21 Publications
2019
A Review of Cell-Based Computational Modeling in Cancer Biology
Metzcar, John⋅Wang, Yafei⋅Heiland, Randy and Macklin, Paul
JCO clinical cancer informatics, vol. 3, (no. 3), pp. 13, 2019-Feb. | Journal Article
 
Learning-accelerated discovery of immune-tumour interactionsElectronic supplementary information (ESI) available: Simulation animations: https://www.youtube.com/watch?v=6GPXZvlNJBg, Software repository: https://github.com/MathCancer/PhysiCell-EMEWS-2/releases/tag/1.0.0http://physicell.mathcancer.orghttp://emews.org
Ozik, Jonathan⋅Collier, Nicholson⋅Heiland, Randy⋅An, Gary and Macklin, Paul
(no. 4), pp. 76, 20190805. | Journal Article
 
Learning-accelerated discovery of immune-tumour interactionsElectronic supplementary information (ESI) available: Simulation animations: https://www.youtube.com/watch?v=6GPXZvlNJBg, Software repository: https://github.com/MathCancer/PhysiCell-EMEWS-2/releases/tag/1.0.0http://physicell.mathcancer.orghttp://emews.org
Ozik, Jonathan⋅Ozik, Jonathan⋅Collier, Nicholson⋅Collier, Nicholson⋅Heiland, Randy⋅Heiland, Randy⋅An, Gary⋅An, Gary⋅Macklin, Paul and Macklin, Paul
(no. 4), pp. 76, 20190805. | Journal Article
 
PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling
Letort, Gaelle⋅Montagud, Arnau⋅Stoll, Gautier⋅Heiland, Randy⋅Barillot, Emmanuel⋅Macklin, Paul⋅Zinovyev, Andrei and Calzone, Laurence
Bioinformatics, vol. 35, (no. 7), pp. 1196, 20190401. | Journal Article
2018
High-throughput cancer hypothesis testing with an integrated PhysiCell-EMEWS workflow
Ozik, Jonathan⋅Ozik, Jonathan⋅Collier, Nicholson⋅Collier, Nicholson⋅Wozniak, Justin M⋅Wozniak, Justin M⋅Macal, Charles⋅Macal, Charles⋅Cockrell, Chase⋅Cockrell, Chase⋅Friedman, Samuel H⋅Friedman, Samuel H⋅Ghaffarizadeh, Ahmadreza⋅Ghaffarizadeh, Ahmadreza⋅Heiland, Randy⋅Heiland, Randy⋅An, Gary⋅An, Gary⋅Macklin, Paul and Macklin, Paul
BMC bioinformatics, vol. 19, (no. Suppl 18), pp. 483, 2018-Dec-21. | Journal Article
 
PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems
Ghaffarizadeh, Ahmadreza⋅Ghaffarizadeh, Ahmadreza⋅Ghaffarizadeh, Ahmadreza⋅Ghaffarizadeh, Ahmadreza⋅Heiland, Randy⋅Heiland, Randy⋅Heiland, Randy⋅Heiland, Randy⋅Friedman, Samuel H⋅Friedman, Samuel H⋅Friedman, Samuel H⋅Friedman, Samuel H.⋅Mumenthaler, Shannon M⋅Mumenthaler, Shannon M.⋅Mumenthaler, Shannon M⋅Mumenthaler, Shannon M⋅Macklin, Paul⋅Macklin, Paul⋅Macklin, Paul and Macklin, Paul
PLoS Computational Biology, vol. 14, (no. 2), 2018-02-01. | Journal Article
2014
The cell behavior ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents
Sluka, James P⋅Sluka, James P⋅Sluka, James P⋅Shirinifard, Abbas⋅Shirinifard, Abbas⋅Shirinifard, Abbas⋅Swat, Maciej⋅Swat, Maciej⋅Swat, Maciej⋅Cosmanescu, Alin⋅Cosmanescu, Alin⋅Cosmanescu, Alin⋅Heiland, Randy W⋅Heiland, Randy W⋅Heiland, Randy W⋅Glazier, James A⋅Glazier, James A and Glazier, James A
Bioinformatics (Oxford, England), vol. 30, (no. 16), pp. 2374, 2014-Aug-15. | Journal Article
2013
Toward a Research Software Security Maturity Model
Heiland, Randy⋅Heiland, Randy⋅Thomas, Betsy⋅Thomas, Betsy⋅Welch, Von⋅Welch, Von⋅Jackson, Craig and Jackson, Craig
2013-09-06. | Journal Article
2011
Extending Transfer Entropy Improves Identification of Effective Connectivity in a Spiking Cortical Network Model
Ito, Shinya⋅Ito, Shinya⋅Hansen, Michael E⋅Hansen, Michael E⋅Heiland, Randy⋅Heiland, Randy⋅Lumsdaine, Andrew⋅Lumsdaine, Andrew⋅Litke, Alan M⋅Litke, Alan M⋅Beggs, John M and Beggs, John
PloS one, vol. 6, (no. 11), pp. e27431, 2011-00-00. | Journal Article
2009
Multicell simulations of development and disease using the CompuCell3D simulation environment
Swat, Maciej H⋅Swat, Maciej H⋅Hester, Susan D⋅Hester, Susan D⋅Balter, Ariel I⋅Balter, Ariel I⋅Heiland, Randy W⋅Heiland, Randy W⋅Zaitlen, Benjamin L⋅Zaitlen, Benjamin L⋅Glazier, James A and Glazier, James A
Methods in molecular biology (Clifton, N.J.), vol. 500, pp. 428, 2009-00-00. | Journal Article
2008
ChemInform Abstract: Visual Methods for Interpreting Optical Nonlinearity at the Molecular Level
Wampler, Ronald D⋅Wampler, Ronald D.⋅Moad, Andrew J.⋅Moad, Andrew J⋅Moad, Charles W⋅Moad, Charles W.⋅Heiland, Randy⋅Heiland, Randy⋅Simpson, Garth J and Simpson, Garth J.
ChemInform, vol. 39, (no. 3), 2008-01-15. | Journal Article
 
