TY  - CHAP
A1  - Swat, M H
A1  - Thomas, G L
A1  - Belmonte, J M
A1  - Shirinifard, A 
A1  - Hmeljak, D 
A1  - Glazier, J A
T1  - Multi-scale modeling of tissues using CompuCell3D.
Y1  - 2012//
N1  - R835001
JF  - METHODS IN CELL BIOLOGY
J1  - METHOD CELL BIOL
VL  - 110
SP  - 325
EP  - 366
ER  - 


TY  - JOUR
A1  - Andasari, V 
A1  - Roper, R T
A1  - Swat, M H
A1  - Chaplain, MA J
T1  - Integrating intracellular dynamics using CompuCell3D and BioNetSolver: applications to multiscale modelling of cancer cell growth and invasion.
Y1  - 2012/03/
N1  - R835001
JF  - PLOS ONE
J1  - PLOS One
VL  - 7
IS  - 3
SP  - e33726
ER  - 


TY  - JOUR
A1  - Petersen, B K
A1  - Ropella, G 
A1  - Hunt, C A
T1  - Toward modular biological models: defining analog modules based on referent physiological mechanisms.
Y1  - 2014/08/16
N1  - R835001
VL  - 8
SP  - 95
ER  - 


TY  - JOUR
A1  - Sluka, J P
A1  - Glazier, J A
A1  - Swat, M 
T1  - Infrastructure requirements for moving multiscale modeling from research tools to the clinical and regulatory domains.
Y1  - 2012/01/
N1  - R835001
VL  - 7
SP  - 12
ER  - 


TY  - JOUR
A1  - Sluka, J 
A1  - Shirinifard, A 
A1  - Swat, M 
A1  - Cosmanescu, A 
A1  - Heiland, R W
A1  - Glazier, J 
T1  - The Cell Behavior Ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents.
Y1  - 2014/08/15
N1  - R835001
VL  - 30
IS  - 16
SP  - 2367
EP  - 2374
ER  - 


TY  - JOUR
A1  - Wambaugh, J F
A1  - Wetmore, B A
A1  - Pearce, R 
A1  - Strope, C 
A1  - Goldsmith, R 
A1  - Sluka, J P
A1  - Sedykh, A 
A1  - Tropsha, A 
A1  - Bosgra, S 
A1  - Shah, I 
A1  - Judson, R 
A1  - Thomas, R S
A1  - Setzer, R W
T1  - Toxicokinetic triage for environmental chemicals.
Y1  - 2015/09/
N1  - R835001
N1  - R835166
JF  - TOXICOLOGICAL SCIENCES
J1  - TOXICOL SCI
J2  - Toxicol.Sci.
J3  - Toxicological Sciences
VL  - 147
IS  - 1
SP  - 55
EP  - 67
ER  - 


TY  - JOUR
A1  - Wang, Y 
A1  - Lin, Z 
A1  - Liu, Z 
A1  - Harris, S 
A1  - Kelly, R 
A1  - Zhang, J 
A1  - Ge, W 
A1  - Chen, M 
A1  - Borlak, J 
A1  - Tong, W 
T1  - A unifying ontology to integrate histological and clinical observations for drug-induced liver injury.
Y1  - 2013/04/
N1  - R835001
JF  - AMERICAN JOURNAL OF PATHOLOGY
J1  - AM J PATHOL
VL  - 182
IS  - 4
SP  - 1180
EP  - 1187
ER  - 


TY  - CONF
A1  - Belmonte, J 
A1  - Fu, X 
A1  - Sluka, J P
A1  - Swat, M 
A1  - Glazier, J A
T1  - Blood flow and oxygen distribution in a simulated 3D liver lobule.
Y1  - 2013/09/
N1  - R835001
ER  - 


TY  - CONF
A1  - Fu, X 
T1  - Flow modeling in simulated liver lobule.
Y1  - 2014/06/15-19
N1  - R835001
ER  - 


TY  - CONF
A1  - Fu, X 
T1  - A simulation framework for modeling acetaminophen induced liver toxicity.
Y1  - 2014/06/25
N1  - R835001
ER  - 


TY  - CONF
A1  - Glazier, J A
T1  - [Presentation].
Y1  - 2011/08/28-1
N1  - R835001
ER  - 


