Genome-Scale Computational Approaches to Memory-Intensive Applications in Systems Biology
SC '05 Proceedings of the 2005 ACM/IEEE conference on Supercomputing
Innovative computational methods for transcriptomic data analysis
Proceedings of the 2006 ACM symposium on Applied computing
A Stochastic Local Search Approach to Vertex Cover
KI '07 Proceedings of the 30th annual German conference on Advances in Artificial Intelligence
Matching of anatomical tree structures for registration of medical images
Image and Vision Computing
Combinatorial genetic regulatory network analysis tools for high throughput transcriptomic data
RECOMB'05 Proceedings of the 2005 joint annual satellite conference on Systems biology and regulatory genomics
Algorithms and theory of computation handbook
The maximum clique enumeration problem: algorithms, applications and implementations
ISBRA'11 Proceedings of the 7th international conference on Bioinformatics research and applications
A systematic comparison of genome scale clustering algorithms
ISBRA'11 Proceedings of the 7th international conference on Bioinformatics research and applications
The cluster editing problem: implementations and experiments
IWPEC'06 Proceedings of the Second international conference on Parameterized and Exact Computation
A parameterized complexity tutorial
LATA'12 Proceedings of the 6th international conference on Language and Automata Theory and Applications
A basic parameterized complexity primer
The Multivariate Algorithmic Revolution and Beyond
Distributed memorization for the k-vertex cover problem
ISPA'07 Proceedings of the 5th international conference on Parallel and Distributed Processing and Applications
Parallel vertex cover: a case study in dynamic load balancing
AusPDC '11 Proceedings of the Ninth Australasian Symposium on Parallel and Distributed Computing - Volume 118
The use of fast approximate graph coloring to enhance exact parallel algorithm performance
AusPDC '12 Proceedings of the Tenth Australasian Symposium on Parallel and Distributed Computing - Volume 127
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Algorithmic methods based on the theory of fixed-parameter tractability are combined with powerful computational platforms to launch systematic attacks on combinatorial problems of significance. As a case study, optimal solutions to very large instances of the NP-hard vertex cover problem are computed. To accomplish this, an efficient sequential algorithm and various forms of parallel algorithms are devised, implemented, and compared. The importance of maintaining a balanced decomposition of the search space is shown to be critical to achieving scalability. Target problems need only be amenable to reduction and decomposition. Applications in high throughput computational biology are also discussed.