Editorials

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

Sequence Analysis and Alignment

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  Sören Sonnenburg, Alexander Zien, Petra Philips, Gunnar Rätsch: POIMs: positional oligomer importance matrices - understanding support vector machine-based signal detectors. 6-14
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  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
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  Thomas Abeel, Yvan Saeys, Pierre Rouzé, Yves Van de Peer: ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles. 24-31
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  Iman Hajirasouliha, Fereydoun Hormozdiari, Süleyman Cenk Sahinalp, Inanç Birol: Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies. 32-40
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  Yaniv Loewenstein, Elon Portugaly, Menachem Fromer, Michal Linial: Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space. 41-49
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  Yunpen Xu, Xuefeng Zhou, Weixiong Zhang: MicroRNA prediction with a novel ranking algorithm based on random walks. 50-58
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  Seunghak Lee, Elango Cheran, Michael Brudno: A robust framework for detecting structural variations in a genome. 59-67
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  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

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  Simon Wong, Mark A. Ragan: MACHOS: Markov clusters of homologous subsequences. 77-85
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  Jun Liu, Sanjay Ranka, Tamer Kahveci: Classification and feature selection algorithms for multi-class CGH data. 86-95
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  Chunfang Zheng, Qian Zhu, Zaky Adam, David Sankoff: Guided genome halving: hardness, heuristics and the history of the Hemiascomycetes. 96-104
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  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

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

Gene Regulation and Transcriptomics

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

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

Protein Interactions and Molecular Networks

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  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
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  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
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  Noga Alon, Phuong Dao, Iman Hajirasouliha, Fereydoun Hormozdiari, Süleyman Cenk Sahinalp: Biomolecular network motif counting and discovery by color coding. 241-249
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  Yanjun Qi, Fernanda Balem, Christos Faloutsos, Judith Klein-Seetharaman, Ziv Bar-Joseph: Protein complex identification by supervised graph local clustering. 250-268

Text Mining

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  Thomas J. Lee, Ian T. Paulsen, Peter D. Karp: Annotation-based inference of transporter function. 259-267
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  Roman Klinger, Corinna Kolárik, Juliane Fluck, Martin Hofmann-Apitius, Christoph M. Friedrich: Detection of IUPAC and IUPAC-like chemical names. 268-276
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  Arzucan Özgür, Thuy Vu, Günes Erkan, Dragomir R. Radev: Identifying gene-disease associations using centrality on a literature mined gene-interaction network. 277-285
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  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

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  Larisa N. Soldatova, Wayne Aubrey, Ross D. King, Amanda Clare: The EXACT description of biomedical protocols. 295-303
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  Kenneth McLeod, Albert Burger: Towards the use of argumentation in bioinformatics: a gene expression case study. 304-312
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  Stefan Schulz, Holger Stenzhorn, Martin Boeker: The ontology of biological taxa. 313-321
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  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

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  Curtis Huttenhower, Olga G. Troyanskaya: Assessing the functional structure of genomic data. 330-338
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  Sean McIlwain, David Page, Edward L. Huttlin, Michael R. Sussman: Matching isotopic distributions from metabolically labeled samples. 339-347
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  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
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  Pierre Baldi, Ryan W. Benz: BLASTing small molecules - statistics and extreme statistics of chemical similarity scores. 357-365
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  Yiqun Cao, Tao Jiang, Thomas Girke: A maximum common substructure-based algorithm for searching and predicting drug-like compounds. 366-374
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  Franck Rapaport, Emmanuel Barillot, Jean-Philippe Vert: Classification of arrayCGH data using fused SVM. 375-382

Bioinformatics of Disease

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  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
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  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
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  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
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  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

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

last updated on Tue May 21 02:13:15 2013 by the dblp team
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