MBI Publications

MBI Publications for 2007 (35)

  • J. Tian
    On several types of Universal invariants of framed links and 3-manifolds, derived from hopf algebras.
    Math. Proc. Cam. Phil. Soc.Vol. 142 (2007) pp. 73-92

    Abstract

  • P. Blower, J. Verducci, S. Lin, J. Zhou, C. Liu, W. Reinhold, C. Croce , J. Weinstein and W. Sadee
    MicroRNA microarray expression profiles for the NCI60 cancer cell panel
    Molecular Cancer TherapeuticsVol. 6 (2007) pp. 1483-1491

    Abstract

  • S. Sun, C. Greenwood and R. Neal
    Haplotype inference using a Bayesian Hidden Markov Model
    Genetic EpidemiologyVol. 31 No. 8 (2007) pp. 937-948

    Abstract

  • K. Rejniak
    An immersed boundary framework for modelling the growth of individual cells: an application to the early tumour development
    J. Theor. Biology (2007) pp. 186-204

    Abstract

  • K. Rejniak and R. Dillon
    A single cell based model of the ductal tumour microarchitecture
    Computational and Mathematical Methods in MedicineVol. 8 No. 1 (2007) pp. 51-69

    Abstract

  • K. Rejniak
    Modelling the Development of Complex Tissues using Individual Viscoelastic Cells, in "Single-Cell-Based Models in Biology and Medicine"
    Birkhauser-Verlag (2007) pp. book chapter

    Abstract

  • G. Wright, J. Mustard, S. Kottcamp and B. Smith
    Olfactory memory formation and the influence of reward pathway during olfactory learning by honeybees
    Journal of Experimental BiologyVol. 210 (2007) pp. 4024-4033

    Abstract

  • M. Djordjevic
    SELEX experiments: novel prospects applications and data analysis for inferring regulatory pathways
    Biomol EngVol. 24 No. 2 (2007) pp. 179

    Abstract

  • E. Dimitrova, A. Jarrah, R. Laubenbacher and B. Stigler
    A Grobner Fan Method for Biochemical Network Modeling
    ISSAC Proceedings (2007) pp. 122-126

    Abstract

  • Z. Liu and J. Tian
    Coalescent Random Walks on graph
    Journal of Computational and Applied MathematicsVol. 202 (2007) pp. 144-154

    Abstract

  • A. Nevai, K. Passino and T. Waite
    State subsidies induce gray jays to accept greater danger: an ecologically rational response?
    Behav. Ecol. Sociobiol.Vol. 61 (2007) pp. 1261-1266

    Abstract

  • A. Nevai and R. Vance
    Plant population growth and competition in a light gradient: a mathematical model of canopy partitioning
    J. Theor. Biol.Vol. 245 (2007) pp. 210-219

    Abstract

  • L. Allen, B. Bolker, Y. Lou and A. Nevai
    Asymptotic profile of the steady states for an SIS epidemic patch model
    SIAM J. Appl. Math.Vol. 67 (2007) pp. 1283-1309

    Abstract

  • A. Jarrah, R. Laubenbacher, B. Stigler and M. Stillman
    Reverse Engineering of Polynomial Dynamical Systems
    Advances in Applied MathematicsVol. 39 No. 4 (2007) pp. 477-489

    Abstract

  • R. Ahmad, D. Vikram, B. Clymer, L. Potter, Y. Deng, P. Srinivasan, J. Zweier and P. Kuppusamy
    Uniform distribution of projection data for improved reconstruction quality of 4D EPR imaging
    Journal of Magnetic ResonanceVol. 187 (2007) pp. 277-287

    Abstract

  • E. Higgins, P. Goel, J. Puglisi, D. Bers, M. Cannell and J. Sneyd
    Modeling Calcium Microdomains using Homogenisation
    Journal of Theoretical BiologyVol. 247 No. 4 (2007) pp. 623-644

    Abstract

  • K. Robenack and P. Goel
    Observer Based Measurement of the Input Current of a Neuron
    The Mediterranean Journal of Measurement and ControlVol. 3 No. 1 (2007) pp. 22-29

    Abstract

  • A. Sevostyanova, M. Djordjevic, K. Kuznedelov, T. Naryshkina, M. Gelfand, K. Severinov and L. Minakhin
    Temporal regulation of viral transcription during development of Thermus thermophilus bacteriophage phiYS40
    J Mol BiolVol. 366 No. 2 (2007) pp. 420

    Abstract

  • A. Nevai, K. Passino and T. Waite
    State-dependent choice and ecological rationality
    J. Theor. Biol.Vol. 247 (2007) pp. 471-479

    Abstract

  • B. Stigler, A. Jarrah, M. Stillman and R. Laubenbacher
    Reverse Engineering of Dynamic Networks
    In Reverse Engineering Biological Networks: Opportunities and Challenges in Computational Methods for Pathway InferenceVol. 115 (2007) pp. 168-177

    Abstract

  • J. Tian
    On several types of Universal invariants of framed links and 3-manifolds, derived from hopf algebras
    Mathematical Proceedings of the Cambridge Philosophical SocietyVol. 142 (2007) pp. 73-92

    Abstract

  • Z. Liu and J. Tian
    Coalescent Random Walks on graph
    Vol. 202 (2007) pp. 144-154

    Abstract

  • A. Nevai and R. Vance
    Plant interspecies competition for sunlight: a mathematical model of canopy partitioning
    J. Math. Biol.Vol. 55 (2007) pp. 105-145

