Welcome to Julie's CSB webpage

Julie Bernauer

Contact address

Levitt group
Computational Structural Biology
MC 5126 - Department of Structural Biology
Fairchild Science Building
Stanford School of Medicine
Stanford, CA 94305-5126
Tel: +1 (650) 723 5720
Fax: +1 (650) 724 4021
E-mail: bernauer@stanford.edu
http://www.stanford.edu/~bernauer

Education

September 2006 to present	Post-Doc Levitt Group. Computational Structural Biology Stanford University.
April 2006 to August 2006	Teaching Assistant. IBBMC Université Paris-Sud.
September 2002 to April 2006	Ph.D. Yeast Structural Genomics. IBBMC Université Paris-Sud / LEBS CNRS Gif-sur-Yvette.
September 2002 to January 2003	Master of Science (2^nd year) in Algorithmics (DEA d'Algorithmique de Paris) - Algorithms Science and Algorithmic Geometry Courses. Université Paris-Sud (Orsay) & École Normale Supérieure de Cachan (Institute of Higher Education where students, after highly selective entrance exams, are trained over four years both as future professors and researchers).
September 2001 to August 2002	Master of Science in Molecular Physico-Chemistry (Magistère Physico-Chimie Moléculaire). Université Paris-Sud (Orsay) & École Normale Supérieure de Cachan
September 2001 to August 2002	Master of Science (2^nd year) in Biological Crystallography and NMR (DEA Cristallographie et RMN biologiques). Université Paris-Sud (Orsay) & École Normale Supérieure de Cachan
September 2000 to August 2001	Master of Science (1^st year) in Molecular Physico-Chemistry with Specialization in Biological Physico-Chemistry and Industry Research (Maîtrise Physico-Chimie Moléculaire). Université Paris-Sud (Orsay) & École Normale Supérieure de Cachan
September 1999 to August 2000	B.S. in Molecular Physico-Chemistry with Specialization in Industry Research (Licence Physico-Chimie Moléculaire). Université Paris-Sud (Orsay) & École Normale Supérieure de Cachan
September 1997 to August 1999	Preparatory classes with specialization in Physics and Chemistry. Lycée Louis-le-Grand Paris. Two-year class preparing for highly selective national entrance exam to Grandes Écoles
July 1997	High School Diploma with Specialization in Sciences (Physics and Chemistry) (Baccalauré Série S). Lycée Colbert Reims.
July 1997	Technical School Certificate in Maintenance of Automated Industrial Systems (BEP MSMA). Lycée Croix Cordier Reims.

Training and Professional Experience

September 2006 to present	Post-Doc Research with Pr. Michael Levitt and Pr. Leo Guibas. Stanford University.
February 2002 to August 2006	Doctoral and Master's research with Dr. Anne Poupon. IBBMC Université Paris-Sud / LEBS CNRS Gif-sur-Yvette. Use of Voronoï tessellation for the modelling of protein-protein complexes.
May 2001 to August 2001	Master's Research intership with Dr. Masayuki Takeda. Mitsubishi Chemical Corporation Electrochemical Laboratory - Tsukuba Research Center - Japan. Evaluation of electrochemical stability of electrolyte solutions for double layer capacitors by linear sweep voltammetry.
March 2001	Research intership with Dr. Ronald Melki. Université Paris-Sud / LEBS CNRS Gif-sur-Yvette. Deleting flexible part of Ure2p yeast prion protein.
June 2000 to August 2000	Research intership with Pr. Pierre Audebert. Université Paris-Sud / PPSM ENS Cachan. Synthesis of electropolymerisables cyclophanes.

Awards and Honors

French Cancer Research Association (ARC) Post-Doctoral Fellowship. (2006-2007)
Ph.D. Defense: Mention Très Honorable. (April 2006)
Therapeutic Innovation Doctoral Studies Oral Communication Prize. (June 2005)
French Government / ENS Cachan Doctoral Fellowship. (2003-2006)
B.S. and Master of Science with honors.
French Government / ENS Cachan Civil Servant Fellowship (1999-2003)
Women's Scientific and Technological Vocation Prize - Champagne-Ardennes Region. (July 1997)
High School Diploma with Highest Honors. (July 1997)

Teaching Experience

Graduate	Computer Science Additional Skills for Scientists Professionnal Master of Science: Introduction to Unix/Linux (10 hours/year) (2003-2006), Algorithms and Programming (50 hours/year), exams and interships reviewing (2003-2005). Université Paris-Sud. 'Introduction to Docking' Lectures for Master students at INAPG (Paris) and Genomics Master students at Université Paris-Sud. (2004-2006)
Undergraduate	Bioinformatics B.S.: Introduction to Unix/Linux, Algorithms and Programming (50 hours), exams and internships reviewing. (2006)

Student internship supervision

Julien Neel, 1^st master of science in Bioinformatics training period. Co-Supervision with Dr. Jérôme Azé. (March-June 2006) Impact study of missing data in machine learning for protein-protein docking scoring functions.

