Biography: Dr. Lemkin is a Principal Investigator in the Image Processing and Database Analysis Group, Laboratory of Experimental and Computational Biology, CCR, NCI. Dr. Lemkin received his Ph.D. from the University of Maryland, Department of Computer Science. The focus of his Ph.D. dissertation was the computer analysis of microscope cell images. He has concentrated on applying image analysis, database, exploratory analysis, and Internet technologies to the automation of microarray and proteomics data mining, 2D PAGE protein gel analysis, and other biomedical databases. He has a long-standing interest in the application of exploratory data analysis, image processing, database techniques, Internet technologies, and collaborative computing to the analysis of biomedical problems.
Research Areas: The Image Processing Section conducts research in applying image analysis, database, exploratory analysis, and internet technologies to the computer analysis of biomedical problems. Current research areas include: 1) Open2Dprot - a community effort to create an n-dimensional protein expression data analysis system facility for various types of protein expression sources (open source at open2dprot.sourceforge.net); 2) image flicker comparison of 2D PAGE gels with integration with Internet reference databases; 3) MAExplorer - the MicroArray Explorer data mining tool for data discovery in cDNA and oligo microarrays (open source at maexplorer.sourceforge.net); 4) ProtPlot virtual 2D gel ProtPlot is a data-mining software tool for virtual 2D gels. Much of the work in the above projects was based on previous computer aided two-dimensional electrophoretic gel analysis using GELLAB-II system he developed in the 1980s-1990s and its integration with the Web for collaborative computing.
Currently 2D gel spot segmentation Seg2Dgel and 2D spot list matching CmpSpots pipeline module programs are available. See the Open2Dprot sub-projects Web page for the current status of additional pipeline processing modules, documentation and downloads.
The GELLAB-II software system
was an exploratory data analysis system for the analysis of sets of 2D
electrophoretic protein gel images. Much of the flavor of the
Open2Dprot, Flicker and MAExplorer proteomic and genomic data-mining
systems was based on ideas from the GELLAB-II project.
GELLAB-II incorporated image acquisition, processing, database
manipulation, graphics and statistical analysis. It had been applied
to a variety of experimental systems to track quantitative and
qualitative changes in one or more proteins among hundreds or
thousands of unaltered proteins. A composite gel database could be
"viewed" under different exploratory data analysis conditions and
statistical differences and subtle patterns elucidated from "slices"
of an effectively 3D database. Results were presented in a variety of
tables, plots or synthesized images [Lemkin PF et al.
Electrophoresis 1989;10(2):122-140; Robinson MK et
al. Electrophoresis 1995;16(7);1176-1183; Myrick JE et al.
Appl. & Theor. Electrophoresis 1993;335-346]. GELLAB-II
technology was transferred via a CRADA to CSPI/Scanalytics Inc. which
made a base-line version of this technology more readily available to
cancer researchers on inexpensive Microsoft Windows PCs as the GELLAB-II+ system.
Although the old GELLAB-II software is no longer available, much of
its functionality is now being incorporated in the more general and
modern open-source Open2Dprot.
Some of the data from previously analyzed with GELLAB-II projects
has been released for public use in the LECB
2D-gel databases. These consist of a number of 2D gel GIF image data
sets (over 300 gels) with machine readable annotation and landmark
databases.
Publications:
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Contact |
P. Lemkin |
LECB |
CCR, NCI
]
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