Plant stem cell maintenance involves direct transcriptional repression of differentiation program
R.K. Yadav, M. Perales, J. Gruel, C. Ohno, M. Heisler, T. Girke, H. Jönsson, and G.V. Reddy
Molecular Systems Biology 9:654 (2013)
[ HTML at journal ]

On evaluating models in Computational Morphodynamics
H. Jönsson, J. Gruel, P. Krupinski, and C. Troein
Current Opinion in Plant Biology 15:103-110 (2012)
[ HTML at journal ]

WUSCHEL protein movement mediates stem cell homeostasis in the Arabidopsis shoot apex R.K. Yadav, M. Perales, J. Gruel, T. Girke, H. Jönsson, and G.V. Reddy Genes & Development 25:2025-2030 (2011) [ HTML at journal ]

Models of sequestration and receptor cross-talk for explaining multiple mutants in plant stem cell regulation
P. Sahlin, P. Melke, and H. Jönsson
BMC Systems Biology 5:2 (2011)
[ HTML at journal ]

Alignment between PIN1 Polarity and Microtubule Orientation in the Shoot Apical Meristem Reveals a Tight Coupling between Morphogenesis and Auxin Transport
M. Heisler, O. Hamant, P. Krupinski, M. Uyttewaal, C. Ohno, H. Jönsson, J. Traas, E. Meyerowitz
PLoS Biology 8(10):e1000516 (2010)
[ HTML at journal ]

A modeling study on how cell division affects properties of epithelial tissues under isotropic growth
P. Sahlin, H. Jönsson
PLoS ONE 5(7):e11750 (2010)
[ HTML at journal ]

A cell-based model for quorum sensing in heterogeneous bacterial colonies
P. Melke, P. Sahlin, A. Levchenko, and H. Jönsson
PLoS Computational Biology 6(6):e1000819 (2010)
[ HTML at journal ]

Modeling auxin-regulated Development
P. Krupinski and H. Jönsson
Cold Spring Harb Persp Biol 2, a001560 (2010)
[ HTML at journal ]

Modeling plant growth and pattern formation H. Jönsson and P. Krupinski Current Opinion in Plant Biology 13,5-11 (2010) [ HTML at journal ]

Regulated transport as a mechanism for pattern generation: Capabilities for phyllotaxis and beyond
P. Sahlin, B. Söderberg, and H. Jönsson
Journal of Theoretical Biology 258, 60-70 (2009)
[ HTML at journal ]

Developmental patterning by mechanical signals in Arabidopsis O. Hamant, M. Heisler, H. Jönsson, P. Krupinski, M. Uyttewaal, P. Bokov, F. Corson, P. Sahlin, A. Boudaoud, E. M. Meyerowitz, Y. Couder, and J. Traas Science 322, 1650-1655 (2008) [ HTML at journal ]

Self-organization in high density bacterial colonies: Efficient crowd control
H. J. Cho, H. Jönsson, J. K. Cambell, P. Melke, J. W. Williams, B. Jedynak, A. M. Stevens, A. Groisman, and A. Levchenko
PLoS Biology 5, e302 (2007)
[ HTML at journal ]
See also comments in Research Highlight from Nature 450(7168):322 and Nature Reviews Microbiology, 5(12):904.

Modelling meristem development in plants
M. Heisler and H. Jönsson
Current Opinion in Plant Biology 10, 92-97 (2007)
[ HTML at journal ]

Computer modeling of plant development
M. Heisler and H. Jönsson
Journal of Plant Growth Regulation 25, 267-269 (2006)
[ HTML at journal ]

Modeling auxin transport and plant development
M. Heisler and H. Jönsson
Journal of Plant Growth Regulation 25, 302-312 (2006)
[ HTML at journal ]

A rate equation approach to elucidate the kinetics and robustness of the TGF-β pathway
P. Melke, H. Jönsson, E. Pardali, P. ten Dijke, and C. Peterson
Biophysical Journal 96, 4368-4380 (2006)
[ HTML at journal ]

An auxin-driven polarized transport model for phyllotaxis
H. Jönsson, M. Heisler, B.E. Shapiro, E.M. Meyerowitz, and E. Mjolsness
Proceedings of the National Academy of Sciences USA 103, 1633-1638 (2006)
[ abs ] [ PDF at journal ] [ Supplement at journal ]
See also comment in In this issue from PNAS.

