Education

• Ph.D. in Computational and Molecular Biology
  (with highest honors)
  Jan. 2005
  Paris VI (Pierre & Marie Curie) University. Paris, France
• M.S. (french “DEA”) in Molecular Biology
  (with honors)
  Jun. 2001
  Paris VI (Pierre & Marie Curie) University. Paris, France
• B.S. (french “maîtrise”) in Biochemistry
  Jun. 2000
  Paris VI (Pierre & Marie Curie) University. Paris, France

Positions

• Consultant, Golden Helix
  Jul. 2012 - Present
  Golden Helix, Inc. (Bozeman, MT, USA)
  Bioinformatics data analyses performed on behalf of Golden Helix—a bioinformatics company providing software and services for researchers to find or diagnose the genetic causes of disease, drug safety, and drug efficacy. Projects involve the analysis of microarray expression datasets to isolate candidate markers of cystic fibrosis in cohorts of patients, and of patients and parents.
• Consultant, Floragenex
  Apr. 2012 - Present
  Floragenex, Inc. (Eugene, OR, USA)
  Bioinformatics data analyses and software development performed on behalf of Floragenex—a genomics company specialized in SNP discovery in plants and animals using RAD sequencing. Projects involve the review of functionality and design of existing Floragenex tools and data processing infrastructure, followed by the optimization of this infrastructure to automatize further analyzes.
• Assistant Research Professor, Department of Microbiology
  Dec. 2010 - Present
  Department of Microbiology. Montana State University (Bozeman, MT, USA)
  Research projects focused on the structure and evolution of metabolic networks organization at two scales—intracellular, and within microbial communities. Development of software pipelines to help interpreting transcriptomics, metabolomics and metagenomics data by placing molecular events into functional context.
• Director, Bioinformatics Core
  Sep. 2009 - Present
  Bioinformatics Core. Montana State University (Bozeman, MT, USA)
  Involvement in various genomics and metagenomics projects as consultant or co-PI, including: Characterization of archaeal virus population structure and dynamics in acidic hot springs using metagenomics and custom-made document-oriented databases (Mark Young, PI, MSU); Transcriptional profiling of Pseudomonas aeruginosa under various experimental conditions, including biofilm formation (1 article; Philip Stewart, PI, MSU); Characterization of, and biomarkers identification for hypoxia response in Aspergillus fumigatus using microarrays, RNA-seq and ChIP-seq (2 articles; Robert Cramer, PI, MSU); Characterization of lipid accumulation in Phaeodactylum tricornutum using RNA-seq (1 article; Matthew Fields, PI, MSU); Mutagenesis of honey bee olfactive receptors (Kevin Wanner, PI, MSU).
• Senior Post-Doctoral Research Fellow, Systems Biology Lab
  Nov. 2006 - Jul. 2009
  Systems Biology Lab. Institut Pasteur (Paris, France) • PI: Benno Schwikowski, Ph.D.
  Research projects focused on the impact of evolutionary pressures on metabolic network organization (1 article) and the identification of functional modules from genome-scale, high-throughput data.
• Post-Doctoral Research Fellow, Center for the Study of Biological Complexity
  May. 2005 - Oct. 2006
  Center for the Study of Biological Complexity. Virginia Commonwealth University (Richmond, VA, USA) • PI: Gregory A. Buck, Ph.D.
  Research projects focused on the relationship between phylogeny and metabolic network organization (1 articles, 1 book chapter), the inference of gene essentiality from post-genomics data (1 article), the characterization of metabolic capabilities from expression data (1 article) and comparative genomics of two Cryptosporidium species.
• Ph.D. Candidate
  Oct. 2001 - Jan. 2005
  Laboratoire de Génétique de la Neurotransmission CNRS UMR 7091. Hôpital Pitié-Salpêtrière (Paris, France) • Advisor: Jacques Mallet, Ph.D.
  Research projects focused on the small-scale organization of gene regulatory networks (1 article, 1 book chapter), the inference of gene regulatory networks structure from expression data (1 article, 2 book chapters; Florence d'Alché-Buc, PI, Université Evry-Val d'Essonne, France), and the development of double-channel radioactive microarray technology (1 article; Hélène Salin, PI).

