Engineering Director

CURRICULUM VITAE

Robert F. Murphy

Ray and Stephanie Lane Professor of Computational Biology

Professor of Biological Sciences, Biomedical Engineering and Machine LearningCarnegie Mellon

University Telephone: 412-***-****

5000 Forbes Avenue FAX: 412-***-****

Pittsburgh, Pennsylvania 15213 Email: ******@***.***

EDUCATION

Columbia University, New York, B.A., 1974, Biochemistry.

California Institute of Technology, Pasadena, CA, Ph.D., 1980, Biochemistry (Dr. James

Bonner)

PROFESSIONAL EXPERIENCE

Ray and Stephanie Lane Professor of Computational Biology, Carnegie Mellon U., 2007

-

Director (Department Head), Ray and Stephanie Lane Center for Computational Biology,

Carnegie Mellon U. 2007-

Professor of Machine Learning, Carnegie Mellon U., 2006-

Professor of Biological Sciences and Biomedical Engineering, Carnegie Mellon U., 2003-

Honorary Professor of Biology, Albert Ludwig University of Freiburg, 2011-

External Senior Fellow, Freiburg Institute for Advanced Studies, Freiburg, Germany 2008-

Founding Director, Joint CMU-Pitt Ph.D. Program in Computational Biology, 2005-2009

Founding Director, Center for Bioimage Informatics, Carnegie Mellon U., 2004-2008

Associate Professor of Biological Sciences, Carnegie Mellon University, 1989-2003

Associate Professor of Biomedical Engineering (by courtesy), 2002-2003

Voting Faculty Member, Center for Automated Learning and Discovery, 2002-2006

Director, Merck Computational Biology and Chemistry Program, 1999-2004

Director, Summer Undergraduate Research Program, Dept. Biological Sciences, 1996-2004

Member,

University of Pittsburgh Cancer Institute, 1994-present

.

Faculty of Biomedical Engineering, Carnegie Mellon University, 1998-2002

Faculty Member and Program Leader for Undergraduate and Graduate Education, Center for

Light Microscope Imaging and Biotechnology, 1991-2002

.

Undergraduate Research Advisor, Dept. of Biological Sciences, Carnegie Mellon Univ., 1996

-

2000

Director, Beckman Scholars Program at Carnegie Mellon University, 1998-1999

Visiting Associate Professor of Biology, Johns Hopkins University, 1994

.

Associate Member, Pittsburgh Cancer Institute, 1986-1993.

Founding Member, Center for Fluorescence Research in Biomedical Sciences, 1983-1991

Assistant Professor of Biological Sciences, Carnegie Mellon University, 1983-1989

Consultant, Becton Dickinson Immunocytometry Systems, 1982-1992

.

Postdoctoral Research Associate, Columbia University, Dr. Charles Cantor, Departments of

Chemistry and Human Genetics, 1979-1983

.

HONORS

Earle C. Anthony Fellowship, Caltech, 1974

Damon Runyon-Walter Winchell Cancer Foundation Fellowship, 1979

Presidential Young Investigator Award, 1984

Fellow, American Institute of Medical and Biological Engineering, 2007

Senior Member, IEEE, 2007

Alexander von Humboldt Foundation Research Award, 2008

Honorary Professor of Biology, Albert Ludwig University of Freiburg, 2011

PROFESSIONAL SERVICE

2008

Member, Editorial Board, Biology Direct: Genomics, bioinformatics and systems biology

section, March 2007-

Member, Editorial Board, Cytometry Part A, May 2007-

Member, Editorial Board, Biology Direct: Discovery notes section, October 2007-

Software Section Editor, PLOS Computational Biology, March 2009-

Associate Editor, BMC Bioinformatics, May 2011-

Committee and Society Positions

Member, Data Standards Committee, International Soc. Analytical Cytology, Jan. 1990-March

2003 (Chair, Jan. 1998-March 2003)

Member, Publications Committee, International Society for Computational Biology, January

