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James A. Glazier - Publications

Affiliations: 
Indiana University, Bloomington, Bloomington, IN, United States 
Area:
Biophysics
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68 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Sego TJ, Glazier JA, Tovar A. Unification of aggregate growth models by emergence from cellular and intracellular mechanisms. Royal Society Open Science. 7: 192148. PMID 32968501 DOI: 10.1098/Rsos.192148  0.32
2020 Fortuna I, Perrone GC, Krug MS, Susin E, Belmonte JM, Thomas GL, Glazier JA, de Almeida RMC. CompuCell3D Simulations Reproduce Mesenchymal Cell Migration on Flat Substrates. Biophysical Journal. PMID 32407685 DOI: 10.1016/j.bpj.2020.04.024  0.355
2016 Belmonte JM, Swat MH, Glazier JA. Filopodial-Tension Model of Convergent-Extension of Tissues. Plos Computational Biology. 12: e1004952. PMID 27322528 DOI: 10.1371/journal.pcbi.1004952  0.328
2016 Belmonte JM, Clendenon SG, Oliveira GM, Swat MH, Greene EV, Jeyaraman S, Glazier JA, Bacallao RL. Virtual-Tissue Computer Simulations Define the Roles of Cell Adhesion and Proliferation in the Onset of Kidney Cystic Disease. Molecular Biology of the Cell. PMID 27193300 DOI: 10.1091/mbc.E16-01-0059  0.333
2015 Swat MH, Thomas GL, Shirinifard A, Clendenon SG, Glazier JA. Emergent Stratification in Solid Tumors Selects for Reduced Cohesion of Tumor Cells: A Multi-Cell, Virtual-Tissue Model of Tumor Evolution Using CompuCell3D. Plos One. 10: e0127972. PMID 26083246 DOI: 10.1371/Journal.Pone.0127972  0.69
2014 Sluka JP, Shirinifard A, Swat M, Cosmanescu A, Heiland RW, Glazier JA. The cell behavior ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents. Bioinformatics (Oxford, England). 30: 2367-74. PMID 24755304 DOI: 10.1093/Bioinformatics/Btu210  0.69
2014 Dy AJ, Cosmanescu A, Sluka J, Glazier JA, Stupack D, Amarie D. Fabricating microfluidic valve master molds in SU-8 photoresist Journal of Micromechanics and Microengineering. 24. DOI: 10.1088/0960-1317/24/5/057001  0.739
2013 Shirinifard A, McCollum CW, Bolin MB, Gustafsson JÃ…, Glazier JA, Clendenon SG. 3D quantitative analyses of angiogenic sprout growth dynamics. Developmental Dynamics : An Official Publication of the American Association of Anatomists. 242: 518-26. PMID 23417958 DOI: 10.1002/Dvdy.23946  0.682
2013 Clendenon S, Ganapathi Sankaran D, Shirinifard A, McCollum C, Bondesson Bolin M, Gustafsson J, Glazier J. Arsenic Exposure Inhibits Angiogenesis in Zebrafish via Downregulation of both VEGFA and VEGFR2 Microscopy and Microanalysis. 19: 778-779. DOI: 10.1017/S1431927613005886  0.647
2013 Glazier J, Belmonte J, Clendenon S, Gens J, Shirinifard A, Bacallao R, Mosaliganti R, Megason S, Swat M. The Role of Virtual-Tissue Computer Simulations in the Interpretation of Four-Dimensional Microscopy of Developing Tissues: The Example of Polycystic Kidney Disease Microscopy and Microanalysis. 19: 756-757. DOI: 10.1017/S1431927613005771  0.669
2012 Amarie D, Glazier JA. Label-free microcavity biosensors: steps towards personalized medicine. Sensors (Basel, Switzerland). 12: 17262-94. PMID 23443397 DOI: 10.3390/S121217262  0.734