Technical skills

Bioinformatics techniques Transcriptomics data analysis (selection of statistical tests, functional analysis of ranked lists or subset of genes using graph theory and gene set enrichment analysis, identification of best predictors or biomarkers of quantitative or qualitative phenotypes using machine learning and statistics), Next generation sequencing data analysis (reads processing—denoising and dereplication—and quality control, genome assembly, de novo and ab initio RNA-seq, ChIP-seq peak calling), Metagenomics data analysis (evaluation of community membership and comparison of communities membership—alpha and beta diversity, relationship between community membership and environment), Network-based data analysis (representation of biological systems as networks, characterization of the organization of these networks using graph theory, characterization of the dynamic of these networks using Petri nets, cellular automata or flux models), Development of ad-hoc analysis pipelines (programming, data parsing and format conversion, identifier mapping, data visualization, database development).

Bioinformatics toolkits Use and administration of BioJava, BioPython, Taverna, BioMoby, Cytoscape, EMBOSS, Galaxy.

Knowledge representation and inference Machine learning (Weka, Orange toolkits), statistics (R, JMP), rules engines (CLIPS, Jess).

Knowledge representation Population and query of relational databases (MySQL, PostgreSQL), document-oriented databases (MongoDB) and graph databases (Neo4j). Query and parsing of XML documents (XPath, XSLT) and RDF/OWL ontologies (SparQL).

Software development in Python, Java (J2SE), PHP, Perl, C/C++. Use of the Git distributed revision control system.

Web development HTML₄ and HTML₅, CSS₃, JavaScript, RPC (SOAP), REST, CGI (Python and Perl).

Grid computing Amazon Web Services platform (EC2, EBS, S3). OpenPBS (Portable Batch System) and SGE (Sun Grid Engine) schedulers, on local hardware and on EC2 using StarCluster.

Operating systems administration Windows (95 to 7), Linux, MacOS X.

Examples of bioinformatics tools developed at http://github.com/ajmazurie

Publications

(Legend: published as principal investigator, co-principal investigator, or consultant)

Papers (9) in refereed international journals:

• Potential role of multiple carbon fixation pathways during lipid accumulation in Phaeodactylum tricornutum
  Valenzuela J, Mazurie A, Carlson RP, Gerlach R, Cooksey KE, Peyton BM, Fields MW
  Biotechnology for Biofuels, Jun 2012; 5:40 — Impact Factor: 6.09.
• Transcriptomic and proteomic analyses of the Aspergillus fumigatus hypoxia response using an oxygen-controlled fermenter
  Barker BM, Kroll K, Vödisch M, Mazurie A, Kniemeyer O, Cramer RA
  BMC Genomics, Feb 2012; 13(1):62
• SREBP coordinates iron and ergosterol homeostasis to mediate triazole drug and hypoxia responses in the human fungal pathogen Aspergillus fumigatus
  Blatzer M, Barker BM, Willger SD, Beckmann N, Blosser SJ, Cornish EJ, Mazurie A, Grahl N, Haas H, Cramer RA
  PLoS Genetics, Dec 2011; 7(12): e1002374
• Physiology of Pseudomonas aeruginosa in biofilms as revealed by transcriptome analysis
  Folsom JP, Richards L, Pitts B, Roe F, Ehrlich GD, Parker A, Mazurie A, Stewart PS
  BMC Microbiology, Nov 2010; 10:294 — Impact Factor: 2.96. Tagged as 'Highly accessed' with 3008 accesses as of June 2011.
• Evolution of metabolic network organization
  Mazurie A, Bonchev D, Schwikowski B, Buck GA
  BMC Systems Biology, May 2010; 4(1):59 — Impact Factor: 3.57. Cites by two publications* and tagged as 'Highly accessed' with 2670 accesses as of June 2011.
• Phylogenetic distances are encoded in networks of interacting pathways
  Mazurie A, Bonchev D, Schwikowski B, Buck GA
  Bioinformatics, Nov 2008; 24(22):2579-2585 — Impact Factor: 5.468. Cited by 16 publications* and accessed 1698 times as of June 2011.
• An evolutionary and functional assessment of regulatory network motifs
  Mazurie A, Bottani S, Vergassola M
  Genome Biology, Mar 2005; 6(4):R35 — Impact Factor: 9.04. Rated as 'Must Read' (Factor 6.4) by the Faculty of 1000 Biology. Cited by 16 publications* and accessed 6961 times as of June 2011.
• Gene networks inference using dynamic Bayesian networks
  Perrin BE, Ralaivola L, Mazurie A, Bottani S, Mallet J, d'Alché-Buc F
  Bioinformatics, Oct 2003; 19(2):II138-II148 — Impact Factor: 5.468. Cited by 128 publications* as of June 2011.
• A novel sensitive microarray approach for differential screening using probes labeled with two different radio-elements
  Salin H, Vujasinovic T, Mazurie A, Maitrejean S, Menini C, Mallet J, Dumas S
  Nucleic Acids Research, Feb 2002; 30(4):e17 — Impact Factor: 7.836. Cited by 22 publications* as of June 2011.

