Data and Software used for:

H. Sun, X. Fu, S. Abraham, S. Jin and R. F. Murphy (2022) Improving And Evaluating Deep Learning Models Of Cellular Organization. Bioinformatics, in press (Preprint bioRxiv 2022.05.24.493229).

Data and Software used for:

H. Sun and R. F. Murphy (2021) Evaluation of Categorical Matrix Completion Algorithms: Towards Improved Active Learning for Drug Discovery. Bioinformatics 37:3538–3545 [DOI]

Data and Software used for:

H. Sun and R. F. Murphy (2020) An Improved Matrix Completion Algorithm For Categorical Variables: Application to Active Learning of Drug Responses. Proceedings of the ICML 2020 Workshop on Real World Experiment Design and Active Learning. [PDF]

Data and Software used for:

X. Ruan, G. R. Johnson, I. Bierschenk, R. Nitschke, M. Boerries, H. Busch and R. F. Murphy (2019) Image-derived Models of Cell Organization Changes During Differentiation and Drug Treatments, Molecular Biology of the Cell, in press. (DOI)

Data and Software used for:

X. Ruan and R. F. Murphy (2019) Evaluation of methods for generative modeling of cell and nuclear shape. Bioinformatics 35:2475-2489 (DOI)

Data and Software used for:

T. Majarian, R. F. Murphy, and S. Lakdawala (2018) Learning the sequence of influenza A genome assembly during viral replication using point process models and fluorescence in situ hybridization, PLoS Computational Biology 15(1): e1006199 and bioRxiv. (DOI)

Data and Software used for:

X. Ruan, C. Wülfing, and R. F. Murphy (2017) Image-based Spatiotemporal Causality Inference for Protein Signaling Networks. Bioinformatics 33:i217-i224. (DOI)

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:

• J. Newberg and R. F. Murphy (2008). A Framework for the Automated Analysis of Subcellular Patterns in Human Protein Atlas Images. J. Proteome Res. 7:2300-2308.

Data and Software used for the paper:

• Y. Qian and R.F. Murphy. (2007). Improved Recognition of Figures containing Fluorescence Microscope Images in Online Journal Articles using Graphical Models. Bioinformatics 24:569-576.

Data and Software used for the paper:

• T. Zhao and R.F. Murphy. (2007) Automated learning of generative models for subcellular location: Building blocks for systems biology. Cytometry 71A:978-990.

Data and Software used for the paper:

• S.-C. Chen, T. Zhao, G. J. Gordon and R. F. Murphy (2007) Automated Image Analysis of Protein Localization in Budding Yeast. Bioinformatics 23:i6-i71.

Software used for the paper:

• E. Garcia Osuna, J. Hua, N.W. Bateman, T. Zhao, P.B. Berget and R.F. Murphy (2007). Large-Scale Automated Analysis of Location Patterns in Randomly Tagged 3T3 Cells. Annals Biomed. Eng. 35:1081-1087.
  

Data and Software used for the paper:

• T. Zhao, S. Soto and R. F. Murphy (2006). Improved Comparison of Subcellular Location Patterns. Proceedings of the 2006 International Symposium on Biomedical Imaging, pp. 562-565.
  

Data and Software used for the paper:

• S.-C. Chen, G. Gordon and R.F. Murphy. (2006) A Novel Approximate Inference Approach To Automated Classification Of Protein Subcellular Location Patterns In Multi-Cell Images. Proceedings of the 2006 International Symposium on Biomedical Imaging, pp. 558-561.
  

Data and Software used for the paper:

• S.-C. Chen and R.F. Murphy. (2006) A Graphical Model Approach to Automated Classification of Protein Subcellular Location Patterns in Multi-Cell Images. BMC Bioinformatics 7:90.
  

Software used for the paper:

• M.V. Boland, R.F. Murphy. (2001) A Neural Network Classifier Capable of Recognizing the Patterns of all Major Subcellular Structures in Fluorescence Microscope Images of HeLa Cells. Bioinformatics 17:1213-1223.
  

Last Updated: 17 Oct 2022

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