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BOOKS

1. Applications of Fluorescence in the Biomedical Sciences (1986) D. L. Taylor, A. S. Waggoner, R. F. Murphy, F. Lanni, R. Birge (eds.), Alan R. Liss, Inc., New York.

2. Endosomes and Lysosomes: A Dynamic Relationship (1993) B. Storrie and R. F. Murphy (eds.), JAI Press.

PUBLICATIONS

1. R. F. Murphy and J. Bonner (1975). Alkaline Extraction of Non-Histone Proteins from Rat Liver Chromatin. Biochim. Biophys. Acta 405:62-66.

2. J. M. Gottesfeld, R. F. Murphy and J. Bonner (1975). Structure of Transcriptionally Active Chromatin. Proc. Natl. Acad. Sci. USA 72:4404-4408.

3. R. B. Wallace, T. D. Sargent, R. F. Murphy and J. Bonner (1977). Physical Properties of Chemically Acetylated Rat Liver Chromatin. Proc. Natl. Acad. Sci. USA 74:3244-3248.

4. J. Bonner, R. B. Wallace, T. D. Sargent, R. F. Murphy and S. K. Dube (1977). The Expressed Portion of Eukaryotic Chromatin. Cold Spring Harbor Symp. Quant. Biol. 42:851-857.

5. R. F. Murphy, R. B. Wallace and J. Bonner (1978). Altered Nucleosome Spacing in Newly Replicated Chromatin from Friend Leukemia Cells. Proc. Natl. Acad. Sci. USA 75:5903-5907.

6. R. B. Wallace, J. Schaeffer, R. F. Murphy, T. Hirosa, K. Itakura and J. Bonner (1979). Hybridization of Synthetic Oligodeoxyribonucleotides to fX174 DNA: The Effect of Single Base Pair Mismatch. Nucleic Acids Res. 6:3543-3557.

7. R. F. Murphy, W. R. Pearson and J. Bonner (1979). Computer Programs for Analysis of Nucleic Acid Hybridization, Thermal Denaturation and Gel Electrophoresis Data. Nucleic Acids Res. 6:3911-3921.

8. R. F. Murphy, R. B. Wallace and J. Bonner (1980). Isolation of Newly-Replicated Chromatin by Using Shallow Metrizamide Gradients. Proc. Natl. Acad. Sci. USA 77:3336-3340.

9. R. F. Murphy (1980). Chromosomal Protein-DNA Interactions. Doctoral Thesis. California Institute of Technology.

10. R. F. Murphy, J. R. Daban and C. R. Cantor (1981). Flow Cytofluorometric Analysis of the Nuclear Division Cycle of Physarum Polycephalum Plasmodia. Cytometry 2:26-30.

11. R. F. Murphy, E. D. Jorgensen and C. R. Cantor (1982). Kinetics of Histone Endocytosis in Chinese Hamster Ovary Cells: A Flow Cytofluorometric Analysis. J. Biol. Chem. 257:1695-1701.

12. R. F. Murphy, S. Powers, M. Vderame, C. R. Cantor and R. Pollack (1982). Flow Cytofluorometric Analysis of Insulin Binding and Internalization by Swiss 3T3 Cells. Cytometry 2:402-406.

13. R. Haas, R. F. Murphy and C. R. Cantor (1982). Testing Models of the Arrangement of DNA Inside Bacteriophage Lambda by Crosslinking the Packaged DNA. J. Mol. Biol. 159:71-92.

14. P. L. McNeil, R. F. Murphy, F. Lanni and D. L. Taylor (1984). A Method for Incorporating Macromolecules into Adherent Cells. J. Cell Biol. 98:1556-1564.

15. R. F. Murphy, S. Powers and C. R. Cantor (1984). Endosome pH Measured in Single Cells by Dual Fluorescence Flow Cytometry: Rapid Acidification of Insulin to pH 6. J. Cell Biol. 98:1757-1762.

16. R. F. Murphy, S. Powers, C. R. Cantor and R. Pollack (1984). Reduced Insulin Endocytosis in Serum Transformed Fibroblasts Demonstrated by Flow Cytometry. Cytometry 5:275-280.

17. W. Hiddemann, J. Schumann, M. Andreeff, B. Barlogie, C. J. Herman, R. C. Leif, B. H. Mayall, R. F. Murphy, A. A. Sandberg (1984). Convention on Nomenclature for DNA Cytometry. Cytometry 5:445-446.

18. R. F. Murphy and T. M. Chused (1984). A Proposal for a Flow Cytometric Data File Standard. Cytometry 5:553-555.

19. R. F. Murphy, D. B. Tse, C. R. Cantor and B. Pernis (1984). Acidification of Internalized Class I MHC Antigen by T Lymphoblasts. Cell. Immunol. 88:336-342.

20. R. F. Murphy, E. Bisaccia, C. R. Cantor, C. Berger and R. L. Edelson (1984). Internalization and Acidification of Insulin by Activated Human Lymphocytes. J. Cell. Physiol. 121:351-356.

21. P. L. Wollenzien, C. F. Hui, C. Kang, R. F. Murphy and C. R. Cantor (1984) RNA structure, Free and on the Ribosome, as Revealed by Chemical and Enzymatic Studies. In: Mechanisms of Protein Synthesis, Bermek, (ed.), Springer-Verlag, Berlin.

22. P. L. McNeil, A. L. Kennedy, A. S. Waggoner, D. L. Taylor and R. F. Murphy (1985). Light Scattering Changes During Chemotactic Stimulation of Human Neutrophils: Kinetics Followed by Flow Cytometry. Cytometry 6:7-12.

23. R. F. Murphy (1985). Automatic Identification of Subpopulations in Flow Cytometric List Mode Data Using Cluster Analysis. Cytometry 6:302-309.

24. P. L. Wollenzien, R. F. Murphy, C. R. Cantor, A. Expert-Bezancon and D. H. Hayes (1985). Structure of the E. coli 16S rRNA. Psoralen Crosslinks and N-Acetyl-N'-(p-Glyoxylylbenzoyl) Cystamine Crosslinks Detected by Electron Microscopy. J. Mol. Biol. 184:67-80.

