Carl Troein's publications:

• Carl Troein, Syahril Siregar, Michiel Op De Beeck, Carsten Peterson, Anders Tunlid and Per Persson
  OCTAVVS: A graphical toolbox for high-throughput preprocessing and analysis of vibrational spectroscopy imaging data
  Methods and Protocols 3, 34 (2020)
  [ Journal/DOI, BioRxiv, Google Scholar ]
• Adriaan Merlevede and Carl Troein
  Perfect edge-transmitting recombination of permutations
  Submitted (2020)
  [ arXiv, Google Scholar ]
• Michiel Op De Beeck, Carl Troein, Syahril Siregar, Luigi Gentile, Giuseppe Abbondanza, Carsten Peterson, Per Persson and Anders Tunlid
  Regulation of fungal decomposition at single-cell level
  The ISME Journal 14, 896-905 (2020)
  [ Journal/DOI, Google Scholar ]
• Adriaan Merlevede, Henrik Åhl and Carl Troein
  Homology and linkage in crossover for linear genomes of variable length
  PLOS ONE 14, e0209712 (2019)
  [ Journal/DOI, Google Scholar ]
• César Nicolás, Tomas Martin-Bertelsen, Dimitrios Floudas, Johan Bentzer, Mark Smits, Tomas Johansson, Carl Troein, Per Persson and Anders Tunlid
  The soil organic matter decomposition mechanisms in ectomycorrhizal fungi are tuned for liberating soil organic nitrogen
  The ISME Journal 13, 977-988 (2019)
  [ Journal/DOI, Google Scholar ]
• Michiel Op De Beeck, Carl Troein, Carsten Peterson, Per Persson and Anders Tunlid
  Fenton reaction facilitates organic nitrogen acquisition by an ectomycorrhizal fungus
  The New Phytologist 218, 335-343 (2018)
  [ Journal/DOI, Google Scholar ]
• Karl Fogelmark, Carsten Peterson and Carl Troein
  Selection shapes transcriptional logic and regulatory specialization in genetic networks
  PLOS ONE 11, e0150340 (2016)
  [ Journal/DOI, Google Scholar ]
• Karl Fogelmark and Carl Troein
  Rethinking transcriptional activation in the Arabidopsis circadian clock
  PLoS Computational Biology 10, e1003705 (2014)
  [ Journal/DOI, Google Scholar, Software supplement ]
• Laura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman and Andrew J. Millar
  Light and circadian regulation of clock components aids flexible responses to environmental signals
  The New Phytologist 203, 568–577 (2014)
  [ Journal/DOI, Google Scholar ]
• 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
  The ISME Journal 7, 2010–2022 (2013)
  [ Journal/DOI, Google Scholar ]
• 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 29, 664–665 (2013)
  [ 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, Supplementary data ]
• 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 }
• 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 }
• Doctoral dissertation:
  Gene Regulatory Networks: Dynamics and Stability
  Printed by Media-Tryck AB, Lund 2007
  ISBN 978-91-628-7118-5
  [ Abstract, PDF, Library, Errata ]
• Carl Troein, Dag Ahrén, Morten Krogh and Carsten Peterson
  Is transcriptional regulation of metabolic pathways an optimal strategy for fitness?
  PLoS ONE 2, e855 (2007)
  [ Abstract, PDF, Journal/DOI, Google Scholar ]
• Vijay Chickarmane, Carl Troein, Ulrike A. Nuber, Herbert M. Sauro and Carsten Peterson
  Transcriptional dynamics of the embryonic stem cell switch
  PLoS Computational Biology 2, e123 (2006)
  [ Abstract, PDF, Journal/DOI, Google Scholar ]
• Björn Samuelsson and Carl Troein
  Random maps and attractors in random Boolean networks
  Physical Review E 72, 046112 (2005)
  [ Abstract, Preprint (PDF), Journal/DOI, Google Scholar, Errata ]
• Thomas Breslin, Morten Krogh, Carsten Peterson and Carl Troein
  Signal transduction pathway profiling of individual tumor samples
  BMC Bioinformatics 6, 163 (2005)
  [ Abstract, PDF, Journal/DOI, Supplement, Google Scholar, Errata ]
• Stuart Kauffman, Carsten Peterson, Björn Samuelsson and Carl Troein
  Genetic networks with canalyzing Boolean rules are always stable
  Proceedings of the National Academy of Sciences USA 101, 17102–17107 (2004)
  [ Abstract, PDF, Supplement (PDF), Journal/DOI, Google Scholar ]
• Dag Ahrén, Carl Troein, Tomas Johansson and Anders Tunlid
  PHOREST: A web-based tool for comparative analyses of expressed sequence tag data
  Molecular Ecology Notes 4, 311–314 (2004)
  [ Abstract, Journal/DOI, Google Scholar ]
• Stuart Kauffman, Carsten Peterson, Björn Samuelsson and Carl Troein
  Random Boolean network models and the yeast transcriptional network
  Proceedings of the National Academy of Sciences USA 100, 14796–14799 (2003)
  [ Abstract, PDF, Supplement (PDF), Journal/DOI, Google Scholar ]
• Björn Samuelsson and Carl Troein
  Superpolynomial growth in the number of attractors in Kauffman networks
  Physical Review Letters 90, 098701 (2003)
  [ Abstract, Preprint (PDF), Journal/DOI, FAQ, Google Scholar, Errata ]
• Lao H. Saal, Carl Troein, Johan Vallon-Christersson, Sofia Gruvberger, Åke Borg and Carsten Peterson
  BioArray Software Environment (BASE): A platform for comprehensive management and analysis of microarray data
  Genome Biology 3, software0003.1–0003.6 (2002)
  [ Abstract, PDF, Journal/DOI, Google Scholar ]
• Anders Irbäck and Carl Troein
  Enumerating designing sequences in the HP model
  Journal of Biological Physics 28, 1–15 (2002)
  [ Abstract, Preprint (PDF), Data, Journal/DOI, Google Scholar ]

Proceedings, book chapters &c.:

• 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, Johan Vallon-Christersson and Lao H. Saal
  An introduction to BioArray Software Environment
  In Methods in Enzymology 411, DNA Microarrays, Part B: Databases and Statistics, eds. A. Kimmel and B. Oliver, 99–119, Elsevier (2006)
  [ Abstract, Publisher Google Scholar ]
• Björn Samuelsson and Carl Troein
  Superpolynomial growth in the number of attractors in Kauffman networks
  Acta Physica Polonica B 34, 5051–5061 (2003)
  [ Abstract, Preprint (PDF), Journal ]