CURRICULUM VITAE

Robert F. Murphy

Ray and Stephanie Lane Professor of Computational Biology Emeritus

 

Carnegie Mellon University                                       Email:             murphy@cmu.edu

5000 Forbes Avenue                                                  

Pittsburgh, Pennsylvania 15213                                

 

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 Emeritus, Carnegie Mellon U., 2021-

Ray and Stephanie Lane Professor of Computational Biology, Carnegie Mellon U., 2007-2021

Founding Head, Computational Biology Department (originally called the Lane Center for Computational Biology, which received department status in the School of Computer Science in September 2009; name changed to Computational Biology Department in January 2015), Carnegie Mellon University, 2007-2020

Professor of Machine Learning, Carnegie Mellon U., 2006-2021

Professor of Biological Sciences and Biomedical Engineering, Carnegie Mellon U., 2003-2021

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

Founder and Board Member, Quantitative Medicine LLC, 2012-2020 (sold to Predictive Oncology, Inc.)

Senior Fellow, Allen Institute for Cell Science, 2015-2020

External Senior Fellow, Freiburg Institute for Advanced Studies, Freiburg, Germany 2008-2017

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, 1994-2021.

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, 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

 

Fellow, IEEE, 2020

Senior Member, International Society for Computational Biology, 2018

Distinguished Service Award, International Society for Advancement of Cytometry, 2016

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

Alexander von Humboldt Foundation Research Award, 2008

Senior Member, IEEE, 2007

Fellow, American Institute of Medical and Biological Engineering, 2007

Presidential Young Investigator Award, 1984

Damon Runyon-Walter Winchell Cancer Foundation Fellowship, 1979

Earle C. Anthony Fellowship, Caltech, 1974

 

PROFESSIONAL SERVICE

Editorial

Guest Editor (with Gaudenz Danuser and Erik Meijering), Special Issue on Molecular and Cellular Bioimaging, IEEE Transactions on Image Processing, September 2005

Guest Editor (with Jelena Kovacevic), Special Issue on Molecular and Cellular Bioimaging, IEEE Signal Processing Magazine, May 2006

Member, Editorial Advisory Board, Journal of Proteome Research, January 2006-December 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-March 2015

Associate Editor, BMC Bioinformatics, May 2011-May 2016

Associate Editor, Bioinformatics, January 2014-

Member, Editorial Board, Scientific Data, January 2014-

Guest Editor (with Thilo Figge), Special Issue on Image-Based Systems Biology, Cytometry Part A, June 2015

 

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 2004-2014

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 2010-2012

Member, Steering Committee, Bioimage Informatics Conferences, November 2011-2014

 

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 2010-2014

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

Member, Review Panel, NSF-NIH BIGDATA initiative, October-November, 2012

Member, X02 Review Working Group, NIGMS, February 2013

Member, External Advisor Board, Bioinformatics Core Facility, University of Texas Southwestern Medical Center, January 15-

Member, Fellowship Selection Committee, Freiburg Institute for Advanced Studies, February 2015

Chair, External Advisory Board, MEP-LINCS program, Oregon Health & Science University, April 11-12, 2016 & November 28-29, 2016

Member, CTSA Collaborative Innovation Award Application (U01) Special Emphasis Panel ZTR1 CI-9 (01), National Center For Advancing Translational Sciences, May 11-12, 2016

Member, Special Emphasis Panel, ZCA1 RTRB-R J2 R on Research Centers for Cancer Systems Biology, November 9-10, 2016

Ad Hoc Member, National Institute of Allergy and Infectious Diseases Division of Intramural Research Board of Scientific Counselors, December 9-10, 2016

Chair, External Advisory Board, National Resource for Imaging Mass Spectrometry, Vanderbilt University, January 13, 2017

Member, Scientific Advisory Board, Morgridge Institute for Research, June 2017-June 2022

Chair, CTSA Program Data to Health Coordinating Center (U24) Special Emphasis Panel, ZTR1 CI-9 (01), National Center For Advancing Translational Sciences, May 17, 2017

Member, National Science Foundation Signal Transduction panel, February 21-23, 2018

Member, CTSA review Special Emphasis Panel ZTR1 CI-9 (01), June 14, 2018

Member, Special Emphasis Panel, ZRG1 BST-J (50) R, Tissue Mapping Centers for the Human BioMolecular Atlas Program (U54), June 28, 2018

Member, External Advisory Board, National Resource for Imaging Mass Spectrometry, Vanderbilt University, August 9, 2018

Member, Data Science Working Group, National Institutes of Health HubMAP Program, December 2018-present

Member, Schmidt Science Fellows Review Panel, December 2018-January 2019

Member, NIH Director’s Transformative Research Award Editorial Board, November 2018-April 3, 2019

Member, CTSA review Special Emphasis Panel ZTR1 CI-9 (01), September 11-12, 2019

Member, Schmidt Science Fellows Review Panel, December 2019-January 2020

Selector, Schmidt Science Fellows Program, March 2020

Member, NIH Director’s Transformative Research Award Editorial Board, December 2019-April 7, 2020

