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Robert F. Murphy (computational biologist)

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Bob Murphy
Alma mater
Scientific career
Fields
Institutions
Doctoral advisorJames F. Bonner
Websitewww.andrew.cmu.edu/user/murphy/

Robert F. Murphy is Ray and Stephanie Lane Professor of Computational Biology Emeritus and Director of the M.S. Program in Automated Science at Carnegie Mellon University. Prior to his retirement in May 2021, he was the Ray and Stephanie Lane Professor of Computational Biology as well as Professor of Biological Sciences, Biomedical Engineering, and Machine Learning. He was founding Director (with Jelena Kovacevic[1]) of the Center for Bioimage Informatics at Carnegie Mellon and founded (with Ivet Bahar) the Joint CMU-Pitt Ph.D. Program in Computational Biology. He also founded the Computational Biology Department at Carnegie Mellon University (originally the Lane Center for Computational Biology) and served as its head from 2009 to 2020.

Biography

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Prior to arriving at Carnegie Mellon, Murphy was a Damon Runyon Cancer Research Foundation postdoctoral fellow with Dr. Charles R. Cantor at Columbia University from 1979 through 1983. Murphy earned an A. B. in biochemistry from Columbia College in 1974 and a Ph.D. in biochemistry from the California Institute of Technology in 1980. He received a Presidential Young Investigator Award[2] from the National Science Foundation shortly after joining the faculty at Carnegie Mellon in 1983. In 2005, NIH selected him as the first full-term chair of its new Biodata Management and Analysis Study Section.[3] In 2006, he was named a Fellow of the American Institute for Medical and Biological Engineering.[4] In 2019, he was elected as a Fellow of the IEEE for his contributions to machine learning algorithms for biological images.[5] Murphy has received research grants from the National Institutes of Health, the National Science Foundation, the American Cancer Society, the American Heart Association, the Arthritis Foundation, and the Rockefeller Brothers Fund. He has co-edited two books and two special journal issues on “Cell and Molecular Imaging,” and published over 200 research papers.[6] He served as President of the International Society for the Advancement of Cytometry,[7] was named as the first External Senior Fellow of the School of Life Sciences in the Freiburg (Germany) Institute for Advanced Studies, and has been named as an Honorary Professor at the University of Freiburg. He was a member of the National Advisory General Medical Sciences Council and the National Institutes of Health Council of Councils.[8]

Murphy’s career has centered on combining fluorescence-based cell measurement methods with quantitative and computational methods. He and his collaborators did extensive work on the application of flow cytometry to analyze endocytic membrane traffic beginning in the early 1980s[9][10][11] and pioneered the application of machine learning methods to high-resolution fluorescence microscope images depicting subcellular location patterns in the mid-1990s.[12][13] This work led to the development of the first systems for automatically recognizing all major organelle patterns in 2D and 3D images.[14][15][16] He founded the CellOrganizer project for learning generative models of cell organization directly from microscope images. He also leads the image analysis and modeling efforts for the National Center for Multiscale Modeling of Biological Systems. He has also done extensive work on using active machine learning to drive biomedical discovery,[17][18][19] and founded the world’s first M.S. program in Automated Science. His research publications have been cited over 13,000 times and his h-index is 57[20]

Murphy’s leadership experience includes developing the first formal undergraduate program in computational biology in 1987 and founding the Merck Computational Biology and Chemistry program at Carnegie Mellon in 1999. These programs were important forerunners to the 2005 establishment of a Ph.D. program in computational biology in partnership with the University of Pittsburgh. Murphy cofounded Quantitative Medicine, LLC based upon work from his research group.[citation needed] The company was sold to Predictive Oncology, Inc.[21] in 2020.