Reviews (1) in refereed international journals:

• Integrating genome-scale data for gene essentiality prediction
  Roberts SB, Mazurie A, Buck GA
  Chemistry and Biodiversity, Nov 2007; 4(11):2618-2630 — Impact Factor: 1.926
  Cited by 2 publications* as of June 2011.

Papers (2) in refereed international conferences:

• Understanding metabolic network evolution with stochastic simulations
  Jolley CC, Mazurie A, Young M, Douglas T
  Biophysical Society 54th Annual Meeting, San Francisco CA, Feb 2010
• Path-a-Way: a strategy for network analysis of microarray data
  Arasappan D, Mazurie A, Alves J, Bonchev D, Buck GA
  International Conference on BioMedical Engineering and Informatics, p. 432-436 (2008)

Book chapters (5):

• Metabolic networks and the phylogeny of species
  Mazurie A, Bonchev D, Buck GA
  In 'Analysis of biomolecular structures and interaction networks', Kuznetsov VA editor, CRC/Taylor & Francis (2008)
• Genetic networks: between theory and experimentation
  Bottani S, Mazurie A
  In 'Complex population dynamics: nonlinear modeling in ecology, epidemiology and genetics', Blasius B, Kurths J, and Stone L editors, World Scientific, pp. 215-236 (2007)
• Genomes to networks, pathways and function
  Buck GA, Mazurie A, Roberts SB, Alves J, Arassapan D, Serrano M, Manque P
  In 'Recent progress in computational sciences and engineering: Lecture series on computer and computational sciences', Volume 7, Simos T and Maroulis G editors, Brill Academics, pp. 758-763 (2006)
• A dynamic model of gene regulatory networks based on inertia principle
  d'Alché-Buc F, Lahaye PJ, Perrin BE, Ralaivola L, Vujasinovic T, Mazurie A, Bottani S
  In 'Bioinformatics using Computational Intelligence Paradigms', Seiffert U editor, Springer, pp. 93-118 (2005)
• Réseaux bayésiens dynamiques pour l'inférence de structure de réseaux de régulation
  Ralaivola L, Perrin BE, d'Alché-Buc F, Mazurie A, Bottani S
  In 'Informatique pour l'analyse du transcriptome', Boulicaut JF and Gandrillon O editors, Lavoisier, pp. 291-319 (2004)

Invited talks (7):

