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DALIX: Optimal DALI Protein Structure Alignment
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Inken Wohlers,Rumen Andonov,Gunnar W. Klau
Issue Date:January 2013
pp. 26-36
We present a mathematical model and exact algorithm for optimally aligning protein structures using the DALI scoring model. This scoring model is based on comparing the interresidue distance matrices of proteins and is used in the popular DALI software too...
 
FROST: Revisited and Distributed
Found in: Parallel and Distributed Processing Symposium, International
By Vincent Poirriez, Rumen Andonov, Antoine Marin, Jean-François Gibrat
Issue Date:April 2005
pp. 200a
FROST (Fold Recognition-Oriented Search Tool) is a software whose purpose is to assign a 3D structure to a protein sequence. It is based on a series of filters and uses a database of about 1200 known 3D structures, each one associated with empirically dete...
 
Dynamic Programming for LR-PCR Segmention of Bacterium Genomes
Found in: Parallel and Distributed Processing Symposium, International
By Rumen Andonov, Dominique Lavenier, Philippe Veber, Nicola Yanev
Issue Date:April 2004
pp. 190a
Bacterium genome plasticity can efficiently be studied by Long-Range PCR: genomes of different strains are split into hundreds of short segments which, after LR-PCR amplification, are used to sketch profiles. The segments have : (1) to cover the entire gen...
 
Optimal Semi-Oblique Tiling
Found in: IEEE Transactions on Parallel and Distributed Systems
By Rumen Andonov, Stefan Balev, Sanjay Rajopadhye, Nicola Yanev
Issue Date:September 2003
pp. 944-960
<p><b>Abstract</b>—For 2D iteration space tiling, we address the problem of determining the tile parameters that minimize the total execution time on a parallel machine. We consider uniform dependency computations tiled so that (at least)...
 
Solving the Protein Threading Problem in Parallel
Found in: Parallel and Distributed Processing Symposium, International
By Nicola Yanev, Rumen Andonov
Issue Date:April 2003
pp. 157a
We propose a network flow formulation for protein threading and show its equivalence with the shortest path problem on a graph with a particular structure. The underlying Mixed Integer Programming (MIP) model proves to be very appropriate-huge real-life in...
 
Knapsack on VLSI: from Algorithm to Optimal Circuit
Found in: IEEE Transactions on Parallel and Distributed Systems
By Rumen Andonov, Sanjay Rajopadhye
Issue Date:June 1997
pp. 545-561
<p><b>Abstract</b>—We present a parallel solution to the unbounded knapsack problem on a linear systolic array. It achieves optimal speedup for this well-known, NP-hard problem on a model of computation that is weaker than the PRAM. Our a...
 
DALIX: Optimal DALI Protein Structure Alignment
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Gunnar W. Klau, Inken Wohlers, Rumen Andonov
Issue Date:January 2013
pp. 26-36
We present a mathematical model and exact algorithm for optimally aligning protein structures using the dali scoring model. This scoring model is based on comparing the interresidue distance matrices of proteins and is used in the popular dali software too...
     
Optimal tiling for the RNA base pairing problem
Found in: Proceedings of the fourteenth annual ACM symposium on Parallel algorithms and architectures (SPAA '02)
By Casiano Rodriguez, Daniel Gonzalez, Francisco Almeida, Luz M. Moreno, Rumen Andonov, Vincent Poirriez
Issue Date:August 2002
pp. 173-182
Dynamic programming is an important combinatorial optimization technique that has been widely used in various fields such as control theory, operations research, computational biology and computer science. Many authors have described parallel dynamic progr...
     
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