Carnegie Mellon
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SUREBET summer program

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Jelena Kovacevic and Robert F. Murphy, Directors

Research Publications

supported by NSF ITR grant EF-0331657

supported by NIH grant GM068845

supported by Pennsylvania Tobacco Settlement Fund grant 017393

supported by Pennsylvania Tobbaco Settlement Fund Kamlet-Smith Bioinformatics Grant

A. K. Singh, B.S. Manjunath, and R. F. Murphy (2004) A Distributed Database for Bio-Molecular Images. SIGMOD Record 33(2).

X. Chen and R. F. Murphy (2004) Robust Classification of Subcellular Location Patterns in High Resolution 3D Fluorescence Microscope Images. Proceedings of the 26th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, pp. 1632-1635.

X. Chen and R. F. Murphy (2004). Location Proteomics: Determing the Optimal Groupings of Proteins according to their Subcellular Location Patterns as determined from Fluorescence Microscope Images. Proceedings of the 38th Asilomar Conference on Signals, Systems and Computers, pp. 50-54.

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X. Chen and R. F. Murphy (2005). Automated interpretation of protein subcellular location. Biophotonics Intl 12(3):34-35.

P. Hennings Yeomans, J. Thornton, J. Kovačević and B.V.K.V. Kumar (2005) Wavelet packet correlation methods in biometrics, Applied Optics, 44:637-646.

T.E. Merryman Jr., J. Kovacevic, R. F. Murphy, and E. Garcia Osuna (2005). Adaptive Multirate Data Acquisition of 3D Cell Images. Proceedings of ICASSP 2005, pp. II-133-136.

J.T. Thornton, P. Hennings Yeomans, J. Kovačević and B.V.K.V. Kumar (2005) Wavelet packet correlation methods in biometrics. Proceedings of ICASSP 2005, pp. II:81-84.

A. Jacquin, E. Causevic, E.R. John and J. Kovačević (2005) Adaptive complex wavelet-based filtering of EEG for extraction of evoked potential responses. Proceedings of ICASSP 2005, pp. V:393-396.
M. Pueschel and J. Kovačević (2005) Real, Tight Frames with Maximal Robustness to Erasures. Proc. Data Compr. Conf., pp. 63-72.

R.F. Murphy (2005). Location Proteomics: A Systems Approach to Subcellular Location. Biochem. Soc. Trans. 33:535-538. [Article at journal web site]

X. Chen and R. F. Murphy (2005). Objective Clustering of Proteins Based on Subcellular Location Patterns. J. Biomed. Biotech. 2005(2):87-95. [Article at journal web site]

Z. Kou, W.W. Cohen and R.F. Murphy (2005). High-recall protein entity recognition using a dictionary. Bioinformatics 21(suppl_1):i266-i273. [Article at journal web site]

P. Nair, B.E. Schaub, K. Huang, X. Chen, R.F. Murphy, J.M. Griffith, H.J. Geuze, and J. Rohrer (2005). Characterization of the TGN Exit Signal of the human Mannose 6-Phosphate Uncovering Enzyme. J. Cell Sci. 118:2949-2956. [Article at journal web site]

R.F. Murphy (2005). Location Proteomics: Providing Critical Information for systems Biology. Bioforum Europe, 2005/04.

R.F. Murphy (2005). Location Proteomics. GIT Imaging & Microscopy, 2005/02.

T. Merryman and J. Kovacevic (2005). An adaptive multirate algorithm for acquisition of fluorescence microscopy data sets. IEEE Trans. Image Proc. 14:1351-1359

T. Zhao, M. Velliste, M.V. Boland, and R.F. Murphy (2005). Object Type Recognition for Automated Analysis of Protein Subcellular Location. IEEE Trans. Image Proc. 14:1351-1359

R.F. Murphy (2005). Cytomics and Location Proteomics: Automated Interpretation of Subcellular Patterns in Fluorescence Microscope Images. Cytometry 67A:1-3

A. Bhattacharya, V. Ljosa, J.-Y. Pan, M. Verardo, H. Yang, C. Faloutsos and A. Singh (2005). ViVo: Visual Vocabulary Construction for Mining Biomedical Images. Proceedings of ICDM.

G. Valet, R.F. Murphy, J.P. Robinson, A. Tarnok and A. Kriete (2006). Cytomics - from cell states to predictive medicine. In: Computational Systems Biology (A. Kriete and R. Eils, eds.), pp. 363-381.

