Murphy Lab - Home

New! v1.8! New! v1.1.2!

Welcome to the Murphy lab at Carnegie Mellon University. The lab is a multidisciplinary environment with people working on projects in computational cell biology.

April 2, 2013	CellOrganizer v1.8.1 has been released. The primary goal of this release was to add the resolution of the dataset to the model trainer graphical user interface.
March 11, 2013	CellOrganizer v1.8.0 has been released. The primary new feature is the ability to generate cell and nuclear shapes from diffeomorphic models.
January 24, 2013	Congratulations to Dr. Joshua Kangas for successfully defending his thesis entitled, "Active Learning for Drug Discovery." Dr. Kangas will be joining a new startup, Quantitative Medicine, LLC, as cofounder and Chief Science Officer.
January 15, 2013	A review article from our group on automated image analysis methods for high-content screening and analysis was awarded the 2013 JBC Authors' Choice Award at the annual meeting of the Society for Laboratory Automation and Screening.
January 9, 2013	A new version of OMERO.searcher Local Client has been released, along with a content database for the PSLID RandTag2 database also released today. This version permits searching of both OMERO and non-OMERO databases and supports user-defined feature sets.
January 9, 2013	A significantly expanded collection of images and sequences from the RandTag project has been released. Automated analysis of the images of CD-tagged NIH 3T3 clones in which the tagged gene has been identified permitted the assignment of subcellular location for a number of previously unannotated or minimally-annotated proteins.
November 30, 2012	Two articles in PLoS ONE describe results from our collaboration with the Human Protein Atlas. In the first, analysis of images of eleven cultured cell lines reveals that accounting for differences in cell shape and size reduces apparent variation in microtubule distribution. Accounting for this, three groups of cell lines remain distinguishable. In the second, computational analysis identified proteins whose annotations from visual analysis were incorrect.
November 28, 2012	Congratulations to Dr. Jieyue Li for successfully defending his thesis entitled, "Automated Learning of Subcellular Location Patterns in Confocal Fluorescence Images from Human Protein Atlas." Dr. Li has accepted a position as Machine Learning Expert at ZestFinance in Los Angeles, California.
September 4, 2012	CellOrganizer v1.7.1 released. Support added for exporting object files from TIF files of synthesized images.
August 8, 2012	CellOrganizer v1.7 released. Support added for output as indexed images, blender object files, and SBML Spatial extension.
May 16, 2012	OMERO.searcher v.1.1.2 released! Provides content-based searching of OMERO databases with local or remote images.
April 13, 2012	CellOrganizer v1.6 released! Supports 2D/3D images and vesicle and microtubule pattern models.
December 19, 2011	Dr. Murphy named to the NIH Council of Councils.
September 7, 2011	Murphy Lab member Luis Pedro Coelho named to the 2012 class of Siebel Scholars. The Siebel Scholars program recognizes the most talented students at the world's leading graduate schools of business, bioengineering, and computer science.
September 5, 2011	Video of Dr. Murphy's talk at the COMBINE 2011 meeting is available online.
January 10, 2011	Work from Murphy group featured in Nature Biotechnology article on Computational Biology breakthroughs in 2010.
September 18, 2010	Murphy Lab member Tao Peng wins the 2009 Research Award from Carnegie Mellon's Biomedical Engineering Department. One award is given each year to the BME graduate student judged to have the most outstanding research achievement.
July 11, 2010	New release 2.0 of PatternUnmixer (formerly called PUnmix). The new version supports reading images from OMERO servers, displaying object distributions, checking for the presence of unknown patterns, and exporting unmixing fractions. See the Software link.
August 22, 2009	Murphy Lab member Luis Pedro Coelho wins the CPCB Outstanding Research Achievement Award.
July 8, 2009	Collection of hand-segmented nuclear images and python code for comparing segmentation methods released. See the Software link.
July 1, 2009	New PSLID release containing images from over 2,500 clones generated by the RandTag project.
April 6, 2009	Releases of SLML Tools and PUnmix are available under the Software link. These packages implement learned, generative models of subcellular patterns and estimation of pattern unmixing fractions, respectively. Matlab source code, as well as compiled versions for Linux, Mac OS, and Windows, are available.

The primary focus of current work in the lab is on automated interpretation of fluorescence microscope images.

If you are interested in reading more about our work, a list of publications is available.

Slides from Dr. Murphy's tutorials at meetings like the ISAC Congress and the SBS Conference are available under the presentations link.

Select data generated from Murphy Lab projects is available for download.

Last Updated: 03 Apr 2013

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