TY  - CONF
A1  - Glazier, J A
A1  - Swat, M 
A1  - Sluka, J P
T1  - Challenges for multi-scale virtual tissues: where we are and where we need to go: computational component libraries and biological component libraries.
Y1  - 2014/09/3-4
N1  - R835001
ER  - 


TY  - CONF
A1  - Glazier, J 
T1  - From molecules to tissues: multiscale modeling from a multicellular viewpoint.
Y1  - 2012/12/13-14
N1  - R835001
ER  - 


TY  - CONF
A1  - Hunt, C A
A1  - Ropella, G 
A1  - Smith, A 
T1  - Explanatory, concrete insight Into location-dependent, multiscale aspects of APAP-induced liver injury.
Y1  - 2013/09/
N1  - R835001
ER  - 


TY  - CONF
A1  - Ropella, G 
A1  - Petersen, B 
A1  - Hunt, C A
T1  - Exploring two modularity techniques for agent-based models.
Y1  - 2014/09/3-4
N1  - R835001
ER  - 


TY  - CONF
A1  - Sluka, J P
A1  - Cosmanescu, A 
A1  - Swat, M 
A1  - Glazier, J A
T1  - From macro to micro dosimetry, pharmacology and toxicity: a multiscale modeling framework of xenobiotics using open source tools.
Y1  - 2012/09/
N1  - R835001
ER  - 


TY  - CONF
A1  - Sluka, J P
A1  - Fu, X 
A1  - Swat, M 
A1  - Glazier, J A
T1  - Parameter sensitivities in a multiscale model of acetaminophen metabolism: from whole-body to subcellular reaction kinetics.
Y1  - 2014/09/3-4
N1  - R835001
ER  - 


TY  - CONF
A1  - Sluka, J 
T1  - Optimizing model specification in cross-scale computational biology.
Y1  - 2012/12/13-14
N1  - R835001
ER  - 


TY  - CONF
A1  - Sluka, J 
A1  - Fu, X 
A1  - Belmonte, J 
A1  - Cosmanescu, A 
A1  - Swat, M 
A1  - Glazier, J A
T1  - A multiscale in silica modeling framework of xenobiotics.
Y1  - 2014/03/23-27
N1  - R835001
ER  - 


TY  - CONF
A1  - Smith, A 
A1  - Ropella, G 
A1  - Hunt, C A
T1  - Explaining complex phenomena by discovering, validating, and falsifying in silico mechanistic hypotheses: a demonstration focused on multiple features of acetaminophen hepatotoxicity.
Y1  - 2014/09/3-4
N1  - R835001
ER  - 


TY  - CONF
A1  - Swat, M 
T1  - Multicell modelling using CompuCell3D.
Y1  - 2012/12/13-14
N1  - R835001
ER  - 


TY  - CONF
A1  - Wambaugh, J 
A1  - Strope, C 
A1  - Nicolas, C 
A1  - Pearce, R 
A1  - Judson, R 
A1  - Goldsmith, R 
A1  - El-Masri, H 
A1  - Wetmore, B 
A1  - Sluka, J 
A1  - Tropsha, A 
A1  - Bosgra, S 
A1  - Shah, I 
A1  - Thomas, R 
A1  - Setzer, R W
T1  - High throughput pharmacokinetics for environmental chemicals.
Y1  - 2014/03/23-27
N1  - R835001
ER  - 


TY  - CONF
A1  - Heiland, R 
A1  - Swat, M 
A1  - Sluka, J 
A1  - Zaitlen, B 
A1  - Shirinifard, A 
A1  - Thomas, G 
A1  - Lumsdaine, A 
A1  - Glazier, J 
T1  - Visualizing cells and their connectivity graphs for CompuCell3D.
Y1  - 2012/10/14-19
N1  - R835001
SP  - 85
EP  - 90
ER  - 


TY  - CONF
A1  - Smith, A 
A1  - Ropella, G 
A1  - Kaplowitz, N 
A1  - Ookhtens, M 
A1  - Hunt, C A
T1  - Mechanistic agent-based damage and repair models as hypotheses for patterns of necrosis caused by drug induced liver injury.
Y1  - 2014//
N1  - R835001
ER  -