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Murphy Lab - Software - Software from papers


Data and Software for the following paper will be available here shortly:

    Y. Li, T. D. Majarian, A. W. Naik, G. R. Johnson, and R. F. Murphy (2016) Point process models for localization and interdependence of punctate cellular structures. Cytometry Part A 89:633-643. (DOI)

Data and Software used for:

    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.

Data and Software used for:

    A.W. Naik, J.D. Kangas, D. P. Sullivan, and R. F. Murphy (2016) Active Machine Learning-driven Experimentation to Determine Compound Effects on Protein Patterns, eLife 5:e10047. (DOI)

Data and Software used for:

    G. R. Johnson, J. Li, A. Shariff, G.K.Rohde, and R.F. Murphy (2015) Automated Learning of Subcellular Variation among Punctate Protein Patterns and a Generative Model of their Relation to Microtubules. PLoS Computational Biology 11(12): e1004614.

Data and Software used for:

    G. R. Johnson, T. E. Buck, D. P. Sullivan, G. K. Rohde, and R. F. Murphy (2015) Joint modeling of cell and nuclear shape variation. Molecular Biology of the Cell 26: 4046-4056. (DOI)

Data and Software used for:

    M. Temerinac-Ott, A. W. Naik, and R. F. Murphy (2015) Deciding when to stop: Efficient experimentation to learn to predict drug-target interactions. BMC Bioinformatics 16:213.

Data and Software used for:

    A. W. Naik, J. D. Kangas, C. J. Langmead, and R. F. Murphy (2013) Efficient Modeling and Active Learning Discovery of Biological Responses. PLoS ONE 8: e83996.

Data and Software used for:

    L. P. Coelho, J. D. Kangas, A. Naik, E. Osuna-Highley, E. Glory-Afshar, M. Fuhrman, R. Simha, P. B. Berget, J. W. Jarvik, and R. F. Murphy (2013) Determining the subcellular location of new proteins from microscope images using local features. Bioinformatics 29:2343-2349.

Data and Software used for:

    J. Li, J.Y. Newberg, M. Uhlen, E. Lundberg, and R.F. Murphy (2012) Automated Analysis and Reannotation of Subcellular Locations in Confocal Images from the Human Protein Atlas. PLoS ONE 7:e0050514.

Data and Software used for:

    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.

Data and Software used for:

    B.H. Cho, I. Cao-Berg, J.A. Bakal, and R.F. Murphy (2012) OMERO.searcher: Content-based image search for microscope images. Nature Methods 9:633-634.

Data and Software used for:

    J. Li, L. Xiong, J. Schneider and R. F. Murphy (2012) Protein Subcellular Location Pattern Classification in Cellular Images Using Latent Discriminative Models. Proceedings of ISMB 2012.

Data and Software used for:

    C. Jackson, E. Glory, R. F. Murphy and J. Kovacevic (2011) Model building and intelligent acquisition with application to protein subcellular location classification. Bioinformatics 27:1854-1859.

Data and Software used for:

    T. Peng and R.F. Murphy (2011) Image-derived, Three-dimensional Generative Models of Cellular Organization. Cytometry Part A 79A:383-391.

Data and Software used for the paper:

    T. Lin, Z. Bar-Joseph, and R. F. Murphy (2011) Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs. Lecture Notes in Bioinformatics (Proceedings of RECOMB 2011) 6577:204-221.

Data and Software used for the paper:

    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.

Data and Software used for the paper:

    T. Lin, R.F. Murphy, and Z. Bar-Joseph (2010) Discriminative Motif Finding for Predicting Protein Subcellular Localization. IEEE/ACM Transactions on Computational Biology and Bioinformatics 8:441-451.

Data and Software used for the paper:

    Y. Hu, E. Garcia Osuna, J. Hua, J. Carmona, T. S. Nowicki, R. Stolz, C. McKayle and R. F. Murphy (2010) Automated Analysis of Protein Subcellular Locations in Time Series Images. Bioinformatics 26:1630-1636.

Data and Software used for the paper:

    L. P. Coelho, T. Peng, and R. F. Murphy (2010) Quantifying the distribution of probes between subcellular locations using unsupervised pattern unmixing. Bioinformatics 26:i7-i12.

Data and Software used for the paper:

    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 Part A 77A:457-466.

Data and Software used for the paper:

    T. Peng, G.M.C. Bonamy, E. Glory, D. Rines, S. K. Chanda, and R. F. Murphy (2010) Automated Unmixing Of Subcellular Patterns: Determining the Distribution of Probes Between Different Subcellular Locations. Proc. Natl. Acad. Sci. U.S.A. 107:2944-2949.

Data and Software used for

  • T. E. Buck, A. Rao, L. P. Coelho, M. Fuhrman, J. W. Jarvik, P. B. Berget, and R. F. Murphy (2009) Protein Localization Dependence on Cell Cycle Inferred from Static, Asynchronous Images. Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society, pp. 1016-1019.

Software used for:

  • C. Jackson, R. F. Murphy, and J. Kovacevic (2009) Intelligent Acquisition and Learning of Fluorescence Microscope Data Models. IEEE Trans Image Proc. 18:2071-2084.

Data and Software used for the paper:

  • L.P. Coelho, A. Shariff and R. F. Murphy (2009). Nuclear segmentation in microsope cell images: A hand-segmented dataset and comparison of algorithms. Proceedings of the 2009 IEEE International Symposium on Biomedical Imaging (ISBI 2009), pp. 518-521.

Data and Software used for:

  • J. H. Boysen, S. Fanning, J. Newberg, R. F. Murphy, and A. P. Mitchell (2009). Detection of protein-protein interactions through vesicle targeting. Genetics 181:33-39.

Data and Software used for the paper:

Data and Software used for the paper:

Data and Software used for the paper:

Data and Software used for the paper:

Software used for the paper:

Data and Software used for the paper:

Data and Software used for the paper:

Data and Software used for the paper:

Software used for the paper:




Last Updated: 23 Feb 2017




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