25. C. R. Cantor, D. B. Tse, J. McDowell, R. Murphy, and B. Pernis (1985). Internalization of Histocompatibility Antigens Studied by Flow Cytometry. In: Cell Biology of the Major Histocompatibility Complex, B. Pernis & H. J. Vogel (eds.), Academic Press, New York, pp. 165-172.

26. R. F. Murphy (1985). Analysis and Isolation of Endocytic Vesicles by Flow Cytometry and Sorting: Demonstration of Three Kinetically Distinct Compartments Involved in Fluid-Phase Endocytosis. Proc. Natl. Acad. Sci. USA 82:8523-8526.

27. M. Fechheimer, C. Denny, R. F. Murphy, and D. L. Taylor (1986).Measurement of cytoplasmic pH in Dictyostelium discoideum by using a new method for introducing macromolecules into living cells. Eur. J. Cell Biol. 40:242-247.

28. R. F. Murphy (1986). Flow Cytometry in Cell Biology. In: Applications of Fluorescence in the Biomedical Sciences, D. L. Taylor, A. S. Waggoner, R. F. Murphy, F. Lanni, R. Birge (eds.), Alan R. Liss, Inc., New York, pp. 525-530.

29. R. F. Murphy and M. Roederer (1986). Flow Cytometric Analysis of Endocytic Pathways. In: Applications of Fluorescence in the Biomedical Sciences, D. L. Taylor, A. S. Waggoner, R. F. Murphy, F. Lanni, R. Birge (eds.), Alan R. Liss, Inc., New York, pp. 545-566.

30. C. C. Cain and R. F. Murphy (1986). Growth Inhibition of 3T3 Fibroblasts by Lysosomotropic Amines: Correlation with Effects on Intravesicular pH but Not Vacuolation. J. Cell. Physiol. 129:65-70.

31. M. Roederer and R. F. Murphy (1986). Cell-By-Cell Autofluorescence Correction for Low Signal-to-Noise Systems: Application to EGF Endocytosis by 3T3 Fibroblasts. Cytometry 7:558-565.

32. M. Roederer, R. Bowser, and R. F. Murphy (1987). Kinetics and Temperature Dependence of Exposure of Endocytosed Material to Proteolytic Enzymes and Low pH: Evidence for a Maturation Model for the Formation of Lysosomes. J. Cell. Physiol. 131:200-209.

33. S. Taylor, M. Roederer, and R. F. Murphy (1987). Flow Cytometric DNA Analysis of Adrenocortical Tumors in Children. Cancer 59:2059-2063.

34. D. M. Sipe and R. F. Murphy (1987). High resolution kinetics of transferrin acidification in Balb/c 3T3 cells: Exposure to pH 6 followed by temperature-sensitive alkalinization during recycling. Proc. Natl. Acad. Sci. USA 84:7119-7123.

35. R. A. Preston, R. F. Murphy, and E. W. Jones (1987). Apparent Endocytosis of FITC-Dextran by Saccharomyces cerevisiae Reflects Uptake of Low Molecular Weight Impurities, not Dextran. J. Cell Biol. 105:1981-1987.

36. C. C. Cain and R. F. Murphy (1988). A Chloroquine-resistant Swiss 3T3 Cell Line with a Defect in Late Endocytic Acidification. J. Cell Biol. 106:269-277.

37. S. Taylor, J. Blatt, J. Costantino, M. Roederer, and R. F. Murphy (1988). Flow Cytometric DNA Analysis of Neuroblastoma and Ganglioneuroma: a 10-year Retrospective Study. Cancer 62:749-754.

38. R. F. Murphy (1988). Processing of Endocytosed Material. Adv. Cell Biol. 2:159-180.

39. C. C. Cain, D. M. Sipe and R. F. Murphy (1989). Regulation of Endocytic pH by the Na⁺ /K⁺-ATPase in Living Cells. Proc. Natl. Acad. Sci. USA 86:544-548.

40. M. Roederer, R. W. Mays and R. F. Murphy (1989). Effect of Confluence on Endocytosis by 3T3 Fibroblasts: Increased Rate of Pinocytosis and Accumulation of Residual Bodies. Eur. J. Cell Biol. 48:37-44.

41. C. R. Abramowsky, S. R. Taylor, A. H. Anton, A. Berk, M. Roederer and R. F. Murphy (1989). Flow Cytometry DNA Ploidy Analysis and Catecholamine Secretion Profiles in Neuroblastoma. Cancer 63:1752-1756.

42. R. B. Wilson and R. F. Murphy (1989). Flow Cytometric Analysis of Endocytic Compartments. Methods Cell Biol. 31:293-317.

43. R. F. Murphy (1989). Flow Cytometric Analysis of Ligand Binding and Endocytosis. In: Microspectrofluorometry of Single Cells, E. Kohen and J. G. Hirschberg (eds.), Academic Press, New York, pp. 363-376.

44. R. F. Murphy, M. Roederer, D. M. Sipe, C. Cain, and R. Bowser (1989). Determination of the Biochemical Characteristics of Endocytic Compartments by Flow Cytometric and Fluorometric Analysis of Cells and Organelles. In: Flow Cytometry: Advanced Research and Clinical Applications, Volume II, A. Yen (ed.), CRC Press, Boca Raton, FL, pp. 221-254.

45. R. A. Preston, R. F. Murphy and E. W. Jones (1989). Assay of Vacuolar pH in Yeast and Identification of Acidification-defective Mutants. Proc. Natl. Acad. Sci. USA 86:7027-7031.

46. R. F. Murphy (1990). Ligand Binding, Endocytosis, and Processing. In: Flow Cytometry and Sorting, Second Edition, M. R. Melamed, T. Lindmo, M. L. Mendelsohn (eds.), Wiley-Liss, Inc., New York, pp. 355-366.

47. R. Bowser and R. F. Murphy (1990). Kinetics of Hydrolysis of Endocytosed Substrates by Mammalian Cultured Cells: Early Introduction of Lysosomal Enzymes into the Endocytic Pathway. J. Cell. Physiol. 143:110-117.