2004-present

Councillor, International Society for Analytical Cytology, May 2004-May 2006

Chair, Scientific Communications Committee, International Society for Analytical

Cytology,

May 2004-May 2006

Member, International Society for Analytical Cytology Management Task Force, March 2005 -

September 2006

President-elect, International Society for Advancement of Cytometry, May 2006-May 2008

President, International Society for Advancement of Cytometry, May 2008-May 2010

Immediate Past-President, International Society for Advancement of Cytometry, May 2010-

Advisory Panels

Member, American Heart Association Western Pa. Peer Review Committee, March 1987-1991

Member, National Science Foundation Cell Biology Review Panel B, October 1989-March 1992

NIH, Special Study Section A (Biomedical Instrumentation), September 1990, June 1991

NIH, Biological Sciences 2 Study Section (Special Reviewer), July 1991, November 1991

NIH, Reviewers Reserve, December 1991-June 1993

Member, NIH Biological Sciences 2 Study Section, July 1993-June 1997

Chair, Carnegie Mellon University Faculty Development Fund, July 1996-June 1997

Member, NSF Research Experience for Undergraduates Review Panel, November 1996-1998

Member, NIH, ZRG2 CBY-1, March 1997, June 1997

Member, NIH, ZRG2 CBY-2, July, Dec. 1998 (Chair), March, July, Nov. 1999, March, June

2000

Member, NSF Research Experience for Undergraduates Review Panel, November 2000

Member, NSF Graduate Research Fellowship Panel, February 2001, February 2002

Member, Visiting Review Committee, Biological and Medical Informatics Program, University

of California, San Francisco, March 28-29, 2002

Member, Scientific Advisory Board, Sequel Genetics, 2002-2003

Member, NIH SSS-U (Instrumentation), August 2002

Member, NIH SSS-H (Computational Biology), June 2002, November 2002, February 2003,June

2003, November 2003

Member, Visiting Review Committee, Image Analysis Laboratory, National Cancer Institute,

Frederick, MD, January 2004

Member, NIH BDMA Study Section, March 2004

Chair, NIH BDMA Study Section, June 2004-June 2006

Member, NIH ZGM1 BRT-9 (KR) Study Section, August 2006

Member, NIH ZRG1 CB-B (40) Study Section, November 2006

Member, NIH ZRG1 BST-R (30) Study Section, October 2007

Member, NIH NIGMS Advisory Council, January 2009-December 2012

Member, Advisory Board, Caribbean Computing Center for Excellence, September 2010-

Member, NIH Council of Councils, November 2011-October 2014

Program Committees

Chair, Cytometry Development Workshop, November 1998-October 2006

Scientific and Medical Advisory Board, Pittsburgh Bone Symposium, August 2003

Member, Program Committee, IEEE International Workshop on Neural Networks in Signal

Processing, September 2003

Finance Chair, IEEE International Symposium on Biomedical Imaging, April 2006

Member, Organizing Committee, International Society for Analytical Cytology XXIII

Congress,

May 2006

Member, Program Committee, MICCAI Workshop on Microscopic Image Analysis with

Applications in Biology, October 1, 2006

Member, Program Committee, International

Invited Faculty Member, Short Course on High-Content Analysis, Society for Biomolecular

Sciences Conference 2005, Geneva, Switzerland, September 11, 2005

Invited Tutorial Image Analysis of Subcellular Patterns for High Throughput Screening

and

Systems Biology, International Society for Analytical Cytology XXIII Congress, Quebec

City, Quebec, Canada, May 20, 2006

Invited Tutorial Basics of Machine Learning for Image or Flow (Cytometry),

International

Society for Analytical Cytology XXIII Congress, Quebec City, Quebec, Canada, May 20,

2006

Invited Faculty Member, Short Course on High-Content Analysis, Society for Biomolecular

Sciences Conference 2006, Seattle, Washington, September 17, 2006

Faculty Member, Machine Learning Department Autumn Course on Data Mining from Text and