• Evolution of metabolic networks organization
  Applied Mathematics Seminar Series, Dept. of Mathematics, Montana State University, Bozeman MT (Mar 3, 2011)
  Seminar at the Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond VA (Mar 2, 2010)
• Statistical challenges in bioinformatics and systems biology
  Annual meeting of the Montana Chapter of the American Statistical Association, Montana State University, Bozeman MT (Sep 14, 2010)
• Interaction networks
  Guest lecturer for the Introductory Bioinformatics Laboratory 535 course (Marcie McClure, lecturer), Montana State University, Bozeman MT (Nov 17-19, 2010)
• An evolutionary perspective on functional modules in metabolic networks
  Workshop on Systems Biology & Networks, Institut Pasteur, Paris (Sep 22, 2008)
• Modularity in intracellular systems
  3ème Journée de Biologie Systémique, Paris V (Descartes) University, Paris (Apr 16, 2008)
• Functional modules in intracellular systems: where are we?
  Modularity in Synthetic Biology, Genopole, Evry (Mar 21, 2008)
• An evolutionary and functional assessment of regulatory network motifs
  Modularité, Compositionalité et Abstraction dans les réseaux géniques et protéiques, Institut Henry Poincaré, Paris (Nov 21, 2007)
• Identification of biologically relevant modules in cells
  Journées départementales de l'Institut Pasteur, Institut Pasteur, Paris (Jun 14, 2007)

Reviewer for Bioinformatics, BMC Systems Biology, PLoS Computational Biology, PLoS ONE, Nature Protocols, Cancer Informatics, Critical Reviews in Biotechnology, and Interface.

*sources: Google Scholar, PubMed and ISI Web of Knowledge

Grants

• Modeling infectious and environmental factors affecting transmission of honey bee diseases
  Flenniken M (PI, MSU), Mazurie A, Sagili R, Hooven L, Bothner B
  National Science Foundation; Pending
• Determining residue defense across classes of endemic wheat pathogens
  Dyer A (PI, MSU), Mazurie A
  US Department of Agriculture; Pending
• Modulation of amino acid networks for controlled tuning of chemosensory receptors
  MacAllister IE (PI, ERDC-CERL), Mazurie A, Grimme S, Wanner K
  US Army Engineer Research and Development Center (#W9132T-11-2-0004); Mar. 2011 - Mar. 2014; $744,000
• Integrated analysis of extremophile biology from genes to metabolites
  Bothner B (PI, MSU), Mazurie A, Young M, McDermott T
  National Science Foundation (#1022481); Jan. 2011 - Dec. 2014; $354,000

Reviewer for the NIH grant evaluation panel 'SBIR (small business innovative research)', NSF grant evaluation panel 'Advancing theory in biology', and French National Research Agency (ANR) panel 'Genomics, genetics, bioinformatics and systems biology'.

Teaching

• Instructor of record
  Jan. 2010 - Present
  Montana State University
  MBSP 579, 'Programming for Life Scientists' (3 credits). Syllabus: http://goo.gl/EygYg
  IGERT DGED 614, 'Introduction to programming' (2 credits)
• Instructor
  Dec. 2010 - Present
  Montana State University
  Bi-annual workshop, 'Introduction to Programming'. Syllabus: http://goo.gl/jTlUR
• Lecturer (french “vacataire”)
  Oct. 2001 - Apr. 2005
  Paris XIII University. Bobigny, France
  'Introduction to Bioinformatics' (100 hours). Audience: biology undergraduate students.
  Cellular Biology, Genetics, Embryology (120 hours). Audience: biology undergrads and medschool students.
• Tutor
  Private courses in mathematics. Audience: high school students.

Other

Community involvement Secretary of the french BioDocs association in 2003, helping contacts between private research companies and PhDs. Co-organizer of the Paris, France edition of BioTechno2002 and BioTechno2003 forums.

Memberships AAAS (American Association for the Advancement of Science), ISCB (International Society for Computational Biology).