48. M. Roederer, J. Barry, R. B. Wilson and R. F. Murphy (1990). Endosomes Can Undergo an ATP-dependent Density Increase in the Absence of Dense Lysosomes. Eur. J. Cell Biol. 51:229-234.

49. P. N. Dean, C. B. Bagwell, T. Lindmo, R. F. Murphy, and G. C. Salzman (1990). Data File Standard for Flow Cytometry. Cytometry 11:323-332.

50. D. M. Sipe, A. Jesurum and R. F. Murphy (1991). Absence of Na⁺,K⁺-ATPase Regulation of Endosomal pH in K562 Erythroleukemia Cells: Analysis via Inhibition of Transferrin Recycling by Low Temperatures. J. Biol. Chem. 266:3469-3474.

51. D. M. Sipe and R. F. Murphy (1991). Binding to Cellular Receptors Results in Increased Iron Release from Transferrin at Mildly Acidic pH. J. Biol. Chem. 266:8002-8007. [Copy as Word 97/98 document: high-resolution (1.5 MB) low-resolution (856 KB)]

52. C. C. Cain, R. B. Wilson and R. F. Murphy (1991). Isolation by Fluorescence-Activated Cell Sorting of Chinese Hamster Ovary Cell Lines with Pleiotropic, Temperature-Conditional Defects in Receptor Recycling. J. Biol. Chem. 266:11746-11752.

53. R. F. Murphy (1991). Maturation Models for Endosome and Lysosome Biogenesis. Trends Cell Biol. 1:77-82.

54. R. F. Murphy, M. Roederer, D. M. Sipe, C. C. Cain and R. B. Wilson (1992). Endosomal pH Regulation and the Maturation Model for Lysosome Biogenesis. In: Endocytosis: From Cell Biology to Health, Disease and Therapy (Proceedings of the NATO Advanced Research Workshop on Endocytosis), P. J. Courtoy (ed.), NATO ASI Series H, Vol. 62, Springer Verlag, pp. 91-95.

55. R. E. Valdes-Perez, H. A. Simon, and R. F. Murphy (1992) Discovery of pathways in science. In: Proceedings of the ML92 Workshop on Machine Discovery, J. Zytkow (ed.), Aberdeen, Scotland, pp. 51-57.

56. R. F. Murphy (1992) Scatchard analysis by flow cytometry. In: Flow Cytometry and Cell Sorting, A. Radbruch (ed.), Springer Verlag, Berlin, pp. 59-62.

57. R. F. Murphy (1992) Ligand acidification by non-adherent cells. In: Flow Cytometry and Cell Sorting, A. Radbruch (ed.), Springer Verlag, Berlin, pp. 124-129.

58. S. A. Brockman and R. F. Murphy (1993) Endosomal and Lysosomal Hydrolases. In: Biological Barriers to Protein Delivery (Pharmaceutical Biotechnology, Vol. 4), K. L. Audus and T. J. Raub (eds.), Plenum Press, New York, pp. 51-70.

59. R. F. Murphy (1993) Models of Endosome and Lysosome Traffic. Adv. Cell Mol. Biol. Memb. 1:1-17.

60. R. F. Murphy, J. Schmid and R. Fuchs (1993) Endosome maturation: Insights from somatic cell genetics and cell-free analysis. Biochem. Soc. Trans. 21:716-720.

61. R. B. Wilson, C. C. Mastick and R. F. Murphy (1993). A Chinese Hamster Ovary Cell Line with a Temperature-Conditional Defect in Receptor Recycling is Pleiotropically Defective in Lysosome Biogenesis. J. Biol. Chem. 268:25357-25363.

62. M. Bucci, T. W. Moyer, C. M. Brown, R. B. Wilson and R. F. Murphy (1994). The receptor-recycling and lysosome biogenesis mutant TfT1.11 belongs to a new complementation group, End6. Somatic Cell Mol. Genet. 20:47-54.

63. S. A. Brockman and R. F. Murphy (1994). Isolation and Analysis of Somatic Cell Mutants with Defects in Endocytic Traffic. Methods Cell Biol. 42:131-148.

64. L.C. Seamer, C.B. Bagwell, L. Barden, D. Redelman, G.C. Salzman, J.C. Wood, R.F. Murphy (1997). Proposed new data file standard for flow cytometry, version FCS 3.0. Cytometry 28:118-122.

65. S. L. Rybak, F. Lanni and R. F. Murphy (1997). Theoretical considerations on the role of membrane potential in the regulation of endosomal pH. Biophys. J. 73:674-687. [Article at BJ web site] [Project Description]

66. M. V. Boland, M. K. Markey and R. F. Murphy (1997) Automated Classification of Cellular Protein Localization Patterns Obtained via Fluorescence Microscopy. Proceedings of the 19th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, pp. 594-597. [Project Description]

67. M. V. Boland and R. F. Murphy (1998) Multivariate Analysis. In: Current Protocols in Cytometry, pp. 10.8.1-10.8.21.

68. S. L. Rybak and R. F. Murphy (1998) Primary Cell Cultures from Murine Kidney and Heart Differ in Endosomal pH. J. Cell. Physiol. 176:216-222.

69. M. V. Boland, M. K. Markey and R. F. Murphy (1998) Automated Recognition of Patterns Characteristic of Subcellular Structures in Fluorescence Microscopy Images. Cytometry 33: 366-375. [Project Description] [Dataset Download]

70. N. Bayer, D. Schober, E. Prchla, R. F. Murphy, D. Blass, and R. Fuchs (1998) Effect of bafilomycin A1 and nocodazole on endocytic transport in HeLa cells: Implications for viral uncoating and infection. J. Virol. 72: 9645-55.

71. D. Schober, N. Bayer, R.F. Muphy, E. Wagner, and R. Fuchs (1999). Establishment of an assay to determine adenovirus-induced endosome rupture required for receptor-mediated gene delivery. Gene Therapy Mol. Biol. 3:1-9.

