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Items: 1 to 50 of 81


Modeling of xenobiotic transport and metabolism in virtual hepatic lobule models.

Fu X, Sluka JP, Clendenon SG, Dunn KW, Wang Z, Klaunig JE, Glazier JA.

PLoS One. 2018 Sep 13;13(9):e0198060. doi: 10.1371/journal.pone.0198060. eCollection 2018.


Molecular jenga: the percolation phase transition (collapse) in virus capsids.

Brunk NE, Lee LS, Glazier JA, Butske W, Zlotnick A.

Phys Biol. 2018 Jun 6;15(5):056005. doi: 10.1088/1478-3975/aac194.



Somogyi E, Hagar A, Glazier JA.

Proc Winter Simul Conf. 2016 Dec;2016:1230-1240. doi: 10.1109/WSC.2016.7822179. Epub 2017 Jan 19.


A Notch positive feedback in the intestinal stem cell niche is essential for stem cell self-renewal.

Chen KY, Srinivasan T, Tung KL, Belmonte JM, Wang L, Murthy PKL, Choi J, Rakhilin N, King S, Varanko AK, Witherspoon M, Nishimura N, Glazier JA, Lipkin SM, Bu P, Shen X.

Mol Syst Biol. 2017 Apr 28;13(4):927. doi: 10.15252/msb.20167324.


Transcriptome analysis reveals manifold mechanisms of cyst development in ADPKD.

de Almeida RM, Clendenon SG, Richards WG, Boedigheimer M, Damore M, Rossetti S, Harris PC, Herbert BS, Xu WM, Wandinger-Ness A, Ward HH, Glazier JA, Bacallao RL.

Hum Genomics. 2016 Nov 21;10(1):37.


A Computational Model of Peripheral Photocoagulation for the Prevention of Progressive Diabetic Capillary Occlusion.

Gast TJ, Fu X, Gens JS, Glazier JA.

J Diabetes Res. 2016;2016:2508381. Epub 2016 Oct 25.


Virtual-tissue computer simulations define the roles of cell adhesion and proliferation in the onset of kidney cystic disease.

Belmonte JM, Clendenon SG, Oliveira GM, Swat MH, Greene EV, Jeyaraman S, Glazier JA, Bacallao RL.

Mol Biol Cell. 2016 Nov 7;27(22):3673-3685. Epub 2016 May 18.


Formalizing Knowledge in Multi-Scale Agent-Based Simulations.

Somogyi E, Sluka JP, Glazier JA.

Model Driven Eng Lang Syst. 2016 Oct;16:115-122. doi: 10.1145/2976767.2976790.


A Liver-Centric Multiscale Modeling Framework for Xenobiotics.

Sluka JP, Fu X, Swat M, Belmonte JM, Cosmanescu A, Clendenon SG, Wambaugh JF, Glazier JA.

PLoS One. 2016 Sep 16;11(9):e0162428. doi: 10.1371/journal.pone.0162428. eCollection 2016.


Filopodial-Tension Model of Convergent-Extension of Tissues.

Belmonte JM, Swat MH, Glazier JA.

PLoS Comput Biol. 2016 Jun 20;12(6):e1004952. doi: 10.1371/journal.pcbi.1004952. eCollection 2016 Jun.


Progression of Diabetic Capillary Occlusion: A Model.

Fu X, Gens JS, Glazier JA, Burns SA, Gast TJ.

PLoS Comput Biol. 2016 Jun 14;12(6):e1004932. doi: 10.1371/journal.pcbi.1004932. eCollection 2016 Jun.


libRoadRunner: a high performance SBML simulation and analysis library.

Somogyi ET, Bouteiller JM, Glazier JA, König M, Medley JK, Swat MH, Sauro HM.

Bioinformatics. 2015 Oct 15;31(20):3315-21. doi: 10.1093/bioinformatics/btv363. Epub 2015 Jun 17.


Emergent Stratification in Solid Tumors Selects for Reduced Cohesion of Tumor Cells: A Multi-Cell, Virtual-Tissue Model of Tumor Evolution Using CompuCell3D.

Swat MH, Thomas GL, Shirinifard A, Clendenon SG, Glazier JA.

PLoS One. 2015 Jun 17;10(6):e0127972. doi: 10.1371/journal.pone.0127972. eCollection 2015.


3D simulations of wet foam coarsening evidence a self similar growth regime.

