Computational Biology and Biological Physics

Carl Troein Assistant Professor (Forskarassistent) Computational Biology & Biological Physics, Department of Astronomy and Theoretical Physics, Lund University Phone: +46 46 2223003 Email: carl@thep.NOSPAM.lu.se

Research interests:

I am interested in the function and evolutionary origins of gene regulatory systems, in particular the circadian clocks of plants. My current aim is to gain a better understanding of how and which environmental and functional requirements cause circadian clocks to generally require a large number of light inputs, negative feedback loops and so forth.

Recent publications (Full publication list; Citations):

• François Rineau, Firoz Shah, Mark M. Smits, Per Persson, Tomas Johansson, Robert Carleer, Carl Troein and Anders Tunlid
  Carbon availability triggers the decomposition of plant litter and assimilation of nitrogen by an ectomycorrhizal fungus
  Submitted
  
• Richard Adams, Allan Clark, Azusa Yamaguchi, Neil Hanlon, Nikos Tsorman, Shakir Ali, Galina Lebedeva, Alexey Goltsov, Anatoly Sorokin, Ozgur E. Akman, Carl Troein, Andrew J. Millar, Igor Goryanin and Stephen Gilmore
  SBSI: An extensible distributed software infrastructure for parameter estimation in systems biology
  Bioinformatics 2013; doi 10.1093/bioinformatics/btt023
  [ Journal/DOI, Google Scholar ]
• Henrik Jönsson, Jérémy Gruel, Pawel Krupinski and Carl Troein
  On evaluating models in Computational Morphodynamics
  Current Opinion in Plant Biology 15, 103–110 (2012)
  [ Journal/DOI, Google Scholar ]
• Christian Holzgräfe, Anders Irbäck and Carl Troein
  Mutation-induced fold switching among lattice proteins
  The Journal of Chemical Physics 135, 195101 (2011)
  [ Journal/DOI, Google Scholar ]
• Gerben van Ooijen, Laura E. Dixon, Carl Troein and Andrew J. Millar
  Proteasome function is required for biological timing throughout the twenty-four hour cycle
  Current Biology 21, 869–875 (2011)
  [ Journal/DOI, Google Scholar ] ( Commentary )
• Carl Troein, Florence Corellou, Laura E. Dixon, Gerben van Ooijen, John S. O'Neill, François-Yves Bouget and Andrew J. Millar
  Multiple light inputs to a simple clock circuit allow complex biological rhythms
  The Plant Journal 66, 375–385 (2011)
  [ Journal/DOI, Google Scholar ]
• John S. O'Neill, Gerben van Ooijen, Laura E. Dixon, Carl Troein, Florence Corellou, François-Yves Bouget, Akhilesh B. Reddy and Andrew J. Millar
  Circadian rhythms persist without transcription in a eukaryote
  Nature 469, 554–558 (2011)
  [ Journal/DOI, Google Scholar ] ( Commentary ) { The Scientist, Coturnix/SciAm }
• Ozgur E. Akman, Maria Luisa Guerriero, Laurence Loewe and Carl Troein
  Complementary approaches to understanding the plant circadian clock
  Proceedings of From Biology To Concurrency and back 2010 (FBTC'10)
  EPTCS 19, 1–19 (2010)
  [ Abstract, PDF, Journal/DOI, Google Scholar ]
• Carl Troein, James C. W. Locke, Matthew S. Turner and Andrew J. Millar
  Weather and seasons together demand complex biological clocks
  Current Biology 19, 1961–1964 (2009)
  [ Abstract, Preprint (PDF), Journal/DOI, Google Scholar ] ( Commentary ) { BBC news }

Brief CV:

• 2001 – MSc, Physics, Lund University.
• 2007 – PhD, Theoretical physics, Lund University.
• 2007 – Postdoc, Millar lab, School of Biological Sciences, University of Edinburgh.
• 2008–2010 – HFPS Cross-Disciplinary Fellowship at University of Edinburgh.
• 2010–2011 – Postdoc, CBBP, Dept. of Astr. and Theor. Phys., Lund University.
• 2011– – Assistant Professor, CBBP, Dept. of Astr. and Theor. Phys., Lund University.

For students:

• C++ course for PhD students, summer 2011.
• Systems biology course for PhD students, spring 2013.

Software:

• BASE – BioArray Software Environment: A Platform for Comprehensive Management and Analysis of Microarray Data
• Benchmarks of local computers

PhD position:

PhD position in computational biology with focus on dynamical modelling of biological networks, in particular in relation to network evolution and circadian rhythms. This position has now been filled. Karl Fogelmark has joined the group. If the opportunity arises to recruit additional PhD students or postdocs, any open positions will be posted here as well as through the official channels. Until then, we can only consider applications from self-funded candidates.

Last updated (possibly wrong): 15 May 2012