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Integer Programming Approach for Nested Pairs Genome Scaffolding

 Victor Epain , Rumen Andonov
2022
Pré-publication, Document de travail hal-03613353v1
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Comparing Protein 3D Structures Using A_purva

 Noël Malod-Dognin , Nicola Yanev , Rumen Andonov
[Research Report] RR-7464, INRIA. 2010, pp.9
Rapport inria-00539939v1
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Lagrangian Approaches for a class of Matching Problems in Computational Biology

 Nicola Yanev , Rumen Andonov , Philippe Veber , Stefan Balev
[Research Report] PI 1814, 2006, pp.18
Rapport inria-00091944v1

Local protein threading by Mixed Integer Programming

 Guillaume Collet , Rumen Andonov , Jean-François Gibrat , Nicola Yanev
Discrete Applied Mathematics, 2011, 159 (16), pp.1707-1716. ⟨10.1016/j.dam.2010.05.024⟩
Article dans une revue inria-00536537v1
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GenoFrag: software to design primers optimized for whole genome scanning by long-range PCR amplification.

 Nouri Ben Zakour , Michel Gautier , Rumen Andonov , Dominique Lavenier , Marie-Françoise Cochet , et al.
Nucleic Acids Research, 2004, 32 (1), pp.17-24. ⟨10.1093/nar/gkg928⟩
Article dans une revue hal-01454461v1
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Global Optimization for Scafolding and Completing Genome Assemblies

 Sebastien François , Rumen Andonov , Dominique Lavenier , Hristo Djidjev
12th International Workshop on Constraint-Based Methods for Bioinformatics, Sep 2016, Toulouse, France
Communication dans un congrès hal-01567134v1
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Assembling close strains in metagenome assemblies using discrete optimization

 Tam Khac Minh Truong , Roland Faure , Rumen Andonov
BIOINFORMATICS 2024 - 15th International conference on bioinformatics models, methods and algorithms, Feb 2024, Rome, Italy. pp.1-10
Communication dans un congrès hal-04349675v1
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Recent Advances in Solving the Protein Threading Problem

 Rumen Andonov , Guillaume Collet , Jean-François Gibrat , Antoine Marin , Vincent Poirriez , et al.
[Research Report] PI 1856, 2007, pp.38
Rapport inria-00170619v1
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Lagrangian Approaches for a class of Matching Problems in Computational Biology

 Nicola Yanev , Rumen Andonov , Philippe Veber , Stefan Balev
[Research Report] RR-5973, INRIA. 2006
Rapport inria-00090635v2
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A Hybrid Algorithm for the Unbounded Knapsack Problem

 Vincent Poirriez , Nicola Yanev , Rumen Andonov
Discrete Optimization, 2009, 6, pp.110-124. ⟨10.1016/j.disopt.2008.09.004⟩
Article dans une revue inria-00335065v1
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Détection de domaines dans des séquences génomiques : un problème de couverture optimale

 Philippe Veber , Sébastien Tempel , Rumen Andonov , Dominique Lavenier , Jacques Nicolas
FRANCORO V/ROADEF 2007, Feb 2007, Grenoble, France
Communication dans un congrès hal-00186471v1
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Parallel seed-based approach to multiple protein structure similarities detection

 Guillaume Chapuis , Mathilde Le Boudic-Jamin , Rumen Andonov , Hristo Djidjev , Dominique Lavenier
2014
Pré-publication, Document de travail hal-01093809v1

Energy Modeling and Optimization for Tiled Nested-Loop Codes

 Nirmal Prajapati , Waruna Ranasinghe , Vamsi Krishna Tandrapati , Rumen Andonov , Hristo Djidjev , et al.
Parallel and Distributed Processing Symposium Workshop (IPDPSW), May 2015, Hyderabad India. pp.888 - 895 ⟨10.1109/IPDPSW.2015.94⟩
Communication dans un congrès hal-01250602v1

GPU-accelerated shortest paths computations for planar graphs

 Guillaume Chapuis , Hristo Djidjev , Dominique Lavenier , Rumen Andonov
Hamid Azad Advances in GPU Research and Practice , Elsevier, pp.774, 2016, 9780128037386
Chapitre d'ouvrage hal-01385634v1
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Maximum Cliques in Protein Structure Comparison

 Noël Malod-Dognin , Rumen Andonov , Nicola Yanev
SEA 2010 9th International Symposium on Experimental Algorithms, May 2010, Naples, Italy. pp.106-117, ⟨10.1007/978-3-642-13193-6_10⟩
Communication dans un congrès inria-00536700v1
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Automatic Classification of Protein Structure Using the Maximum Contact Map Overlap Metric

