Stan Marée's old webpage
I have recently moved to Norwich, where I have
started as a Project Leader
in the Department of Computational and Systems
Biology
at the John Innes Centre.
My research group focuses on Modelling Animal
and Plant Development.
From 2003-2009 I was a staff member of the Theoretical
Biology / Bioinformatics Group, at the
Utrecht University, the
Netherlands.
The main theme
of my research is ``Modelling morphogenesis on the interface of
subcellular and cellular processes''. Since we have entered the era
of bioinformatics, we continuously gain better understanding of the
processes that take place on the subcellular level. However, there
is limited knowledge how the subcellular processes eventually lead
to morphogenesis, how during embryogenesis tissues, organs, and whole
organisms emerge and are able to grow, develop, and maintain themselves.
We want to fill up the missing link between gene regulation and morphogenesis.
To bridge the gap, we are coupling the cellular Potts model, a cellular
automata-type of model that is very powerful for describing cell dynamics,
to (minimal) models of gene regulation networks. This multi-level
modelling approach, in which all the pre-defined dynamics in the model
are on the (sub)cellular level, while all the interesting behaviour
that emerges from the model take place at different intermediate levels
of organisation, as well as at the level of the whole organism, allows
us to keep a relatively low level of model-complexity, since the complexity
of the morphogenesis itself emerges from the interactions and entanglement
of the different levels. It provides a framework in which cells can
differentiate and generate shape simultaneously, and in which experimental
findings related to gene regulation can be linked to the observed
development, from the cellular level to the level of the whole organism.
From 2001-2003 I have been a MITACS
postdoctoral fellow working with Leah Keshet.
I was a member of the Mathematical Biology research
group
of the Mathematics Department
at the University of British Columbia.
In Vancouver, I have worked on models describing the development of
Type I Diabetes. Type I diabetes is an autoimmune disease which develops
after a prolonged period of inflammation of the pancreatic islets
of Langerhans. The immune system specifically attacks the insulin-producing
beta cells. Progression from hidden inflammation to overt diabetes
is caused by an increase in the fraction of lymphocytes that have
a high affinity and high toxicity to the beta cells. This is called
avidity maturation. Treatment of diabetes-prone mice with peptides
similar to those recognised by the lymphocytes has been observed to
either speed up or slow down the avidity maturation, and thereby the
development of diabetes. The outcome depends in a highly non-linear
way on the dose of the administered peptide. We have developed a number
of ODE models to explore the possible underlying mechanisms of the
avidity maturation and its modulation by peptide treatment. The models
describe the dynamics of lymphocyte populations that have different
affinities for the beta cell peptide, as well as the so-called antigen-presenting
cells, which present these peptides to the lymphocytes.
I have done my PhD studies under supervision of Dr.
Sasha Panfilov
and Prof.
Paulien Hogeweg
in the Theoretical
Biology / Bioinformatics group, Utrecht
University, the Netherlands. In my thesis
I describe a model study of the whole development of the cellular
slime mould Dictyostelium discoideum.
When I was living in Vancouver, I have made a couple of fantastic
hikes through beautiful British Columbia. Here
you can find many nice pictures of our hikes.
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M. Laskowski, V. A. Grieneisen, H. Hofhuis, C. A. ten Hove,
P. Hogeweg, A. F. M. Marée, and B. Scheres.
- Root system architecture from coupling cell shape to auxin transport.
PLoS Biol., 6(12):e307 (2008).
MEDLINE.
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A. F. M. Marée, M. Komba, D. T. Finegood, and L. Edelstein-Keshet.
- A quantitative comparison of rates of phagocytosis and digestion of
apoptotic cells by macrophages from normal (BALB/c) and diabetes-prone
(NOD) mice.
J. Appl. Physiol., 104(1):157-169 (2008).
MEDLINE.
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J. B. Beltman, A. F. M. Marée, J. N. Lynch, M. J. Miller, and R. J.
de Boer.
- Lymph node topology dictates T cell migration behavior.
J. Exp. Med., 204(4):771-780 (2007a).
MEDLINE.
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J. B. Beltman, A. F. M. Marée, and R. J. de Boer.
- Spatial modelling of brief and long interactions between T cells
and dendritic cells.
Immunol. Cell Biol., 85(4):306-314 (2007b).
MEDLINE.
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V. A. Grieneisen, J. Xu, A. F. M. Marée, P. Hogeweg, and B. Scheres.
- Auxin transport is sufficient to generate a maximum and gradient
guiding root growth.
Nature, 449(7165):1008-1013 (2007).
MEDLINE.
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A. Jilkine, A. F. M. Marée, and L. Edelstein-Keshet.
- Mathematical model for spatial segregation of the Rho-family
GTPases based on inhibitory crosstalk.
Bull. Math. Biol., 69(6):1943-1978 (2007).
MEDLINE.
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J. Käfer, T. Hayashi, A. F. M. Marée, R. W. Carthew, and
F. Graner.
- Cell adhesion and cortex contractility determine cell patterning in
the Drosophila retina.
Proc. Natl. Acad. Sci. U.S.A., 104(47):18549-18554 (2007).
MEDLINE.
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A. F. M. Marée, V. A. Grieneisen, and P. Hogeweg.
- The Cellular Potts Model and biophysical properties of cells,
tissues and morphogenesis.
In A. R. A. Anderson, M. A. J. Chaplain, and K. A. Rejniak,
editors, Single-Cell-Based Models in Biology and Medicine, pages
107-136. Birkhäuser Verlag, Basel (2007).
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J. Käfer, P. Hogeweg, and A. F. M. Marée.
