16. ISMB 2008: Toronto, Canada(Supplement of Bioinformatics)

Editorials

• Alfonso Valencia, Ildefonso Cases:
  Editorial.
  
• ISMB 2008 Organization.
  

Sequence Analysis and Alignment

• Sören Sonnenburg, Alexander Zien, Petra Philips, Gunnar Rätsch:
  POIMs: positional oligomer importance matrices - understanding support vector machine-based signal detectors. 6-14
  
• Aleksandar Stojmirovic, E. Michael Gertz, Stephen F. Altschul, Yi-Kuo Yu:
  The effectiveness of position- and composition-specific gap costs for protein similarity searches. 15-23
  
• Thomas Abeel, Yvan Saeys, Pierre Rouzé, Yves Van de Peer:
  ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles. 24-31
  
• Iman Hajirasouliha, Fereydoun Hormozdiari, Süleyman Cenk Sahinalp, Inanç Birol:
  Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies. 32-40
  
• Yaniv Loewenstein, Elon Portugaly, Menachem Fromer, Michal Linial:
  Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space. 41-49
  
• Yunpen Xu, Xuefeng Zhou, Weixiong Zhang:
  MicroRNA prediction with a novel ranking algorithm based on random walks. 50-58
  
• Seunghak Lee, Elango Cheran, Michael Brudno:
  A robust framework for detecting structural variations in a genome. 59-67
  
• Chuong B. Do, Chuan-Sheng Foo, Serafim Batzoglou:
  A max-margin model for efficient simultaneous alignment and folding of RNA sequences. 68-76
  

Comparative Genomics

• Simon Wong, Mark A. Ragan:
  MACHOS: Markov clusters of homologous subsequences. 77-85
  
• Jun Liu, Sanjay Ranka, Tamer Kahveci:
  Classification and feature selection algorithms for multi-class CGH data. 86-95
  
• Chunfang Zheng, Qian Zhu, Zaky Adam, David Sankoff:
  Guided genome halving: hardness, heuristics and the history of the Hemiascomycetes. 96-104
  
• Minzhu Xie, Jianxin Wang, Jianer Chen:
  A model of higher accuracy for the individual haplotyping problem based on weighted SNP fragments and genotype with errors. 105-113
  

Evolution and Phylogeny

• Yu Lin, Bernard M. E. Moret:
  Estimating true evolutionary distances under the DCJ model. 114-122
  
• Cuong Than, R. Sugino, Hideki Innan, Luay Nakhleh:
  Efficient inference of bacterial strain trees from genome-scale multilocus data. 123-131
  
• Mukul S. Bansal, Oliver Eulenstein:
  The multiple gene duplication problem revisited. 132-138
  

Gene Regulation and Transcriptomics

• Moran Yassour, Tommy Kaplan, Ariel Jaimovich, Nir Friedman:
  Nucleosome positioning from tiling microarray data. 139-146
  
• Tien-ho Lin, Naftali Kaminski, Ziv Bar-Joseph:
  Alignment and classification of time series gene expression in clinical studies. 147-155
  
• Ivan G. Costa, Stefan Roepcke, Christoph Hafemeister, Alexander Schliep:
  Inferring differentiation pathways from gene expression. 156-164
  
• Lucas D. Ward, Harmen J. Bussemaker:
  Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences. 165-171
  
• Theo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders:
  Combinatorial influence of environmental parameters on transcription factor activity. 172-181
  

Protein Structure and Function

• Shuai Cheng Li, Dongbo Bu, Xin Gao, Jinbo Xu, Ming Li:
  Designing succinct structural alphabets. 182-189
  
• Ludovica Montanucci, Piero Fariselli, Pier Luigi Martelli, Rita Casadio:
  Predicting protein thermostability changes from sequence upon multiple mutations. 190-195
  
• Ivelin Georgiev, Daniel Keedy, Jane S. Richardson, David C. Richardson, Bruce Randall Donald:
  Algorithm for backrub motions in protein design. 196-204
  
• Fei Xiong, Gopal Pandurangan, Chris Bailey-Kellogg:
  Contact replacement for NMR resonance assignment. 205-213
  
• Menachem Fromer, Chen Yanover:
  A computational framework to empower probabilistic protein design. 214-222
  

