Protein Alignment on UPMEM PiM Architecture
D. Lavenier
1st minisymposium on applications and benefits of UPMEM commercial Massively Parallel Processing-in-Memory Platform, EURO-PAR 2023, Limassol, Cyprus, Aug. 2023
Exploring genomic algorithms on Processing-in-Memory Architecture
Keynote speaker
D. Lavenier
5th Workshop on Accelerator Architecture in Computational Biology and Bioinformatics, ISCA 2023, Orlando, Florida, USA, June 2023
Data Storage on DNA
Invited Speaker
D. Lavenier
IDA 2022, Symposium on Intelligent Data Analysis, 20-22 April 2022, Rennes, France
Storing the declaration of human rights on one data DNA molecule
Gouenou Coatrieux, Chloé Berton, Elsa Dupraz, Belaid Hamoum, Thomas Derrien, Yann Audic, Dominique Lavenier, Jacques Nicolas, Julien Leblanc, Olivier Boulle, Emeline Roux
CominLabs day, Oct 2022, Rennes, France
Hairsplitter: Separating noisy long reads into an unknown number of haplotypes
R. Faure, D. Lavenier
Genome Informatics, Sep 2022, London / Virtual, United Kingdom
Processing-in-Memory to speed up NGS analysis
D. Lavenier
Sequencing to Function: Analysis and Application for the Future, Jun 2022, Santa Fe, United States.
Secure data storage into DNA molecules compliant with biological constraints: Ensuring the confidentiality of data stored into DNA molecules
Chloé Berton, Gouenou Coatrieux, Dominique Lavenier
RITS 2022 – Recherche en Imagerie et Technologies pour la Santé, May 2022, Brest, France
Experimental DNA storage platform
O. Boullé, D. Lavenier
The 1st International Conference on Data Storage in Molecular Media, Mar 2022, Virtual, France
A first proposal fore secure data storage into DNA molecules compliant with biological constraints
C. Berton, G. Coatrieux, D. Lavenier
The 1st International Conference on Data Storage in Molecular Media, Mar 2022, Virtual, France.
Error Correction Schemes for DNA Storage with Nanopore Sequencing
L. Conde-Canencia, B. Hamoum, D. Lavenier, E. Roux
JOBIM 2019 – Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France
SVJedi : Structural variation genotyping using long reads
L. Lecompte, P. Peterlongo, D. Lavenier, C. Lemaitre
HiTSeq 2019 – Conference on High Throughput Sequencing, Jul 2019, Basel, Switzerland
Simka: large scale de novo comparative metagenomics
G. Benoit, P. Peterlongo, M. Mariadassou, E. Drezen, S. Schbath, D. Lavenier, C, Lemaitre
JOBIM 2017 – Journées Ouvertes Biologie Informatique Mathématiques, Jul 2017, Lille, France. pp.234, 2017, JOBIM 2017 LILLE
Simka: fast kmer-based method for estimating the similarity between numerous metagenomic datasets
Best Poster Award
G Benoit, P Peterlongo, D Lavenier, C Lemaitre
JOBIM, French Worshop on Biologie Informatics ans Mathematics, 2015
Assembling Raspberry on Raspberry Pi
D. Lavenier, JM Primat
Personal communication, 2014
The Open Source Genomic Tool Box for Genome Assembly and Analysis
E. Drezen, G. Rizk, R. Chikhi, C. Deltel, C. Lemaitre, P. Peterlongo, D. Lavenier
Bio-IT, Boston, 2014
Speeding up NGS software development
D. Lavenier
Sequencing, Finishing and Analysis in the Future Meeting, Santa Fe, USA, May 2014
MINIA on a Raspberry Pi, Assembling a 100 Mbp Genome on a Credit Card Sized Computer
Best Poster Award
G. Collet, G. Rizk, R. Chikhi, D. Lavenier
JOBIM, French Worshop on Biologie Informatics ans Mathematics, 2013
De novo comparison of metagenomic data.A new tool: Compareads
Best Poster Award
N. Maillet, C. Lemaitre, R. Chikhi, D. Lavenier, P. Peterlongo
JOBIM, French Worshop on Biologie Informatics ans Mathematics, 2012
Next Generation Sequencing Data Processing. How reconfigurable computing can help?
Keynote Speaker
D. Lavenier
International Conference on Engineering of Reconfigurable Systems and Algorithms, 2011
How to accelerate genomic sequence alignment 4X using half an FPGA
A. Cornu, S. Derrien, D. Lavenier,
EE Times Design, vol 7, no 5, 2011
Comparison of large scale metagenomic data in Tara Oceans project
N. Maillet, D. Lavenier, P. Peterlongo
Jacques-Monod Conerence, Integrative Ecological Genomics, 2011
biomanycores.org: a repository of interoperable open-source code for many-core bioinformatics
JF. Berthelot, C. Deltel, M. Giraud, S. Janot,L. Jourdan, D. Lavenier, H. Touzet, JF. Viarré
JOBIM, French Worshop on Biologie Informatics ans Mathematics, 2011
Biomanycores, open-source parallel code for many-core bioinformatics
M. Giraud, S. Janot, JF. Berthelot, C. Deltel, L. Jourdan, D. Lavenier, H. Touzet, JF. Viarré
12th Annual Bioinformatics Open Source Conference, 2011
GPU Accelerted QTLMap
G. Chapuis, O. Filangi, P. Leroy, JM. Elsen, D. Lavenier
15Th QTL-MAS Workshop, 2011
Fine-Grained Parallelism for Genomic Computation
Keynote Speaker
D. Lavenier
SIAM Conf. on Parallel Processing for Scientific Computing, San Francisco, CA, 2006
Optimisation of the NCBI-BLAST code for high throughput in silico comparative genomics in the DEISA project
O. Glorieux, M. Ferré, A, Fouilloux, I. Dupays, D. Raux, D. Lavenier, Y. Malthièry, P. Raynier, Y. Tourmen
JOBIM, French Worshop on Biologie Informatics ans Mathematics, 2005