Member, NIH INCLUDE Transformative R01 Study section, July 19, 2020

Member, AIMBE Review Committee on Biomedical Imaging and Instrumentation, August-September 2020

Member, NCI Subcommittee F study section, February 24, 2021

Final Selection Panel, Schmidt Science Fellows Program, March 2021

Member, NIH Director’s Transformative Research Award Editorial Board, November 2020-April 3, 2021

Member, NIH Director’s Pioneer Award Stage 2 Panel, April 12-14, 2021

Chair, NIH Cellular Senescence Network: Tissue Mapping Centers Panel, June 21-22, 2021

Member, AIMBE Review Committee of Computational Bioengineering, Systems Biology, and Bioinformatics, August-September 2021

Final Selection Panel, Schmidt Science Fellows Program, February 2022

Member, AIMBE Systems Biology Review Committee, August 2022

Chair, Final Selection Panel, Schmidt Science Fellows Program, February 2023

 

Conference Organization and 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 Conference on Bioinformatics Research and Development (BIRD), March 2007

Special Sessions Chair, IEEE International Symposium on Biomedical Imaging, April 2007

Member, Program Committee, Second International Workshop on Microscopic Image Analysis with Applications in Biology, September 21, 2007

Topic Chair, Bioengineering and Imaging Research Opportunities Workshop, January 2008

General Chair, International Society for Analytical Cytology XXIII Congress, May 2008

General Chair, International Conference on Bioinformatics Research and Development (BIRD), July 2008

Workshop Co-Organizer, “Automated Interpretation and Modeling of Cell Images,” International Conference on Machine Learning (ICML), June 2009

Area Chair for Bioimaging (with Eugene Myers), Intelligent Systems for Molecular Biology, July 11-13, 2010

Member, Organizing Committee, Bioimage Informatics 2010, Carnegie Mellon University, September 17-19, 2010

Organizer (with Anne Carpenter), Special Session, International Symposium on Biomedical Imaging, Chicago, Illinois, April 1, 2011

Member, Steering Committee, Great Lakes Bioinformatics Conference 2011, May 2-4, 2011

Member, Organizing Committee, CYTO 2011, Baltimore, Maryland, May 21-25, 2011

Area Chair for Bioimaging and Visualization (with Eugene Myers and Sean O’Donoghue), Intelligent Systems for Molecular Biology, Vienna, Austria, July 15-19, 2011

Chair, “Image-based Models of Cell Organization and Function,” International Conference on Systems Biology, Heidelberg, Germany, August 28-September 1, 2011

Member, Program Committee, Microscopic Image Analysis with Applications in Biology,  Mannheim, Germany, September 2, 2011

Member, Program Committee, International Symposium on Biomedical Imaging, Barcelona, Spain, May 2-5, 2012

Honorary Conference Chair and member of Organizing Committee, GLBIO 2012, Ann Arbor, Michigan, May 15-17, 2012

Member, Organizing Committee, CYTO 2012, Leipzig, Germany, June 22-27, 2012

Area Chair for Bioimaging and Visualization (with Sean O’Donoghue), Intelligent Systems for Molecular Biology, Long Beach, California, July 15-17, 2012

Track Chair for Bioimage Analysis, ACM Conference on Bioinformatics, Computational Biology and Biomedicine, Orlando, Florida, October 7-10, 2012

Special Sessions Chair, IEEE International Symposium on Biomedical Imaging, San Francisco, California, April 7-11, 2013

Steering Committee, GLBIO 2013, Pittsburgh, Pennsylvania, May 13-15, 2013

Member, Organizing Committee, CYTO 2013, San Diego, California, May 19-22, 2013

Track Chair for Bioimage Analysis, ACM Conference on Bioinformatics, Computational Biology and Biomedicine, Washington, DC, 2013

Member, Program Committee, 2nd International Workshop on Pattern Recognition in Proteomics, Structural Biology and Bioinformatics, Naples, Italy, September 10-11, 2013

Member, Organizing Committee, CYTO 2014, Ft. Lauderdale, Florida, May 17-21, 2014

Area Chair for Bioimaging and Visualization, Intelligent Systems for Molecular Biology, Boston, Massachusetts, July 11-15, 2014

Member, Organizing Committee, CYTO 2015, Glasgow, Scotland, June 26-30, 2015

Session Organizer and Chair, Machine-Learning Advances in the Life Sciences, Society for Laboratory Automation and Screening Annual Meeting, Washington, DC, February 9, 2015

Area Chair for Bioimaging and Visualization, Intelligent Systems for Molecular Biology, Dublin Ireland, July 11-15, 2015

Organizer (with James Faeder), National Institute for Mathematical and Biological Synthesis Working Group on “Spatial Cell Simulations, Knoxville, Tennessee, December 1-3, 2015

