Zobrazeno 1 - 10
of 62
pro vyhledávání: '"Rumen Andonov"'
Autor:
Victor Epain, Rumen Andonov
Publikováno v:
Algorithms for Molecular Biology, Vol 19, Iss 1, Pp 1-34 (2024)
Abstract Background Scaffolding is an intermediate stage of fragment assembly. It consists in orienting and ordering the contigs obtained by the assembly of the sequencing reads. In the general case, the problem has been largely studied with the use
Externí odkaz:
https://doaj.org/article/a7a4b8b631c04ecbb5b004b3c43352fb
Publikováno v:
Algorithms, Vol 8, Iss 4, Pp 850-869 (2015)
In this work, we propose a new distance measure for comparing two protein structures based on their contact map representations. We show that our novel measure, which we refer to as the maximum contact map overlap (max-CMO) metric, satisfies all prop
Externí odkaz:
https://doaj.org/article/87bbe85e9a374356bb8d6135c27e34bd
Autor:
Sanjay Rajopadhye, Hristo N. Djidjev, Nandakishore Santhi, Rumen Andonov, Tobias Grosser, Nirmal Prajapati
Publikováno v:
IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. 39:1300-1313
We propose an optimization approach for determining both hardware and software parameters for the efficient implementation of a (family of) applications called dense stencil computations on programmable general purpose computing on graphics processin
Publikováno v:
Journal of Bioinformatics and Computational Biology
Journal of Bioinformatics and Computational Biology, World Scientific Publishing, In press, pp.1-28. ⟨10.1142/S0219720019500148⟩
Journal of Bioinformatics and Computational Biology, In press, pp.1-28. ⟨10.1142/S0219720019500148⟩
Journal of Bioinformatics and Computational Biology, World Scientific Publishing, In press, pp.1-28. ⟨10.1142/S0219720019500148⟩
Journal of Bioinformatics and Computational Biology, In press, pp.1-28. ⟨10.1142/S0219720019500148⟩
International audience; This paper focuses on the last two stages of genome assembly, namely, scaffolding and gap-filling, and shows that they can be solved as part of a single optimization problem. Our approach is based on modeling genome assembly a
Publikováno v:
Algorithms
Algorithms, 2015, Special Issue Algorithmic Themes in Bioinformatics, Volume 8 (Issue 4), pp.20. ⟨10.3390/a8040850⟩
Giuseppe Lancia
Algorithms, MDPI, 2015, Special Issue Algorithmic Themes in Bioinformatics, Volume 8 (Issue 4), pp.20. ⟨10.3390/a8040850⟩
Algorithms, 8(4), 850-869
Algorithms, 2015, 8 (4), ⟨10.3390/a8040850⟩
Algorithms, MDPI, 2015, 8 (4), ⟨10.3390/a8040850⟩
Volume 8
Issue 4
Pages 850-869
Algorithms, 8(4), 850-869. MDPI AG
Algorithms, Vol 8, Iss 4, Pp 850-869 (2015)
Andonov, R, Djidjev, H, Klau, G W, Boudic-Jamin, M L & Wohlers, I 2015, ' Automatic classification of protein structure using the maximum contact map overlap metric ', Algorithms, vol. 8, no. 4, pp. 850-869 . https://doi.org/10.3390/a8040850
Algorithms, 2015, Special Issue Algorithmic Themes in Bioinformatics, Volume 8 (Issue 4), pp.20. ⟨10.3390/a8040850⟩
Giuseppe Lancia
Algorithms, MDPI, 2015, Special Issue Algorithmic Themes in Bioinformatics, Volume 8 (Issue 4), pp.20. ⟨10.3390/a8040850⟩
Algorithms, 8(4), 850-869
Algorithms, 2015, 8 (4), ⟨10.3390/a8040850⟩
Algorithms, MDPI, 2015, 8 (4), ⟨10.3390/a8040850⟩
Volume 8
Issue 4
Pages 850-869
Algorithms, 8(4), 850-869. MDPI AG
Algorithms, Vol 8, Iss 4, Pp 850-869 (2015)
Andonov, R, Djidjev, H, Klau, G W, Boudic-Jamin, M L & Wohlers, I 2015, ' Automatic classification of protein structure using the maximum contact map overlap metric ', Algorithms, vol. 8, no. 4, pp. 850-869 . https://doi.org/10.3390/a8040850
In this work, we propose a new distance measure for comparing two protein structures based on their contact map representations. We show that our novel measure, which we refer to as the maximum contact map overlap (max-CMO) metric, satisfies all prop
Publikováno v:
International Network Optimization Conference
International Network Optimization Conference, European Network Optimization Group (ENOG), Feb 2017, Lisboa, Portugal. pp.15
Electronic Notes in Discrete Mathematics
Electronic Notes in Discrete Mathematics, 2018
International Network Optimization Conference, European Network Optimization Group (ENOG), Feb 2017, Lisboa, Portugal. pp.15