72. M. K. Markey, M. V. Boland and R. F. Murphy (1999). Towards Objective Selection of Representative Microscope Images. Biophys. J. 76:2230-2237. [Article at BJ web site] [Project Description]

73. M. V. Boland and R. F. Murphy (1999). Automated analysis of patterns in fluorescence-microscope images. Trends Cell. Biol. 9(5): 201-202.

74. R. F. Murphy and M. V. Boland (1999). Pattern Analysis Meets Cell Biology. Microsc. Microanal. 5 (Suppl. 2: Proceedings): 510-511.

75. M. V. Boland and R. F. Murphy (1999). After Sequencing: Quantitative Analysis of Protein Localization. IEEE Eng. Med. Biol. Mag. 18(5): 115-119.

76. R. F. Murphy (1999). Scatchard analysis by flow cytometry. In: Flow Cytometry and Cell Sorting, 2nd Ed., A. Radbruch (ed.), Springer Verlag, Berlin, pp. 82-85.

77. R. F. Murphy (1999). Ligand acidification by non-adherent cells. In: Flow Cytometry and Cell Sorting, 2nd Ed., A. Radbruch (ed.), Springer Verlag, Berlin, pp. 186-193.

78. S. L. Rybak and R. F. Murphy (2000). Measurement of Ligand Acidification Kinetics for Adherent and Non-Adherent Cells. In: In Living Color: Protocols in Flow Cytometry and Cell Sorting (R. Diamond and S. DeMaggio, eds.), pp. 496-523.

79. R. F. Murphy, M. V. Boland and M. Velliste (2000). Towards a Systematics for Protein Subcellular Location: Quantitative Description of Protein Localization Patterns and Automated Analysis of Fluorescence Microscope Images. Proc Int Conf Intell Syst Mol Biol (ISMB 2000) 8: 251-259. [ with high res images (3.8 MB)] [ with compressed images (176 K)]