Modeling the organization of the WUSCHEL expression domain in the shoot apical meristem
H. Jönsson, M. Heisler, G.V. Reddy, V. Agrawal, V. Gor, B.E. Shapiro, E. Mjolsness, and E.M. Meyerowitz
Bioinformatics 21(Suppl. 1), i232-i240 (2005)
[ abs ] [ PDF at journal ] [ Supplement ]

An explicit spatial model of yeast microcolony growth
H. Jönsson and A. Levchenko
Multiscale Modeling and Simulation 3, 346-361 (2005).
[ abs ] [ pdf ]

An approximate maximum likelihood approach, applied to phylogenetic trees
H. Jönsson and B. Söderberg
Journal of Computational Biology 10, 737-749 (2003)
[ abs ] [ ps.gz ] [ pdf ]

An information-based neural approach to generic constraint satisfaction
H. Jönsson and B. Söderberg
Artificial Intelligence 142:1, 1-17 (2002)
[ abs ] [ ps.gz ] [ pdf ]

An information-based neural approach to constraint satisfaction
H. Jönsson and B. Söderberg
Neural Computation 13, 1827-1838 (2001)
[ abs ] [ ps.gz ] [ pdf ]

Statistical Properties of Cell Topology and Geometry in a Tissue-Growth Model
P. Sahlin, O. Hamant, and H. Jönsson
In J. Zhou (Ed.): Complex 2009, Part I, LNICST 4, pp. 971-979 (2009)

A software architecture for developmental modeling in plants: The computable plant project.
V. Gor, BE. Shapiro, H. Jönsson, M. Heisler, GV. Reddy, EM. Meyerowitz, and E. Mjolsness
in Bioinformatics of Genome Regulation and Structure II, N. Kolchanov, R. Hoffestaedt, L. Milanesi (eds.), pp 345-354, Kluwer Academic Publishers, (2006).
[ abs ]

Modeling plant development with gene regulation networks including signaling and cell division
H. Jönsson, B.E. Shapiro, E.M. Meyerowitz, and E. Mjolsness
in Bioinformatics of Genome Regulation and Structure, N. Kolchanov, R. Hoffestaedt (eds.), pp 311-318, Kluwer Academic Publishers, Boston, (2004). (ISBN 1-4020-7735-1)
[ abs ]

Signalling in multicellular models of plant development
H. Jönsson, B.E. Shapiro, E.M. Meyerowitz, and E. Mjolsness
in On Growth, Form, and Computers, S. Kumar,P. Bentley (eds.), pp 156-161, Academic Press, London, (2003). (ISBN 0-12-428765-4)
[ abs ]

Variational methods in combinatorial optimization and
phylogeny reconstruction
Henrik Jönsson
PhD Thesis, Date of issue: 2001-11-01, ISBN 91-7874-161-1
Thesis advisor: Bo Söderberg.
[ about ] [ pdf ]

Deterministic annealing and nonlinear assignment
H. Jönsson and B. Söderberg
LU TP 01-16
[ abs ] [ ps.gz ] [ pdf ]

Neural network approaches to Jobshop problems
Henrik Jönsson Master thesis, LU TP 97-xx, Thesis advisor: Bo Söderberg.
[ abs ]

Modeling software developed within the computableplant project
H. Jönsson
Oral presentation at the Advanced Workshop: The understanding and modelling of auxin transport in plants , Nottingham, UK, May 14 - 16, 2008.
[ workshop homepage ]

Models of pattern generation in multicellular systems
H. Jönsson
Oral presentation at the SY-STEM meeting , Montpellier, France, April 28 - 29, 2008.

Modeling and live imaging of multicellular pattern-generating systems: from bacteria to plants
H. Jönsson
Oral presentation at the Workshop on Modelling Complex Biological Systems , Uppsala, April 17 - 18, 2008.
[ workshop homepage ]

Models of pattern formation in the plant shoot
H. Jönsson
Oral presentation at Workshop on Pattern Formation and Functional Morphology , Linz, Austria, January 7 - 11, 2008.
[ workshop homepage ]

Modeling and live confocal imaging of plant shoot development
H. Jönsson
Oral presentation at the 8th International Conference on Systems Biology , Long Beach, CA, October 1 - 6, 2007.
[ conference homepage ]

Computational modeling of plant development
H. Jönsson
Oral (keynote) presentation at the Systems Biology Workshop: From Nucleotides to Ecosystems , Melbourne, Australia, May 21 - June 1, 2007.

