Simulations of Biological Systems
Multi-Physics Models of Cancer Cells
Novel Genome-Scale Correlation Between DNA Replication and RNA Transcription During the Cell Cycle in Yeast is Predicted by Data-Driven Models|
O. Alter, G.H. Golub, P.O. Brown, D. Botstein. In Proceedings of the Miami Nature Biotechnology Winter Symposium on the Cell Cycle, Chromosomes and Cancer, Vol. 15, Edited by M.P. Deutscher and S. Black and P.E. Boehmer and G. D'Urso and T. Fletcher and F. Huijing and A. Marshall and B. Pulverer and B. Renault and J.D. Rosenblatt and J.M. Slingerland and W.J. Whelan, 2004.
|Integrative Analysis of Genome-Scale Data by Using Pseudoinverse Projection Predicts Novel Correlation Between DNA Replication and RNA Transcription,
O. Alter, G.H. Golub. In Proceedings of the National Academy of Sciences, Vol. 101, No. 47, Proceedings of the National Academy of Sciences, pp. 16577--16582. November, 2004.
Biomedical Computing and Visualization Software Environments|
C.R. Johnson, R.S. MacLeod, S.G. Parker, D.M. Weinstein. In Comm. ACM, Vol. 47, No. 11, pp. 64--71. 2004.
Influence of Head Tissue Conductivity in Forward and Inverse Magnetoencephalographic Simulations Using Realistic Head Models|
R. Van Uitert, C.R. Johnson, L. Zhukov. In IEEE Trans Biomed. Eng., Vol. 51, No. 12, pp. 2129--2137. 2004.
Three-dimensional Propagation in Mathematic Models: Integrative Model of the Mouse Heart|
C.S. Henriquez, J.V. Tranquillo, D.M. Weinstein, E.W. Hsu, C.R. Johnson. In Cardiac Electrophysiology: From Cell to Bedside, 4th edition, Ch. 30, Edited by D.P. Zipes and J. Jalife, Saunders, pp. 273--281. 2004.
A Software Framework for Solving Problems of Bioelectricity Applying High-Order Finite Elements|
M. Cole, F.B. Sachse, D.M. Weinstein, S.G. Parker, R.M. Kirby. In Proceedings of the IEEE Engineering in Medicine and Biology Society 26th Annual International Conference, Vol. 1, pp. 821--824. 2004.
Generalized Singular Value Decomposition for Comparative Analysis of Genome-Scale Expression Datasets of Two Different Organisms|
O. Alter, P.O. Brown, D. Botstein. In Proceedings of the National Academy of Sciences, Vol. 100, No. 6, Proceedings of the National Academy of Sciences, pp. 3351--3356. March, 2003.
Volume Currents in Forward and Inverse Magnetoencephalographic Simulations Using Realistic Head Models|
R. Van Uitert, D. Weinstein, C.R. Johnson. In Annals of Biomedical Engineering, Vol. 31, pp. 21--31. 2003.
Minimum Support MEG (Magnetoencephalography) Imaging: Study on Effects of Noise, Discretization, Depth, and Separation of Multiple Sources|
D. Hwang, O. Portniaguine, S. Nagarajan, C.R. Johnson, K. Sekihara. In World Congress on Medical Physics and Biomedical Engineering, August, 2003.
Influence of Brain Conductivity on Magnetoencephalographic Simulations in Realistic Head Models|
R. Van Uitert, C.R. Johnson. In The 25th Annual International Conference of the IEEE Engineering In Medicine And Biology Society, Vol. 3, pp. 2136--2139. September, 2003.
BioPSE Case Study: Modeling, Simulation, and Visualization of Three Dimensional Mouse Heart Propagation|
D.M. Weinstein, J.V. Tranquillo, C.S. Henriquez, C.R. Johnson. In International Journal of Bioelectromagnetism, Vol. 5, No. 1, pp. 314--315. 2003.
|Molecular Characterisation of Soft Tissue Tumours: a Gene Expression Study,
T. Nielsen, R.B. West, S.C. Linn, O. Alter, M.A. Knowling, J. O'Connell, S. Zhu, M. Fero, G. Sherlock, J.R. Pollack, P.O. Brown, D. Botstein, M. van de Rijn. In Lancet, Vol. 359, No. 9314, pp. 1301–-1307. April, 2002.
Performance of a Minimum-Support Imaging Method for Biomagnetic Source Localization|
S.S. Nagarajan, O. Portniaguine, K. Sekihara, D. Hwang, C.R. Johnson. In Proceedings of the IEEE Engineering in Medicine and Biology Society 24th Annual International Conference, Houston, Vol. 3, pp. 2006-2007. October, 2002.
Can a Spherical Model Substitute for a Realistic Head Model in Forward and Inverse MEG Simulations?|
R. Van Uitert, C.R. Johnson. In Proceedings of The 13th International Conference on Biomagnetism, Jena, Germany, August, 2002.
Modeling and Simulation in Medicine: Towards an Integrated Framework|
G. Higgins, B. Athey, J. Bassingthwaighte, J. Burgess, H. Champion, K. Cleary, P. Dev, J. Duncan, M. Hopmeier, D. Jenkins, C.R. Johnson, H. Kelly, R. Leitch, W. Lorensen, D. Metaxas, V. Spitzer, N. Vaidehi, K. Vosburgh, R. Winslow. In Computer Aided Surgery, Vol. 6, No. 1, Note: Final report of the meeting of the same title held July 20-21, 2000, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA., 2001.
|Quantum Measurement of a Single System,
O. Alter, Y. Yamamoto. Wiley-Blackwell, May, 2001.
|Processing and Modeling Genome-Wide Expression Data Using Singular Value Decomposition,
O. Alter, P.O. Brown, D. Botstein. In Microarrays: Optical Technologies and Informatics, Vol. 4266, Edited by M.L. Bittner and Y. Chen and A.N. Dorsel and E.R. Dougherty (International Society for Optical Engineering Bellingham), pp. 171--186. 2001.
Multilevel Methods for Inverse Bioelelectric Field Problems|
C.R. Johnson, M. Mohr, U. Ruede, A. Samsonov, K. Zyp. In Lecture Notes in Computational Science and Engineering - Multiscale and Multiresolution Methods: Theory and Applications, Vol. 20, Edited by T.J. Barth and T.F. Chan and R. Haimes, Springer-Verlag Publishing, Heidelberg pp. 331--346. October, 2001.
Finite Element EEG and MEG Simulations for Realistic Head Models: Quadratic vs. Linear Approximations|
R. Van Uitert, D. Weinstein, C.R. Johnson, L. Zhukov. In Biomed. Technik, Vol. 46, pp. 32--34. 2001.
Computational Bioimaging for Medical Diagnosis and Treatment|
C.R. Johnson. In Communications of the ACM, Vol. 44, No. 3, pp. 74--76. March, 2001.