Publications

Latest Selected Publications

Special Issue of the Journal: Biofilms

SIAM Journal of Multiscale Modeling and Simulations:
Special Issue on Multiscale Modeling in Biology

Biological Networks

• H. Jeong, Z. N. Oltvai, and A.-L. Barabsi, Prediction of protein essentiality based on genomic data, ComplexUs 1, 19-28 (2003).
• I. Farkas, H. Jeong, T. Vicsek, A.-L. Barabsi, and Z.N. Oltvai, The topology of transcription regulatory network in the yeast, Saccharomyces cerevisiae, Physica A 318, 601-612 (2003).
• S. Y. Gerdes, M. D. Scholle, J. W. Campbell, G. Balzsi, E. Ravasz, M. D. Daugherty, A. L. Somera, N. C. Kyrpides, I. Anderson, M. S. Gelfand, A. Bhattacharya, V. Kapatral, M. D'Souza, M. V. Baev, Y. Grechkin, F. Mseeh, M. Y. Fonstein, R. Overbeek, A.-L. Barabsi, Z. N. Oltvai, and A. L. Osterman, Experimental Determination and System Level Analysis of Essential Genes in Escherichia coli MG1655, Journal of Bacteriology 185, 5673-5684 (2003).
• S. Wuchty, E. Ravasz and A.-L. Barabsi, The Architecture of Biological Networks, in T.S. Deisboeck, J. Yasha Kresh and T.B. Kepler (eds.), Complex Systems in Biomedicine, Kluwer Academic Publishing, New York (2003).
• S. Wuchty, Z. N. Oltvai and A.-L. Barabsi, Evolutionary conservation of motif constituents in the yeast protein interaction network, Nature Genetics 35, 176-179 (2003).

Organogenesis and Tissue Development

• Alber, M.S., Kiskowski, M.A., Glazier, J.A., and Jiang, Y., On Cellular Automaton Approaches 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, 2003, p.1-40.
• 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.
• Hentschel, H. G. E., T. Glimm, J. A. Glazier, S. A. Newman, Dynamical mechanisms for skeletal pattern formation in the vertebrate limb. Proc. R. Soc. Lond: Bio. Sciences 271 (2004) 1713-1722.
• Izaguirre, J. A., Chaturvedi, R., Huang, C., Cickovski, T., Coffland, 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.
• Kiskowski, M.A., M.S. Alber, G.L. Thomas, J.A. Glazier, N. Bronstein, J. Pu, and Newman, S.A. [2004], Interaction between activator-inhibitor coupling and cell-matrix adhesion in a cellular automaton model for chondrogenic patterning, Developmental Biology 271, 372--387 (corresponding authors: M.Alber and S. Newman).
• Alber, M.S., Y. Jiang, and M.A. Kiskowski. [2004], Lattice gas cellular automaton model for rippling and aggregation in myxobacteria, Physica D 191, 343--358.
• Alber, M.S., M.A. Kiskowski, and Y. Jiang [2004], Two-stage aggregate formation via streams in myxobacteria, Phys. Rev. Lett. 93 068301.
• Alber, M., T. Glimm, H.G.E. Hentschel, B. Kazmierczak, S. Newman. [2005], Stability of n-Dimensional Patterns in a Generalized Turing System: implications for Biological Pattern Formation, Nonlinearity 18 125 -138.
• Kiskowski, M.A., Y. Jiang, M.S. Alber [2004], Role of Streams in Myxobacteria Aggregate Formation, Physical Biology 1 173-183.
• Chaturvedi, R., C. Huang, J. A. Izaguirre, S. A. Newman, J. A. Glazier, M. Alber [2004], A Hybrid Discrete- Continuum Model for 3-D Skeletogenesis of Vertebrate Limb, Lecture Notes in Computer Science, Vol. 3305, Springer-Verlag, New York, 543-552.
• Alber, M.S., M.A. Kiskowski, Y. Jiang and S.A. Newman [2004], Biological Lattice Gas Models, in Dynamics and Bifurcation of Patterns in Dissipative Systems, G. Dangelmayr and I. Oprea (eds.), World Scientific Series on Nonlinear Science, Vol. 12, World Scientific, Singapore, 2004, pp 274-291.
• Alber, M., H.G.E. Hentschel, B. Kazmierczak, S.A. Newman, Existence of Solutions to a New Model of Biological Pattern Formation, Journal of Mathematical Analysis and Applications (to appear)
• Chaturvedi, R., C. Huang, B. Kazmierczak, Schneider. A. Izaguirre, T. Glimm, G.E. Hentschel, S. A. Newman, J. A. Glazier, M. Alber, On Multiscale Approaches to Three-Dimensional Modeling of Morphogenesis (submitted).