2012 Shirinifard A, Glazier JA, Swat M, Gens JS, Family F, Jiang Y, Grossniklaus HE. Adhesion failures determine the pattern of choroidal neovascularization in the eye: a computer simulation study. Plos Computational Biology. 8: e1002440. PMID 22570603 DOI: 10.1371/Journal.Pcbi.1002440  0.694
2012 Swat MH, Thomas GL, Belmonte JM, Shirinifard A, Hmeljak D, Glazier JA. Multi-scale modeling of tissues using CompuCell3D. Methods in Cell Biology. 110: 325-66. PMID 22482955 DOI: 10.1016/B978-0-12-388403-9.00013-8  0.713
2012 Heiland R, Shirinifard A, Swat M, Thomas GL, Sluka J, Lumsdaine A, Zaitlen B, Glazier JA. Visualizing cells and their connectivity graphs for CompuCell3D Ieee Symposium On Biological Data Visualization 2012, Biovis 2012 - Proceedings. 85-90. DOI: 10.1109/BioVis.2012.6378597  0.63
2011 Zhang Y, Thomas GL, Swat M, Shirinifard A, Glazier JA. Computer simulations of cell sorting due to differential adhesion. Plos One. 6: e24999. PMID 22028771 DOI: 10.1371/Journal.Pone.0024999  0.699
2011 Hester SD, Belmonte JM, Gens JS, Clendenon SG, Glazier JA. A multi-cell, multi-scale model of vertebrate segmentation and somite formation. Plos Computational Biology. 7: e1002155. PMID 21998560 DOI: 10.1371/Journal.Pcbi.1002155  0.649
2010 Larson DE, Johnson RI, Swat M, Cordero JB, Glazier JA, Cagan RL. Computer simulation of cellular patterning within the Drosophila pupal eye. Plos Computational Biology. 6: e1000841. PMID 20617161 DOI: 10.1371/Journal.Pcbi.1000841  0.345
2010 Poplawski NJ, Shirinifard A, Agero U, Gens JS, Swat M, Glazier JA. Front instabilities and invasiveness of simulated 3D avascular tumors. Plos One. 5: e10641. PMID 20520818 DOI: 10.1371/Journal.Pone.0010641  0.669
2010 Vasiev B, Balter A, Chaplain M, Glazier JA, Weijer CJ. Modeling gastrulation in the chick embryo: formation of the primitive streak. Plos One. 5: e10571. PMID 20485500 DOI: 10.1371/Journal.Pone.0010571  0.364
2010 Amarie D, Alileche A, Dragnea B, Glazier JA. Microfluidic devices integrating microcavity surface-plasmon-resonance sensors: glucose oxidase binding-activity detection. Analytical Chemistry. 82: 343-52. PMID 19968248 DOI: 10.1021/Ac902038D  0.729
2009 Shirinifard A, Gens JS, Zaitlen BL, PopÅ‚awski NJ, Swat M, Glazier JA. 3D multi-cell simulation of tumor growth and angiogenesis. Plos One. 4: e7190. PMID 19834621 DOI: 10.1371/Journal.Pone.0007190  0.67
2009 Swat MH, Hester SD, Balter AI, Heiland RW, Zaitlen BL, Glazier JA. Multicell simulations of development and disease using the CompuCell3D simulation environment. Methods in Molecular Biology (Clifton, N.J.). 500: 361-428. PMID 19399437 DOI: 10.1007/978-1-59745-525-1_13  0.617
2008 Merks RM, Perryn ED, Shirinifard A, Glazier JA. Contact-inhibited chemotaxis in de novo and sprouting blood-vessel growth. Plos Computational Biology. 4: e1000163. PMID 18802455 DOI: 10.1371/Journal.Pcbi.1000163  0.703
2008 PopÅ‚awski NJ, Shirinifard A, Swat M, Glazier JA. Simulation of single-species bacterial-biofilm growth using the Glazier-Graner-Hogeweg model and the CompuCell3D modeling environment. Mathematical Biosciences and Engineering : Mbe. 5: 355-88. PMID 18613738 DOI: 10.3934/Mbe.2008.5.355  0.705
2008 Glazier JA, Zhang Y, Swat M, Zaitlen B, Schnell S. Coordinated action of N-CAM, N-cadherin, EphA4, and ephrinB2 translates genetic prepatterns into structure during somitogenesis in chick. Current Topics in Developmental Biology. 81: 205-47. PMID 18023729 DOI: 10.1016/S0070-2153(07)81007-6  0.329