80. R. F. Murphy, M. Velliste, J. Yao, and G. Porreca (2001). Searching Online Journals for Fluorescence Microscope Images Depicting Protein Subcellular Location Patterns. Proc IEEE Int Symp Bio-Informat Biomed Eng (BIBE 2001) 2; pp. 119-128.
81. M. V. Boland and 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. [Article at journal web site] ] [Screen PDF] [Software] [Data]
82. S.A. Jesch, A.J. Mehta, M. Velliste, R.F. Murphy and A.D. Linstedt (2001). Mitotic Golgi is in a Dynamic Equilibrium Between Clustered and Free Vesicles Independent of the ER. Traffic 2: 873-884.
83. E.J.S. Roques and R.F. Murphy (2002). Objective evaluation of differences in protein subcellular distribution. Traffic 3: 61-65.
84. C.A. Telmer, P.B. Berget, B. Ballou, R.F. Murphy, and J.W. Jarvik (2002) Epitope tagging genomic DNA usng a CD-tagging Tn10 Minitransposon. Biotechniques 32: 422-430.
85. K. Huang, J. Lin, J.A. Gajnak, and R.F. Murphy (2002) Image Content-based Retrieval and Automated Interpretation of Fluorescence Microscope Images via the Protein Subcellular Location Image Database. Proc 2002 IEEE Intl Symp Biomed Imaging (ISBI 2002), pp. 325-328.
86. M. Velliste and R.F. Murphy (2002) Automated Determination of Protein Subcellular Locations from 3D Fluorescence Microscope Images. Proc 2002 IEEE Intl Symp Biomed Imaging (ISBI 2002), pp. 867-870.
87. R.F. Murphy, M. Velliste and G. Porreca (2002) Robust Classification of Subcellular Location Patterns in Fluorescence Microscope Images. Proc 2002 IEEE Intl Workshop Neural Networks Signal Processing (NNSP 12), pp. 67-76.
88. J. H. Price, A. Goodacre, K. Hahn, L. Hodgson, E. A. Hunter, S. Krajewski, R. F. Murphy, A. Rabinovich, J. C. Reed, and S. Heynen (2002) Advances in Molecular Labeling, High Throughput Imaging and Machine Intelligence Portend Powerful Functional Cellular Biochemistry Tools. J. Cell. Biochem. Supp. 39: 194-210.
89. X. Chen, M. Velliste, S. Weinstein, J.W. Jarvik and R.F. Murphy (2003) Location proteomics - Building subcellular location trees from high resolution 3D fluorescence microscope images of randomly-tagged proteins. Proc. SPIE 4962: 298-306.
90. K. Huang, M. Velliste, and R. F. Murphy (2003) Feature reduction for improved recognition of subcellular location patterns in fluorescence microscope images. Proc. SPIE 4962: 307-318.
91. W. W. Cohen, R. Wang, and R. F. Murphy (2003) Understanding Captions in Biomedical Publications. Proceedings of the Ninth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD-2003), pp. 499-504.
92. Z. Kou, W. W. Cohen, and R. F. Murphy (2003) Extracting information from text and images for location proteomics. Proceedings of the Third ACM SIGKDD Workshop on Data Mining in Bioinformatics (BIOKDD03) pp. 2-9.
93. R. F. Murphy, M. Velliste, and G. Porreca (2003) Robust Numerical Features for Description and Classification of Subcellular Location Patterns in Fluorescence Microscope Images. J. VLSI Sig. Proc. 35: 311-321.
94. S. Puri, H. Telfer, M. Velliste, R.F. Murphy, and A.D. Linstedt (2004). Dispersal of Golgi matrix proteins during mitotic Golgi disassembly. J. Cell Sci. 117:451-456. [Article at JCS web site]
95. R. F. Murphy (2004) Automated Interpretation of Subcellular Location Patterns. Proc 2004 IEEE Intl Symp Biomed Imaging (ISBI 2004), pp. 53-56.
96. K. Huang and R. F. Murphy (2004) Automated Classification of Subcellular Patterns in Multicell images without Segmentation into Single Cells. Proc 2004 IEEE Intl Symp Biomed Imaging (ISBI 2004), pp. 1139-1142.
97. K. Huang and R. F. Murphy (2004) Boosting accuracy of automated classification of fluorescence microscope images for location proteomics. BMC Bioinformatics 5:78. [Article at journal web site]
98. R. F. Murphy (2004) Automated Interpretation of Protein Subcellular Location Patterns: Implications for Early Cancer Detection and Assessment. Annals of the New York Academy of Science 1020:124-131.
99. A. K. Singh, B.S. Manjunath, and R. F. Murphy (2004) A Distributed Database for Bio-Molecular Images. SIGMOD Record 33(2).
100. Y. Hu and R. F. Murphy (2004) Automated Interpretation of Subcellular Patterns from Immunofluorescence Microscopy. J. Immunol. Methods 290:93-105.
101. R. F. Murphy (2004) Automated Determination of Subcellular Location from Confocal Microscope Images. Microsc. Microanal. 10 (Suppl. 2): 1242-1243.
102. K. Huang and R. F. Murphy (2004) From Quantitative Microscopy to Automated Image Understanding. J. Biomed. Optics 9: 893-912.
103. 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.
104. K. Huang and R. F. Murphy (2004) Data Mining Methods for a Systematics of Protein Subcellular Location. In: Data Mining in Bioinformatics (J.T.L. Wang, M.J. Zaki, H.T.T. Toivonen, and D. Shasha, eds.) , Springer-Verlag (London), pp. 143-187. [Book description at Springer web site]
105. R. F. Murphy, Z. Kou, J. Hua, M. Joffe, and W. W. Cohen (2004) Extracting and Structuring Subcellular Location Information from On-line Journal Articles: The Subcellular Location Image Finder. Proceedings of the IASTED International Conference on Knowledge Sharing and Collaborative Engineering (KSCE 2004), pp. 109-114.
106. 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.
107. M. Brabec, D. Schober, E. Wagner, N. Bayer, R.F. Murphy, D. Blaas, and R. Fuchs (2005). Opening of size selective pores in endosomes during human rhinovirus serotype 2 in vivo uncoating monitored by single organelle flow analysis. J. Virol. 79: 1008-1016. [Article at J Virol web site]
108. X. Chen and R. F. Murphy (2005). Automated interpretation of protein subcellular location. Biophotonics Intl 12(3):34-35.
109. 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.
110. G. Baravalle, D. Schober, M. Huber, N. Bayer, R.F. Murphy and R. Fuchs (2005). Transferrin recycling and transport to lysosomes is differentially affected by bafilomycin, nocodazole and low temperature. Cell Tissue Res. 320:99-113. [Article at journal web site]
111. R.F. Murphy (2005). Location Proteomics: A Systems Approach to Subcellular Location. Biochem. Soc. Trans. 33:535-538. [Article at journal web site]
112. 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]
113. Z. Kou, W.W. Cohen and R.F. Murphy (2005). High-recall protein entity recognition using a dictionary. Bioinformatics 21:i266-i273. [Article at journal web site]
114. 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]
115. R.F. Murphy (2005). Location Proteomics: Providing Critical Information for systems Biology. Bioforum Europe, 2005/04.
116. R.F. Murphy (2005). Location Proteomics. GIT Imaging & Microscopy, 2005/02.
117. 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
118. R.F. Murphy (2005). Cytomics and Location Proteomics: Automated Interpretation of Subcellular Patterns in Fluorescence Microscope Images. Cytometry 67A:1-3
119. 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.
120. 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] [Software/Data]
121. 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.
122. 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 IEEE International Symposium on Biomedical Imaging (ISBI 2006), pp. 558-561. [Software/Data]
123. T. Zhao, S. Soto, and R.F. Murphy (2006). Improved Comparison of Protein Subcellular Location Patterns. Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging (ISBI 2006), pp. 562-565.
124. 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 2006 IEEE International Symposium on Biomedical Imaging (ISBI 2006), pp. 566-569.
125. 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 2006 IEEE International Symposium on Biomedical Imaging (ISBI 2006), pp. 1028-1031.
126. X. Chen, and R.F. Murphy (2006). Automated Interpretation of Protein Subcellular Location Patterns. International Review of Cytology 249:193-227.
127. 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.
128. 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 April 19-21, 2006 [Meeting Review]. J. Cell. Biol. 174:1-4.
129. R.F. Murphy (2006). Putting proteins on the map [News and Views]. Nature Biotech. 24:1223-1224.
130. 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 in Bioinformatics and Computational Biology (CIBCB '06), pp. 1-8.
131. Z. Kou, W. W. Cohen, and R.F. Murphy (2007). A Stacked Graphical Model for Associating Information from Text and Images in Figures. Pacific Symposium on Biocomputing 12:257-268. [Article at conference web site]
132. 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]
133. X. Chen and R. F. Murphy (2007). Interpretation of Protein Subcellular Location Patterns in 3D Images Across Cell Types and Resolutions. Lectures Notes in Bioinformatics 4414:328-342.
134. R.F. Murphy (2007). Systematic Description Of Subcellular Location For Integration With Proteomics Databases And Systems Biology Modeling. Proceedings of the 2007 IEEE International Symposium on Biomedical Imaging (ISBI 2007), pp. 1052-1055.
135. J. Hua, O.N. Ayasli, W.W. Cohen, and R.F. Murphy (2007). Identifying Fluorescence Microscope Images in Online Journal Articles Using Both Image and Text Features. Proceedings of the 2007 IEEE International Symposium on Biomedical Imaging (ISBI 2007), pp. 1224-1227.
136. 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.
137. A. Chebira, Y. Barbotin, C. Jackson, T. Merryman, G. Srinivasa, R.F. Murphy, and J. Kovacevic (2007). A multiresolution approach to automated classification of protein subcellular location images. BMC Bioinformatics 8:210. [Article at journal web site]
138. T. Zhao, S.-C. Chen, and R. F. Murphy (2007). Location Proteomics. In: Introduction to Systems Biology. (S. Choi, ed.), Humana Press, pp. 196-214.
139. S.-C. Chen, T. Zhao, G. J. Gordon, and R. F. Murphy (2007). Automated Image Analysis of Protein Localization in Budding Yeast. Bioinformatics 23:i66-i71. [Article at journal web site] [Software/Data]
140. E. Garcia Osuna and R.F. Murphy (2007). Automated, Systematic Determination of Protein Subcellular Location using Fluorescence Microscopy. In: Subcellular Proteomics: From Cell Deconstruction to System Reconstruction (E. Bertrand and M. Faupel, eds.), Springer, pp. 263-278.
141. C. Jackson, R.F. Murphy and J. Kovacevic (2007). Efficient Acquisition and Learning of Fluorescence Microscopy Data Models. Proceedings of 2007 IEEE International Conference on Image Processing.

