| 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 | 568 | 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 | 325 | 2009 |
| 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), eaaz5357, 2020 | 311 | 2020 |
| Contact-inhibited chemotaxis in de novo and sprouting blood-vessel growth RMH Merks, ED Perryn, A Shirinifard, JA Glazier PLoS computational biology 4 (9), e1000163, 2008 | 275 | 2008 |
| 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 | 241 | 2017 |
| 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 | 182 | 2014 |
| 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 | 77 | 2011 |
| 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 | 77 | 2008 |
| 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), 3718, 2019 | 64 | 2019 |
| Ovarian tumor attachment, invasion, and vascularization reflect unique microenvironments in the peritoneum: insights from xenograft and mathematical models MP Steinkamp, KK Winner, S Davies, C Muller, Y Zhang, RM Hoffman, ... Frontiers in oncology 3, 97, 2013 | 62 | 2013 |
| 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 | 60 | 2018 |
| 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 computational biology 8 (5), e1002440, 2012 | 55 | 2012 |
| The tumor cell‐secreted matricellular protein WISP 1 drives pro‐metastatic collagen linearization H Jia, J Janjanam, SC Wu, R Wang, G Pano, M Celestine, O Martinot, ... The EMBO Journal 38 (16), e101302, 2019 | 45 | 2019 |
| 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 | 42 | 2015 |
| 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 | 40 | 2015 |
| 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 | 39 | 2020 |
| 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 | 38 | 2014 |
| 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 | 37 | 2019 |
| Circadian gene variants and the skeletal muscle circadian clock contribute to the evolutionary divergence in longevity across Drosophila populations LC Hunt, J Jiao, YD Wang, D Finkelstein, D Rao, M Curley, ... Genome Research 29 (8), 1262-1276, 2019 | 31 | 2019 |
| 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 | 31 | 2010 |