    Abstract

  • R. Ahmad, D. Vikram, B. Clymer, L. Potter, J. Zweier and P. Kuppusamy
    Uniform data distribution for 4D EPR imaging
    EPR (Conference Proceedings) (2007)

    Abstract

  • G. Enciso
    A dichotomy for a class of cyclic delay systems
    Mathematical BiosciencesVol. 208 (2007) pp. 63-75

    Abstract

  • G. Enciso, M. Hirsch and H. Smith
    Prevalent behavior of strongly order preserving semiflows
    Journal of Dynamics and Differential EquationsVol. 20 No. 1 (2007) pp. 115-132

    Abstract

  • P. Grajdeanu, L. Moore and H. Layton
    Effect of tubular inhomogenities on filter properties of thick ascending limb of loop of Henle
    Mathematical BiosciencesVol. 209 No. 2 (2007) pp. 564-592

    Abstract

  • R. Ahmad, Y. Deng, D. Vikram, B. Clymer, P. Srinivasan, J. Zweier and P. Kuppusamy
    Quasi Monte Carlo-based isotropic distribution of gradient directions for improved reconstruction quality of 3D EPR imaging
    Journal of Magnetic ResonanceVol. 184 (2007) pp. 236-245

    Abstract

  • P. Goloboff and D. Pol
    On Divide-and-Conquer Strategies for Parsimony Analysis of Large Data Sets: Rec-I-dcm3 vs. TNT
    Systematic BiologyVol. 56 (2007) pp. 485-495

    Abstract

  • F. Rassoul-Agha, M. Balazs and T. Seppalainen
     Existence of the zero range process and a deposition model with superlinear growth rates
    Annals of ProbabilityVol. 35 No. 4 (2007) pp. 1201-1249

    Abstract

  • Z. Wang, P. Yan, D. Potter, C. Eng, T. Huang and S. Lin
    Heritable clustering algorithms for recapturing epigenetic progression in breast cancer.
    BMC BioinformaticsVol. 8 No. 38 (2007)

    Abstract

  • Y. Kim and H. Othmer
    A hybrid model for tumor spheroid grown in vitro I: Theoretical development and early results
    Math. Models Methods in Appl ScisVol. 17 (2007) pp. 1773-1798

    Abstract

    Tumor spheroids grown in vitro have been widely used as models of in vivo tumor growth because they display many of the characteristics of in vivo growth, including the effects of nutrient limitations and perhaps the effect of stress on growth. In either case there are numerous biochemical and biophysical processes involved whose interactions can only be understood via a detailed mathematical model. Previous models have focused on either a continuum description or a cell-based description, but both have limitations. In this paper we propose a new mathematical model of tumor spheroid growth that incorporates both continuum and cell-level descriptions, and thereby retains the advantages of each while circumventing some of their disadvantages. In this model the cell-based description is used in the region where the majority of growth and cell division occurs, at the periphery of a tumor, while a continuum description is used for the quiescent and necrotic zones of the tumor and for the extracellular matrix. Reaction-diffusion equations describe the transport and consumption of two important nutrients, oxygen and glucose, throughout the entire domain. The cell-based component of this hybrid model allows us to examine the effects of cell‚€“cell adhesion and variable growth rates at the cellular level rather than at the continuum level. We show that the model can predict a number of cellular behaviors that have been observed experimentally.
  • P. Grajdeanu and L. Moore
    Effect of tubular inhomogeneities on filter properties of thick ascending limb of Henle's loop
    Mathematical BiosciencesVol. 209 No. 2 (2007) pp. 564-592

    Abstract

    We used a simple mathematical model of rat thick ascending limb (TAL) of the loop of Henle to predict the impact of spatially inhomogeneous NaCl permeability, spatially inhomogeneous NaCl active transport, and spatially inhomogeneous tubular radius on luminal NaCl concentration when sustained, sinusoidal perturbations were superimposed on steady-state TAL flow. A mathematical model previously devised by us that used homogeneous TAL transport and fixed TAL radius predicted that such perturbations result in TAL luminal fluid NaCl concentration profiles that are standing waves. That study also predicted that nodes in NaCl concentration occur at the end of the TAL when the tubular fluid transit time equals the period of a periodic perturbation, and that, for non-nodal periods, sinusoidal perturbations generate non-sinusoidal oscillations (and thus a series of harmonics) in NaCl concentration at the TAL end. In the present study we find that the inhomogeneities transform the standing waves and their associated nodes into approximate standing waves and approximate nodes. The impact of inhomogeneous NaCl permeability is small. However, for inhomogeneous active transport or inhomogeneous radius, the oscillations for non-nodal periods tend to be less sinusoidal and more distorted than in the homogeneous case and to thus have stronger harmonics. Both the homogeneous and non-homogeneous cases predict that the TAL, in its transduction of flow oscillations into concentration oscillations, acts as a low-pass filter, but the inhomogeneities result in a less effective filter that has accentuated non-linearities.
  • Z. Wang, S. Lin, M. Popesco and A. Rotter
    Modeling and analysis of multi-library, multi-group SAGE data with application to a study of mouse cerebellum.
    BiometricsVol. 63 (2007) pp. 777-786

    Abstract

  • X. Liu, P. Srinivasan, E. Collard, P. Grajdeanu, J. Zweier and A. Friedman
    Oxygen regulates the flux of nitric oxide diffusion across the vascular wall,
    Conference Proceedings, American Heart Association Scientific Sessions (2007)

    Abstract

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