| 2008 | Guided genome halving: hardness, heuristics and the history of the Hemiascomycetes. | Chunfang Zheng, Qian Zhu, Zaky Adam, David Sankoff |
| 2008 | Nucleosome positioning from tiling microarray data. | Moran Yassour, Tommy Kaplan, Ariel Jaimovich, Nir Friedman |
| 2008 | Prediction of drug-target interaction networks from the integration of chemical and genomic spaces. | Yoshihiro Yamanishi, Michihiro Araki, Alex Gutteridge, Wataru Honda, Minoru Kanehisa |
| 2008 | MicroRNA prediction with a novel ranking algorithm based on random walks. | Yunpen Xu, Xuefeng Zhou, Weixiong Zhang |
| 2008 | Contact replacement for NMR resonance assignment. | Fei Xiong, Gopal Pandurangan, Chris Bailey-Kellogg |
| 2008 | A model of higher accuracy for the individual haplotyping problem based on weighted SNP fragments and genotype with errors. | Minzhu Xie, Jianxin Wang, Jianer Chen |
| 2008 | ISMB 2008 Organization. | |
| 2008 | MACHOS: Markov clusters of homologous subsequences. | Simon Wong, Mark A. Ragan |
| 2008 | Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences. | Lucas D. Ward, Harmen J. Bussemaker |
| 2008 | Reversible jump MCMC approach for peak identification for stroke SELDI mass spectrometry using mixture model. | Yuan Wang, Xiaobo Zhou, Honghui Wang, King C. Li, Lixiu Yao, Stephen T. C. Wong |
| 2008 | Assessment and improvement of the | Ashley Vaughan, Sum-Ying Chiu, Gowthaman Ramasamy, Ling Li, Malcolm J. Gardner, Alice S. Tarun, Stefan H. I. Kappe, Xinxia Peng |
| 2008 | Editorial. | Alfonso Valencia, Ildefonso Cases |
| 2008 | Efficient inference of bacterial strain trees from genome-scale multilocus data. | Cuong Than, R. Sugino, Hideki Innan, Luay Nakhleh |
| 2008 | The effectiveness of position- and composition-specific gap costs for protein similarity searches. | Aleksandar Stojmirovic, E. Michael Gertz, Stephen F. Altschul, Yi-Kuo Yu |
| 2008 | POIMs: positional oligomer importance matrices - understanding support vector machine-based signal detectors. | Sren Sonnenburg, Alexander Zien, Petra Philips, Gunnar Rtsch |
| 2008 | The EXACT description of biomedical protocols. | Larisa N. Soldatova, Wayne Aubrey, Ross D. King, Amanda Clare |
| 2008 | The ontology of biological taxa. | Stefan Schulz, Holger Stenzhorn, Martin Boeker |
| 2008 | Selecting anti-HIV therapies based on a variety of genomic and clinical factors. | Michal Rosen-Zvi, Andr Altmann, Mattia Prosperi, Ehud Aharoni, Hani Neuvirth, Anders Snnerborg, Eugen Schlter, Daniel Struck, Yardena Peres, Francesca Incardona, Rolf Kaiser, Maurizio Zazzi, Thomas Lengauer |
| 2008 | Classification of arrayCGH data using fused SVM. | Franck Rapaport, Emmanuel Barillot, Jean-Philippe Vert |
| 2008 | Protein complex identification by supervised graph local clustering. | Yanjun Qi, Fernanda Balem, Christos Faloutsos, Judith Klein-Seetharaman, Ziv Bar-Joseph |
| 2008 | Identifying gene-disease associations using centrality on a literature mined gene-interaction network. | Arzucan zgr, Thuy Vu, Gnes Erkan, Dragomir R. Radev |
| 2008 | Extracting and Normalizing Gene/Protein Mentions with the Flexible and Trainable Moara Java Library. | Mariana L. Neves, Jos Mara Carazo, Alberto D. Pascual-Montano |
| 2008 | Predicting protein thermostability changes from sequence upon multiple mutations. | Ludovica Montanucci, Piero Fariselli, Pier Luigi Martelli, Rita Casadio |
| 2008 | Towards the use of argumentation in bioinformatics: a gene expression case study. | Kenneth McLeod, Albert Burger |
| 2008 | Matching isotopic distributions from metabolically labeled samples. | Sean McIlwain, David Page, Edward L. Huttlin, Michael R. Sussman |