Nicolas Maillet

nico.maillet@gmail.com
http://siteactif.org
Curriculum Vitae: color or black & white

I am a post-doctoral researcher in bioinformatics at Laboratory of Ecology and Evolution of Plankton in Stazione Zoologica Anton Dohrn of Naples, Italy.
I previously did a PhD in bioinformatics at INRIA/IRISA, Université de Rennes 1, Rennes (France), under the supervision of Dominique Lavenier and Pierre Peterlongo.



Research interests

(Comparative) metagenomics analysis
NGS technology
Algorithms
Interdisciplinary work
Nicolas-Maillet




Software

Meteor (“Metagenome: each one of reads”)
Remove duplicate reads from huge metagenomes. Combined with Commet, it will provide informations about α and β-diversity, in progress.

Commet (“Compare multiple metagenomes”)
Provides a global similarity overview between all datasets of a large metagenomic project, directly from non-assembled reads, described in [5].

Compareads
Extract similar reads between two potentially huge metagenomic datasets, described in [3].



Publications

[5] N. Maillet, G. Collet, T. Vannier, D. Lavenier, P. Peterlongo, Commet: comparing and combining multiple metagenomic datasets, Bioinformatics and Biomedicine (BIBM) (Acceptance ratio: 19%), IEEE International Conference, Belfast (Nov. 2014) [PDF] [Webpage]

[4] K. R. Bradnam, J. N. Fass, A. Alexandrov, P. Baranay, M. Bechner et al., Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species, Gigascience (Jan. 2013) [Open-access]

[3] N. Maillet, C. Lemaitre, R. Chikhi, D. Lavenier, P. Peterlongo, Compareads: comparing huge metagenomic experiments, BMC Bioinformatics (Dec. 2012) [Open-access] [Webpage]

[2] S. Renaut, N. Maillet, E. Normandeau, C. Sauvage, N. Derome, S. M. Rogers, L. Bernatchez, Genome-wide patterns of divergence during speciation: the lake whitefish case study, Philosophical Transactions of the Royal Society B: Biological Sciences (Feb. 2012) [Open-access]

[1] D. Earl, K. Bradnam, J. St John, A. Darling, D. Lin et al., Assemblathon 1: a competitive assessment of de novo short read assembly methods, Genome Research (Dec. 2011) [Open-access]



Award

Best poster among 112 in JOBIM conference, 2012. Compareads: comparing huge metagenomic experiments [PDF]



Reports

N. Maillet, De novo comparision of huge metagenomic experiments coming from NGS technologies : application on Tara Oceans project, PhD Thesis, 2010-2013 [PDF (fr)]




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