Computational models of plant shoot development
H. Jönsson
Oral presentation at the 2nd Workshop on Mathematical Aspects of Systems Biology , Gothenburg, Sweden, March 21-24, 2007.
[ conference homepage ]

Computational modelling and live imaging of plant development
H. Jönsson, M. Heisler, P. Melke, E.M. Meyerowitz, E. Mjolsness, and B. S. Shapiro
Oral presentation at the Basel Computational Biology Conference (USGEB07) , Basel, Switzerland, March 13-14, 2007.
[ conference homepage ]

An auxin transport model for regulation of plant organ initiation
H. Jönsson, M. Heisler, B. E. Shapiro, E.M. Meyerowitz, and E. Mjolsness
Poster presented at the 7th International Conference on Systems Biology, Yokohama, Japan, Oct 9-11, 2006.
[ abstract (pdf) ] [ poster(pdf) ] [ conference homepage ]

Modeling the organization of the WUSCHEL expression domain in the shoot apical meristem
H. Jönsson, M. Heisler, G.V. Reddy, V. Agrawal, V. Gor, B.E. Shapiro, E. Mjolsness, and E.M. Meyerowitz
Oral presentation at the 13th Annual International conference on Intelligent Systems for Molecular Biology (ISMB 2005) , Detroit, USA, June 25-29, 2005.
[ abs ] [ conference homepage ]

Addressing the plant phyllotaxis problem using modeling and in vivo live imaging
H. Jönsson, M. Heisler, G.V. Reddy, B. E. Shapiro, V. Gor, E.M. Meyerowitz, and E. Mjolsness
Oral presentation at the 5th Swedish Bioinformatics Workshop, Lund, Sweden, November 26-27, 2004.
[ abstract (html)] [ workshop homepage ]

A multicellular model of a feedback network regulating spatial gene expression domains in the shoot apical meristem
H. Jönsson, B. E. Shapiro, V. Gor, M. Heisler, G. V. Reddy, M. Heisler, E.M. Meyerowitz, and E. Mjolsness
Poster presented at the 5th International Conference on Systems Biology, Heidelberg, Germany, Oct 9-13, 2004.
[ abstract (pdf) ] [ poster(pdf) ] [ conference homepage ]

Modeling and in vivo live imaging of the Arabidopsis shoot apical meristem
H. Jönsson, M. Heisler, B. E. Shapiro, V. Gor, G. V. Reddy, M. Heisler, E.M. Meyerowitz, and E. Mjolsness
Oral presentation at the 15th International Conference on Arabidopsis Research, Berlin, Germany, July 11-14, 2004.
[ abstract (txt) ] [ conference homepage ]

Inferring gene regulatory networks for plant stem cell regulation
H. Jönsson, E.M. Meyerowitz, and E. Mjolsness
Poster presented at the 4th International Conference on Systems Biology, St Louis, MD, USA, Nov, 2003.
[ extended abstract (pdf) ] [ poster(pdf) ] [ conference homepage ]

Resources and signaling in multicellular models of plant development
H. Jönsson, B.E. Shapiro, E.M. Meyerowitz, and E. Mjolsness
Poster presented at the 3rd International Conference on Systems Biology, Stockholm, Sweden, Dec 11-15, 2002.

The poster is discussed in the Science STKE review of the conference:
E. Werner, In Silico Cell Signaling Underground, Science STKE 2003, pe8 (2003)

Gene regulation networks with signaling and cell division in developmental simulations
E. Mjolsness, B.E. Shapiro, V. Gor, and H. Jönsson
Oral presentation at the Second Joint Meeting of the IEEE Engineering in Medicine and Biology Society (IEEE/EMBS) and the Biomedical Engineering Society (BMES), Houston TX, USA, Oct 23-26, 2002.
[ pdf ]

A neural network approach to Jobshop problems
H. Jönsson
Poster presented at Scientific Applications of Neural Nets, Bad Honnef, Germany, May 11-13, 1998.