Earth Sciences Division (ESD) Department of Energy (DOE) Lawrence Berkeley National Laboratory (LBNL)

Earth Sciences Division Staff: Emmanuel Prestat

Emmanuel Prestat

Emmanuel Prestat

Postdoctoral Fellow

Ecology Department

 

 

Phone: 510-495-8082

Fax: 510-486-7152

Email: eprestat@lbl.gov

Biographical Summary

I am responsible for bioinformatics and statistics analyses of the US Department of Energy BER project: “Meta-“omics” analysis of microbial carbon cycling responses to altered rainfall inputs in native prairie soils” *. Specifically, I am analyzing metagenomics and metaproteomics data obtained from native prairie soil in Kansas.

→ More on the project ←

My previous experience (as a postdoc in “Ecole Centrale de Lyon”, France) focused on mining genes present in soil organisms from 454 and Solexa Next Generation Sequencing datasets. My main research interest was the discovery of new genes, functions, species, ecological mechanisms and how they relate to the environment. Given the complexity of the soil ecosystem (currently known as the most diverse), exploring and discovering novel phenomena, interactions, etc, remains a major challenge.

My PhD thesis aimed to reconstruct gene regulatory networks from microarray data of breast cancer tumors. The method used and extended to achieve this inference was the Bayesian Networks (a method at the interface between graph and probabilistic theories).

* 2010-2012. PI: Ari Jumpponen (Kansas State University), co-PIs: Janet Jansson (Lawrence Berkeley National Laboratory), Charles Rice (Kansas State University), Susannah Tringe (Joint Genome Institute), Robert Hettich & Nathan VerBerkmoes (Oak Ridge National Laboratory). Project coordinator: David Myrold (Oregon State University).

Research Interests

Bioinformatics, biostatistics, bayesian networks, soil ecology, metagenomics, Next Generation Sequencing data analysis, molecular cell networks.

Education

  • Universite Claude Bernard Lyon 1, Villeurbanne, France
    • Ph.D., Biometry and Evolutive Biology Laboratory, May 2010
      • Thesis Topic: Classi cation and capture of genetic regulation networkswith Bayesian Networks in oncology.
      • Advisor: Professor Christian Gautier
      • Area of Study: Bioinformatics
    • Professional Master, Biometry and Evolutive Biology Laboratory, September 2005
      • Thesis Topic: Interactive Microarray Data Management System for PhylochipData Mining
      • Advisor: Professor Christian Gautier
      • Area of Study: Bioinformatics
  • Universite Joseph Fourier, Grenoble, France
    • Research Master, Techniques for biomedical engineering and complexity manage-ment informatics, mathematics and applications Laboratory Grenoble, September2004
      • Thesis Topic: Quality control of the image acquisition step of microarrays: de-velopment of a measurements protocol, and a R implemented method to correctdata extracted from microarray images.
      • Models and Instruments in Medecine and Biology
      • Advisor: Doctor Francoise Giroud

Professional Experience

  • October 2011 to present:  Postdoctoral Fellow
    Earth Sciences Division, Ecology Department, Lawrence Berkeley National Laboratory
    • Topic: Meta-omics analysis of microbial carbon cycling responses to al-tered rainfall inputs in native prairie soils. Biostatistical and bioinfor-matical analyses.
    • Advisors: Ari Jumpponen (associate professor), Kansas State Universityand Janet Jansson (Professor and Senior Sta Scientist), Lawrence Berkeley NationalLaboratory
  • June 2009 to September 2011:  Postdoctoral Fellow
    Environmental Microbial Genomics Group, Ampere Laboratory,Ecole Centrale de Lyon
    • Topic: Exploration of soil metagenomics and metaproteomics data. Bio-statistical and bioinformatical analyses.
    • Advisor: Professor Timothy M. Vogel

Awards

Best poster award (3000 euros price). Using bayesian networks in cancer research. International conference on system science in health care, Lyon, France, 3rd of September, 2008.

Teaching Experience

  • INSA Lyon engineering school, Villeurbanne, France
    • Bioinformatics and modeling - year 4 - 2011 (8h)
      • Transcriptome analysis within the R environment and the Bioconductor package
    • Biochemistry and biotechnology - year 5 2008, 2010 (44h)
      • Introduction to bioinformatics
      • Introduction to transcriptome analysis
      • Databases mining in biology
      • Transcriptome analysis within the R environment and the Bioconductor package
  • Medecine Faculty of Laennec, Universite Claude Bernard Lyon 1, Lyon, France
    • Health and drug engineering - Master 2008 (4h)
      • Introduction to transcriptome analysis with microarrays
      • Using Bayesian Networks to infer biological networks
  • Biology department, Universite Claude Bernard Lyon 1, Villeurbanne, France
    • Life science - 1st year of Master degree 2011 (20h)
      • Solving ordinary di erential equations in R and R2
      • Analysis of dynamic biological systems with ordinary di erential equations.
    • Life science - 2nd year Licence 2006, 2007 (88h)
      • Biostatistics
      • Bioinformatics
      • Relationnal database creation and queries using SQL

Training Experience

  • Analyzing soil microbe community fingerprints (DGGE, RISA) with parametric and non-parametric multivariate statistical methods 2010 (10h)
  • Introduction to Sweave: a R and LATEX framework to edit updatable statistical analysis documents. 2007 (1h)

Statistical & Mathematical Expertise

  • Parametric and non-parametric models to analyse univariate and multivariate datasets (regression, hypothesis testing, NMDS, PCA, Correspondance Analysis, CCA, BGA,WGA, discriminant analysis).
  • Classi cation and clustering (Bayesian Networks, SVM, Naive Bayes, K-Means)
  • Matrix models and ODE for dynamic systems.

Technical Skills

  • Bioinformatics and statistics softwares:
    • R: BioConductor, ADE4, vegan, SeqinR packages.
    • Matlab: Bioinformatics, Bayesian Networks Toolboxes.
    • Weka: A machine learning feature selection, classi cation, and clustering tool.
  • Sequences alignment tools: BLAST, HMMER, SOAP, muscle, clustalw, t co ee.
  • Phylogenetic tree reconstruction: PhyML, Neighbor-Joining, Parsimony, MrBayes.
  • Programming: Python, MPI, R, MatLab, Java, JavaScript, PHP, UNIX shell scripting, SQL.
  • Hardware and software installation, management of multi-processors and -nodes UNIX systems.
  • Computer Applications: TEX (LATEX, BibTEX), Sweave, most common productivity packages (for Windows, Mac OS X, and Linux platforms), Emacs.

Biological Expertise

Metagenomics, transcriptomics, cell molecular networks (genetic and metabolic).