Publications on Generative Models of Subcellular Organization
K. T. Roybal, T. E. Buck, X. Ruan, B. H. Cho, D. J. Clark, R. Ambler, H. M. Tunbridge, J. Zhang, P. Verkade, C. Wülfing, and R. F. Murphy (2016) Computational spatiotemporal analysis identifies WAVE2 and Cofilin as joint regulators of costimulation-mediated T cell actin dynamics. Science Signaling 9:rs3.
R. F. Murphy (2016) Building cell models and simulations from microscope images. Methods 96: 33-39 (Special Issue on High-throughput Imaging).
R. M. Donovan, J.-J. Tapia, D. P. Sullivan, J. R. Faeder , R. F. Murphy , M. Dittrich, D. M. Zuckerman (2016) Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using A Weighted Ensemble Of Trajectories. PLoS Computational Biology 12: e1004611.
G. R. Johnson, J. Li, A. Shariff, G.K.Rohde, and R.F. Murphy (2015) >Automated Learning of Subcellular Pattern Variation among Punctate Proteins and of a Generative Model of their Distributions in Relation to Microtubules. PLoS Computational Biology 11: e1004614.
G. R. Johnson, T.E. Buck, D. P. Sullivan, G. R. Rohde, and R. F. Murphy (2015) Joint Modeling of Cell and Nuclear Shape Variation. Molecular Biology of the Cell 26:4046-4056 (Special Issue on Quantitative Biology).
J. Li, A. Shariff, M. Wiking, E. Lundberg, G.K. Rohde and R.F. Murphy (2012) Estimating microtubule distributions from 2D immunofluorescence microscopy images reveals differences among human cultured cell lines. PLoS ONE 7:e0050292.
T.E. Buck, J. Li, G.K. Rohde, and R.F. Murphy (2012) Towards the virtual cell: Automated approaches to building models of subcellular organization 'learned' from microscopy images. Bioessays 34:791-799.
R. F. Murphy (2012) CellOrganizer: Image-derived Models of Subcellular Organization and Protein Distribution. Methods in Cell Biology 110:179-193.
T. Peng and R.F. Murphy (2011) Image-derived, Three-dimensional Generative Models of Cellular Organization. Cytometry Part A 79A:383-391.
A. Shariff, R.F. Murphy, and G. Rohde (2011) Automated Estimation of Microtubule Model Parameters from 3-D Live Cell Microscopy Images. Proceedings of the 2011 IEEE International Symposium on Biomedical Imaging (ISBI 2011), pp. 1330-1333.
R. F. Murphy (2010) Communicating Subcellular Distributions. Cytometry Part A 77A:686-692.
A. Shariff, G. K. Rohde and R. F. Murphy (2010) A Generative Model of Microtubule Distributions, and Indirect Estimation of its Parameters from Fluorescence Microscopy Images. Cytometry 77A:457-466.
T. Peng, Wei Wang, G. K. Rohde, R. F. Murphy (2009) Instance-Based Generative Biological Shape Modeling. Proceedings of the 2009 IEEE International Symposium on Biomedical Imaging (ISBI 2009), pp. 690-693.
G.K. Rohde, W. Wang, T. Peng, and R.F. Murphy (2008). Deformation-Based Nonlinear Dimension Reduction: Applications To Nuclear Morphometry. Proceedings of the 2008 IEEE International Symposium on Biomedical Imaging (ISBI 2008), pp. 500-503.
G. K. Rohde, A. Ribeiro, K. N. Dahl, and R. F. Murphy (2008). Deformation-based nuclear morphometry: capturing nuclear shape variation in HeLa Cells. Cytometry, 73A:341-350.
T. Zhao and R.F. Murphy (2007). Automated Learning of Generative Models for Subcellular Location: Building Blocks for Systems Biology. Cytometry 71A:978-990.
Support for CellOrganizer has been provided by grants GM075205, GM090033
and GM103712 from the
National Institute of General Medical Sciences, grants MCB1121919 and MCB1121793 from the U.S. National Science Foundation,
by a Forschungspreis from the Alexander von Humboldt Foundation,
and by the Freiburg Institute for Advanced Studies.
Copyright © 2007-2015 by the Murphy Lab, Carnegie Mellon University