Re: biological ABM modelling publications

[Mark H. Butler]

RE: biological ABM modelling publications

I've found my copy of Pankaj Agarwal's PhD thesis - it's got quite a few
references to computer models (but not necessarily agent based models) of
development in tissues. Maybe they are of some use? I haven't read them
though so I can't comment on them .. see the list below ..

> I'm a grad student trying to convince potential advisor(s) of the utility
> of agent based modeling systems in obtaining a better understanding how
> intricate patterns of gene expression are formed in developing tissues of
> embryos.  They (quite understanably) want to see publications in "the
> field".  Can somebody please help me?  

Also I know my supervisor is very keen to run a project (could be PhD or
PostDoc) on agent based modelling of the placenta at the moment - he's got
some contacts in the medical school here who are keen to participate. You'd
have to arrange funding but I expect it could work out cheaper than the
states. So if you fancy a change in continent then why not ask him. His
name is Dr Ray Paton, email address@hidden,
http://www.csc.liv.ac.uk/~rcp You can check out our work in general at
http://www.csc.liv.ac.uk/~biocomp

Please mention my name if you write

Mark H. Butler
address@hidden
http://www.csc.liv.ac.uk/~mhb
Liverpool Biocomputation Group  http://www.csc.liv.ac.uk/~biocomp

++++++++++++++++++++++++++++++++++++++++++++++++

(Aga93)   Pankaj Agarwal.  The Cell Programming Language.  Technical Report
630, Department of Computer Science, Courant Institute of Mathematical
Sciences New York University,1993.

(ARW75)   P. Antonelli, T.D. Rogers, and M. Willard. Cell aggregation
kinetics. In G.D. Mostow, editor, Mathematical Models. for Cell
Rearrangement, chapter 10, pages 176-195. Yale University Press, New
Haven,1975.

(CM8B)    Richard Cowan and Valerie B. Morris. Division rules for polygonal
cells. Journal Of Theoretical Biology,131:33-42,1988.

(CP78)    Stephen Childress and Jerome K. Percus. Mathematical Models in
Developmental Biology.  Courant Institute of Mathematical Sciences Lecture
Notes. New York University,1978.

(FB93)    Kurt Fleischer and Alan H. Barr. A simulation testbed for the
study of multi-cellular development: The multiple mechanisms of
morphogenesis. In Artificial Life III Addison-Wesley, 1993.

(GCG+75)  Narendra Goel, Richard D. Campbell, Richard Gordon, ftobert
Rosen, Hugo Martinez, and Martynas Ycas. Self-sorting of isotropic cells.
In G.D. Mostow, editor, Mathematical Models for Cell Rearrangement, chapter
7, pages 100-144.Yale University Press,1975.

(Gil91)   Scott F. Gilbert. Developmental Bzology. Sinauer Associates,
Sunderland, MA,1991.

(GL75)    Narendra S. Goel and Ardean G. Leith. Self sorting of anisotropic
cells. In G.D.Mostow, editor, Mathematical Models for Cell Rearrangement,
chapter 8, pages 145-158. Yale University Press,1975.

(GR78)    Narendra S. Goel and Gary Rogers.  Computer simulation of
engulfment and   other movements of embryonic tissues. Journal Of
Theoretical Biology, 71:103- 140,1978.

(Har76)   Albert K. Harris. Is cell sorting caused by differences in the
work of intercellular adhesion? A critique of the Steinberg hypothesis.
Journal Of Theoretical Biology, 61:267-285,1976.

(Hon78)   Hisao Honda.  Description of cellular pattern by Dirichlet
domains: The two- dimensional case. Journal Of Theoretical Biology,
72:523-543,1978.

(LG7l)    Ardean G. Leith and Narendra S. Goel. Simulation of movement of
cells during self sorting. Journal Of Theoretzcal Biology, 33:171-188,1971.

(LG75)     Ardean G. Leith and Narendra S. Goel. Simulation of movement of
cells during  self-sorting. In Mathematical Models for Cell Rearrangement,
chapter 9, pages 159-175. Yale University Press,1975.

(Lin68)    Aristid Lindenmayer. Mathematical models for cellular
interaction in development, Journal Of Theoretical Biology,18:280-315,1968.

(Mei82)    Hans Meinhardt. Models of Biological Pattern FoTmation. Academic
Press, New York,1982.

(MF8O)     Raymond J. Matela and Robert J. Fletterick. Computer simulation
of cellular self sorting:  A topological exchange model.  Journal Of
Theoretical Biology, 84:673-690,1980.

(Mos75)    G.D. Mostow.  Mathematical Models for Cell Rearrangement.  Yale
University Press,1975.

(MRB5)     Raymond J. Matela and Robert Ransom. A topological model of cell
division: Structure of the computer program. BioSystems,18:65-78,1985.

(MSR91)    Eric Mjolsness, David H. Sharp, and John Reinitz.  A
connectionist model of development. Journal Of Theoretical
Biology,152:429-453,1991.

(Ran81)    Robert Ransom.  Computers and Embryos: Models in Developmental
Biology.John Wiley, New York,1981.

(RG78)     Gary Rogers and Narendra S. Goel. Computer simulation of
cellular movements: Cell-sorting, cellular migration through a mass of
cells and contact inhibition.Journal Of Theoretical Biology,
71:141-166,1978.

(RM84)     R. Ransom and R.J. Matela. Computer modeling of cell division
during development using a topological approach. Journal of Embryology and
Experimental Morphology: Supplement, 83:233-259,1984.

(RM590)    John Reinitz, Eric Mjolsness, and David H. Sharp.  A
connectionist model of Drosophilia blastoderm. In Principles of
Organization in Organisms, pages 109- 118. Addison-Wesley, 1990.

(5C91)     Hans B. Sieburg and Oliver K. Clay. The cellular device machine
development system for modeling biology on the computer.  Complex Systems,
5:575-601,1991.

(Ste75)   Malcolm S. Steinberg.  Reconstruction of tissues by dissociated
cells. In G.D.Mostow, editor, Mathematical Models for Cell Rearrangement,
chapter 6, pages 82-99. Yale University Press,1975.

(Ste78)   Malcolm S. Steinberg. Cell-cell recognition in multicellular
assembly: levels of specificity.  In Cell-cell recognation, pages 25-49.
Cambridge University Press,Cambridge,1978.

(Sul82)   Deborah Sulsky.  Models of Cell and Tissue Movement.  PhD thesis,
Courant Institute of Mathematical Sciences, June 1982.

(Tur52)   Alan Turing.  The chemical basis of morphogenesis.  Phil. Trans.
Roy. Soc. B, 237:37-72,1952.

(Wad66)   C.H. Waddington.  Principles of Development and Differentation.
Macmillan Company, New York,1966.



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