Associate Editor, IEEE International Symposium on Biomedical Imaging, Prague, Czech Republic, April 13-16, 2016

Member, Organizing Committee, CYTO 2016, Seattle, Washington, June 11-15, 2016

Area Chair for Bioimaging and Visualization, Intelligent Systems for Molecular Biology, Orlando, Florida, July 8-12, 2016

Organizing Committee member, Symposium on Clinical and Pharmaceutical Solutions through Analysis, 2016-2017

Member, Scientific Program Committee, 2018 Annual Meeting, American Association for Cancer Research, Chicago, Illinois, April 14-18, 2018

Member, Program Committee, Intelligent Systems for Molecular Biology, Chicago, Illinois, July 6-10, 2018

Associate Editor, IEEE International Symposium on Biomedical Imaging, Prague, Czech Republic, April 8-11, 2019

Member, Program Committee, Intelligent Systems for Molecular Biology, Basel, Switzerland, July 21-25, 2019

Member, Program Committee, Intelligent Systems for Molecular Biology, Montreal, Canada, July 12-16, 2020

Member, Program Committee, Intelligent Systems for Molecular Biology, Madison, Wisconsin, July 10-14, 2022

Co-Chair, Organizing Committee, 3rd Nobel Turing Challenge Initiative Workshop, Pittsburgh, Pennsylvania, July 11-12, 2023

 

Courses and Tutorials

Invited Tutorial “Signal and Image Processing Issues in Molecular and Cellular Imaging,” ICASSP 2005, Philadelphia, Pennsylvania, March 19, 2005

Invited Tutorial “Signal and Image Processing Issues in Molecular and Cellular Imaging” (with Christos Faloutsos), SIGMOD 2005, Baltimore, Maryland, June 14, 2005

Faculty Member, Tenth Annual Course on 3D Microscopy of Living Cells, University of British Columbia, Vancouver, BC, June 16-24, 2005

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 für Biosystems Analyse, Freiburg, Germany, July 14, 2009

Short Course, “Bioimage Informatics: Automated Image Analysis and Modeling”, Biogem, Ariano Irpino, Italy, July 7-9, 2010

Invited Faculty Member, International Symposium in Applied Bioimaging, Porto, Portugal, September 20-21, 2012

Invited Faculty Member, EMBO Practical Course on “Intravital Microscopy, Flow Cytometry and Cell Sorting”, Berlin, Germany, July 7-12, 2013

Instructor and Co-Organizer, MMBioS Workshop on “Computational Methods for Spatially Realistic Microphysiological Simulations”, Pittsburgh, April 28-30, 2014

Instructor and Co-Organizer, MMBioS Workshop on “Computational Methods for Spatially Realistic Microphysiological Simulations”, Pittsburgh, April 27-29, 2015

Instructor, Bioinformatics Course, University of Freiburg, July 20-24, 2015

Instructor and Co-Organizer, MMBioS Workshop on “Computational Methods for Spatially Realistic Microphysiological Simulations”, Pittsburgh, June 1-3, 2016

Instructor, Bioinformatics Course, University of Freiburg, July 24-27, 2016

Instructor and Co-Organizer, MMBioS Workshop on “Computational Methods for Spatially Realistic Microphysiological Simulations”, Pittsburgh, June 26-28, 2017

Instructor and Co-Organizer, MMBioS Workshop on “Computational Methods for Spatially Realistic Microphysiological Simulations”, Seattle, Washington, March 7-9, 2018

Instructor and Co-Organizer, MMBioS Virtual Workshop on “Cell Modeling”, Pittsburgh, June 22-26, 2020

 

PROFESSIONAL SOCIETIES

 

American Association for Advancement of Science, American Institute for Medical and Biological Engineering (Fellow), American Society for Cell Biology, Institute of Electrical and Electronic Engineers (IEEE, Fellow), International Society for Advancement of Cytometry, International Society for Computational Biology (Senior Member)

 

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.

3.     Bioinformatics Research and Development: Second International Conference, BIRD 2008, Vienna, Austria, July 7-9, 2008 Proceedings (Communications in Computer and Information Science) (2008) M. Elloumi, J. Küng, R. Murphy, K. Schneider, C. Toma (eds.), Springer, Berlin.

4.     New Trends in Image Analysis and Processing, ICIAP 2013 Workshops: Naples, Italy, September 2013, Proceedings (Lecture Notes in Computer Science) (2013) A. Petrosino, L. Maddalena, P. Pala, V. Cantoni, M. Ceccarelli, R. F. Murphy, A. Del Bimbo, M. Pantic, C. Grana, J. Ooomen, G. Serra, M. Leo, D. P. Mandic, G. Pirlo, M. Fairhurst, D. Impedovo (eds.), Springer, Heidelberg.

 

PATENTS

 

R.F. Murphy, A. Rao, E. Glory-Afshar, J.Y. Newberg, S. Bhavani, A. Kumar. Identifying Location Biomarkers. U.S. patent number 9,092,850 (WO 2012100190).