Thomas GL, Belmonte JM, Graner F, Glazier JA, de Almeida RM.

Colloids Surf A Physicochem Eng Asp. 2015 May 20;473:109-114. Epub 2015 Feb 14.


The cell behavior ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents.

Sluka JP, Shirinifard A, Swat M, Cosmanescu A, Heiland RW, Glazier JA.

Bioinformatics. 2014 Aug 15;30(16):2367-74. doi: 10.1093/bioinformatics/btu210. Epub 2014 Apr 22.


Somites without a clock.

Dias AS, de Almeida I, Belmonte JM, Glazier JA, Stern CD.

Science. 2014 Feb 14;343(6172):791-795. doi: 10.1126/science.1247575. Epub 2014 Jan 9.


Label-free microcavity biosensors: steps towards personalized medicine.

Amarie D, Glazier JA.

Sensors (Basel). 2012 Dec 13;12(12):17262-94. doi: 10.3390/s121217262.


3D quantitative analyses of angiogenic sprout growth dynamics.

Shirinifard A, McCollum CW, Bolin MB, Gustafsson JÅ, Glazier JA, Clendenon SG.

Dev Dyn. 2013 May;242(5):518-26. doi: 10.1002/dvdy.23946. Epub 2013 Mar 25.


Adhesion failures determine the pattern of choroidal neovascularization in the eye: a computer simulation study.

Shirinifard A, Glazier JA, Swat M, Gens JS, Family F, Jiang Y, Grossniklaus HE.

PLoS Comput Biol. 2012;8(5):e1002440. doi: 10.1371/journal.pcbi.1002440. Epub 2012 May 3.


Multi-scale modeling of tissues using CompuCell3D.

Swat MH, Thomas GL, Belmonte JM, Shirinifard A, Hmeljak D, Glazier JA.

Methods Cell Biol. 2012;110:325-66. doi: 10.1016/B978-0-12-388403-9.00013-8.


Computer simulations of cell sorting due to differential adhesion.

Zhang Y, Thomas GL, Swat M, Shirinifard A, Glazier JA.

PLoS One. 2011;6(10):e24999. doi: 10.1371/journal.pone.0024999. Epub 2011 Oct 18.


A multi-cell, multi-scale model of vertebrate segmentation and somite formation.

Hester SD, Belmonte JM, Gens JS, Clendenon SG, Glazier JA.

PLoS Comput Biol. 2011 Oct;7(10):e1002155. doi: 10.1371/journal.pcbi.1002155. Epub 2011 Oct 6. Review.


Coarsening foams robustly reach a self-similar growth regime.

Lambert J, Mokso R, Cantat I, Cloetens P, Glazier JA, Graner F, Delannay R.

Phys Rev Lett. 2010 Jun 18;104(24):248304. Epub 2010 Jun 18.


Computer simulation of cellular patterning within the Drosophila pupal eye.

Larson DE, Johnson RI, Swat M, Cordero JB, Glazier JA, Cagan RL.

PLoS Comput Biol. 2010 Jul 1;6:e1000841. doi: 10.1371/journal.pcbi.1000841.


Front instabilities and invasiveness of simulated 3D avascular tumors.

Poplawski NJ, Shirinifard A, Agero U, Gens JS, Swat M, Glazier JA.

PLoS One. 2010 May 26;5(5):e10641. doi: 10.1371/journal.pone.0010641.


Modeling gastrulation in the chick embryo: formation of the primitive streak.

Vasiev B, Balter A, Chaplain M, Glazier JA, Weijer CJ.

PLoS One. 2010 May 11;5(5):e10571. doi: 10.1371/journal.pone.0010571.


Bulk elastic properties of chicken embryos during somitogenesis.

Agero U, Glazier JA, Hosek M.

Biomed Eng Online. 2010 Mar 30;9:19. doi: 10.1186/1475-925X-9-19.


Microfluidic devices integrating microcavity surface-plasmon-resonance sensors: glucose oxidase binding-activity detection.

Amarie D, Alileche A, Dragnea B, Glazier JA.

Anal Chem. 2010 Jan 1;82(1):343-52. doi: 10.1021/ac902038d.


3D multi-cell simulation of tumor growth and angiogenesis.

Shirinifard A, Gens JS, Zaitlen BL, Popławski NJ, Swat M, Glazier JA.

PLoS One. 2009 Oct 16;4(10):e7190. doi: 10.1371/journal.pone.0007190.


