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» Generalization Methods in Bioinformatics
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SAC
2004
ACM
15 years 11 months ago
Guiding motif discovery by iterative pattern refinement
In this paper, we demonstrate that the performance of a motif discovery algorithm can be significantly improved by embedding it into a novel framework that effectively guides the ...
Zhiping Wang, Mehmet M. Dalkilic, Sun Kim
FTML
2008
185views more  FTML 2008»
15 years 6 months ago
Graphical Models, Exponential Families, and Variational Inference
The formalism of probabilistic graphical models provides a unifying framework for capturing complex dependencies among random variables, and building large-scale multivariate stat...
Martin J. Wainwright, Michael I. Jordan
ISBRA
2010
Springer
16 years 22 days ago
Uncovering Hidden Phylogenetic Consensus
Abstract. Many of the steps in phylogenetic reconstruction can be confounded by “rogue” taxa, taxa that cannot be placed with assurance anywhere within the tree—whose locatio...
Nicholas D. Pattengale, Krister M. Swenson, Bernar...
BIBE
2008
IEEE
142views Bioinformatics» more  BIBE 2008»
16 years 22 days ago
Optimizing performance, cost, and sensitivity in pairwise sequence search on a cluster of PlayStations
— The Smith-Waterman algorithm is a dynamic programming method for determining optimal local alignments between nucleotide or protein sequences. However, it suffers from quadrati...
Ashwin M. Aji, Wu-chun Feng
BIBM
2008
IEEE
217views Bioinformatics» more  BIBM 2008»
16 years 22 days ago
Combining Hierarchical Inference in Ontologies with Heterogeneous Data Sources Improves Gene Function Prediction
The study of gene function is critical in various genomic and proteomic fields. Due to the availability of tremendous amounts of different types of protein data, integrating thes...
Xiaoyu Jiang, Naoki Nariai, Martin Steffen, Simon ...