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Special Issues of Journals and Book:

1, Special Issue on Applications to Biology of the Journal of Statistical Physics, Mark Alber, Ray Goldstein, Erwin Frey, Editors, Springer, Volume 128, Issue 1-2, July 2007.

2. Special Issue on Multiscale Modeling in Biology, Multiscale Modeling and Simulation: A SIAM Interdisciplinary Journal, Mark Alber, Thomas Hou, James A. Glazier, Yi Jiang, Editors. Volume 3, Number 2, 2005.

3. Special Issue of the Journal: Biofilms, Clay Fuqua, James A. Glazier,  Yves Brun and Mark S. Alber, Editors, Cambridge University Press,Volume 1, Number 4, 2004.

4. Alber, M.S. , B. Hu and J. Rosenthal, Editors, Current and future directions in applied mathematics [1997]. Papers from the symposium held at the University of Notre Dame,Notre Dame, IN, April 1996. Birkhuser Boston, Inc., Boston, MA x+261.

Peer-reviewed Publications:

1. Zhu, J., Y.-T. Zhang, S.A. Newman and M. Alber, Application of Discontinuous Galerkin Methods for reaction-diffusion systems in developmental biology, Journal of Scientific Computing (in press).

2. Wu, Y., Jiang, Y., Kaiser, D., and M. Alber, Swarming bacteria can sense distant neighbors by cell contacts, Proc. Natl. Acad. Sci. USA (to appear).

3. Xu, Z., Chen, N., Shadden, S., Marsden, J.E., Kamocka, M.M., Rosen, E.D., and M.S.Alber, Study of Blood Flow Impact on Growth of Thrombi Using a Multiscale Model, Soft Matter (to appear).

4. Xu, Z., Chen, N., , Kamocka, M.M., Rosen, E.D., and M.S. Alber [2008], MultiscaleModel of Thrombus Development, Journal of the Royal Society Interface 5 705-722.

5. Alber, M., Glimm, T., Hentschel, H.G.E., Kazmierczak, B., and S. Newman [2008],Pattern formation via the Turing instability in a model of chondrogenesis in vertebratelimb, Bulletin of Mathematical Biology 70 460-483.

6. Alber, M., Chen, N., Lushnikov, P., and S. Newman [2007], Continuous macroscopiclimit of a discrete stochastic model for interaction of living cells, Physical ReviewLetters 99 168102

7. Wu, Y., Jiang, Y., Kaiser, D., and M. Alber [2007], Social Interactions in MyxobacterialSwarming, PLoS Computational Biology 3 12, e253.

8. Christley, S., M. Alber, and S.A. Newman [2007], Patterns of mesenchymal condensation in a multiscale, quasi-3D discrete stochastic model, PLoS Computational Biology 3 4, e76.

9. Chen, N., Glazier, J.A., Izaguirre, J.A. and M.S. Alber [2007], A Parallel Implementa-tion of the Cellular Potts Model for Simulation of Morphogenesis, Computer Physics Communications 76 670-681.

10. Newman, S., Christley, S., Glimm, T., Hentschel, H.G.E., Kazmierczak, B., Zhang,Y.T., Zhu. J., and M. Alber [2007], Multiscale Models for Vertebrate Limb Development, Curr Top Dev Biol 81 311-340.

11. Alber, M., Chen, N., Glimm, T., and P. Lushnikov, A Two-dimensional MultiscaleModel of Cell Motion in a Chemotactic Field, A.R.A Anderson, M.A.J. Chaplain, K.A. Rejniak Eds.,Single Cell Based Models in Biology and Medicine, Birkhauser-Verlag, 2007.

12. Christley, S., Newman, S.A., and M. Alber [2007], Agent-based Simulation for Biological Development, Cybernetics and Systems 38 7, 707-727.

13. Trevor Cickovski, Kedar Aras, Maciej Swat, Roeland M. H. Merks, Tilmann Glimm,H. George E. Hentschel, Mark S. Alber, James A. Glazier, Stuart A. Newman, JesusA. Izaguirre [2007], From Genes To Organisms Via The Cell: A Problem SolvingEnvironment For Multicellular Development, Computing in Science and Engineering 9 4, 50-60.

14. Christley, S., Newman, S.A., and M. Alber, Agent-Based Model for DevelopmentalPattern Formation with Multiscale Dynamics and Varying Cell Geometry. In: Mathematical Modeling of Biological Systems, Volume I. A. Deutsch, L. Brusch, H. Byrne, G. de Vries and H.-P. Herzel (eds). Birkhuser, Boston, 155-167 (2007).

15. Jiang,Y., Sozinova, O., and M. Alber [2006], On Modeling Complex Collective Behavior in Myxobacteria, Advances in Complex Systems 9 4, 1-15.

