CV of Oliver Ruebenacker

Oliver Ruebenacker	Phone: (617) 818-2146
11 Peabody Terrace, Ap 1904	E-Mail: curoli@gmail.com
Cambridge, MA 02138	WWW: http://www.oliver.curiousworld.org

Year	Degree	Institution
2005	PhD (Physics)	University of Massachusetts, Amherst
2001	MS (Physics)	University of Massachusetts, Amherst
2000	Diplom (Physics)	University of Karlsruhe (TH), Germany

Integrating BioPAX pathway knowledge with SBML models
Michael L Blinov, Oliver Ruebenacker, Ion I Moraru
Submitted to IET Systems Biology
Kinetic Modeling Using BioPAX Ontology Oliver Ruebenacker, Ion I Moraru, James C Schaff, Michael L Blinov
IEEE International Conference on Bioinformatics and Biomedicine, 2007, Proceedings, pages 339-348.
Weakly interacting Bose gases in the fluctuation region
Oliver Ruebenacker
PhD thesis at the University of Massachusetts at Amherst, MA, US (2006) Thesis advisor: Nikolay Prokof'ev
"Weakly interacting Bose gas in the vicinity of the critical point"
Nikolay Prokof`ev, Oliver Ruebenacker, Boris Svistunov
Phys. Rev. A 69 , 053625 (2004)
"Critical Point of a Weakly Interacting Two-Dimensional Bose Gas"
Nikolay Prokof`ev, Oliver Ruebenacker, Boris Svistunov
Phys. Rev. Lett. 87 , 160601 (2001)
"Hole Dynamics in a two-dimensional quantum anti-ferromagnet"
Oliver Ruebenacker
Diplom thesis at University of Karlsruhe, Germany, 2000
Thesis advisors: Peter Woelfle and Nikolay Prokof`ev

Towards unifying systems biology - using pathway data in BioPAX format for SBML simulators
Oliver Ruebenacker, Michael L Blinov, Ion I Moraru
Accepted to Second Annual q-bio Conference on Cellular Information Processing (2008)
Submitted to International Conference on Computational Methods in Systems Biology (2008)
Modeling Complex Networks: Integrating Rules (BioNetGen) and Data Mining (BioPAX ontology) into the Virtual Cell Framework
Ion I Moraru, Oliver Ruebenacker, James C Schaff, Leslie M Loew Michael L Blinov
The Eighth International Conference on Systems Biology, 2007
Kinetic Modeling Using BioPAX Ontology
Oliver Ruebenacker, Ion I Moraru, James C Schaff, Michael L Blinov
IEEE International Conference on Bioinformatics and Biomedicine, 2007
Membrane Nano-Structures: The Three Tether Junction
Oliver Ruebenacker, Greg Huber American Physical Society, March Meeting 2006
Three-Dimensional Weakly Interacting Bose Gas in the Vicinity of the Critical Point
Nikolay Prokof`ev, Oliver Ruebenacker, Boris Svistunov
American Physical Society, March Meeting 2004
Worm Algorithm simulations of the hole dynamics in the t-J model
Nikolay Prokof`ev, Oliver Ruebenacker
American Physical Society, March Meeting 2001

Post-doc (February 2007 to August 2009, Center for Cell Analysis and Modeling, University of Connecticut Health Center)
- Part of Virtual Cell team, research software development for simulation of molecular pathways; integration of SBML, SBPAX and BioPAX using Semantic Web technology.
Post-doc (February 2005 to February 2007, Center for Cell Analysis and Modeling, University of Connecticut Health Center)
- Research in biological physics, simulation of membrane mechanics, membrane tether networds (e.g. endoplasmic reticulum)
Instructor (June 2004 to July 2004, Department of Continuing Education, University of Massachusetts at Amherst)
- Teaching Physics 131: Introductory Physics I (Physics for Life Science Majors)
Graduate Teaching Assistant (September 2003 to August 2004, Department of Physics, University of Massachusetts at Amherst)
- General physics lab, including grading
- department resource room, tutoring students of all classes
Graduate Research Assistant (September 1999 to August 2003, Dep. of Physics, UMass Amherst)
- PhD research in condensed matter theory involving analytical and numerical methods applied to statistical physics, such as holes in a two-dimensional quantum antiferromagnet and Bose and psi-4 gases in two and three dimensions
- Setup and maintainance of research computer systems, including two Redhat Linux Beowulf clusters (15 and 12 nodes)

Semantic Web: XML, RDF, OWL, SPARQL queries, Jena, automatic reasoning
Programming Languages and Software Development: Java, Java Swing, C++, C, Perl, Fortran 95, ML, PostScript, Eclipse, Subversion
Systems Biology Data: BioPAX, SBPAX, SBML, libSBML
Document Processing: LaTeX/TeX and relatives, LaTeX Beamer, PostScript, MS Office, OpenOffice, HTML, Perl Template Toolkit
System Administration: Hardware and software maintanence including Linux, Windows, Mac, Beowulf cluster, Apple G5 cluster
Languages: German (mothertongue), English (fluent), Turkish (some)
Awards: Won prizes at German federal and state math competitions.

Physics Graduate Student Association: President (2001-2003), Chair of Academic and Research Committee (2003-2004)
Graduate Employee Organization/UAW Local 2322: Steering committee (2001), Physics Department steward (2000-2003), chair of by-laws committee (2001-2002)
GRIPS (math and science student club): Chair, Vice-Chair
Schachfreunde Kraichtal (Local Chess Club): Treasurer, Captain of first team, Youth Leader