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16th ISMB 2008: Toronto, Canada (Supplement of Bioinformatics)
- Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), Toronto, Canada, July 19-23, 2008. 2008
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
The effectiveness of position- and composition-specific gap costs for protein similarity searches. 15-23 - Thomas Abeel
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
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
Estimating true evolutionary distances under the DCJ model. 114-122 - Cuong Than, R. Sugino, Hideki Innan
Efficient inference of bacterial strain trees from genome-scale multilocus data. 123-131 - Mukul S. Bansal
The multiple gene duplication problem revisited. 132-138
Gene Regulation and Transcriptomics
- Moran Yassour
Nucleosome positioning from tiling microarray data. 139-146 - Tien-ho Lin, Naftali Kaminski
Alignment and classification of time series gene expression in clinical studies. 147-155 - Ivan G. Costa
Inferring differentiation pathways from gene expression. 156-164 - Lucas D. Ward
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
Designing succinct structural alphabets. 182-189 - Ludovica Montanucci
Predicting protein thermostability changes from sequence upon multiple mutations. 190-195 - Ivelin Georgiev, Daniel A. Keedy
Algorithm for backrub motions in protein design. 196-204 - Fei Xiong, Gopal Pandurangan
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
Identifying functional modules in protein-protein interaction networks: an integrated exact approach. 223-231 - Yoshihiro Yamanishi, Michihiro Araki, Alex Gutteridge
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
Protein complex identification by supervised graph local clustering. 250-268
Text Mining
- Thomas J. Lee, Ian T. Paulsen
Annotation-based inference of transporter function. 259-267 - Roman Klinger
Detection of IUPAC and IUPAC-like chemical names. 268-276 - Arzucan Özgür
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
The EXACT description of biomedical protocols. 295-303 - Kenneth McLeod
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
GenoQuery: a new querying module for functional annotation in a genomic warehouse. 322-329
Other Bioinformatics Applications and Methods
- Curtis Huttenhower
Assessing the functional structure of genomic data. 330-338 - Sean McIlwain, David Page, Edward L. Huttlin
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
A maximum common substructure-based algorithm for searching and predicting drug-like compounds. 366-374 - Franck Rapaport
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
Assessment and improvement of the Plasmodium yoelii yoelii genome annotation through comparative analysis. 383-389 - Joshua Wing Kei Ho
Differential variability analysis of gene expression and its application to human diseases. 390-398 - Michal Rosen-Zvi
Selecting anti-HIV therapies based on a variety of genomic and clinical factors. 399-406 - Yuan Wang, Xiaobo Zhou, Honghui Wang, King C. Li
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
Multi-spectra peptide sequencing and its applications to multistage mass spectrometry. 416-423
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