@misc {23713,
	title = {Simulations of Heart Function (editorial)},
	howpublished = {BioMed Research International},
	year = {2015},
	pages = { 3 pages},
	publisher = {Hindawi Publishing Corporation},
	author = {Rodrigo Weber dos {Santos} and Alonso, Sergio and Elizabeth M {Cherry} and Sundnes, Joakim}
}
@inproceedings {Simula.simula.2708,
	title = {3D Heart Modeling With Cellular Automata, Mass-Spring System and CUDA},
	journal = {Parallel computing technologies},
	volume = {7979},
	year = {2013},
	pages = {296-309},
	publisher = {Springer},
	type = {Conference},
	abstract = {The mechanical behavior of the heart is guided by the propagation of an electrical wave, called action potential. Many diseases have multiple effects on both electrical and mechanical cardiac physiology. To support a better understanding of the multi-scale and multi-physics processes involved in physiological and pathological cardiac conditions, a lot of work has been done in developing computational tools to simulate the electro-mechanical behavior of the heart. In this work, we implemented an aplication to mimic the heart tissue behavior, based on cellular automaton, mass-spring system and parallel computing with CUDA. Our application performed 3D simulations in a very short time. In order to assess the simulation results, we compared them with another synthetic model based on well-known partial differential equations(PDE). Preliminary results suggest our application was able to reproduce the PDE results with much less computational effort.},
	author = {Ricardo Silva {Campos} and Ronan Mendonca {Amorim} and Bernardo Lino {de Oliveira} and Sundnes, Joakim and Luis Paulo da S {Barra} and Lobosco, Marcelo and Rodrigo Weber dos {Santos}},
	editor = {Malyshkin, Victor}
}
@article {Simula.simula.1440,
	title = {Effects of Deformation on Transmural Dispersion of Repolarization Using in Silico Models of Human Left Ventricular Wedge},
	journal = {International Journal for Numerical Methods in Biomedical Engineering},
	volume = {29},
	number = {12},
	year = {2013},
	pages = {1323-1337},
	abstract = {Mechanical deformation affects the electrical activity of the heart through multiple feedback loops. The purpose of this work is to study the effect of deformation on transmural dispersion of repolarization and on surface electrograms using an in silico human ventricular wedge. To achieve this purpose, we developed a strongly coupled electromechanical cell model by coupling a human left ventricle electrophysiology model and an active contraction model reparameterized for human cells. This model was then embedded in tissue simulations on the basis of bidomain equations and nonlinear solid mechanics. The coupled model was used to evaluate effects of mechanical deformation on important features of repolarization and electrograms. Our results indicate an increase in the T-wave amplitude of the surface electrograms in simulations that account for the effects of cardiac deformation. This increased T-wave amplitude can be explained by changes to the coupling between neighboring myocytes, also known as electrotonic effect. The thickening of the ventricular wall during repolarization contributes to the decoupling of cells in the transmural direction, enhancing action potential heterogeneity and increasing both transmural repolarization dispersion and T-wave amplitude of surface electrograms. The simulations suggest that a considerable percentage of the T-wave amplitude (15\%) may be related to cardiac deformation.},
	author = {Bernardo Lino {de Oliveira} and Luis Paulo da S {Barra} and Elson Magalh{\~a}es {Toledo} and Sundnes, Joakim and Rodrigo Weber dos {Santos}}
}
@inproceedings {Simula.sc.1170,
	title = {Biomedical and Bioinformatics Challenges to Computer Science},
	journal = {Proceedings of the International Conference on Computational Science, ICCS},
	year = {2010},
	publisher = {Elsevier},
	type = {1},
	isbn = {1877-0509},
