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 |
0.695 |
|
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, Popławski 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 |
Popławski 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 |
0.47 |
|
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 |
0.485 |
|
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 |
0.366 |
|
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 |
0.355 |
|
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 |
0.389 |
|
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 |
0.435 |
|
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 |
0.448 |
|
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 |
0.387 |
|
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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