Rumen Andonov

According to our database, Rumen Andonov authored at least 57 papers between 1991 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

Global exact optimisations for chloroplast structural haplotype scaffolding.

Victor Epain, Rumen Andonov

Algorithms Mol. Biol., December, 2024

Assembling Close Strains in Metagenome Assemblies Using Discrete Optimization.

Tam Khac Minh Truong, Roland Faure, Rumen Andonov

Proceedings of the 17th International Joint Conference on Biomedical Engineering Systems and Technologies, 2024

2020

Optimization Approach to Accelerator Codesign.

Nirmal Prajapati, Sanjay V. Rajopadhye, Hristo N. Djidjev, Nandakishore Santhi, Tobias Grosser, Rumen Andonov

IEEE Trans. Comput. Aided Des. Integr. Circuits Syst., 2020

2019

Complete assembly of circular and chloroplast genomes based on global optimization.

Rumen Andonov, Hristo N. Djidjev, Sebastien François, Dominique Lavenier

J. Bioinform. Comput. Biol., 2019

2018

Global Optimization for Scaffolding and Completing Genome Assemblies.

Sebastien François, Rumen Andonov, Dominique Lavenier, Hristo N. Djidjev

Electron. Notes Discret. Math., 2018

2017

Accelerator Codesign as Non-Linear Optimization.

Nirmal Prajapati, Sanjay V. Rajopadhye, Hristo N. Djidjev, Nandakishore Santhi, Tobias Grosser, Rumen Andonov

CoRR, 2017

Simple, Accurate, Analytical Time Modeling and Optimal Tile Size Selection for GPGPU Stencils.

Nirmal Prajapati, Waruna Ranasinghe, Sanjay V. Rajopadhye, Rumen Andonov, Hristo N. Djidjev, Tobias Grosser

Proceedings of the 22nd ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, 2017

2015

Parallel Seed-Based Approach to Multiple Protein Structure Similarities Detection.

Guillaume Chapuis, Mathilde Le Boudic-Jamin, Rumen Andonov, Hristo N. Djidjev, Dominique Lavenier

Sci. Program., 2015

All-Pairs Shortest Path algorithms for planar graph for GPU-accelerated clusters.

Hristo N. Djidjev, Guillaume Chapuis, Rumen Andonov, Sunil Thulasidasan, Dominique Lavenier

J. Parallel Distributed Comput., 2015

Automatic Classification of Protein Structure Using the Maximum Contact Map Overlap Metric.

Rumen Andonov, Hristo N. Djidjev, Gunnar W. Klau, Mathilde Le Boudic-Jamin, Inken Wohlers

Algorithms, 2015

Energy Modeling and Optimization for Tiled Nested-Loop Codes.

Nirmal Prajapati, Waruna Ranasinghe, Vamshi Tandrapati, Rumen Andonov, Hristo N. Djidjev, Sanjay V. Rajopadhye

Proceedings of the 2015 IEEE International Parallel and Distributed Processing Symposium Workshop, 2015

2014

Efficient Multi-GPU Computation of All-Pairs Shortest Paths.

Hristo N. Djidjev, Sunil Thulasidasan, Guillaume Chapuis, Rumen Andonov, Dominique Lavenier

Proceedings of the 2014 IEEE 28th International Parallel and Distributed Processing Symposium, 2014

Exact Protein Structure Classification Using the Maximum Contact Map Overlap Metric.

Inken Wohlers, Mathilde Le Boudic-Jamin, Hristo N. Djidjev, Gunnar W. Klau, Rumen Andonov

Proceedings of the Algorithms for Computational Biology - First International Conference, 2014

2013

DALIX: Optimal DALI Protein Structure Alignment.

Inken Wohlers, Rumen Andonov, Gunnar W. Klau

IEEE ACM Trans. Comput. Biol. Bioinform., 2013

Parallel Seed-Based Approach to Protein Structure Similarity Detection.

Guillaume Chapuis, Mathilde Le Boudic-Jamin, Rumen Andonov, Hristo N. Djidjev, Dominique Lavenier

Proceedings of the Parallel Processing and Applied Mathematics, 2013

2012

CSA: comprehensive comparison of pairwise protein structure alignments.

Inken Wohlers, Noël Malod-Dognin, Rumen Andonov, Gunnar W. Klau

Nucleic Acids Res., 2012

2011

Algorithm engineering for optimal alignment of protein structure distance matrices.