Protein Interactions and Molecular Networks

• Marcus T. Dittrich, Gunnar W. Klau, Andreas Rosenwald, Thomas Dandekar, Tobias Müller:
  Identifying functional modules in protein-protein interaction networks: an integrated exact approach. 223-231
  
• Yoshihiro Yamanishi, Michihiro Araki, Alex Gutteridge, Wataru Honda, Minoru Kanehisa:
  Prediction of drug-target interaction networks from the integration of chemical and genomic spaces. 232-240
  
• Noga Alon, Phuong Dao, Iman Hajirasouliha, Fereydoun Hormozdiari, Süleyman Cenk Sahinalp:
  Biomolecular network motif counting and discovery by color coding. 241-249
  
• Yanjun Qi, Fernanda Balem, Christos Faloutsos, Judith Klein-Seetharaman, Ziv Bar-Joseph:
  Protein complex identification by supervised graph local clustering. 250-268
  

Text Mining

• Thomas J. Lee, Ian T. Paulsen, Peter D. Karp:
  Annotation-based inference of transporter function. 259-267
  
• Roman Klinger, Corinna Kolárik, Juliane Fluck, Martin Hofmann-Apitius, Christoph M. Friedrich:
  Detection of IUPAC and IUPAC-like chemical names. 268-276
  
• Arzucan Özgür, Thuy Vu, Günes Erkan, Dragomir R. Radev:
  Identifying gene-disease associations using centrality on a literature mined gene-interaction network. 277-285
  
• Chun-Nan Hsu, Yu-Ming Chang, Cheng-Ju Kuo, Yu-Shi Lin, Han-Shen Huang, I-Fang Chung:
  Integrating high dimensional bi-directional parsing models for gene mention tagging. 286-294
  

Databases and Ontologies

• Larisa N. Soldatova, Wayne Aubrey, Ross D. King, Amanda Clare:
  The EXACT description of biomedical protocols. 295-303
  
• Kenneth McLeod, Albert Burger:
  Towards the use of argumentation in bioinformatics: a gene expression case study. 304-312
  
• Stefan Schulz, Holger Stenzhorn, Martin Boeker:
  The ontology of biological taxa. 313-321
  
• Frédéric Lemoine, Bernard Labedan, Christine Froidevaux:
  GenoQuery: a new querying module for functional annotation in a genomic warehouse. 322-329
  

Other Bioinformatics Applications and Methods

• Curtis Huttenhower, Olga G. Troyanskaya:
  Assessing the functional structure of genomic data. 330-338
  
• Sean McIlwain, David Page, Edward L. Huttlin, Michael R. Sussman:
  Matching isotopic distributions from metabolically labeled samples. 339-347
  
• Aaron A. Klammer, Sheila M. Reynolds, Jeff A. Bilmes, Michael J. MacCoss, William Stafford Noble:
  Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification. 348-356
  
• Pierre Baldi, Ryan W. Benz:
  BLASTing small molecules - statistics and extreme statistics of chemical similarity scores. 357-365
  
• Yiqun Cao, Tao Jiang, Thomas Girke:
  A maximum common substructure-based algorithm for searching and predicting drug-like compounds. 366-374
  
• Franck Rapaport, Emmanuel Barillot, Jean-Philippe Vert:
  Classification of arrayCGH data using fused SVM. 375-382
  

Bioinformatics of Disease

• Ashley Vaughan, Sum-Ying Chiu, Gowthaman Ramasamy, Ling Li, Malcolm J. Gardner, Alice S. Tarun, Stefan H. I. Kappe, Xinxia Peng:
  Assessment and improvement of the Plasmodium yoelii yoelii genome annotation through comparative analysis. 383-389
  
• Joshua W. K. Ho, Maurizio Stefani, Cristobal G. dos Remedios, Michael A. Charleston:
  Differential variability analysis of gene expression and its application to human diseases. 390-398
  
• Michal 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:
  Selecting anti-HIV therapies based on a variety of genomic and clinical factors. 399-406
  
• Yuan Wang, Xiaobo Zhou, Honghui Wang, King Li, Lixiu Yao, Stephen T. C. Wong:
  Reversible jump MCMC approach for peak identification for stroke SELDI mass spectrometry using mixture model. 407-413
  

Other Bioinformatics Applications and Methods

• Nuno Bandeira, Jesper V. Olsen, Matthias Mann, Pavel A. Pevzner:
  Multi-spectra peptide sequencing and its applications to multistage mass spectrometry. 416-423