142. T. Zhao and R. F. Murphy (2007). Automated learning of generative models for subcellular location: Building blocks for systems biology. Cytometry 71A:978-990. [Article at journal web site] [Software/Data]
143. Y. Qian and R.F. Murphy (2008). Improved Recognition of Figures containing Fluorescence Microscope Images in Online Journal Articles using Graphical Models. Bioinformatics 24:569-576. [Article at journal web site]
144. 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. [Article at journal web site]
145. S.-C. Chen, G. J. Gordon, and R.F. Murphy (2008). Graphical Models for Structured Classification, with an Application to Interpreting Images of Protein Subcellular Location Patterns. J. Machine Learning Res. 9:.651-682. [Article at journal web site]
146. 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. [Article at journal web site] [Software/Data]
147. E. Glory, J. Newberg, and R.F. Murphy (2008). Automated Comparison Of Protein Subcellular Location Patterns Between Images Of Normal And Cancerous Tissues. Proceedings of the 2008 IEEE International Symposium on Biomedical Imaging (ISBI 2008), pp. 304-307.
148. R.F. Murphy (2008). Automated Proteome-Wide Determination Of Subcellular Location Using High Throughput Microscopy. Proceedings of the 2008 IEEE International Symposium on Biomedical Imaging (ISBI 2008), pp. 308-311.
149. 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.
150. L. P. Coelho and R.F. Murphy (2008). Identifying Subcellular Locations from Images of Unknown Resolution. Communications in Computer and Information Science 13:235-242.
151. W. Hendee, K. Cleary, R. Ehman, G. Fullerton, W. Grundfest, J. Haller, C. Kelley, A. Meyer, R. F. Murphy, W. Phillips, V. Torchlin (2008). Bioengineering and Imaging Research Opportunities Workshop V: A White Paper on Imaging and Characterizing Structure and Function in Native and Engineered Tissues. Medical Physics 35:3428. [Full Report] [Report Summary]
152. J. Newberg, J. Hua, and R.F. Murphy (2009). Location Proteomics: Systematic Determination of Protein Subcellular Location. Methods in Molecular Biology, Systems Biology, volume 500, I. Maly (ed.), Humana Press, pp. 313-332.
153. 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.
154. A. Shariff, G. K. Rohde, and R. F. Murphy (2009) Indirect learning of generative models for microtubule distribution from fluorescence microscope images. Proceedings of the ICML-UAI-COLT 2009 Workshop on Automated Interpretation and Modeling of Cell Images (Cell-Image Learning 2009).
155. L. P. Coelho and R. F. Murphy (2009) Unsupervised Unmixing of Subcellular Location Patterns. Proceedings of the ICML-UAI-COLT 2009 Workshop on Automated Interpretation and Modeling of Cell Images (Cell-Image Learning 2009).
156. A. Ahmed, A. Arnold, L. P. Coelho, J. Kangas, A.-S. Sheikh, E. Xing, W. Cohen, and R. F. Murphy (2009) Structured Literature Image Finder. Proceedings of the Ninth Annual Meeting of the ISMB BioLINK Special Interest Group, pp. 209-212.
157. L. P. Coelho, A. Shariff, and R. F. Murphy (2009) Nuclei Segmentation In Microscope 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. [Software/Data]
158. T. Peng, Wei Wang, G. K. Rohde1, 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.
159. J. Y. Newberg, J. Li, A. Rao, E. Lundberg, F. Ponten, M. Uhlen and R. F. Murphy (2009) Automated Analysis Of Human Protein Atlas Immunofluorescence Images. Proceedings of the 2009 IEEE International Symposium on Biomedical Imaging (ISBI 2009), pp. 1023-1026.
160. A. Ahmed, E. Xing, W. Cohen, and R. F. Murphy (2009) Structured Correspondence Topic Models for Mining Captioned Figures in Biological Literature. Proceedings of the Fifteenth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD-2009), pp. 39-47.
161. 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.
162. 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. [Data/Software]
163. S. Huh, D. Lee and R. F. Murphy (2009) Efficient framework for automated classification of subcellular patterns in budding yeast. Cytometry 75A:934-940.
164. J. Spidlen, W. Moore, D. Parks, M. Goldberg, C. Bray, V. Cordioli, P. Gorombey, B. Hyun, M. Hubbard, R. Lefebvre, R. Leif, M. Naivar, D. Novo, L. Ostruszka, A. Treister, J. Wood, R. F. Murphy, M. Roederer, D. Sudar, R. Zigon, and R. R. Brinkman (2010) Data File Standard for Flow Cytometry: Version FCS 3.1. Cytometry 77A:97-100.
165. T. Peng, G.M.C. Bonamy, E. Glory, D. Rines, S. K. Chanda, and R. F. Murphy (2010) Determining the distribution of probes between different subcellular locations through automated unmixing of subcellular patterns. Proc. Natl. Acad. Sci. U.S.A. 107:2944-2949. [Supporting Information]
166. 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/Software]
167. E. Glory-Afshar, E. Garcia Osuna, B. Granger, and R. F. Murphy (2010) A Graphical Model To Determine The Subcellular Protein Location In Artificial Tissues. Proceedings of the 2010 IEEE International Symposium on Biomedical Imaging (ISBI 2010), pp. 1037-1040.
168. L. P. Coelho, E. Glory-Afshar, J. Kangas, S. Quinn, A. Shariff, and R. F. Murphy (2010) Principles of Bioimage Informatics: Focus on machine learning of cell patterns. Lecture Notes in Computer Science 6004:.8-18.
169. L. P. Coelho, A. Ahmed, A. Arnold, J. Kangas, A.-S. Sheikh, E. Xing, W. Cohen, and R. F. Murphy (2010) Structured Literature Image Finder: Extracting, Information from Text and Images in Biomedical Literature. Lecture Notes in Computer Science 6004:23-32.
170. 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. [Article at journal web site] [Data/Software]
171. A. Ahmed, A. Arnold, L. P. Coelho, J. Kangas, A.-S. Sheikh, E. Xing, W. Cohen, and R. F. Murphy (2010) Structured Literature Image Finder: Parsing Text and Figures in Biomedical Literature. Web Semantics: Science, Services and Agents on the World Wide Web 8:151-154. [DOI]
172. 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. [DOI] [Data/Software]
173. R. F. Murphy (2010) Communicating Subcellular Distributions. Cytometry Part A 77A:686-692. [DOI]
174. A. Shariff, J. Kangas, L.P. Coelho, S. Quinn and R.F. Murphy (2010) Automated Image Analysis for High Content Screening and Analysis. J. Biomolec. Screening 15:726-734. [DOI]
175. A.-S. Sheikh, A. Ahmed, A. Arnold, L. P. Coelho, J. Kangas, E. P. Xing, W. Cohen, and R. F. Murphy (2010) Structured literature image finder: Open source software for extracting and disseminating information from text and figures in biomedical literature. Carnegie Mellon University School of Computer Science Technical Report CMU-CB-09-101.

