Abbas Shirinifard
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Multi-scale modeling of tissues using CompuCell3D
MH Swat, GL Thomas, JM Belmonte, A Shirinifard, D Hmeljak, JA Glazier
Methods in cell biology 110, 325-366, 2012
3D multi-cell simulation of tumor growth and angiogenesis
A Shirinifard, JS Gens, BL Zaitlen, NJ Popławski, M Swat, JA Glazier
PloS one 4 (10), e7190, 2009
Contact-inhibited chemotaxis in de novo and sprouting blood-vessel growth
RMH Merks, ED Perryn, A Shirinifard, JA Glazier
PLoS Comput Biol 4 (9), e1000163, 2008
Targeting the DNA repair pathway in Ewing sarcoma
E Stewart, R Goshorn, C Bradley, LM Griffiths, C Benavente, NR Twarog, ...
Cell reports 9 (3), 829-840, 2014
The dynamic epigenetic landscape of the retina during development, reprogramming, and tumorigenesis
I Aldiri, B Xu, L Wang, X Chen, D Hiler, L Griffiths, M Valentine, ...
Neuron 94 (3), 550-568. e10, 2017
Correlative three-dimensional super-resolution and block-face electron microscopy of whole vitreously frozen cells
DP Hoffman, G Shtengel, CS Xu, KR Campbell, M Freeman, L Wang, ...
Science 367 (6475), 2020
Simulation of single-species bacterial-biofilm growth using the Glazier-Graner-Hogeweg model and the CompuCell3D modeling environment
NJ Popławski, A Shirinifard, M Swat, JA Glazier
Mathematical biosciences and engineering: MBE 5 (2), 355, 2008
Computer simulations of cell sorting due to differential adhesion
Y Zhang, GL Thomas, M Swat, A Shirinifard, JA Glazier
PloS one 6 (10), e24999, 2011
Ovarian tumor attachment, invasion, and vascularization reflect unique microenvironments in the peritoneum: insights from xenograft and mathematical models
MP Steinkamp, K Kanigel-Winner, S Davies, CY Muller, Y Zhang, ...
Frontiers in oncology 3, 97, 2013
Adhesion failures determine the pattern of choroidal neovascularization in the eye: a computer simulation study
A Shirinifard, JA Glazier, M Swat, JS Gens, F Family, Y Jiang, ...
PLoS Comput Biol 8 (5), e1002440, 2012
The cell behavior ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents
JP Sluka, A Shirinifard, M Swat, A Cosmanescu, RW Heiland, JA Glazier
Bioinformatics 30 (16), 2367-2374, 2014
Retinal cell type DNA methylation and histone modifications predict reprogramming efficiency and retinogenesis in 3D organoid cultures
L Wang, D Hiler, B Xu, I AlDiri, X Chen, X Zhou, L Griffiths, M Valentine, ...
Cell reports 22 (10), 2601-2614, 2018
Development and characterization of a human orthotopic neuroblastoma xenograft
E Stewart, A Shelat, C Bradley, X Chen, S Federico, S Thiagarajan, ...
Developmental biology 407 (2), 344-355, 2015
Emergent stratification in solid tumors selects for reduced cohesion of tumor cells: a multi-cell, virtual-tissue model of tumor evolution using compucell3d
MH Swat, GL Thomas, A Shirinifard, SG Clendenon, JA Glazier
PloS one 10 (6), e0127972, 2015
Front instabilities and invasiveness of simulated 3D avascular tumors
NJ Poplawski, A Shirinifard, U Agero, JS Gens, M Swat, JA Glazier
PloS one 5 (5), e10641, 2010
Deep multiomics profiling of brain tumors identifies signaling networks downstream of cancer driver genes
H Wang, AK Diaz, TI Shaw, Y Li, M Niu, JH Cho, BS Paugh, Y Zhang, ...
Nature communications 10 (1), 1-15, 2019
Interleukin-15 enhances anti-GD2 antibody-mediated cytotoxicity in an orthotopic PDX model of neuroblastoma
R Nguyen, A Moustaki, JL Norrie, S Brown, WJ Akers, A Shirinifard, ...
Clinical Cancer Research 25 (24), 7554-7564, 2019
Oxygen tension and the VHL-Hif1α pathway determine onset of neuronal polarization and cerebellar germinal zone exit
JA Kullmann, N Trivedi, D Howell, C Laumonnerie, V Nguyen, ...
Neuron 106 (4), 607-623. e5, 2020
St. Jude Children’s Research Hospital-Washington University Pediatric Cancer Genome Project. The dynamic epigenetic landscape of the retina during development, reprogramming…
I Aldiri, B Xu, L Wang, X Chen, D Hiler, L Griffiths, M Valentine, ...
Neuron 94 (550-568), e10, 2017
3D quantitative analyses of angiogenic sprout growth dynamics
A Shirinifard, CW McCollum, MB Bolin, J Gustafsson, JA Glazier, ...
Developmental Dynamics 242 (5), 518-526, 2013
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