2007 Pop?awski NJ, Swat M, Gens JS, Glazier JA. Adhesion between cells, diffusion of growth factors, and elasticity of the AER produce the paddle shape of the chick limb. Physica A. 373: 521-532. PMID 18167520 DOI: 10.1016/J.Physa.2006.05.028  0.353
2007 Chen N, Glazier JA, Izaguirre JA, Alber MS. A parallel implementation of the Cellular Potts Model for simulation of cell-based morphogenesis. Computer Physics Communications. 176: 670-681. PMID 18084624 DOI: 10.1016/J.Cpc.2007.03.007  0.309
2007 Amarie D, Glazier JA, Jacobson SC. Compact microfluidic structures for generating spatial and temporal gradients. Analytical Chemistry. 79: 9471-7. PMID 17999467 DOI: 10.1021/Ac0714967  0.732
2006 Chuai M, Zeng W, Yang X, Boychenko V, Glazier JA, Weijer CJ. Cell movement during chick primitive streak formation. Developmental Biology. 296: 137-49. PMID 16725136 DOI: 10.1016/J.Ydbio.2006.04.451  0.469
2006 Merks RM, Brodsky SV, Goligorksy MS, Newman SA, Glazier JA. Cell elongation is key to in silico replication of in vitro vasculogenesis and subsequent remodeling. Developmental Biology. 289: 44-54. PMID 16325173 DOI: 10.1016/J.Ydbio.2005.10.003  0.34
2005 Cickovski TM, Huang C, Chaturvedi R, Glimm T, Hentschel HG, Alber MS, Glazier JA, Newman SA, Izaguirre JA. A framework for three-dimensional simulation of morphogenesis. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 2: 273-88. PMID 17044166 DOI: 10.1109/Tcbb.2005.46  0.318
2005 Chaturvedi R, Huang C, Kazmierczak B, Schneider T, Izaguirre JA, Glimm T, Hentschel HG, Glazier JA, Newman SA, Alber MS. On multiscale approaches to three-dimensional modelling of morphogenesis. Journal of the Royal Society, Interface / the Royal Society. 2: 237-53. PMID 16849182 DOI: 10.1098/Rsif.2005.0033  0.334
2005 Cui C, Yang X, Chuai M, Glazier JA, Weijer CJ. Analysis of tissue flow patterns during primitive streak formation in the chick embryo. Developmental Biology. 284: 37-47. PMID 15950214 DOI: 10.1016/J.Ydbio.2005.04.021  0.54
2004 Hentschel HG, Glimm T, Glazier JA, Newman SA. Dynamical mechanisms for skeletal pattern formation in the vertebrate limb. Proceedings. Biological Sciences / the Royal Society. 271: 1713-22. PMID 15306292 DOI: 10.1098/Rspb.2004.2772  0.302
2004 Kiskowski MA, Alber MS, Thomas GL, Glazier JA, Bronstein NB, Pu J, Newman SA. Interplay between activator-inhibitor coupling and cell-matrix adhesion in a cellular automaton model for chondrogenic patterning. Developmental Biology. 271: 372-87. PMID 15223341 DOI: 10.1016/J.Ydbio.2004.03.038  0.76
2004 Izaguirre JA, Chaturvedi R, Huang C, Cickovski T, Coffland J, Thomas G, Forgacs G, Alber M, Hentschel G, Newman SA, Glazier JA. CompuCell, a multi-model framework for simulation of morphogenesis. Bioinformatics (Oxford, England). 20: 1129-37. PMID 14764549 DOI: 10.1093/Bioinformatics/Bth050  0.358
2004 Zeng W, Thomas GL, Glazier JA. Non-turing stripes and spots: A novel mechanism for biological cell clustering Physica a: Statistical Mechanics and Its Applications. 341: 482-494. DOI: 10.1016/J.Physa.2004.03.089  0.484
2003 Zajac M, Jones GL, Glazier JA. Simulating convergent extension by way of anisotropic differential adhesion. Journal of Theoretical Biology. 222: 247-59. PMID 12727459 DOI: 10.1016/S0022-5193(03)00033-X  0.624