176. 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 6577:204-221.
177. 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/Software]
178. A. Rao and R.F. Murphy (2011) Determination of Protein Location Diversity Via Analysis of Immunohistochemical Images from the Human Protein Atlas. Proceedings of the 2011 IEEE International Symposium on Biomedical Imaging (ISBI 2011), pp. 1727-1729.

179. 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. [DOI}

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

181. R. F. Murphy (2011) An active role for machine learning in drug development. Nature Chemical Biology 7:327-330. [Article at journal web site]

182. 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/Software]
183. T. Lin, Z. Bar-Joseph, and R. F. Murphy (2011) Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs. Journal of Computational Biology 18: 1709-1722.

184. R. F. Murphy (2012) CellOrganizer: Image-derived Models of Subcellular Organization and Protein Distribution. Methods in Cell Biology 110:179-193.

185. J. Li, L. Xiong, J. Schneider, and R.F. Murphy (2012) Protein Subcellular Location Pattern Classification in Cellular Images Using Latent Discriminative Models. Bioinformatics 28:i32-39. [Data/Software]

186. 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/Software]

187. K.W. Eliceiri, M.R. Berthold, I.G. Golberg, L. Ibanez, B.S. Manjunath, M.E. Martone, R.F. Murphy, H. Peng, A.L. Plant, B. Roysam, N. Stuurmann, J.R.Swedlow, P. Tomancak, and A.E. Carpenter (2012) Biological Imaging Software Tools. Nature Methods 9:697-710.

188. 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.

189. 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. [DOI] [Data/Software]

190. 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. [DOI] [Data/Software]

191. S. Weber, M.L. Fernanndez-Cachon, J. M. Nascimento, S. Knauer, B. Offermann, R.F. Murphy, M. Boerries, and H. Busch (2013) Label-free detection of neuronal differentiation in cell populations Using High-Throughput Live-Cell Imaging of PC12 Cells. PLoS ONE 8:e56690 [DOI]

192. C. Stadler, E. Rexhepaj, V.R. Singan, R.F. Murphy, R. Pepperkok, M. Uhlen, J.C. Simpson, and E. Lundberg (2013) Immunofluorescence and fluorescent protein-tagging are complementary techniques with high correlation for subcellular investigation of the human proteome in mammalian cells. Nature Methods 10:315-323 [DOI]

193. 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. [DOI] [Video Abstract]

194. K.T. Roybal, P. Sinai, P. Verkade, R. F. Murphy, and Christoph Wülfing (2013) The actin-driven spatiotemporal organization of signaling in T cells activated by antigen presenting cells. Immunological Reviews 256: 133-147. [DOI]

195. 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. [DOI]

196. A. Gough, T. Lezon, J. Faeder, C. Chennubhotla, R. F. Murphy, R. Critchley-Thorne and D. L. Taylor (2014) High-Content Analysis with Cellular and Tissue Systems Biology: A Bridge between Cancel Cell Biology and Tissue-Based Diagnostics. In: The Molecular Basis of Cancer, 4th edition (J. Mendelsohn, J. W. Gray, P. M. Howley, M. A. Israel, and C. B. Thompson, eds.), pp. 369-392 [Link to book]

197. R. F. Murphy (2014) A new era in bioimage informatics. Bioinformatics 30:1353. [DOI]

198. J.D. Kangas, A.W. Naik, and R.F. Murphy (2014) Prediction of Biological Responses Using Protein and Compound Features and their Discovery using Active Learning. BMC Bioinformatics 15:143. [DOI]

199. A. Kumar, A. Rao, S. Bhavani, J.Y. Newberg, and R. F. Murphy (2014) Automated Analysis of Immunohistochemical Images Identifies Candidate Location Biomarkers for Cancers. Proc. Natl. Acad. Sci. U.S.A. 111:18249-18254. [DOI]

200. 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 (also selected for presentation in the Proceedings track of RECOMB 2015). [DOI]

201. 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). [DOI]

202. 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. [DOI]

203. 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(2): e1004611. [DOI]

204. R. F. Murphy (2016) Building cell models and simulations from microscope images. Methods 96:33-39 (Special Issue on High-throughput Imaging). [DOI]

205. 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]

206. 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.

