Carnegie Mellon University

 Robert F. Murphy

Ray and Stephanie Lane Professor of Computational Biology Emeritus

Administrative Assistant: Erin Driskill

 

Dr. Murphy’s group does both experimental and computational cell biology, with a particular emphasis on developing fully-automated methods to understand the subcellular locations of proteins and how they change during development or disease (location proteomics). They use machine learning methods to compare, classify and cluster spatiotemporal patterns in microscope images and construct generative models directly from images to capture the essence of each subcellular pattern as well as the variation in pattern from cell to cell. The goal is to identify all “subcellular location families”, how they change (especially during oncogenesis) and to provide generative models for each family that can be incorporated into systems biology simulations. They are particularly interested in active learning approaches to create closed loop systems of interpretation, modeling, experiment planning and automated data acquisition, enabling automated scientific discovery.

 Haoran Chen

Ph.D Student

 Jiayi Li

MS Student

 Paul Sun

Ph.D. Student

 Melody Wang

MS Student

 Gary Wilkins

Ph.D. Student

 Ted Zhang

Senior Research Programmer/Analyst

Highlighted Publications

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. 

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. 

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.

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. 

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. 

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. 

H. Sun and R.F. Murphy (2021) Evaluation of categorical matrix completion algorithms: toward improved active learning for drug discovery. Bioinformatics, in press.

Google Scholar

Highlighted Software

CellOrganizer v2.7.2 for Matlab, Docker and Galaxy [August 13, 2018]

OMERO.searcher LocalClient v1.3 [July 11, 2013]

SLIF release 2-2 [February 3, 2013]

OMERO.searcher Server v1.1.2 (for OMERO version 4.3.3) [May 16, 2012]

Software from Papers