Table of Contents

• ISMB 2008 Organization [doi]
• EditorialAlfonso Valencia, Ildefonso Cases. [doi]
• POIMs: positional oligomer importance matrices - understanding support vector machine-based signal detectorsSören Sonnenburg, Alexander Zien, Petra Philips, Gunnar Rätsch. 6-14 [doi]
• The effectiveness of position- and composition-specific gap costs for protein similarity searchesAleksandar Stojmirovic, E. Michael Gertz, Stephen F. Altschul, Yi-Kuo Yu. 15-23 [doi]
• ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profilesThomas Abeel, Yvan Saeys, Pierre Rouzé, Yves Van de Peer. 24-31 [doi]
• Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologiesIman Hajirasouliha, Fereydoun Hormozdiari, Süleyman Cenk Sahinalp, Inanç Birol. 32-40 [doi]
• Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein spaceYaniv Loewenstein, Elon Portugaly, Menachem Fromer, Michal Linial. 41-49 [doi]
• MicroRNA prediction with a novel ranking algorithm based on random walksYunpen Xu, Xuefeng Zhou, Weixiong Zhang. 50-58 [doi]
• A robust framework for detecting structural variations in a genomeSeunghak Lee, Elango Cheran, Michael Brudno. 59-67 [doi]
• A max-margin model for efficient simultaneous alignment and folding of RNA sequencesChuong B. Do, Chuan-Sheng Foo, Serafim Batzoglou. 68-76 [doi]
• MACHOS: Markov clusters of homologous subsequencesSimon Wong, Mark A. Ragan. 77-85 [doi]
• Classification and feature selection algorithms for multi-class CGH dataJun Liu, Sanjay Ranka, Tamer Kahveci. 86-95 [doi]
• Guided genome halving: hardness, heuristics and the history of the HemiascomycetesChunfang Zheng, Qian Zhu, Zaky Adam, David Sankoff. 96-104 [doi]
• A model of higher accuracy for the individual haplotyping problem based on weighted SNP fragments and genotype with errorsMinzhu Xie, Jianxin Wang, Jianer Chen. 105-113 [doi]
• Estimating true evolutionary distances under the DCJ modelYu Lin, Bernard M. E. Moret. 114-122 [doi]
• Efficient inference of bacterial strain trees from genome-scale multilocus dataCuong Than, R. Sugino, Hideki Innan, Luay Nakhleh. 123-131 [doi]
• The multiple gene duplication problem revisitedMukul S. Bansal, Oliver Eulenstein. 132-138 [doi]
• Nucleosome positioning from tiling microarray dataMoran Yassour, Tommy Kaplan, Ariel Jaimovich, Nir Friedman. 139-146 [doi]
• Alignment and classification of time series gene expression in clinical studiesTien-ho Lin, Naftali Kaminski, Ziv Bar-Joseph. 147-155 [doi]
• Inferring differentiation pathways from gene expressionIvan G. Costa, Stefan Roepcke, Christoph Hafemeister, Alexander Schliep. 156-164 [doi]
• Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequencesLucas D. Ward, Harmen J. Bussemaker. 165-171 [doi]
• Combinatorial influence of environmental parameters on transcription factor activityTheo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders. 172-181 [doi]
• Designing succinct structural alphabetsShuai Cheng Li, Dongbo Bu, Xin Gao, Jinbo Xu, Ming Li. 182-189 [doi]
• Predicting protein thermostability changes from sequence upon multiple mutationsLudovica Montanucci, Piero Fariselli, Pier Luigi Martelli, Rita Casadio. 190-195 [doi]
• Algorithm for backrub motions in protein designIvelin Georgiev, Daniel Keedy, Jane S. Richardson, David C. Richardson, Bruce Randall Donald. 196-204 [doi]
• Contact replacement for NMR resonance assignmentFei Xiong, Gopal Pandurangan, Chris Bailey-Kellogg. 205-213 [doi]
• A computational framework to empower probabilistic protein designMenachem Fromer, Chen Yanover. 214-222 [doi]
• Identifying functional modules in protein-protein interaction networks: an integrated exact approachMarcus T. Dittrich, Gunnar W. Klau, Andreas Rosenwald, Thomas Dandekar, Tobias Müller. 223-231 [doi]