MutDB: update on development of tools for the biochemical analysis of genetic variation
Singh, Arti⋅Singh, Arti⋅Olowoyeye, Adebayo⋅Olowoyeye, Adebayo⋅Baenziger, Peter H⋅Baenziger, Peter H⋅Dantzer, Jessica⋅Dantzer, Jessica⋅Kann, Maricel G⋅Kann, Maricel G⋅Radivojac, Predrag⋅Radivojac, Predrag⋅Heiland, Randy⋅Heiland, Randy⋅Mooney, Sean D and Mooney, Sean D
Nucleic Acids Research, vol. 36, (no. suppl_1), pp. D819, 20080100. | Journal Article
2007
NLOPredict: Visualization and data analysis software for nonlinear optics
Moad, Andrew J⋅Moad, Andrew J⋅Moad, Charles W⋅Moad, Charles W⋅Perry, John M⋅Perry, John M⋅Wampler, Ronald D⋅Wampler, Ronald D⋅Goeken, G S⋅Goeken, G Scott⋅Begue, Nathan J⋅Begue, Nathan J⋅Shen, Tian⋅Shen, Tian⋅Heiland, Randy⋅Heiland, Randy⋅Simpson, Garth J and Simpson, Garth J
Journal of computational chemistry, vol. 28, (no. 12), pp. 2002, 2007-Sep. | Journal Article
 
Visual Methods for Interpreting Optical Nonlinearity at the Molecular Level
Wampler, Ronald D⋅Wampler, Ronald D⋅Moad, Andrew J⋅Moad, Andrew J⋅Moad, Charles W⋅Moad, Charles W⋅Heiland, Randy⋅Heiland, Randy⋅Simpson, Garth J and Simpson, Garth J
Accounts of chemical research, vol. 40, (no. 10), pp. 960, 2007-Oct. | Journal Article
 
Web Service Infrastructure for Chemoinformatics
Dong, Xiao⋅Dong, Xiao⋅Dong, Xiao⋅Gilbert, Kevin E⋅Gilbert, Kevin E⋅Gilbert, Kevin E⋅Guha, Rajarshi⋅Guha, Rajarshi⋅Guha, Rajarshi⋅Heiland, Randy⋅Heiland, Randy⋅Heiland, Randy⋅Kim, Jungkee⋅Kim, Jungkee⋅Kim, Jungkee⋅Pierce, Marlon E⋅Pierce, Marlon E⋅Pierce, Marlon E⋅Fox, Geoffrey C⋅Fox, Geoffrey C⋅Fox, Geoffrey C⋅Wild, David J⋅Wild, David J and Wild, David J
Journal of chemical information and modeling, vol. 47, (no. 4), pp. 1307, 2007 Jul-Aug. | Journal Article
2006
Identification of similar regions of protein structures using integrated sequence and structure analysis tools
Peters, Brandon⋅Peters, Brandon⋅Moad, Charles⋅Moad, Charles⋅Youn, Eunseog⋅Youn, Eunseog⋅Buffington, Kris⋅Buffington, Kris⋅Heiland, Randy⋅Heiland, Randy⋅Mooney, Sean and Mooney, Sean
BMC structural biology, vol. 6, (no. 1), pp. 4, 2006-Mar-09. | Journal Article
 
XML for BioinformaticsEthan CeramiBerlin: Springer-Verlag;ISBN: 0-387-23028-9; 304pp.;2005; £42.50
Heiland, Randy
Briefings in Bioinformatics, vol. 7, (no. 1), pp. 125, 2006-03-01. | Journal Article
2005
MutDB services: interactive structural analysis of mutation data
Dantzer, Jessica⋅Dantzer, Jessica⋅Moad, Charles⋅Moad, Charles⋅Heiland, Randy⋅Heiland, Randy⋅Mooney, Sean and Mooney, Sean
Nucleic acids research, vol. 33, (no. Web Server issue), pp. W314, 2005-Jul-01. | Journal Article
2002
Visual methods for interpreting optical nonlinearity at the molecular level
Wampler, Ronald⋅Wampler, Ronald⋅Moad, Andrew⋅Moad, Andrew⋅Moad, Charles⋅Moad, Charles⋅Heiland, Randy⋅Heiland, Randy⋅Simpson, Garth and Simpson, Garth
Accounts of Chemical Research, vol. 35, (no. 6), pp. 953, 20020601. | Journal Article
1994
k l t o o l: A tool to analyze spatiotemporal complexity
Armbruster, Dieter⋅Heiland, Randy and Kostelich, Eric J
Chaos: An Interdisciplinary Journal of Nonlinear Science, vol. 4, (no. 2), pp. 424, 19940600. | Journal Article
1992
Phase-space analysis of bursting behavior in Kolmogorov flow
Armbruster, Dieter⋅Heiland, Randy⋅Kostelich, Eric J and Nicolaenko, Basil
Physica D: Nonlinear Phenomena, vol. 58, (no. 1), pp. 401, 1992. | Journal Article