16. Christley, S., Newman, S.A., and M. Alber, Toward Agent-based Simulation in Development Biology, Proceedings of the Agent-directed Simulation Symposium of the Spring Simulation Multi conference (Ed's. Hamilton et al.), pp. 149-156. April 2-6, 2006, Huntsville, Alabama. SCS Press.

17. Sozinova, O., Y. Jiang, D. Kaiser, and M. Alber [2006], A Three-Dimensional Modelof Fruiting Body Formation, Proc. Natl. Acad. Sci. USA 103 No.46, 17255-17259.

18. Christley, S., Newman, S.A., and M. Alber, Agent-based Simulation for Biological De-velopment, Proceedings of the Eighteenth European Meeting on Cybernetics and Systems Research, Robert Trappl (ed). Austrian Society for Cybernetic Studies, (2006).

19. Gregoretti, I., Margolin, G., Alber, M., and H. Goodson [2006], Modeling microtubuledynamic instability, Journal of Cell Science 119 (22) 4781-4788.

20. Margolin, G., Gregoretti, I., H. Goodson, and Alber, M. [2006], Analysis of a microscopic stochastic model of microtubule dynamic instability Phys. Rev. E. 74 041920.

21. Christley, S., Newman, S.A., and M. Alber, Modeling of Pattern Formation in CellCultures, Proceedings of the Tenth International Conference on the Simulation andSynthesis of Living Systems, Luis M. Rocha, Larry S. Yaeger, Mark A. Bedau, DarioFloreano, Robert L. Goldstone and Alessandro Vespignani, editors, MIT Press, Cambridge, MA, 49-55 (2006)

22. Yilin Wu, Nan Chen, Matthew Rissler, Yi Jiang, Dale Kaiser, and Mark Alber, CAModels of Myxobacteria Swarming,S. El Yacoubi, B. Chopard, and S. Bandini (Eds.):ACRI 2006, LNCS 4173, Springer-Verlag Berlin Heidelberg, pp. 192-203, 2006.

23. N. Chen, J.A. Glazier and M.S. Alber, A Parallel Implementation of the Cellular PottsModel for Simulation of Cell-Based Morphogenesis, S. El Yacoubi, B. Chopard, andS. Bandini (Eds.): ACRI 2006, LNCS 4173, Springer-Verlag Berlin Heidelberg, pp.58-67, 2006.

24. Alber, M., Chen, N., Glimm, T., and P. Lushnikov [2006], Multiscale dynamics ofbiological cells with chemotactic interactions: From a discrete stochastic model to acontinuous description, Phys. Rev. E. 73 051901.

25. Sozinova, O., Y. Jiang, D. Kaiser, and M. Alber [2005], A Three-Dimensional Modelof Myxobacterial Aggregation by Contact-mediated Interactions, Proc. Natl. Acad. Sci. USA 102 No.32, 11308-11312.

26. Cickovski, T., C. Huang, R. Chaturvedi, T. Glimm, H.G.E. Hentschel, M. Alber, J. A.Glazier, S. A. Newman, J. A. Izaguirre [2005], A Framework for Three-DimensionalSimulation of Morphogenesis, IEEE/ACM Transactions on Computational Biology and Bioinformatics 2 3, 1545-5963.

27. Casal, A., C. Sumen, T. Reddy, M. Alber. P. Lee [2005], Agent-Based Modeling ofthe Context Dependency in T Cell recognition, Journal of Theoretical Biology 236 376-391 (corresponding authors: M.Alber and P. Lee).

28. Chaturvedi, R., C. Huang, B. Kazmierczak, T. Schneider, J. A. Izaguirre, T. Glimm,H.G.E. Hentschel, J. A. Glazier, S. A. Newman, M. Alber [2005], On MultiscaleApproaches to 3-Dimensional Modeling of Morphogenesis, Journal of the Royal Society Interface 2 3, 237-253.

29. Alber, M., H.G.E. Hentschel, B. Kazmierczak, S.A. Newman [2005], Existence ofSolutions to a New Model of Biological Pattern Formation, Journal of MathematicalAnalysis and Applications 308 1 175-194.

30. Alber, M., Glimm, T., Hentschel, H.G.E., Kazmierczak, B., and S. Newman [2005],Stability of n-Dimensional Patterns in a Generalized Turing System: Implications for Biological Pattern Formation, Nonlinearity 18 125-138.

31. Alber, M.S., M.A. Kiskowski, Y. Jiang and S.A. Newman [2004], Biological LatticeGas Models, in Dynamics and Bifurcation of Patterns in Dissipative Systems, G.Dangelmayr and I. Oprea (eds.), World Scienti¯c Series on Nonlinear Science, Vol. 12, World Scienti¯c, Singapore, 2004, pp 274-291.