Electronic Notes in Discrete Mathematics
Electronic Notes in Discrete Mathematics, 2018
International audience; This work focuses simultaneously on both the scaffolding and gap filling phases of de nouveau genome assembly. Given a set of contigs and their relationships--overlaps and/or remoteness in terms of distances between them--we p
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::02d5532ed4328caa15971b8c6b3cdcaf
https://inria.hal.science/hal-01499859
https://inria.hal.science/hal-01499859
Autor:
Waruna Ranasinghe, Nirmal Prajapati, Hristo N. Djidjev, Rumen Andonov, Sanjay Rajopadhye, Tobias Grosser
Publikováno v:
PPOPP
Stencil computations are an important class of compute and data intensive programs that occur widely in scientific and engineeringapplications. A number of tools use sophisticated tiling, parallelization, and memory mapping strategies, and generate c
Publikováno v:
Wohlers, I, Andonov, R & Klau, G W 2013, ' DALIX: Optimal DALI protein structure alignment ', IEEE/ACM Transactions on Computational Biology and Bioinformatics, no. 10, pp. 26-36 . https://doi.org/10.1109/TCBB.2012.143
IEEE/ACM Transactions on Computational Biology and Bioinformatics
IEEE/ACM Transactions on Computational Biology and Bioinformatics, Institute of Electrical and Electronics Engineers, 2013, IEEE/ACM Transactions on Computational Biology and Bioinformatics 10 (1), pp.20
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2013, IEEE/ACM Transactions on Computational Biology and Bioinformatics 10 (1), pp.20
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 26-36. Institute of Electrical and Electronics Engineers Inc.
ISSUE=10;STARTPAGE=26;ENDPAGE=36;ISSN=1545-5963;TITLE=IEEE/ACM Transactions on Computational Biology and Bioinformatics
IEEE/ACM Transactions on Computational Biology and Bioinformatics
IEEE/ACM Transactions on Computational Biology and Bioinformatics, Institute of Electrical and Electronics Engineers, 2013, IEEE/ACM Transactions on Computational Biology and Bioinformatics 10 (1), pp.20
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2013, IEEE/ACM Transactions on Computational Biology and Bioinformatics 10 (1), pp.20
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 26-36. Institute of Electrical and Electronics Engineers Inc.
ISSUE=10;STARTPAGE=26;ENDPAGE=36;ISSN=1545-5963;TITLE=IEEE/ACM Transactions on Computational Biology and Bioinformatics
International audience; We present a mathematical model and exact algorithm for protein structure alignment using dali scoring, which is an NP-hard problem. dali scoring is based on comparing the inter-residue distance matrices of proteins and is the
Publikováno v:
Advances in GPU Research and Practice
Hamid Azad Advances in GPU Research and Practice, Elsevier, pp.774, 2016, 9780128037386
Hamid Azad Advances in GPU Research and Practice, Elsevier, pp.774, 2016, 9780128037386
We describe three algorithms and their associated graphics processing unit (GPU) implementations for two types of shortest path problems. These implementations target computations on graphs with up to millions of vertices and executions on GPU cluste
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9b191ede6891c6b9fbbc4f4852d5c9e4
https://hal.inria.fr/hal-01385634
https://hal.inria.fr/hal-01385634
Publikováno v:
Journal of Parallel and Distributed Computing
Journal of Parallel and Distributed Computing, Elsevier, 2015, 85, pp.91-103. ⟨10.1016/j.jpdc.2015.06.008⟩
Journal of Parallel and Distributed Computing, 2015, 85, pp.91-103. ⟨10.1016/j.jpdc.2015.06.008⟩
Journal of Parallel and Distributed Computing, Elsevier, 2015, 85, pp.91-103. ⟨10.1016/j.jpdc.2015.06.008⟩
Journal of Parallel and Distributed Computing, 2015, 85, pp.91-103. ⟨10.1016/j.jpdc.2015.06.008⟩
International audience; • We develop a new approach for the All-Pairs Shortest Path problem in planar graphs. • We target execution on large CPU–GPU clusters and graphs with millions of vertices. • We design a centralized (master/slave) and a
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c5153d5fe813a596b8988c2e5ad746d6
https://hal.inria.fr/hal-01235348/file/APSP-JPDC2.pdf
https://hal.inria.fr/hal-01235348/file/APSP-JPDC2.pdf