Anthony Mathelier Ph.D. Postdoctoral Research Fellow Group Wasserman Lab Email Direct line Fax +1 (604) 875-3819

ADDITIONAL CONTACT INFORMATION

EDUCATION

• 2006-2010: PhD under the supervision of Professor Alessandra Carbone ­- Laboratory Genomics of Microorganisms - FRE3214 ­CNRS-UPMC. PhD thesis titled \"Analysis of signals in genomic sequences : Finding microRNAs in eukaryotes - Study of genes distribution in Escherichia coli\" defended in 2010, Sep. 29th
• 2009-2010: Teaching Assistant (Attaché Temporaire d\'Enseignement et de Recherche) - UPMC / UFR Ingénierie 919
• 2006-2009: Teaching Assistant (Moniteur) - CIES-Jussieu ­- UPMC ­/ UFR Ingénierie 919
• 2004-2006: Master of Computer Science (speciality Software Sciences and Technologies) ­- UPMC
• 2003-2004: Bachelor of Computer Science ­- UPMC

RESEARCH INTERESTS

I am currently working as a postdoctoral fellow in Dr. Wyeth W. Wasserman\'s lab on computational prediction of transcription factor binding sites.
During my PhD, I looked for different kind of signals in eukaryotic and prokaryotic genomes.
MicroRNAs are a class of endogenes of 18-25nt long derived from a precursor and involved in post-transcriptional regulation. Studies showed that the analysis of microRNAs\' expression levels may improve the diagnostic of unknown cancers. We proposed two complementary in silico approaches for finding microRNAs in eukaryotic genomes. The first one predicts microRNAs from already known microRNAs or from deep sequencing data and uses secondary structure properties of precursors for computational validation. The second approach looks for new microRNAs organized in clusters using a novel ab initio methodology without any a priori knowledge and possibly deep sequencing data.
The structure of dynamic folds in microbial genomes is largely unknown. We look for genes periodicity within genomes, using a parametrized spectral analysis approach based on single genome analysis. We found, in Escherichia coli, a global genomic period suggesting an encoded three-dimensional chromosomal organization that highlights two independent positional networks of functional genes. The methodology developed in this analysis can be applied to any set of genes and can be taken as a footprint for large scale bacterial and archaeal analysis.

COLLABORATORS

I am currently a postdoctoral fellow under the supervision of Dr. Wyeth Wasserman. During my PhD, my supervisor was Prof. Alessandra Carbone.

AWARDS & HONORS

• 2009: ISMB/ECCB Travel Fellowship from the International Society for Computational Biology (ISCB) funded by BioSapiens

PRESENTATIONS

Conferences

• Integrative Post-Genomics 2009. International multidisciplinary meeting on Post-Genomics, Lyon, France, 2009. Chromosomal periodicity and positional networks of genes in Escherichia coli.
• Interactions between bioinformatics and marine biology. Workshop organized by the Laboratory of \"Genomics of Microorganisms\", Paris, France, 2009. Périodicité chromosomique et réseaux génétiques positionnels chez Escherichia coli.
• Algorithmique, combinatoire du texte et applications en bioinformatique. Meeting on algorithmic and combinatorics of text and applications in bioinformatics, Marne La Vallée, France, 2007. Algorithmes rapides de recherche d\'un motif approché par minimisation des erreurs ou par maximisation des identités dans des fenêtres minimales.

Seminars

• Laboratoire de Recherche en Informatique (LRI) / Laboratoire d\'Informatique de l\'Ecole Polytechnique (LIX) seminar, Orsay, France, 2010. Prédiction de nouveaux microARN dans les génomes.
• Interdisciplinary working group on computation and simulation / Université Pierre et Marie Curie, Paris, France, 2010. Recherche de signaux biologiques chez les eucaryotes et les procaryotes à l\'échelle des génomes.
• Laboratoire d\'Informatique de Paris 6 / PhD students seminar, Paris, France, 2009. Algorithmes et méthodologie pour la recherche de micro-ARN dans les génomes.
• First meeting of the Laboratory of \"Genomics of Microorganisms\", Paris, France, 2008. Prédiction de micro-ARN et pré-micro-ARN, clusters de micro-ARN et évolution.

Posters

• 2009: A. Mathelier, A. Carbone, Finding miRNAs homologs in genomes with no learning. Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Nantes, France
• 2009: A. Mathelier, A. Carbone, A novel ab initio method finding microRNA clusters. International conference on Intelligent Systems for Molecular Biology and European Conference on Computational Biology (ISMB/ECCB), Stockholm, Sweden

Publications