PhD

• Title: Parallel computing for intensive comparison of genomic sequences

• Manuscript (2.5 MB french)

• Slides (3 MB french)

Journals

• V.H. Nguyen, D. Lavenier, PLAST: parallel local alignment search tool for database comparison, BMC Bioinformatics 2009 10(329). (link)

• P. Peterlongo, L. Noé, D. Lavenier, V.H. Nguyen, G. Kucherov, M. Giraud, Optimal neighborhood indexing for protein similarity search, BMC Bioinformatics 2008 9(534). (link)

Conferences

• V.H. Nguyen, A. Cornu, D. Lavenier, Implementing Protein Seed-Based Comparison Algorithm on the SGI RASC-100 Platform, 16th Reconfigurable Architectures Workshop - IPDPS, Rome, Italy, May 2009. (pdf)

• Y. Xiaochun, V.H. Nguyen, D. Lavenier, F. Dongruy, Efficient Parallelization of a Protein Sequence Comparison Algorithm on Manycore Architecture, Ninth International Conference on Parallel and Distributed Computing, Applications and Technologies, Dunedin, New Zealand, 2008. (pdf)

• V.H. Nguyen, D. Lavenier, Speeding up Subset Seed Algorithm for Intensive Protein Sequence Comparison, 6th IEEE International Conference on research, innovation & vision for the future, Ho Chi Minh Ville, Vietnam, 2008. (pdf)

• V.H. Nguyen, D. Lavenier, Comparaison intensive des séquences protéiques : indexation des banques et usage des instructions SIMD des microprocesseurs, JOBIM 2008, Lille, France, 2008. (pdf)

• V.H. Nguyen, D. Lavenier, Parallélisation de la recherche de similarités entre séquences protéiques sur GPU, RenPar'18 : Rencontres francophones du Parallélisme, Fribourg, Suisse, 2008. (pdf)

• V.H. Nguyen, D. Lavenier, Recherche dans les banques d'ADN par indexation parallèle, 4th International Conference on research, innovation & vision for the future, Ho Chi Minh Ville, Vietnam, 2006. (pdf)

Reports

• V.H. Nguyen, D. Lavenier, Fine-grained Parallelization of Similarity Search Between Protein Sequences, INRIA Report, (RR-6513), 2008. (pdf)

Available tool

• PLAST: parallel local alignment search tool for database comparison