Unsupervised Learning of Multiple Motifs in Biopolymers Using Expectation Maximization
Machine Learning - Special issue on applications in molecular biology
Finding similar regions in many strings
STOC '99 Proceedings of the thirty-first annual ACM symposium on Theory of computing
Algorithms for phylogenetic footprinting
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
Finding motifs using random projections
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology
Combinatorial Approaches to Finding Subtle Signals in DNA Sequences
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
Spelling Approximate Repeated or Common Motifs Using a Suffix Tree
LATIN '98 Proceedings of the Third Latin American Symposium on Theoretical Informatics
Search algorithms for biosequences using random projection
Search algorithms for biosequences using random projection
Cooperative Metaheuristics for Exploring Proteomic Data
Artificial Intelligence Review
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Verbumculus and the discovery of unusual words
Journal of Computer Science and Technology - Special issue on bioinformatics
Motif discovery by monotone scores
Discrete Applied Mathematics
A new approach to the assessment of the quality of predictions of transcription factor binding sites
Journal of Biomedical Informatics
DNA Motif Representation with Nucleotide Dependency
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Efficient composite pattern finding from monad patterns
International Journal of Bioinformatics Research and Applications
Detection of subtle variations as consensus motifs
Theoretical Computer Science
Efficient discovery of unusual patterns in time series
New Generation Computing
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CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
VARUN: Discovering Extensible Motifs under Saturation Constraints
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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CPM'05 Proceedings of the 16th annual conference on Combinatorial Pattern Matching
Flexible pattern discovery with (extended) disjunctive logic programming
ISMIS'05 Proceedings of the 15th international conference on Foundations of Intelligent Systems
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We introduce the notion of a multiprofile and use it for finding subtle motifs in DNA sequences. Multiprofiles generalize the notion of a profile and allow one to detect subtle consensus sequences that escape detection by the standard profiles. Our MULTIPROFILER algorithm outperforms other leading motif finding algorithms in a number of synthetic models. Moreover, it can be shown that in some previously studied motif models, MULTIPROFILER is capable of pushing the performance envelope to its theoretical limits.