32. Kiskowski, M.A., Y. Jiang, M.S. Alber [2004], Role of Streams in Myxobacteria Ag-gregate Formation, Physical Biology 1 173-183.

33. Casal, A., C. Sumen, T. Reddy, M. Alber. P. Lee, A Cellular Automata Model ofEarly T Cell Recognition, Lecture Notes in Computer Science, Springer-Verlag, Vol. 3305, Springer-Verlag, New York, pp. 553-560, 2004 (corresponding authors: M.Alber and P. Lee).

34. Chaturvedi, R., C. Huang, J. A. Izaguirre, S. A. Newman, J. A. Glazier, M. Alber, A Hybrid Discrete-Continuum Model for 3-D Skeletogenesis of Vertebrate Limb, LectureNotes in Computer Science, Vol. 3305, Springer-Verlag, New York, pp. 543-552, 2004.

35. Alber, M.S., M.A. Kiskowski, and Y. Jiang [2004], Two-stage aggregate formation viastreams in myxobacteria, Phys. Rev. Lett. 93 068301.

36. Alber, M.S., Y. Jiang, and M.A. Kiskowski. [2004], Lattice gas cellular automatonmodel for rippling and aggregation in myxobacteria, Physica D 191, 343-358.

37. Kiskowski, M.A., M.S. Alber, G.L. Thomas, J.A. Glazier, N. Bronstein, J. Pu, andNewman, S.A. [2004], Interaction between activator-inhibitor coupling and cell-matrixadhesion in a cellular automaton model for chondrogenic patterning, Developmental Biology 271, 372-387 (corresponding authors: M.Alber and S. Newman).

38. Izaguirre, J. A., Chaturvedi, R., Huang, C., Cickovski, T., Co²and, J., Thomas,G., Forgacs, G., Alber, M., Hentschel, G., Newman, S.A., and Glazier, J.A. [2004],CompuCell, a multi-model framework for simulation of morphogenesis, Bioinformatics 20, 1129-1137.

39. Chaturvedi, R., Izaguirre, J. A., Huang, C., Cickovski, T., Virtue, P., Thomas, G.,Forgacs, G., Alber, M., Hentschel, G., Newman, S. A., and Glazier, J. A. [2003], Multi-model simulations of chicken limb morphogenesis, Lecture Notes in Computer Science, Volume 2659, Springer-Verlag, New York, 39-49.

40. Alber, M.S., Kiskowski, M.A., Glazier, J.A., and Jiang, Y., On Cellular AutomatonApproaches to Modeling Biological Cells, in J. Rosenthal and D.S. Gilliam (Eds.), Mathematical Systems Theory in Biology, Communication, and Finance, IMA Volume 134, Springer-Verlag, New York, 1-39, 2003.

41. Alber, M.S. and M.A. Kiskowski, M.A. [2001], On Aggregation in CA Models inBiology, J. Phys. A: Math. Gen., 34 10707-10714.

42. Alber, M.S., R. Camassa, Y. Fedorov, D.D. Holm and J.E. Marsden [2001], The Complex Geometry of Weak Piecewise Smooth Solutions of Integrable Nonlinear PDE's of Shallow Water and Dym Type, Commun.Math.Phys. 221 197-227.

43. Alber, M.S. and Yu.N. Fedorov [2001], Algebraic Geometrical Solutions for CertainEvolution Equations and Hamiltonian Flows on Nonlinear Subvarieties of Generalized Jacobians, Inverse Problems 17 1-26.

44. Alber, M.S., and C. Miller [2001], On Peakon Solutions of the Shallow Water Equation, Appl.Math.Lett. 14 1, 93-98.

45. Alber, M.S. and Yu.N. Fedorov [2000], Wave Solutions of Evolution Equations andHamiltonian Flows on Nonlinear Subvarieties of Generalized Jacobians, J.Phys.A:Math.Gen. 33 8409-8425.

46. Alber, M.S. [2000], N-Component integrable systems and geometric asymptotics. In\Integrability: the Seiberg-Witten and Whitham equations", eds H.W. Braden and I.M. Krichever, 1{10. Amsterdam: Gordon and Breach Science Publishers.

47. Luther, G.G., M.S. Alber, M.S., J.E. Marsden and J.W. Robbins [2000], Geometryand control of Â(2) processes and the generalized Poincar¶e sphere, J. Opt. Soc. Amer.B. 17 6, 932{941.

48. Alber, M.S., R. Camassa and M. Gekhtman [2000], On billiard weak solutions ofnonlinear PDE's and Toda °ows, CRM Proc. & Lecture Notes, AMS, 25 1-11.

49. Alber, M.S., G.G. Luther and C. Miller [2000], On Soliton-type Solutions of theEquations Associated with N-component Systems, J. Math. Phys. 41 1, 284-316.

