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Carl Troein – 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)
    DOI 10.3390/mps3020034, BioRxiv 2019.12.17.879387
  • Adriaan Merlevede and Carl Troein
    Perfect edge-transmitting recombination of permutations
    Submitted (2020)
    arXiv 2005.01113
  • 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)
    DOI 10.1038/s41396-019-0583-9
  • Adriaan Merlevede, Henrik Åhl and Carl Troein
    Homology and linkage in crossover for linear genomes of variable length
    PLOS ONE 14, e0209712 (2019)
    DOI 10.1371/journal.pone.0209712
  • 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)
    DOI 10.1038/s41396-018-0331-6
  • 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)
    DOI 10.1111/nph.14971
  • Karl Fogelmark, Carsten Peterson and Carl Troein
    Selection shapes transcriptional logic and regulatory specialization in genetic networks
    PLOS ONE 11, e0150340 (2016)
    DOI 10.1371/journal.pone.0150340
  • Karl Fogelmark and Carl Troein
    Rethinking transcriptional activation in the Arabidopsis circadian clock
    PLoS Computational Biology 10, e1003705 (2014)
    DOI 10.1371/journal.pcbi.1003705, 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)
    DOI 10.1111/nph.12853
  • 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)
    DOI 10.1038/ismej.2013.91
  • 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)
    DOI 10.1093/bioinformatics/btt023
  • Henrik Jönsson, Jérémy Gruel, Pawel Krupinski and Carl Troein
    On evaluating models in Computational Morphodynamics
    Current Opinion in Plant Biology 15, 103–110 (2012)
    DOI 10.1016/j.pbi.2011.09.007
  • Christian Holzgräfe, Anders Irbäck and Carl Troein
    Mutation-induced fold switching among lattice proteins
    The Journal of Chemical Physics 135, 195101 (2011)
    DOI 10.1063/1.3660691, 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)
    DOI 10.1016/j.cub.2011.03.060, Commentary article
  • 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)
    DOI 10.1111/j.1365-313X.2011.04489.x
  • 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)
    DOI 10.1038/nature09654, Commentary article, 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)
    DOI 10.1016/j.cub.2009.09.024, Preprint (PDF), Commentary article, BBC news item
  • Doctoral dissertation:
    Gene Regulatory Networks: Dynamics and Stability
    Printed by Media-Tryck AB, Lund 2007
    ISBN 978-91-628-7118-5
    Abstract, Full PDF, 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)
    DOI 10.1371/journal.pone.0000855, Preprint (PDF)
  • 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)
    DOI 10.1371/journal.pcbi.0020123, Preprint (PDF)
  • Björn Samuelsson and Carl Troein
    Random maps and attractors in random Boolean networks
    Physical Review E 72, 046112 (2005)
    DOI 10.1103/PhysRevE.72.046112, Preprint (PDF), Errata
  • Thomas Breslin, Morten Krogh, Carsten Peterson and Carl Troein
    Signal transduction pathway profiling of individual tumor samples
    BMC Bioinformatics 6, 163 (2005)
    DOI 10.1186/1471-2105-6-163, Preprint (PDF), Supplement, 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)
    DOI 10.1073/pnas.0407783101, Preprint (PDF), Supplement (PDF)
  • 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)
    DOI 10.1111/j.1471-8286.2004.00613.x, Abstract
  • 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)
    DOI 10.1073/pnas.2036429100. Preprint (PDF), Supplement (PDF)
  • Björn Samuelsson and Carl Troein
    Superpolynomial growth in the number of attractors in Kauffman networks
    Physical Review Letters 90, 098701 (2003)
    DOI 10.1103/PhysRevLett.90.098701, Preprint (PDF), FAQ, 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)
    DOI 10.1186/gb-2002-3-8-software0003, Preprint (PDF)
  • Anders Irbäck and Carl Troein
    Enumerating designing sequences in the HP model
    Journal of Biological Physics 28, 1–15 (2002)
    DOI 10.1023/A:1016225010659, Preprint (PDF), Data supplement

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)
    DOI 10.4204/EPTCS.19.1, Article (PDF)
  • 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
  • Björn Samuelsson and Carl Troein
    Superpolynomial growth in the number of attractors in Kauffman networks
    Acta Physica Polonica B 34, 5051–5061 (2003)
    Preprint (PDF), Journal

  • Doctoral dissertation
    Gene Regulatory Networks: Dynamics and Stability
    Printed by Media-Tryck AB, Lund 2007
    ISBN 978-91-628-7118-5
    • On page 2, last line:
      if should be of
    • On page 12, last paragraph:
      these database should be these databases and the the DNA sequence should be the DNA sequence
    • On page 17, paragraph 4:
      the { should be {the
    • On page 21, last paragraph:
      number of nodes should be mean number of nodes and equilibrium should be its equilibrium distribution of TRUE and FALSE
    • On page 66, III.3, item 2):
      flatter should be steeper
    • On page 76, above eq. (III.B9):
      retrieving should be receiving
    • On page 94, paragraph 3:
      the most one should be the most significant one
    • On page 97, eq. (IV.8):
      \binom{i}{N} should be \binom{N}{i}
    • On page 147, second paragraph:
      bride this gap should be brigde this gap
    • On page 153, last paragraph:
      the the parameters should be the parameters
  • T. Breslin, M. Krogh, C. Peterson, and C. Troein
    Signal transduction pathway profiling of individual tumor samples
    BMC Bioinformatics 6, 163 (2005)
    • On page 8, figures 6 and 7:
      van't Veer should be van 't Veer
    • On page 9, at the column break:
      Uni Gene should be UniGene
    • On page 10, the last equation:
      \binom{i}{N} should be \binom{N}{i}
  • B. Samuelsson and C. Troein
    Superpolynomial growth in the number of attractors in Kauffman Networks
    Physical Review Letters 90, 098701 (2003)
    • On page 098701-3, in the first line after eq. (13):
      h1 and h2 should be k1 and k2
    • On page 098701-4, second paragraph of the summary:
      C2 should be CL
    • On page 098701-4, reference 5 (6 in the preprint):
      Savageua should be Savageau
  • B. Samuelsson and C. Troein
    Random maps and attractors in random Boolean networks
    Physical Review E 72, 046112 (2005)
    • On page 046112-18, reference 11:
      H. J. Kjær should be N. J. Kjær