• Prediction of drug-target interaction networks from the integration of chemical and genomic spacesYoshihiro Yamanishi, Michihiro Araki, Alex Gutteridge, Wataru Honda, Minoru Kanehisa. 232-240 [doi]
• Biomolecular network motif counting and discovery by color codingNoga Alon, Phuong Dao, Iman Hajirasouliha, Fereydoun Hormozdiari, Süleyman Cenk Sahinalp. 241-249 [doi]
• Protein complex identification by supervised graph local clusteringYanjun Qi, Fernanda Balem, Christos Faloutsos, Judith Klein-Seetharaman, Ziv Bar-Joseph. 250-268 [doi]
• Annotation-based inference of transporter functionThomas J. Lee, Ian T. Paulsen, Peter D. Karp. 259-267 [doi]
• Detection of IUPAC and IUPAC-like chemical namesRoman Klinger, Corinna Kolárik, Juliane Fluck, Martin Hofmann-Apitius, Christoph M. Friedrich. 268-276 [doi]
• Identifying gene-disease associations using centrality on a literature mined gene-interaction networkArzucan Özgür, Thuy Vu, Günes Erkan, Dragomir R. Radev. 277-285 [doi]
• Integrating high dimensional bi-directional parsing models for gene mention taggingChun-Nan Hsu, Yu-Ming Chang, Cheng-Ju Kuo, Yu-Shi Lin, Han-Shen Huang, I-Fang Chung. 286-294 [doi]
• The EXACT description of biomedical protocolsLarisa N. Soldatova, Wayne Aubrey, Ross D. King, Amanda Clare. 295-303 [doi]
• Towards the use of argumentation in bioinformatics: a gene expression case studyKenneth McLeod, Albert Burger. 304-312 [doi]
• The ontology of biological taxaStefan Schulz, Holger Stenzhorn, Martin Boeker. 313-321 [doi]
• GenoQuery: a new querying module for functional annotation in a genomic warehouseFrédéric Lemoine, Bernard Labedan, Christine Froidevaux. 322-329 [doi]
• Assessing the functional structure of genomic dataCurtis Huttenhower, Olga G. Troyanskaya. 330-338 [doi]
• Matching isotopic distributions from metabolically labeled samplesSean McIlwain, David Page, Edward L. Huttlin, Michael R. Sussman. 339-347 [doi]
• Modeling peptide fragmentation with dynamic Bayesian networks for peptide identificationAaron A. Klammer, Sheila M. Reynolds, Jeff A. Bilmes, Michael J. MacCoss, William Stafford Noble. 348-356 [doi]
• BLASTing small molecules - statistics and extreme statistics of chemical similarity scoresPierre Baldi, Ryan W. Benz. 357-365 [doi]
• A maximum common substructure-based algorithm for searching and predicting drug-like compoundsYiqun Cao, Tao Jiang, Thomas Girke. 366-374 [doi]
• Classification of arrayCGH data using fused SVMFranck Rapaport, Emmanuel Barillot, Jean-Philippe Vert. 375-382 [doi]
• Assessment and improvement of the ::::Plasmodium yoelii yoelii:::: genome annotation through comparative analysisAshley Vaughan, Sum-Ying Chiu, Gowthaman Ramasamy, Ling Li, Malcolm J. Gardner, Alice S. Tarun, Stefan H. I. Kappe, Xinxia Peng. 383-389 [doi]
• Differential variability analysis of gene expression and its application to human diseasesJoshua W. K. Ho, Maurizio Stefani, Cristobal G. dos Remedios, Michael A. Charleston. 390-398 [doi]
• Selecting anti-HIV therapies based on a variety of genomic and clinical factorsMichal Rosen-Zvi, André Altmann, Mattia C. F. Prosperi, Ehud Aharoni, Hani Neuvirth, Anders Sönnerborg, Eugen Schülter, Daniel Struck, Yardena Peres, Francesca Incardona, Rolf Kaiser, Maurizio Zazzi, Thomas Lengauer. 399-406 [doi]
• Reversible jump MCMC approach for peak identification for stroke SELDI mass spectrometry using mixture modelYuan Wang, Xiaobo Zhou, Honghui Wang, King Li, Lixiu Yao, Stephen T. C. Wong. 407-413 [doi]
• Multi-spectra peptide sequencing and its applications to multistage mass spectrometryNuno Bandeira, Jesper V. Olsen, Matthias Mann, Pavel A. Pevzner. 416-423 [doi]