References

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  1. ^ http://jelena.ece.cmu.edu/
  2. ^ "NSF Award Search: Award#8351364 - Presidential Young Investigator Award". www.nsf.gov. Retrieved 2016-03-29.
  3. ^ "Carnegie Mellon Press Release: March 3, 2005". www.cmu.edu. Archived from the original on 2016-03-07. Retrieved 2016-03-04.
  4. ^ "Fellow Directory - AIMBE". aimbe.org. Retrieved 2016-03-04.
  5. ^ "About the IEEE Fellow Program". IEEE. Retrieved 2019-12-09.
  6. ^ "Robert F. Murphy - Google Scholar Citations". scholar.google.com. Retrieved 2016-03-04.
  7. ^ International Society for the Advancement of Cytometry Past Presidents
  8. ^ New NIH Council of Councils members named, December 10, 2011
  9. ^ Murphy, R. F.; Jorgensen, E. D.; Cantor, C. R. (1982-02-25). "Kinetics of histone endocytosis in Chinese hamster ovary cells. A flow cytofluorometric analysis". Journal of Biological Chemistry. 257 (4): 1695–1701. doi:10.1016/S0021-9258(19)68093-2. ISSN 0021-9258. PMID 7056738.
  10. ^ Murphy, R. F.; Powers, S.; Cantor, C. R. (1984-05-01). "Endosome pH measured in single cells by dual fluorescence flow cytometry: rapid acidification of insulin to pH 6". The Journal of Cell Biology. 98 (5): 1757–1762. doi:10.1083/jcb.98.5.1757. ISSN 0021-9525. PMC 2113196. PMID 6144684.
  11. ^ Cain, C. C.; Sipe, D. M.; Murphy, R. F. (1989-01-01). "Regulation of endocytic pH by the Na+,K+-ATPase in living cells". Proceedings of the National Academy of Sciences of the United States of America. 86 (2): 544–548. Bibcode:1989PNAS...86..544C. doi:10.1073/pnas.86.2.544. ISSN 0027-8424. PMC 286508. PMID 2536168.
  12. ^ Boland, M. V.; Markey, M. K.; Murphy, R. F. (1997-10-01). "Classification of protein localization patterns obtained via fluorescence light microscopy". Proceedings of the 19th Annual International Conference of the IEEE Engineering in Medicine and Biology Society. 'Magnificent Milestones and Emerging Opportunities in Medical Engineering' (Cat. No.97CH36136). Vol. 2. pp. 594–597 vol.2. doi:10.1109/IEMBS.1997.757680. ISBN 978-0-7803-4262-0. S2CID 13518296.
  13. ^ Baker, Monya (2012-07-01). "The author file: Robert F. Murphy". Nature Methods. 9 (7): 629. doi:10.1038/nmeth.2088. ISSN 1548-7091.
  14. ^ Boland, M. V.; Murphy, R. F. (2001-12-01). "A neural network classifier capable of recognizing the patterns of all major subcellular structures in fluorescence microscope images of HeLa cells". Bioinformatics. 17 (12): 1213–1223. doi:10.1093/bioinformatics/17.12.1213. ISSN 1367-4803. PMID 11751230.
  15. ^ Glory, Estelle; Murphy, Robert F. (2007-01-01). "Automated subcellular location determination and high-throughput microscopy". Developmental Cell. 12 (1): 7–16. doi:10.1016/j.devcel.2006.12.007. ISSN 1534-5807. PMID 17199037.
  16. ^ Velliste, M.; Murphy, R. F. (2002-01-01). "Automated determination of protein subcellular locations from 3D fluorescence microscope images". Proceedings IEEE International Symposium on Biomedical Imaging. pp. 867–870. doi:10.1109/ISBI.2002.1029397. ISBN 978-0-7803-7584-0. S2CID 2730192.
  17. ^ Naik, Armaghan W.; Kangas, Joshua D.; Langmead, Christopher J; Murphy, Robert F. (2013-12-17). "Efficient Modeling and Active Learning Discovery of Biological Responses". PLOS ONE. 8 (12): e83996. Bibcode:2013PLoSO...883996N. doi:10.1371/journal.pone.0083996. PMC 3866149. PMID 24358322.
  18. ^ Naik, Armaghan W; Kangas, Joshua D; Sullivan, Devin P; Murphy, Robert F (2016-02-03). Ohler, Uwe (ed.). "Active machine learning-driven experimentation to determine compound effects on protein patterns". eLife. 5: e10047. doi:10.7554/eLife.10047. ISSN 2050-084X. PMC 4798950. PMID 26840049.
  19. ^ Sun, Huangqingbo (2021-10-15). "Evaluation of categorical matrix completion algorithms: toward improved active learning for drug discovery". Bioinformatics. 37 (20): 3538–3545. doi:10.1093/bioinformatics/btab322. PMC 8545350. PMID 33983377.
  20. ^ "Robert F. Murphy". scholar.google.com. Retrieved 2022-02-10.
  21. ^ "Predictive Oncology Completes Acquisition of Quantitative Medicine". GlobeNewsWire.
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