe Dessimoz. Editorial: Orthology and applications |
| 377 | -- | 378 | Eugene V. Koonin. Obituary: Walter Fitch and the orthology paradigm |
| 379 | -- | 391 | David M. Kristensen, Yuri I. Wolf, Arcady R. Mushegian, Eugene V. Koonin. Computational methods for Gene Orthology inference |
| 392 | -- | 400 | Jean-Philippe Doyon, Vincent Ranwez, Vincent Daubin, Vincent Berry. Models, algorithms and programs for phylogeny reconciliation |
| 401 | -- | 412 | Colin N. Dewey. Positional orthology: putting genomic evolutionary relationships into context |
| 413 | -- | 422 | Kimmen Sjölander, Ruchira S. Datta, Yaoqing Shen, Grant M. Shoffner. Ortholog identification in the presence of domain architecture rearrangement |
| 423 | -- | 435 | Brigitte Boeckmann, Marc Robinson-Rechavi, Ioannis Xenarios, Christophe Dessimoz. Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees |
| 436 | -- | 441 | Walid H. Gharib, Marc Robinson-Rechavi. When orthologs diverge between human and mouse |
| 442 | -- | 448 | Jaime Huerta-Cepas, Joaquín Dopazo, Martijn A. Huynen, Toni Gabaldón. Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication |
| 449 | -- | 462 | Pascale Gaudet, Michael S. Livstone, Suzanna E. Lewis, Paul D. Thomas. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium |
| 463 | -- | 473 | Kristoffer Forslund, Fabian Schreiber, Nattaphon Thanintorn, Erik L. L. Sonnhammer. OrthoDisease: tracking disease gene orthologs across 100 species |
| 474 | -- | 484 | Christophe Dessimoz, Stefan Zoller, Tereza Manousaki, Huan Qiu, Axel Meyer, Shigehiro Kuraku. Callorhinchus milii (Holocephali, Chondrichthyes) |
| 485 | -- | 488 | Thomas Schmitt, David N. Messina, Fabian Schreiber, Erik L. L. Sonnhammer. Letter to the Editor: SeqXML and OrthoXML: standards for sequence and orthology information |
| 489 | -- | 497 | Christian Ledergerber, Christophe Dessimoz. Base-calling for next-generation sequencing platforms |
| 498 | -- | 513 | Alan Wee-Chung Liew, Ngai-Fong Law, Hong Yan. Missing value imputation for gene expression data: computational techniques to recover missing data from available information |
| 514 | -- | 517 | Nicolas von Ahsen, Carl T. Wittwer, Ekkehard Schütz. m prediction - recommendations for Primer3 usage |
| 518 | -- | 529 | Rob Jelier, Jelle J. Goeman, Kristina M. Hettne, Martijn J. Schuemie, Johan T. den Dunnen, Peter A. C. 't Hoen. Literature-aided interpretation of gene expression data with the weighted global test |
| 530 | -- | 544 | Yves Sucaet, Taru Deva. Evolution and applications of plant pathway resources and databases |
| 545 | -- | 546 | Adam Wittek, Karol Miller. Letter to the Editor: Current progress in patient-specific modeling by Neal and Kerckhoffs (2010) |