An object-oriented modelling framework for the arterial wall.

Balaguera MI, Briceño JC, Glazier JA.

Comput Methods Biomech Biomed Engin. 2010 Feb;13(1):135-42. doi: 10.1080/10255842.2010.495873.


A threaded Java concurrent implementation of the Monte-Carlo Metropolis Ising model.

Castañeda-Marroquín C, de la Puente AO, Alfonseca M, Glazier JA, Swat M.

Int Work Conf Interp Nat Artif Comput. 2009 Jun 1;2009:103-110.


Multicell simulations of development and disease using the CompuCell3D simulation environment.

Swat MH, Hester SD, Balter AI, Heiland RW, Zaitlen BL, Glazier JA.

Methods Mol Biol. 2009;500:361-428. doi: 10.1007/978-1-59745-525-1_13.


Front instabilities and invasiveness of simulated avascular tumors.

Popławski NJ, Agero U, Gens JS, Swat M, Glazier JA, Anderson AR.

Bull Math Biol. 2009 Jul;71(5):1189-227. doi: 10.1007/s11538-009-9399-5. Epub 2009 Feb 21.


Contact-inhibited chemotaxis in de novo and sprouting blood-vessel growth.

Merks RM, Perryn ED, Shirinifard A, Glazier JA.

PLoS Comput Biol. 2008 Sep 19;4(9):e1000163. doi: 10.1371/journal.pcbi.1000163. Erratum in: PLoS Comput Biol. 2015 Apr;11(4):e1004163.


A parallel implementation of the Cellular Potts Model for simulation of cell-based morphogenesis.

Chen N, Glazier JA, Izaguirre JA, Alber MS.

Comput Phys Commun. 2007 Jun;176(11-12):670-681.


Compact microfluidic structures for generating spatial and temporal gradients.

Amarie D, Glazier JA, Jacobson SC.

Anal Chem. 2007 Dec 15;79(24):9471-7. Epub 2007 Nov 14.


Experimental growth law for bubbles in a moderately "wet" 3D liquid foam.

Lambert J, Cantat I, Delannay R, Mokso R, Cloetens P, Glazier JA, Graner F.

Phys Rev Lett. 2007 Aug 3;99(5):058304. Epub 2007 Aug 2.


From Genes to Organisms Via the Cell A Problem-Solving Environment for Multicellular Development.

Cickovski T, Aras K, Alber MS, Izaguirre JA, Swat M, Glazier JA, Merks RM, Glimm T, Hentschel HG, Newman SA.

Comput Sci Eng. 2007;9(4):50-60.


A framework for three-dimensional simulation of morphogenesis.

Cickovski TM, Huang C, Chaturvedi R, Glimm T, Hentschel HG, Alber MS, Glazier JA, Newman SA, Izaguirre JA.

IEEE/ACM Trans Comput Biol Bioinform. 2005 Oct-Dec;2(4):273-88.


On multiscale approaches to three-dimensional modelling of morphogenesis.

Chaturvedi R, Huang C, Kazmierczak B, Schneider T, Izaguirre JA, Glimm T, Hentschel HG, Glazier JA, Newman SA, Alber MS.

J R Soc Interface. 2005 Jun 22;2(3):237-53.


Cell movement during chick primitive streak formation.

Chuai M, Zeng W, Yang X, Boychenko V, Glazier JA, Weijer CJ.

Dev Biol. 2006 Aug 1;296(1):137-49. Epub 2006 Apr 26.


Dynamic mechanisms of blood vessel growth.

Merks RM, Glazier JA.

Nonlinearity. 2006;19(1):C1-C10.


Solving the advection-diffusion equations in biological contexts using the cellular Potts model.

Dan D, Mueller C, Chen K, Glazier JA.

Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Oct;72(4 Pt 1):041909. Epub 2005 Oct 10.


Cell elongation is key to in silico replication of in vitro vasculogenesis and subsequent remodeling.

Merks RM, Brodsky SV, Goligorksy MS, Newman SA, Glazier JA.

Dev Biol. 2006 Jan 1;289(1):44-54. Epub 2005 Dec 1.


Analysis of tissue flow patterns during primitive streak formation in the chick embryo.

Cui C, Yang X, Chuai M, Glazier JA, Weijer CJ.

Dev Biol. 2005 Aug 1;284(1):37-47.

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