207. 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]

208. B. Diedrich, K.G. Rigbolt, M. Röring, R. Herr, S. Kaeser-Pebernard, C. Gretzmeier, R.F. Murphy, T. Brummer, and J. Dengjel (2017) Discrete cytosolic macromolecular BRAF complexes exhibit distinct activities and composition. EMBO J 36646-663. [DOI]

209. R. Ambler, X. Ruan, R.F. Murphy, and C. Wülfing (2017) Systems Imaging of the immune synapse. The Immune Synapse: Methods and Protocols (C. T. Baldari and M. L. Dustin, eds.), Methods in Molecular Biology 1584:409-421. [DOI]

210. G. R. Johnson, J. D. Kangas, A. Dovzhekno, R. Trojok, K. Voigt, T. D. Majarian, K. Palme, and R. F. Murphy (2017) A Method for Characterizing Phenotypic Changes in Highly Variable Cell Populations and its Application to High Content Screening of Arabidopsis thaliana Protoplasts. Cytometry Part A 91A:326-335. [DOI]

211. C. Gretzmeier, S. Eiselein, G. R. Johnson, R. Engelke, H. Nowag, M. Zarei, V. Küttner, A. C. Becker, K. T. G. Rigbolt, M. Høyer-Hansen, J. S. Andersen, C. Münz, R. F. Murphy, and J. Dengjel (2017) Degradation of protein translation machinery by amino acid starvation-induced macroautophagy. Autophagy 13:1064-1075. [DOI] [Cover image]

212. X. Ruan, C. Wülfing, and R. F. Murphy (2017) Image-based Spatiotemporal Causality Inference for Protein Signaling Networks. Bioinformatics 33:i217-i224 (Proceedings of 25th Annual International Conference on Intelligent Systems in Molecular Biology; only 16% of submitted papers accepted). [DOI]

213. P. Spealman, A.W. Naik, G.E. May, S. Kuersten, L. Freeberg, R.F. Murphy, and J. McManus (2018) Conserved non-AUG uORFs revealed by a novel regression analysis of ribosome profiling data. Genome Research 28:214-222. [DOI]

214. L. Han, R. F. Murphy, and D. Ramanan (2018) Learning Generative Models of Tissue Organization with Supervised GANs. Proceedings of the 2018 IEEE Winter Conf. on Applications of Computer Vision, pp. 682-690. [DOI]

215. T. Majarian, I. Cao-Berg, X. Ruan, and R. F. Murphy (2019) CellOrganizer: Learning and Using Cell Geometries for Spatial Cell Simulations. Methods in Molecular Biology 1945:251-264. [DOI]

216. T. D. Majarian, R.F. Murphy, and S.S. Lakdawala (2019) 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 [DOI Open Access] [Cover Image]

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

218. .J. Lugo-Martinez, J. Dengjel, Z. Bar-Joseph, and R. F. Murphy (2019) Integration of heterogeneous experimental data improves global map of human protein complexes. Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, pp. 144-153. [DOI]

219. The HuBMAP Consortium (2019) The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. Nature 574:187-192.

220. D. J. Clark, L.E. McMillan, S.L. Tan, G. Bellomo, C. Massou, H. Thompson, L. Mykhaylechko, D. Alibhai, X. Ruan, K.L. Singleton, M. Du, A.J. Hedges, P.L. Schwartzberg, P. Verkade, R.F. Murphy, and C. Wülfing (2019) Transient protein accumulation at the center of the T cell antigen presenting cell interface drives efficient IL-2 secretion. eLife 8:e45789. [DOI]

221. Y.-Y. Xu, H.-B. Shen and R. F. Murphy (2019) Learning complex subcellular distribution pattern of proteins via analysis of immunohistochemistry images. Bioinformatics 36(6):1908-1914. [DOI]

222. 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 31(7):655-666. [DOI]

223. 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.

224. R. Ambler, G. L. Edmunds, S. L. Tan, S. Cirillo, J. I. Pernes, X. Ruan, J. Huete Carrasco, C.C.W. Wong, J. Lu, J. Ward, G. Toti, A. J. Hedges, S.J. Dovedi, R. F. Murphy, D. J. Morgan and C. Wülfing (2020) PD-1 suppresses the maintenance of cell couples between cytotoxic T cells and tumor target cells within the tumor. Science Signaling 13:eaau4518. [Supplementary Materials] [DOI]

225. Y.-Y. Xu, H. Zhou, R. F. Murphy, and H.-B. Shen (2021) Consistency and variation of protein subcellular location annotations. PROTEINS: Structure, Function, and Bioinformatics 89(2):242-250. [DOI]

226. M. E. Johnson, A. Chen, J. R. Faeder, P. Henning, I. I. Moraru, M. Meier-Schellersheim, R. F. Murphy, T. Prüstel, J. A. Theriot, and A. M. Uhrmacher (2021) Quantifying the roles of space and stochasticity in computer simulations for cell biology and cellular biochemistry. Molecular Biology of the Cell 32(2):91-210. [Supplementary Materials] [DOI]

227. H. Sun and R.F. Murphy (2021) Evaluation of categorical matrix completion algorithms: toward improved active learning for drug discovery. Bioinformatics 37,3538-3545. [DOI]

228. H. Sun, X. Fu, S. Abraham, J. Shen and R.F. Murphy (2022) Improving and evaluating deep learning models of cellular organization. Bioinformatics 38, 5299-5306. [DOI]

229. H. Chen and R. F. Murphy (2023) Evaluation of cell segmentation methods without reference segmentations. Molecular Biology of the Cell 34:ar50:1-11. [DOI]

230. H. Sun, A. W. J. Soh, L. E. Mitchell, C. G. Pearson, R. F. Murphy (2023) Basal body organization and cell geometry during the cell cycle in Tetrahymena thermophila. Molecular Biology of the Cell 34:ar53:1-13. [DOI]

231. J. C. Schaff, A. Lakshminarayana, R. F. Murphy, F.T. Bergmann, A. Funahashi, D. P. Sullivan, L. P. Smith (2023) SBML Level 3 Package: Spatial Processes, Version 1, Release 1. Journal of Integrative Bioinformatics, pp. 20220054. [DOI]

Last Updated: 15 May 2023

Copyright © 1996-2019 by the Murphy Lab, Computational Biology Department at Carnegie Mellon University