50. Alber, M.S., R. Camassa, Y. Fedorov, D.D. Holm and J.E. Marsden [1999], On BilliardSolutions of Nonlinear PDE's, Phys. Lett. A 264 171-178.

51. Alber, M.S., G.G. Luther, J.E. Marsden and J.W. Robbins [1999], Geometry andControl of Three-Wave Interactions, Fields Inst. Commun. 24 55-80.

52. Alber, M.S., G.G. Luther, J.E. Marsden and J.M. Robbins [1998], Geometric phases,reduction and Lie-Poisson structure for the resonant three-wave interaction, Physica D 123 271-290.

53. Alber, M.S. and G.G. Luther [1997], Nonlinear Waves, Nonlinear Optics and the Future of Communications, Nonlinear Science Today 4.

54. Alber, M.S., G.G. Luther and J.E. Marsden [1997], Energy Dependent SchrodingerOperators and Complex Hamiltonian Systems on Riemann Surfaces, Nonlinearity 10 223-242.

55. Alber, M.S., G.G. Luther and J.E. Marsden [1997], Complex Billiard HamiltonianSystems and Nonlinear Waves, Algebraic aspects of integrable systems, 1-16, Progr. Nonlinear Differential Equations Appl., 26, Birkhuser, Boston, MA.

56. Alber, M.S. and J.E. Marsden [1996], Semiclassical Monodromy and the SphericalPendulum as a Complex Hamiltonian System, Fields Inst. Commun. 8 1-18.

57. Alber, M.S., R. Camassa, D.D. Holm and J.E. Marsden [1995], The geometry ofweak solitons of certain integrable nonlinear pde's, Proc. Int. Workshop, NonlinearEvolution Equations and Dynamical Systems, NEEDS'94, Los Alamos Natl. Lab., NM (World Scientific) 3-8.

58. Alber, M.S., R. Camassa, D.D. Holm and J.E. Marsden [1995], On Umbilic Geodesicsand Soliton Solutions of Nonlinear PDE's, Proc. R. Soc. London Ser. A 450 677-692.

59. Alber, M.S. and J.E. Marsden [1994], Complex Geometric Asymptotics for NonlinearSystems on Complex Varieties, Topol. Methods Nonlinear Anal. 4 237-251.

60. Alber, M.S., R. Camassa, D.D. Holm and J.E. Marsden [1994], The geometry of peaked solitons and billiard solutions of a class of integrable pde's, Lett. Math. Phys. 32137-151.

61. Alber, M.S. and J.E. Marsden [1994], Resonant Geometric Phases for Soliton Equations, Fields Inst. Commun. 3 1-26.

62. Alber, M.S. and J.E. Marsden [1994], Geometric Phases and Monodromy at Singularities, N.M. Ercolani et al., eds., NATO ASI Series B (Plenum Press, New York) 320 273-296.

63. Alber, M.S. and J.E. Marsden [1992], On Geometric Phases for Soliton Equations,Commun. Math. Phys. 149 217-240.

64. Alber, M.S. [1992], Complex geometric asymptotics, geometric phases and nonlinearintegrable problems. Huygens' principle 1690{1990: theory and applications (The Hague and Scheveningen, 1990), 415-427, Stud. Math. Phys., 3, North-Holland, Amsterdam.

65. Alber, M.S. [1992], On geometric phases and braid groups. Proceedings of the XXthInternational Conference on Di®erential Geometric Methods in Theoretical Physics, Vol. 1, 2 (New York, 1991), 439{453, World Sci. Publishing, River Edge, NJ.

66. Alber, M.S. [1991], Hyperbolic Geometric Asymptotics, Asymptotic Anal. 5 161-172.

67. Alber, M.S. [1990], Geometric Asymptotics for Integrable Systems, Proc.of the CRMWorkshop on Hamiltonian Systems, Transformation Groups and Spectral Transform Methods, CRM, Universite de Montreal (Marquis, Montmagny, Qc).

68. Alber, M.S. [1989], On integrable systems and semiclassical solutions of the stationary Schrodinger equations, Inverse Problems 5 131-148.

69. Alber, M.S. and S.J. Alber [1987], Hamiltonian formalism for nonlinear Schr}odingerequations and sine-Gordon equations, J. London Math. Soc. (2) 36 176-192.

70. Alber, M.S. [1987], Hamiltonian formalism for ¯nite-zone solutions of nonlinear integrable equations. VIIIth international congress on mathematical physics (Marseille, 1986), 447-462, World Sci. Publishing, Singapore.

71. Alber, M.S. and S.J. Alber [1985], Hamiltonian formalism for ¯nite-zone solutions of integrable equations, C. R. Acad. Sci. Paris Sr. I Math. 301 777-781.