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Abbas Shirinifard, Ph.D. - Publications

Affiliations: 
Physics Indiana University, Bloomington, Bloomington, IN, United States 
Area:
Biophysics
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22 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 Hoffman DP, Shtengel G, Xu CS, Campbell KR, Freeman M, Wang L, Milkie DE, Pasolli HA, Iyer N, Bogovic JA, Stabley DR, Shirinifard A, Pang S, Peale D, Schaefer K, et al. Correlative three-dimensional super-resolution and block-face electron microscopy of whole vitreously frozen cells. Science (New York, N.Y.). 367. PMID 31949053 DOI: 10.1126/Science.Aaz5357  0.305
2019 Jia H, Janjanam J, Wu SC, Wang R, Pano G, Celestine M, Martinot O, Breeze-Jones H, Clayton G, Garcin C, Shirinifard A, Zaske AM, Finkelstein D, Labelle M. The tumor cell-secreted matricellular protein WISP1 drives pro-metastatic collagen linearization. The Embo Journal. e101302. PMID 31294477 DOI: 10.15252/Embj.2018101302  0.394
2017 Shirinifard A, Thiagarajan S, Patel YT, Davis AD, Jacus MO, Roberts J, Stewart CF, Sablauer A. Abstract A33: An individualized predictive 3D model of tumor response to topotecan for a patient-derived orthotopic xenograft model of pediatric neuroblastoma Cancer Research. 77. DOI: 10.1158/1538-7445.Epso16-A33  0.323
2016 Shirinifard A, Thiagarajan S, Vogel P, Sablauer A. Detection of Phenotypic Alterations Using High-Content Analysis of Whole-Slide Images. The Journal of Histochemistry and Cytochemistry : Official Journal of the Histochemistry Society. PMID 27026297 DOI: 10.1369/0022155416639884  0.32
2016 Shirinifard A, Thiagarajan S, Patel YT, Davis AD, Jacus MO, Throm SL, Roberts J, Daryani V, Stewart CF, AS. Abstract 2708: Development of an individualized 3D transport model of topotecan for a patient-derived orthotopic xenograft model of pediatric neuroblastoma Cancer Research. 76: 2708-2708. DOI: 10.1158/1538-7445.Am2016-2708  0.389
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  0.622
2015 Patel YT, Jacus MO, Shirinifard A, Davis AD, Thiagarajan S, Throm SL, Daryani VM, Sablauer A, Stewart CF. Abstract 4519: Development of a whole body physiologically-based pharmacokinetic (PBPK) model with individualized tumor compartment for topotecan (TPT) in mice bearing neuroblastoma (NB) Cancer Research. 75: 4519-4519. DOI: 10.1158/1538-7445.Am2015-4519  0.369
2015 Thiagarajan S, Shirinifard A, Jacus MO, Davis AD, Patel YT, Throm SL, Daryani V, Stewart CF, Sablauer A. Abstract 1496: Quantification of tumor blood perfusion of an orthotopic mouse model of neuroblastoma using nonlinear contrast-enhanced ultrasound imaging Cancer Research. 75: 1496-1496. DOI: 10.1158/1538-7445.Am2015-1496  0.369
2015 Shirinifard A, Thiagarajan S, Sablauer A. Abstract 1495: Quantification of blood perfusion in rhabdomyosarcoma xenograft in 3D using contrast-enhanced ultrasound imaging Cancer Research. 75: 1495-1495. DOI: 10.1158/1538-7445.Am2015-1495  0.363
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  0.577
2013 Steinkamp MP, Winner KK, Davies S, Muller C, Zhang Y, Hoffman RM, Shirinifard A, Moses M, Jiang Y, Wilson BS. Ovarian tumor attachment, invasion, and vascularization reflect unique microenvironments in the peritoneum: insights from xenograft and mathematical models. Frontiers in Oncology. 3: 97. PMID 23730620 DOI: 10.3389/Fonc.2013.00097  0.514
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  0.545
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  0.509
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  0.54
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  0.576
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  0.608
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  0.462
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  0.587
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  0.568
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  0.596
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  0.603
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  0.593
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