Jan B. Valentin  



The Bioinformatics Centre
Department of Biology
University of Copenhagen
Ole Maaloes Vej
2200 Copenhagen N

Office: 1.2.18

E-mail: valentin (-at-) binf.ku.dk




Position

Ph.D. student in Bioinformatics at the Bioinformatics Center, University of Copenhagen, in the Structural Bioinformatics group led by Thomas Hamelryck.

Supervisors: Thomas Hamelryck and Jesper Ferkinghoff-Borg (DTU Elektro).

Research Interests

  • Classical mechanics
  • Dynamical systems, incl.:
    • Runge-kutta methods
    • Chaos
    • Fluid dynamics
  • Statistics, incl.:
    • Bayesian networks
    • Monte Carlo simulation
    • Statistical mechanics

Education

  • Ph.D. in Bioinformatics at the University of Copenhagen, 2013 (expected).
  • Master of Science in Physics at the Niels Bohr Institute, University of Copenhagen, 2010.
  • Bachelor of Science in Physics and Mathematics at Aalborg University, 2007.

Publications

  • Wouter Boomsma, Jes Frellsen, Tim Harder, Sandro Bottaro, Kristoffer E. Johansson, Pengfei Tian, Kasper Stovgaard, Christian Andreetta, Anders S. Christensen, Simon Olsson, Jan Valentin, Mikael Borg, Jesper Ferkinghoff-Borg and Thomas Hamelryck (2012) PHAISTOS: A Framework for Markov Chain Monte Carlo Simulation of Proteins ()

Presentations (talks)

Presentations (posters)

Current Work

Protein structure prediction using Knowledge Based Potentials (KBP) and Monte Carlo simulation implementing generalized ensembles.

Unpublished Work

  • "On the Spectral Method as a Tool for Topology Optimization in a Viscous and Compressible Navier-Stokes Flow", master thesis, 2010 under the supervision of Mogens Høgh Jensen.
  • "Kilde- og Kanalkodning", bachelor thesis, 2007, under the supervision of Christian Thommesen.
  • Various Java applets/simulations, which can be found at physics.skyphysics.dk

Teaching

Lecturer

Assistant

  • Statistical Physics (fysik 7) at NBI, Fall 2008.

Software Competencies

Programming Languages

  • Java
  • c++ incl. boost libraries, serialization, message passing interface (MPI) etc.

Programs

Scripting

  • Python incl. numpy, scipy, biopython etc.
  • Gnuplot
  • Bash, AWK
  • MatLab/Octave

Other

I am currently administrating the computer cluster owned by the Structural Bioinformatics group.