 Rumen Andonov , Hristo Djidjev , Gunnar Klau , Mathilde Boudic-Jamin , Inken Wohlers
Algorithms, 2015, 8 (4), ⟨10.3390/a8040850⟩
Article dans une revue hal-01248543v1

Lagrangian approaches for a class of matching problems in computational biology

 Nicola Yanev , Rumen Andonov , Philippe Veber , Stefan Balev
Computers & Mathematics with Applications, 2008, 55 (Issue 5 (March 2008)), pp.1054-1067. ⟨10.1016/j.camwa.2006.12.103⟩
Article dans une revue inria-00335126v1
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Assemblage de Novo de Longues Lectures Par Programmation Linéaire

 Victor Epain , Rumen Andonov , Hristo Djidjev , Dominique Lavenier
2020
Pré-publication, Document de travail hal-03007132v1
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Solving Maximum Clique Problem for Protein Structure Similarity

 Noël Malod-Dognin , Rumen Andonov , Nicola Yanev
[Research Report] RR-6818, INRIA. 2009, pp.12
Rapport inria-00356816v1

Solving Maximum Clique Problem for Protein Structure Similarity

 Noël Malod-Dognin , Rumen Andonov , Nicola Yanev
Serdica Journal of Computing, 2010, 4 (1), pp.93--100
Article dans une revue hal-00849979v1
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The PROTEUS project: Improving large-scale structure prediction for proteins

 T. Simonson , R. Andonov , Jean-François Gibrat , J. Pothier , Yh Sanejouand
journée restitution ANR Calcul Intensif et Simulation, Feb 2010, Paris, France. 39 p
Communication dans un congrès hal-02818506v1
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Automatic Classification of Protein Structures Using the Maximum Contact Map Overlap Metric

 Rumen Andonov , Hristo Djidjev , Klau Gunnar , Mathilde Le Boudic-Jamin , Inken Wohlers
Algorithms, 2015, Special Issue Algorithmic Themes in Bioinformatics, Volume 8 (Issue 4), pp.20. ⟨10.3390/a8040850⟩
Article dans une revue hal-01250539v1
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Maximum Cliques in Protein Structure Comparison

 Noël Malod-Dognin , Rumen Andonov , Nicola Yanev
[Research Report] RR-7053, INRIA. 2009, pp.19
Rapport inria-00422198v1

Le projet GénoGRID : une grille expérimentale pour la génomique

 Dominique Lavenier , Hugues Leroy , Michel Hurfin , Rumen Andonov , L. Mouchard , et al.
Journées Ouvertes Biologie Informatique et Mathématiques, 2002, Saint Malo, France. pp.27-32
Communication dans un congrès hal-00465092v1
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Overlap Graphs for Assembling and Scaffolding Algorithms: Paradigm Review and Implementation Proposals

 Victor Epain , Rumen Andonov
2022
Pré-publication, Document de travail hal-03878293v1
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Inverted Repeats Scaffolding for a Dedicated Chloroplast Genome Assembler

 Victor Epain , Dominique Lavenier , Rumen Andonov
2022
Pré-publication, Document de travail hal-03684406v1
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Global Optimization for Scaffolding and Completing Genome Assemblies

 Sebastien François , Rumen Andonov , Dominique Lavenier , Hristo Djidjev
Electronic Notes in Discrete Mathematics, 2018
Article dans une revue hal-03697534v1
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Global Optimization for Scaffolding and Completing Genome Assemblies

 Sebastien François , Rumen Andonov , Dominique Lavenier , Hristo Djidjev
International Network Optimization Conference , European Network Optimization Group (ENOG), Feb 2017, Lisboa, Portugal. pp.15
Communication dans un congrès hal-01499859v1
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Towards Structural Classification of Proteins based on Contact Map Overlap

 Rumen Andonov , Nicola Yanev , Noël Malod-Dognin
[Research Report] RR-6370, INRIA. 2007, pp.20
Rapport inria-00192206v2
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Efficient Multi-GPU Algorithm for All-Pairs Shortest Paths

 Guillaume Chapuis , Hristo Djidjev , Rumen Andonov , Sunil Thulasidasan , Dominique Lavenier
IPDPS 2014, Manish Parashar, May 2014, Phoenix, United States
Communication dans un congrès hal-00905738v1
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