Image, Pittsburgh, PA, September 27, 2006

Invited Tutorial Machine Learning Approaches to Information Extraction from Text and

Images

in Biomedical Journal Articles, International Association of Science and Technology for

Development Biomed 2007 and Signal Processing, Pattern Recognition, and Applications

2007, Innsbruck, Austria, February 15, 2007

Invited Faculty Member, IV Interactive Course in Cytometry, Modena, Italy, March 6-9,

2007

Faculty Member, Twelfth Annual Course on 3D Microscopy of Living Cells, University of

British Columbia, Vancouver, BC, June 29-July 2, 2007

Invited Faculty Member, Short Course on High-Content Analysis, Society for Biomolecular

Sciences Conference 2008, St. Louis, Missouri, April 6, 2008

Faculty Member, Thirteenth Annual Course on 3D Microscopy of Living Cells, University of

British Columbia, Vancouver, BC, June 28-30, 2008

Short Course, Machine Learning Approaches to Biological Research: Bioimage Informatics

and

Beyond, Freiburg Institute for Advanced Studies, Freiburg, Germany, September 29-

October 1, 2008

Selected Tutorial Automated Proteome-wide Determination and Modeling of Subcellular

Location, Sixth Conference on Computational Methods in Systems Biology, Rostock,

Germany, October 12, 2008

Invited Faculty Member, V Advanced Course in Cytometry, Modena, Italy, March 3-8, 2009

Invited Speaker, EMBO Practical Course on Light Microscopy of Living Cells, Oeiras,

Portugal,

May 29-June 5, 2009

Lecture on Advanced Image Analysis, Life Cell Imaging Workshop, Zentrum fUr Biosystems

Analyse, Freiburg, Germany, July 14, 2009

Short Course, Bioimage Informatics: Automated Image Analysis and Modeling, Biogem,

Ariano Irpino, Italy, July 7-9, 2010

PROFESSIONAL SOCIETIES

American Association for the Advancement of Science, American Institute for Medical and

Biological Engineering (Fellow), American Society for Cell Biology, Biomedical

Engineering

Society, Human Proteome Organization, Institute of Electrical and Electronic Engineers

(IEEE,

Senior Fellow), International Clinical Cytometry Society, International Society for

Advancement

of Cytometry, International Society for Computational Biology, Sigma Xi

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. [144 citations according to ISI as of

June 2007]

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. [47

citations according to ISI as of June 2007]

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. [32 citations according to ISI as of June 2007]

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. [520 citations according to ISI as of

Nov 2009]

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. [31 citations according to ISI as of June 2007]

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. [34 citations according to ISI as of June 2007]

12. R. F. Murphy, S. Powers, M. Verderame, C. R. Cantor and R. Pollack (1982). Flow

Cytofluorometric Analysis of Insulin Binding and Internalization by Swiss 3T3 Cells.

Cytometry 2:402-406. [44 citations according to ISI as of June 2007]

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. [227 citations according

to

ISI as of Nov 2009]

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. [118 citations according to ISI as of Nov 2009]

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.

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. [30 citations according to ISI as of June 2007]

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. [41 citations according to ISI as of June 2007]

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. [116

citations according to ISI as of June 2007]

33. S. Taylor, M. Roederer, and R. F. Murphy (1987). Flow Cytometric DNA Analysis of

Adrenocortical Tumors in Children. Cancer 59:2059-2063. [33 citations according to ISI as

of June 2007]

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. [51 citations according to ISI as of

June

2007]

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. [61 citations according to ISI as of June 2007]

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. [105 citations according to ISI as of June 2007]

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. [133 citations

according to ISI as of November 2009]

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.

[115 citations according to ISI as of Nov 2009]

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

RECOMB 2011) 6577:204-221.

180.T. Peng and R.F. Murphy (2011) Image-derived, Three-dimensional Generative Models of

Cellular Organization. Cytometry Part A 79A:383-391.

181.R. F. Murphy (2011) An active role for machine learning in drug development. Nature

Chemical Biology 7:327-330.

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.

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, in press.

S

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