2003 Ouchi NB, Glazier JA, Rieu JP, Upadhyaya A, Sawada Y. Improving the realism of the cellular Potts model in simulations of biological cells Physica a: Statistical Mechanics and Its Applications. 329: 451-458. DOI: 10.1016/S0378-4371(03)00574-0  0.584
2003 Vasconcelos IF, Cantat I, Glazier JA. Dynamics and topological aspects of a reconstructed two-dimensional foam time series using Potts Model on a pinned lattice Journal of Computational Physics. 192: 1-20. DOI: 10.1016/J.Jcp.2003.06.001  0.314
2003 Asipauskas M, Aubouy M, Glazier JA, Graner F, Jiang Y. A texture tensor to quantify deformations: The example of two-dimensional flowing foams Granular Matter. 5: 71-74. DOI: 10.1007/S10035-003-0127-9  0.363
2003 Aubouy M, Jiang Y, Glazier JA, Graner F. A texture tensor to quantify deformations Granular Matter. 5: 67-70. DOI: 10.1007/S10035-003-0126-X  0.352
2001 Mombach JCM, De Almeida RMC, Thomas GL, Upadhyaya A, Glazier JA. Bursts and cavity formation in Hydra cells aggregates: Experiments and simulations Physica a: Statistical Mechanics and Its Applications. 297: 495-508. DOI: 10.1016/S0378-4371(01)00199-6  0.579
2001 Upadhyaya A, Rieu JP, Glazier JA, Sawada Y. Anomalous diffusion and non-Gaussian velocity distribution of Hydra cells in cellular aggregates Physica a: Statistical Mechanics and Its Applications. 293: 549-558. DOI: 10.1016/S0378-4371(01)00009-7  0.535
2000 Rieu JP, Upadhyaya A, Glazier JA, Ouchi NB, Sawada Y. Diffusion and deformations of single hydra cells in cellular aggregates. Biophysical Journal. 79: 1903-14. PMID 11023896 DOI: 10.1016/S0006-3495(00)76440-X  0.558
2000 Zajac M, Jones GL, Glazier JA. Model of convergent extension in animal morphogenesis. Physical Review Letters. 85: 2022-5. PMID 10970673 DOI: 10.1103/Physrevlett.85.2022  0.603
1999 Jiang Y, Swart PJ, Saxena A, Asipauskas M, Glazier JA. Hysteresis and avalanches in two-dimensional foam rheology simulations. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 59: 5819-32. PMID 11969562 DOI: 10.1103/Physreve.59.5819  0.387
1999 Raghavachari S, Glazier JA. Waves in diffusively coupled bursting cells Physical Review Letters. 82: 2991-2994. DOI: 10.1103/Physrevlett.82.2991  0.656
1999 Elias F, Flament C, Glazier JA, Graner F, Jiang Y. Foams out of stable equilibrium: Cell elongation and side swapping Philosophical Magazine B: Physics of Condensed Matter; Statistical Mechanics, Electronic, Optical and Magnetic Properties. 79: 729-751. DOI: 10.1080/13642819908205746  0.433
1998 Jiang Y, Levine H, Glazier J. Possible cooperation of differential adhesion and chemotaxis in mound formation of Dictyostelium Biophysical Journal. 75: 2615-2625. PMID 9826586 DOI: 10.1016/S0006-3495(98)77707-0  0.446
1997 Jiang Y, Glazier JA. Foam drainage: extended large-Q potts model simulation Materials Research Society Symposium - Proceedings. 463: 307-312. DOI: 10.1557/Proc-463-307  0.385
1995 Gonatas CP, Leigh JS, Yodh AG, Glazier JA, Prause B. Magnetic resonance images of coarsening inside a foam. Physical Review Letters. 75: 573-576. PMID 10060055 DOI: 10.1103/Physrevlett.75.573  0.719