Inken Wohlers, Rumen Andonov, Gunnar W. Klau

Optim. Lett., 2011

Maximum Contact Map Overlap Revisited.

Rumen Andonov, Noël Malod-Dognin, Nicola Yanev

J. Comput. Biol., 2011

Local protein threading by Mixed Integer Programming.

Guillaume Collet, Rumen Andonov, Nicola Yanev, Jean-François Gibrat

Discret. Appl. Math., 2011

Using Dominances for Solving the Protein Family Identification Problem.

Noël Malod-Dognin, Mathilde Le Boudic-Jamin, Pritish Kamath, Rumen Andonov

Proceedings of the Algorithms in Bioinformatics - 11th International Workshop, 2011

Sparsifying Distance Matrices for Protein-Protein Structure Alignments.

Antonio Mucherino, Inken Wohlers, Gunnar W. Klau, Rumen Andonov

Proceedings of the 10th Cologne-Twente Workshop on graphs and combinatorial optimization. Extended Abstracts, 2011

2010

Maximum Cliques in Protein Structure Comparison.

Noël Malod-Dognin, Rumen Andonov, Nicola Yanev

Proceedings of the Experimental Algorithms, 9th International Symposium, 2010

SHREC'10 Track: Protein Model Classification.

Lazaros Mavridis, Vishwesh Venkatraman, David W. Ritchie, Naoto Morikawa, Rumen Andonov, Alexandre Cornu, Noël Malod-Dognin, Jacques Nicolas, Maja Temerinac-Ott, Marco Reisert, Hans Burkhardt, Apostolos Axenopoulos, Petros Daras

Proceedings of the 3rd Eurographics Workshop on 3D Object Retrieval, 2010

2009

A hybrid algorithm for the unbounded knapsack problem.

Vincent Poirriez, Nicola Yanev, Rumen Andonov

Discret. Optim., 2009

Protein Threading.

Guillaume Collet, Rumen Andonov, Nicola Yanev, Jean-François Gibrat

Proceedings of the 8th Cologne-Twente Workshop on Graphs and Combinatorial Optimization, 2009

2008

A dynamic programming based reduction procedure for the multidimensional 0-1 knapsack problem.

Stefan Balev, Nicola Yanev, Arnaud Fréville, Rumen Andonov

Eur. J. Oper. Res., 2008

Lagrangian approaches for a class of matching problems in computational biology.

Nicola Yanev, Rumen Andonov, Philippe Veber, Stefan Balev

Comput. Math. Appl., 2008

An Efficient Lagrangian Relaxation for the Contact Map Overlap Problem.

Rumen Andonov, Nicola Yanev, Noël Malod-Dognin

Proceedings of the Algorithms in Bioinformatics, 8th International Workshop, 2008

2007

Recent Advances in Solving the Protein Threading Problem

Rumen Andonov, Guillaume Collet, Jean-François Gibrat, Antoine Marin, Vincent Poirriez, Nicola Yanev

CoRR, 2007

Recent Advances in Solving the Protein Threading Problem.

Rumen Andonov, Guillaume Collet, Jean-François Gibrat, Antoine Marin, Vincent Poirriez, Nicola Yanev

Proceedings of the Grid Computing for Bioinformatics and Computational Biology, 2007

2005

Dynamic programming for LR-PCR segmentation of bacterium genomes.

Rumen Andonov, Dominique Lavenier, Philippe Veber, Nicola Yanev

Concurr. Comput. Pract. Exp., 2005

Optimal Protein Threading by Cost-Splitting.

Philippe Veber, Nicola Yanev, Rumen Andonov, Vincent Poirriez

Proceedings of the Algorithms in Bioinformatics, 5th International Workshop, 2005

FROST: Revisited and Distributed.

Vincent Poirriez, Rumen Andonov, Antoine Marin, Jean-François Gibrat

Proceedings of the 19th International Parallel and Distributed Processing Symposium (IPDPS 2005), 2005

2004

Protein Threading: From Mathematical Models to Parallel Implementations.

Rumen Andonov, Stefan Balev, Nicola Yanev

INFORMS J. Comput., 2004

Parallel divide and conquer approach for the protein threading problem.

Nicola Yanev, Rumen Andonov

Concurr. Pract. Exp., 2004

Dynamic Programming for LR-PCR Segmention of Bacterium Genomes.

Rumen Andonov, Dominique Lavenier, Philippe Veber, Nicola Yanev

Proceedings of the 18th International Parallel and Distributed Processing Symposium (IPDPS 2004), 2004

2003

Optimal Semi-Oblique Tiling.