	author = {Cannataro, Mario and Rodrigo Weber dos {Santos} and Sundnes, Joakim},
	editor = {Sloot, P.M.A. and van Albada, G.D. and Dongarra, J.}
}
@inproceedings {Simula.sc.1182,
	title = {The Development of a New Computational Model for the Electromechanics of the Human Myocyte},
	journal = {2010 Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)},
	year = {2010},
	publisher = {IEEE},
	type = {Conference},
	isbn = {978-1-4244-4124-2},
	author = {Bernardo Lino {de Oliveira} and Sundnes, Joakim and Rodrigo Weber dos {Santos}},
	editor = {Nigel Lovell et {al}}
}
@article {Simula.SC.602,
	title = {Aproaching Cardiac Modeling Challenges to Computer Science With CellMl-Based Web Tools},
	journal = {Future Generation Computer Systems},
	volume = {26},
	number = {3},
	year = {2009},
	pages = {462-470},
	publisher = {Elsevier},
	author = {Ricardo Silva {Campos} and Ronan Mendonca {Amorim} and C. M. {Costa} and Bernardo Lino {de Oliveira} and Barbosa, C. and Sundnes, Joakim and Rodrigo Weber dos {Santos}}
}
@inproceedings {Simula.sc.1164,
	title = {Bioinformatics{\textquoteright} Challenges to Computer Science: Bioinformatics Tools and Biomedical Modeling},
	journal = {Proceedings of the International Conference on Computational Science, ICCS},
	year = {2009},
	publisher = {Springer},
	type = {1},
	isbn = {978-3-642-01969-2},
	author = {Cannataro, Mario and Rodrigo Weber dos {Santos} and Sundnes, Joakim},
	editor = {Allen, G. and Nabrzyski, J. and Seidel, E. and G. D. {van Albada} and Dongarra, J. and P. M. A. {Sloot}}
}
@inproceedings {Simula.SC.598,
	title = {A Two Dimensional Model of Coupled Electromechanics in Cardiac Tissue},
	journal = {Proceedings of the World Congress on Medical Physics and Biomedical Engineering},
	year = {2009},
	publisher = {Springer},
	type = {Conference},
	isbn = {978-3-642-03881-5},
	author = {Bernardo Martins {Rocha} and Bernardo Lino {de Oliveira} and Rodrigo Weber dos {Santos} and E. T. {Magalh{\~a}es} and Luis Paulo da S {Barra} and Sundnes, Joakim},
	editor = {Schlegel, W. and D{\"o}ssel, O.}
}
@article {Simula.simula.1442,
	title = {Automatic Segmentation of Cardiac MRI Using Snakes and Genetic Algorithms},
	journal = {Lecture Notes in Computer Science},
	volume = {5103},
	number = {1},
	year = {2008},
	pages = {168-177},
	abstract = {In this work we study and implement techniques for the automatic segmentation of cardiac Magnetic Resonance Images. The methods are based on the active contours algorithm called Snakes, which are adapted and tailored to the specific task of automatic segmentation of the left ventricle of the heart in Magnetic Resonance Images. We propose a new external force to improve the convergence of the Snakes method. In addition, a genetic algorithm is used to find the best set of configuration parameters for the Snakes method. The algorithms are implemented in Java and threads are used to explore data parallelism on shared-memory machines. Tests are performed on 150 short-axis images acquired from two healthy volunteers. Preliminary results suggest the proposed methods are promising and with further development and validation may be used, for instance, for the automatic calculation of cardiac ejection fraction.},
	author = {Gustavo Miranda {Teixeira} and Igor Ramalho {Pommeranzenbaum} and Bernardo Lino {de Oliveira} and Lobosco, Marcelo and Rodrigo Weber dos {Santos}}
}
@inproceedings {Simula.sc.1168,
	title = {Bioinformatics{\textquoteright} Challenges to Computer Science},
	journal = {Proceedings of the 8th international conference on Computational Science, Part III},
	year = {2008},
	pages = {67-69},
	publisher = {Springer},
	type = {Conference},
	isbn = {978-3-540-69383-3},
	doi = {10.1007/978-3-540-69389-5\_9},
	author = {Cannataro, Mario and Romberg, Mathilde and Rodrigo Weber dos {Santos} and Sundnes, Joakim},
	editor = {Bubak, Marian and Geert Dick {van Albada} and Dongarra, Jack and Peter M.A. {Sloot}}
}