Jonathan Piard, B.S. in Molecular Physico-Chemistry training period. (May-August 2005) Modelling of protein-protein interactions in viral capsids.

Tom Dreyfus, 1^st year master of science in Bioinformatics training period. (May-June 2005) Design of a web server for graph representation and analysis of multiproteic complexes.

Cyprien Bole, 3^rd year agronomy engineering degree. Co-supervision with Dr. Anne Poupon. (February-September 2004) Statistical analysis of protein-protein complexes interfaces.

Xavier Brochet, 1^st year master of science in Bioinformatics training period. Co-supervision with Dr. Anne Poupon. (April-June 2003) Comparison of different molecular replacement softwares, influence of their parameters and of the starting model.

Skills

Programming	Languages: C, C++, Fortran 77 and 90, Sparc Assembly Language, Python, BASH, awk, R, LaTeX, markup languages (html, xml).
Bioinformatics	Sequence analysis, homology modelling, protein structural model design.
Crystallography	X-ray protein structure determination and associated computer tools: CNS, CCP4, Mosflm, Denzo, Turbo, Pymol.
Linux/Unix	Hardware management, device adaptation, installation, upgrades ad maintenance of different types of servers and 3D workstations: Linux, Windows, Mac, IRIX. Associated network security and tools. Cluster management systems: PBS, OpenSSI.
Languages	Native French. Good English. Average German. Average Japanese.

Other Interests

Community Life	2001: Active member of the computer network students' association at ENS Cachan. 2000: Secretary of ENS Cachan student association. 2000: Secretary of ENS Cachan sport association.
Entomology	Stick insect breeding.

Publications

Reviewed papers

Bernauer J, Azé J, Janin J, Poupon A: A new protein-protein docking function based on interface residues properties. Bioinformatics 2007.
Graziani S, Bernauer J*, Skouloubris S, Graille M, Zhou C-Z, Marchand C, van Tilbeurgh H, Myllykalio H, Liebl U: Catalytic mechanism and structure of a viral flavin-dependent thymidylate synthase ThyX. Journal of Biological Chemistry 2006, 281(33):24048-57.
* First two authors contributed equally to the work.
Bernauer J, Azé J, Janin J, Poupon A: Une nouvelle fonction de score pour l'amarrage protéine-protéine fondée sur les diagrammes de Voronoï. In proceedings of Journées Ouvertes de Biologie Informatique Mathématiques; Lyon, France. 2005:459-469
Bernauer J, Poupon A, Azé J, Janin J: A docking analysis of the statistical physics of protein-protein recognition.Physical Biology 2005, 2:S17-S23.
Prilusky J, Oeuillet E, Ulryck N, Pajon A, Bernauer J, Krimm I, Quevillon-Cheruel S, Leulliot N, Graille M, Liger D, et al.: HalX: an open-source LIMS (Laboratory Information Management System) for small- to large-scale laboratories. Acta Crystallogr D Biol Crystallogr 2005, 61:671-678.
Takeda M, Bernauer J, Toriumi A, Takehara M, Ue M: Electrolyte linear sweep voltammetry for double layer capacitors. (in Japanese). In proceeding of the 68^th Annual Meeting of the Electrochemical Society of Japan; Tokyo, Japan. 2001

International Conferences

Use of Voronoi tessellation for the prediction of macromolecular assemblies. In American Chemical Society 232^nd National Meeting & Exposition; San Francisco, USA. September 10^th-14^th, 2006.
A new protein-protein docking scoring function based on interface residues properties. In Fifth Virtual Conference on Genomics and Bioinformatics; Arlington, USA. October 25^th-28^th, 2005.
A new docking scoring function for protein-protein docking based on Voronoi tessellation. In Journées ouvertes de Biologie Informatique Mathématiques; Lyon, France. July 6^th-8^th, 2005.
A new docking scoring function based on interface geometry and physico-chemical residue properties. Poster communication at CECAM Workshop on Flexible Macromolecular Docking; Lyon, France. April 28^th-30^th, 2005.
A new docking scoring function based on Voronoi tessellation. In The Second CAPRI Evaluation Meeting; Gaeta, Italy. December 8^th-10^th, 2004.
Modeling of protein-protein complexes in the yeast structural genomics context. In ESF Training course on Molecular Interactions: New Frontiers for Computational Methods; Verona, Italy. July 20^th-25^th, 2002.