1995 Mombach JC, Glazier JA, Raphael RC, Zajac M. Quantitative comparison between differential adhesion models and cell sorting in the presence and absence of fluctuations. Physical Review Letters. 75: 2244-2247. PMID 10059250 DOI: 10.1103/Physrevlett.75.2244  0.605
1995 Raghavachari S, Glazier JA. Spatially coherent states in fractally coupled map lattices. Physical Review Letters. 74: 3297-3300. PMID 10058161 DOI: 10.1103/PhysRevLett.74.3297  0.663
1995 Glazier JA, Raghavachari S, Berthelsen CL, Skolnick MH. Reconstructing phylogeny from the multifractal spectrum of mitochondrial DNA. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 51: 2665-2668. PMID 9962935 DOI: 10.1103/PhysRevE.51.2665  0.63
1995 Prause BA, Glazier JA, Gravina SJ, Montemagno CD. Three-dimensional magnetic resonance imaging of a liquid foam Journal of Physics: Condensed Matter. 7: L511-L516. DOI: 10.1088/0953-8984/7/40/001  0.725
1994 Berthelsen CL, Glazier JA, Raghavachari S. Effective multifractal spectrum of a random walk. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 49: 1860-1864. PMID 9961425 DOI: 10.1103/PhysRevE.49.1860  0.644
1993 Glazier JA, Graner F. Simulation of the differential adhesion driven rearrangement of biological cells. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 47: 2128-2154. PMID 9960234 DOI: 10.1103/PhysRevE.47.2128  0.341
1992 Graner F, Glazier JA. Simulation of biological cell sorting using a two-dimensional extended Potts model. Physical Review Letters. 69: 2013-2016. PMID 10046374 DOI: 10.1103/PhysRevLett.69.2013  0.34
1990 Glazier JA, Anderson MP, Grest GS. Coarsening in the two-dimensional soap froth and the large- Q potts model: A detailed comparison Philosophical Magazine B: Physics of Condensed Matter; Statistical Mechanics, Electronic, Optical and Magnetic Properties. 62: 615-647. DOI: 10.1080/13642819008215259  0.314
1989 Stavans J, Glazier JA. Soap froth revisited: Dynamic scaling in the two-dimensional froth. Physical Review Letters. 62: 1318-1321. PMID 10039639 DOI: 10.1103/PhysRevLett.62.1318  0.604
1989 Glazier JA, Stavans J. Nonideal effects in the two-dimensional soap froth. Physical Review. A. 40: 7398-7401. PMID 9902164 DOI: 10.1103/PhysRevA.40.7398  0.609
1988 Glazier JA, Gunaratne G, Libchaber A. f( alpha ) curves: Experimental results. Physical Review. A. 37: 523-530. PMID 9899681 DOI: 10.1103/Physreva.37.523  0.515
1988 Glazier JA, Libchaber A. Quasi-Periodicity and Dynamical Systems: An Experimentalist's View Ieee Transactions On Circuits and Systems. 35: 790-809. DOI: 10.1109/31.1826  0.527
1988 Glazier JA, Gunaratne G, Libchaber A. F() curves: Experimental results Physical Review A. 37: 523-530. DOI: 10.1103/PhysRevA.37.523  0.441
1987 Glazier JA, Gross SP, Stavans J. Dynamics of two-dimensional soap froths. Physical Review. A. 36: 306-312. PMID 9898684 DOI: 10.1103/Physreva.36.306  0.6
1986 Glazier JA, Jensen MH, Libchaber A, Stavans J. Structure of Arnold tongues and the f( alpha ) spectrum for period doubling: Experimental results. Physical Review. A. 34: 1621-1624. PMID 9897438 DOI: 10.1103/Physreva.34.1621  0.69
1986 Glazier JA, Jensen MH, Libchaber A, Stavans J. Structure of Arnold tongues and the f() spectrum for period doubling: Experimental results Physical Review A. 34: 1621-1624. DOI: 10.1103/PhysRevA.34.1621  0.653
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