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. [Article at journal web site]

T. Zhao and R.F. Murphy (2006). Automated Interpretation of Subcellular Location Patterns from Three Dimensional Confocal Microscopy. In: Handbook of Biological Confocal Microscopy, Third Edition (J.W. Pawley, ed.), pp. 818-828.

X. Chen, and R.F. Murphy (2006). Automated Interpretation of Protein Subcellular Location Patterns. International Review of Cytology 249:193-227.

T. Merryman, K. Williams, G. Srinivasa, A. Chebira and J. Kovacevic (2006). A multiresolution enhancement to generic classifiers of subcellular protein location images. Proceedings of the IEEE International Symposium on Biomedical Imaging (ISBI 2006), pp. 570-573.

L. Coulot, H. Kirschner, A. Chebira, J.M.F. Moura, J. Kovacevic, E. Garcia Osuna, and R.F. Murphy (2006). Topology Preserving STACS Segmentation of Protein Subcellular Location Images. Proceedings of the IEEE International Symposium on Biomedical Imaging (ISBI 2006), pp.566-569

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

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 IEEE International Symposium on Biomedical Imaging (ISBI 2006), pp. 558-561.

Y. Hu, J. Carmona, and R.F. Murphy (2006). Application of Temporal Texture Features to Automated Analysis of Protein Subcellular Locations in Time Series Fluorescence Microscope Images. Proceedings of the IEEE International Symposium on Biomedical Imaging (ISBI 2006), pp. 1028-1031

Y.-L. Wang, K.M. Hahn, R.F. Murphy, and A.F. Horwitz (2006). From imaging to understanding: Frontiers in Live Cell Imaging, Bethesda, MD April19-21, 2006 [Meeting Review]. J. Cell. Biol. 174:1-4.

R.F. Murphy (2006). Putting proteins on the map [News andViews]. Nature Biotech. 24:1223-1224.

G. Srinivasa, T. Merryman, A. Chebira, A. Mintos and J. Kovacevic (2006). Adaptive multiresolution techniques for subcellular protein location image classification. Proceedings of IEEE Intl. Conf. Acoustic, Speech and Signal Processing (ICASSP 2006), pp. 1177-1180.

J. Kovačević and M. Pueschel (2005) Sampling Theorems for Trigonometric Transforms. Proceedings of IEEE Intl. Conf. Acoustic, Speech and Signal Processing (ICASSP 2006) pp. 357-360.

X. Chen, M. Velliste, and R.F. Murphy (2006). Automated Interpretation of Subcellular Patterns in Fluorescence Microscope Images for Location Proteomics. Cytometry 69A:631-640.

S.-C. Chen, T. Zhao, G.J. Gordon and R.F. Murphy (2006).A Novel Graphical Model Approach to Segmenting Cell Images.Proceedings of the 2006 IEEE Symposium on Computational Intelligence inBioinformatics and Computational Biology (CIBCB '06), 1079.

Z. Kou, W. W. Cohen, and R.F. Murphy (2007). A Stacked Graphical Model for Associating Information from Text and Images inFigures. Pacific Symposium on Biocomputing 12:257-268.[Article at conference web site]
E. Glory and R.F. Murphy (2007). Automated Subcellular Location Determination and High Throughput Microscopy.Developmental Cell 12:7-16.[Article at journal web site] [Email Dr. Murphy to request PDF]

X. Chen and R. F. Murphy (2007). Interpretation of Protein Subcellular Location Patterns in 3D Images AcrossCell Types and Resolutions. Lecture Notes in Bioinformatics 4414:328-342.

R.F. Murphy (2007). Systematic Description Of Subcellular Location ForIntegration With Proteomics Databases And Systems Biology Modeling. Proceedingsof the 2007 IEEE International Symposium on Biomedical Imaging (ISBI 2007),pp. 1052-1055.

J. Hua, O.N. Ayasli, W.W. Cohen, and R.F. Murphy (2007). IdentifyingFluorescence Microscope Images in Online Journal Articles Using Both Image andText Features. Proceedings of the 2007 IEEE International Symposium onBiomedical Imaging (ISBI 2007), pp. 1224-1227.

K. Huang, J.H. Henson, J.E. Davis, and R.F. Murphy (2007). Computational Analysis of Confocal Fluorescence Microscopy Images Using the Protein Subcellular Location Image Database (PSLID). In: Confocal Microscopy Methods and Protocols: Second Edition (S. W. Paddock, ed.), in press.