| 2008 | A computational framework to empower probabilistic protein design. Menachem Fromer, Chen Yanover |
| 2008 | A max-margin model for efficient simultaneous alignment and folding of RNA sequences. Chuong B. Do, Chuan-Sheng Foo, Serafim Batzoglou |
| 2008 | A maximum common substructure-based algorithm for searching and predicting drug-like compounds. Yiqun Cao, Tao Jiang, Thomas Girke |
| 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 | A robust framework for detecting structural variations in a genome. Seunghak Lee, Elango Cheran, Michael Brudno |
| 2008 | Algorithm for backrub motions in protein design. Ivelin Georgiev, Daniel A. Keedy, Jane S. Richardson, David C. Richardson, Bruce Randall Donald |
| 2008 | Alignment and classification of time series gene expression in clinical studies. Tien-ho Lin, Naftali Kaminski, Ziv Bar-Joseph |
| 2008 | Annotation-based inference of transporter function. Thomas J. Lee, Ian T. Paulsen, Peter D. Karp |
| 2008 | Assessing the functional structure of genomic data. Curtis Huttenhower, Olga G. Troyanskaya |
| 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 | BLASTing small molecules - statistics and extreme statistics of chemical similarity scores. Pierre Baldi, Ryan W. Benz |
| 2008 | Biomolecular network motif counting and discovery by color coding. Noga Alon, Phuong Dao, Iman Hajirasouliha, Fereydoun Hormozdiari, Süleyman Cenk Sahinalp |
| 2008 | Classification and feature selection algorithms for multi-class CGH data. Jun Liu, Sanjay Ranka, Tamer Kahveci |
| 2008 | Classification of arrayCGH data using fused SVM. Franck Rapaport, Emmanuel Barillot, Jean-Philippe Vert |
| 2008 | Combinatorial influence of environmental parameters on transcription factor activity. Theo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders |
| 2008 | Contact replacement for NMR resonance assignment. Fei Xiong, Gopal Pandurangan, Chris Bailey-Kellogg |
| 2008 | Designing succinct structural alphabets. Shuai Cheng Li, Dongbo Bu, Xin Gao, Jinbo Xu, Ming Li |
| 2008 | Detection of IUPAC and IUPAC-like chemical names. Roman Klinger, Corinna Kolárik, Juliane Fluck, Martin Hofmann-Apitius, Christoph M. Friedrich |
| 2008 | Differential variability analysis of gene expression and its application to human diseases. Joshua Wing Kei Ho, Maurizio Stefani, Cristobal G. dos Remedios, Michael A. Charleston |
| 2008 | Editorial. Alfonso Valencia, Ildefonso Cases |
| 2008 | Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space. Yaniv Loewenstein, Elon Portugaly, Menachem Fromer, Michal Linial |
| 2008 | Efficient inference of bacterial strain trees from genome-scale multilocus data. Cuong Than, R. Sugino, Hideki Innan, Luay Nakhleh |
| 2008 | Estimating true evolutionary distances under the DCJ model. Yu Lin, Bernard M. E. Moret |
| 2008 | GenoQuery: a new querying module for functional annotation in a genomic warehouse. Frédéric Lemoine, Bernard Labedan, Christine Froidevaux |
| 2008 | Guided genome halving: hardness, heuristics and the history of the Hemiascomycetes. Chunfang Zheng, Qian Zhu, Zaky Adam, David Sankoff |
| 2008 | ISMB 2008 Organization. |
| 2008 | Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Marcus T. Dittrich, Gunnar W. Klau, Andreas Rosenwald, Thomas Dandekar, Tobias Müller |
| 2008 | Identifying gene-disease associations using centrality on a literature mined gene-interaction network. Arzucan Özgür, Thuy Vu, Günes Erkan, Dragomir R. Radev |
| 2008 | Inferring differentiation pathways from gene expression. Ivan G. Costa, Stefan Roepcke, Christoph Hafemeister, Alexander Schliep |
| 2008 | Integrating high dimensional bi-directional parsing models for gene mention tagging. Chun-Nan Hsu, Yu-Ming Chang, Cheng-Ju Kuo, Yu-Shi Lin, Han-Shen Huang, I-Fang Chung |
| 2008 | MACHOS: Markov clusters of homologous subsequences. Simon Wong, Mark A. Ragan |
| 2008 | Matching isotopic distributions from metabolically labeled samples. Sean McIlwain, David Page, Edward L. Huttlin, Michael R. Sussman |
| 2008 | MicroRNA prediction with a novel ranking algorithm based on random walks. Yunpen Xu, Xuefeng Zhou, Weixiong Zhang |
| 2008 | Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification. Aaron A. Klammer, Sheila M. Reynolds, Jeff A. Bilmes, Michael J. MacCoss, William Stafford Noble |
| 2008 | Multi-spectra peptide sequencing and its applications to multistage mass spectrometry. Nuno Bandeira, Jesper V. Olsen, Matthias Mann, Pavel A. Pevzner |
| 2008 | Nucleosome positioning from tiling microarray data. Moran Yassour, Tommy Kaplan, Ariel Jaimovich, Nir Friedman |
| 2008 | Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies. Iman Hajirasouliha, Fereydoun Hormozdiari, Süleyman Cenk Sahinalp, Inanç Birol |
| 2008 | POIMs: positional oligomer importance matrices - understanding support vector machine-based signal detectors. Sören Sonnenburg, Alexander Zien, Petra Philips, Gunnar Rätsch |
| 2008 | Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences. Lucas D. Ward, Harmen J. Bussemaker |
| 2008 | Predicting protein thermostability changes from sequence upon multiple mutations. Ludovica Montanucci, Piero Fariselli, Pier Luigi Martelli, Rita Casadio |
| 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 | ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles. Thomas Abeel, Yvan Saeys, Pierre Rouzé, Yves Van de Peer |
| 2008 | Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), Toronto, Canada, July 19-23, 2008 |
| 2008 | Protein complex identification by supervised graph local clustering. Yanjun Qi, Fernanda Balem, Christos Faloutsos, Judith Klein-Seetharaman, Ziv Bar-Joseph |
| 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 | Selecting anti-HIV therapies based on a variety of genomic and clinical factors. Michal Rosen-Zvi, André Altmann, Mattia Prosperi, Ehud Aharoni, Hani Neuvirth, Anders Sönnerborg, Eugen Schülter, Daniel Struck, Yardena Peres, Francesca Incardona, Rolf Kaiser, Maurizio Zazzi, Thomas Lengauer |
| 2008 | The EXACT description of biomedical protocols. Larisa N. Soldatova, Wayne Aubrey, Ross D. King, Amanda Clare |
| 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 | The multiple gene duplication problem revisited. Mukul S. Bansal, Oliver Eulenstein |
| 2008 | The ontology of biological taxa. Stefan Schulz, Holger Stenzhorn, Martin Boeker |
| 2008 | Towards the use of argumentation in bioinformatics: a gene expression case study. Kenneth McLeod, Albert Burger |