Rumen Andonov, Stephan Balev, Sanjay V. Rajopadhye, Nicola Yanev

IEEE Trans. Parallel Distributed Syst., 2003

On the parallel prediction of the RNA secondary structure.

Francisco Almeida, Rumen Andonov, Luz Marina Moreno, Vincent Poirriez, Melquíades Pérez Pérez, Casiano Rodríguez

Proceedings of the Parallel Computing: Software Technology, 2003

Solving the Protein Threading Problem in Parallel.

Nicola Yanev, Rumen Andonov

Proceedings of the 17th International Parallel and Distributed Processing Symposium (IPDPS 2003), 2003

2002

Optimal tiling for the RNA base pairing problem.

Francisco Almeida, Rumen Andonov, Daniel González, Luz Marina Moreno, Vincent Poirriez, Casiano Rodríguez

Proceedings of the Fourteenth Annual ACM Symposium on Parallel Algorithms and Architectures, 2002

2000

Unbounded knapsack problem: Dynamic programming revisited.

Rumen Andonov, Vincent Poirriez, Sanjay V. Rajopadhye

Eur. J. Oper. Res., 2000

1999

Tiling and Processors Allocation for Three Dimensional Iteration Space.

Hafid Bourzoufi, Benamar Sidi-Boulenouar, Rumen Andonov

Proceedings of the High Performance Computing, 1999

A Parallel Branch-and-Bound Algorithm for the Classification Problem.

Stephan Balev, Rumen Andonov, Arnaud Fréville

Proceedings of the High Performance Computing, 1999

1998

Optimal Orthogonal Tiling.

Rumen Andonov, Sanjay V. Rajopadhye, Nicola Yanev

Proceedings of the Euro-Par '98 Parallel Processing, 1998

1997

Knapsack on VLSI: from Algorithm to Optimal Circuit.

Rumen Andonov, Sanjay V. Rajopadhye

IEEE Trans. Parallel Distributed Syst., 1997

Optimal Orthogonal Tiling of 2-D Iterations.

Rumen Andonov, Sanjay V. Rajopadhye

J. Parallel Distributed Comput., 1997

Three-dimensional orthogonal tile sizing problem: mathematical programming approach.

Rumen Andonov, Nicola Yanev, Hafid Bourzoufi

Proceedings of the 1997 International Conference on Application-Specific Systems, 1997

1996

A Regular VLSI Array for an Irregular Algorithm.

Florent de Dinechin, Doran Wilde, Sanjay V. Rajopadhye, Rumen Andonov

Proceedings of the Parallel Algorithms for Irregularly Structured Problems, 1996

Two-dimensional orthogonal tiling: from theory to practice.

Rumen Andonov, Hafid Bourzoufi, Sanjay V. Rajopadhye

Proceedings of the 3rd International Conference on High Performance Computing, 1996

1995

A Shift Registered-Based Systolic Array for the Unbounded Knapsack Problem.

Rumen Andonov, Patrice Quinton, Sanjay V. Rajopadhye, Doran Wilde

Parallel Process. Lett., 1995

1994

Pure Systolic Array for a Class of Dynamic Dependency Recurrences.

Rumen Andonov, Patrice Quinton, Sanjay V. Rajopadhye, Doran Wilde

Proceedings of the Parcella 1994, 1994

Optimal Tile Sizing.

Rumen Andonov, Sanjay V. Rajopadhye

Proceedings of the Parallel Processing: CONPAR 94, 1994

A sparse knapsack algo-tech-cuit and its synthesis.

Rumen Andonov, Sanjay V. Rajopadhye

Proceedings of the International Conference on Application Specific Array Processors, 1994

1993

An optimal algo-tech-cuit for the knapsack problem.

Rumen Andonov, Sanjay V. Rajopadhye

Proceedings of the International Conference on Application-Specific Array Processors, 1993

1992

Efficient Linear Systolic Array for the Knapsack Problem.

Rumen Andonov, Patrice Quinton

Proceedings of the Parallel Processing: CONPAR 92, 1992

1991

A 2D toroidal systolic array for the knapsack problem.

Rumen Andonov, Frédéric Gruau

Proceedings of the Algorithms and Parallel VLSI Architectures II, 1991

A modular systolic 2-D torus for the general knapsack problem.

Rumen Andonov, Frédéric Gruau

Proceedings of the Application Specific Array Processors, 1991