- Moving forward moving backward: directional sorting of chemotactic
cells due to size and adhesion differences.
PLoS Comput. Biol., 2(6):e56 (2006).
MEDLINE.
DownLoad
PDF.
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A. F. M. Marée, A. Jilkine, A. Dawes, V. A. Grieneisen, and
L. Edelstein-Keshet.
- Polarization and movement of keratocytes: a multiscale modelling
approach.
Bull. Math. Biol., 68(5):1169-1211 (2006a).
MEDLINE.
Web Page.
DownLoad
PDF.
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A. F. M. Marée, P. Santamaria, and L. Edelstein-Keshet.
- Modeling competition among autoreactive CD8+
mathend000# T cells in
autoimmune diabetes: implications for antigen-specific therapy.
Int. Immunol., 18(7):1067-1077 (2006b).
MEDLINE.
DownLoad
PDF.
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A. F. M. Marée, R. Kublik, D. T. Finegood, and L. Edelstein-Keshet.
- Modelling the onset of Type 1 diabetes: can impaired macrophage
phagocytosis make the difference between health and disease?
Philos. Transact. A., 364(1842):1267-1282
(2006c).
MEDLINE.
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PDF.
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M. A. C. Groenenboom, A. F. M. Marée, and P. Hogeweg.
- The RNA silencing pathway: the bits and pieces that matter.
PLoS Comput. Biol., 1(2):155-165 (2005).
MEDLINE.
DownLoad
PDF.
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B. Han, P. Serra, A. Amrani, J. Yamanouchi, A. F. M. Marée,
L. Edelstein-Keshet, and P. Santamaria.
- Prevention of diabetes by manipulation of anti-IGRP autoimmunity:
high efficiency of a low-affinity peptide.
Nat. Med., 11(6):645-652 (2005).
MEDLINE.
DownLoad
PDF.
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A. F. M. Marée, M. Komba, C. Dyck, M.
abeçki, D. T.
Finegood, and L. Edelstein-Keshet.
- Quantifying macrophage defects in type 1 diabetes.
J. Theor. Biol., 233(4):533-551 (2005).
MEDLINE.
DownLoad
PDF.
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A. F. M. Marée and P. Hogeweg.
- Modelling Dictyostelium discoideum
morphogenesis: the culmination.
Bull. Math. Biol., 64(2):327-353 (2002).
MEDLINE.
Web Page.
DownLoad
PDF.
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A. F. M. Marée and P. Hogeweg.
- How amoeboids self-organize into a fruiting body: multicellular
coordination in Dictyostelium discoideum.
Proc. Natl. Acad. Sci. U.S.A., 98(7):3879-3883 (2001).
MEDLINE.
Web Page.
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PDF.
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V. Müller, A. F. M. Marée, and R. J. de Boer.
- Release of virus from lymphoid tissue affects human immunodeficiency
virus type 1 and hepatitis C virus kinetics in the blood.
J. Virol., 75(6):2597-2603 (2001a).
MEDLINE.
DownLoad
PDF.
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V. Müller, A. F. M. Marée, and R. J. de Boer.
- Small variations in multiple parameters account for wide variations
in HIV-1 set-points: a novel modelling approach.
Proc. R. Soc. Lond. B., 268(1464):235-242
(2001b).
MEDLINE.
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PDF.
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A. F. M. Marée, W. Keulen, C. A. B. Boucher, and R. J.
de Boer.
- Estimating relative fitness in viral competition experiments.
J. Virol., 74(23):11067-11072 (2000).
MEDLINE.
Web
Page.
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PDF.
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A. F. M. Marée, A. V. Panfilov, and P. Hogeweg.
- Migration and thermotaxis of Dictyostelium
discoideum slugs, a model study.
J. Theor. Biol., 199(3):297-309 (1999a).
MEDLINE.
Web
Page.
DownLoad
PDF.
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A. F. M. Marée, A. V. Panfilov, and P. Hogeweg.
- Phototaxis during the slug stage of Dictyostelium
discoideum: a model study.
Proc. R. Soc. Lond. Ser. B, 266:1351-1360
(1999b).
Web
Page.
DownLoad
PDF.
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A. F. M. Marée and A. V. Panfilov.
- Spiral breakup in excitable tissue due to lateral instability.
Phys. Rev. Lett., 78:1819-1822 (1997).
Web
Page.
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PDF.
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R. J. A. van Wezel, M. J. M. Lankheet, F. A. J. Verstraten,
A. F. M. Marée, and W. A. van de Grind.
- Responses of complex cells in area 17 of the cat to bi-vectorial
transparent motion.
Vision Res., 36(18):2805-2813 (1996).
MEDLINE.
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PDF.
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A. F. M. Marée, R. J. A. van Wezel, F. A. J. Verstraten,
and W. A. van de Grind.
- Processing of transparent motion information in area 17 complex cells
of the cat.
Perception (suppl.), 23:57-58 (1994).
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R. J. A. van Wezel, F. A. J. Verstraten, A. F. M. Marée,
and W. A. van de Grind.
- Responses of complex cells in area 17 of the cat to transparent
motion.
Invest. Ophthalmol. Vis. Sci. (suppl.), 35:1973 (1994).
| Address: |
Dr. Stan Marée |
|---|
| |
John Innes Centre |
| |
Norwich Research Park |
| |
Colney, Norwich |
| |
UK |
| Office location: |
Genome Centre, Room 101d |
|---|
| Phone: |
+44-1603-450828 |
|---|
| Email: |
Stan.Maree@bbsrc.ac.uk |
|---|