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.

1. Open2Dprot open2dprot.sourceforge.net is a community effort to create an open source n-dimensional (n-D) protein expression data analysis system. It is being designed for a variety of protein data sources including 2D gels, 2D LC-MS, protein arrays and others. It is downloadable and could be used for data mining protein expression across sets of n-D data from research experiments. In the initial phase, pipeline processing modules are being created for 2-dimensional data including 2D-PAGE (polyacrylamide gel electrophoresis) and initial support for 2D LC-MS and other data. In the second phase, it will be expanded to handle a variety of data types from other n-D protein separation methods. Some of the modules have been released including sample accessioning, spot segmentation, spot pairing between samples.

   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.

2. Scientists around the world often work on similar image data, so the need to share results and compare data arises periodically. The new (Lemkin, 2005) open source http://open2dprot.sourceforge.net/Flickersoftware integrates access to Web reference gel databases to allow users to putatively identify proteins in their own gels by comparison with reference gel databases with identified proteins such as those on Swiss-2DPAGE. The Flicker computer method [Lemkin PF Electrophoresis, 1997;18:461-470.] was developed for comparing two 2-dimensional (2D) protein gels and other biomedical materials across the Internet as a Web applet. It uses image processing techniques including spatial warping, edge ehancement, etc. prior to image comparison using image flickering to make images easier to compare. Comparing similar samples created in different laboratories may help identify or suggest protein spot identification. 2D gel images and associated databases identifying proteins in these gels are more frequently appearing on the Internet. This now opens up the possibility of visually comparing one's own experimental 2D gel image data with data from another gel in a remote Internet database. An offshoot of this research has led to the creation of the 2DWG meta-database catalog of 2D gel images found on the World Wide Web. This searchable database is integrated with the Flicker Web tool to facilitate comparisons between gel images across the Internet and between labs.

3. MAExplorer (or MicroArray Explorer) maexplorer.sourceforge.net is an open source Java application running on a researcher's computer (Lemkin etal. Nucleic Acids Research 20(22) 4452-4459]. MAExplorer allows the exploratory data analysis of quantitative cDNA and ologo expression profiles across multiple microarrays. Data may be viewed and directly manipulated in images, scatter plots, histograms, tables, etc. with access to GeneBank and other Internet databases for sets of clones found to be of interest. It was being developed in a collaboration between the Laboratory of Genetics and Physiology (LGP, NIDDK) and the Laboratory of Exeperimental and Computational Biology (LECB,NCI). LGP has established a program designed to identify and understand genetic pathways operative during normal mammary gland development and tumorigenesis. It was initially used as a Web applet data mining as part of the Mammary Genome Anatomy Project (MGAP). It was rewritten as a Java application and made open-source on the http://maexplorer.sourceforge.net/ Web site contains extensive documentation, tutorials, downloads (both binary installers and source code), plug-in extensions and documentation on writing plugins, a data conversion wizard, etc.

4. ProtPlot is an open-source Java-based data-mining software tool for virtual 2D gels as part of the TMAP (Tissue Molecular Anatomy Program) Medhedad D, et.al., (2003) Proteomics 3(8): 1445-1453. It may be downloaded from http://tmap.sourceforge.net/ and run as a stand-alone application on your computer. An exploratory data analysis environment provides tools (scatter plots, expression profiles, clustering) for the data-mining of quantified virtual 2D gel (pIe, Mw, expression) data of estimated expression from the CGAP EST mRNA tissue expression database. This lets you look at the aggregated data in new ways using scatter plots, expression profiles and clustering using various data filtering criteria. As is well known, mRNA expression generally does not correlate well with protein expression as seen in 2D-PAGE gels (Ideker et.al., Science 292: 929-934, 2001). However, some new insights may occur by viewing the transcription data in the protein domain. If actual protein expression data is available for some of these tissues, it might be useful to compare mRNA estimated expression and actual protein expression. This tool may help find those proteins with similar expression and those that have quite different expression. This might be useful in thinking about new hypotheses for protein post-modifications or mRNA post-transcription processing. ProtPlot Java software is available at http://tmap.sourceforge.net/ and could be used with other types of protein expression data.

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:

1. Medjahed D, Lemkin P (2005) Proteome knowledge bases in the context of cancer. In Jorde, L. B., Little, P., Dunn, M., and Subramaniam, S. (Eds.): Genetics, Genomics, Proteomics and Bioinformatics, CRC Press, pp. 109-141.
   
2. Lemkin PF, Thornwall G, Evans J (2005) Comparing 2D Electrophoretic Gels Across Internet Databases. In J. Walker (ed), Protein Protocols Handbook, 3rd Edition. Humana Press, Totowa, NJ. pp 279-306. (PDF) (12Mb)
3. Ravichandran, V., Lubell, J., Vasquez, G. B., Lemkin, P., Sriram, R. D., and Gilliland, G. L. (2004) Ongoing development of two-dimensional polyacrylamide gel electrophoresis data standards. Electrophoresis 25(2): 297-308.
4. Medjahed D, Luke BT, Tontesh TS, Smythers GW, Munroe DJ, Lemkin PF (2003) Tissue Molecular Anatomy Project (TMAP): an expression database for comparative cancer proteomics.Proteomics 3(8): 1445-1453.
5. Lemkin PF (2003) Reference Manual - MAExplorer Microarray Exploratory Data Analysis. (Current version) (PDF).
6. Medjahed D, Smythers GW, Powell DA, Stephens RM, Lemkin PF, Munroe DJ (2003) "VIRTUAL2D" A web-accessible predictive database for proteomics analysis, Proteomics, 3(2): 129-138.
7. Lemkin PF, Thornwall G (2002) Comparing 2D Electrophoretic Gels Across Internet Databases. In J. Walker (ed), Protein Protocols Handbook, 2nd Edition. Humana Press, Totowa, NJ, pp. 197-214.
8. Lemkin PF, Thornwall G, Hennighausen L (2001) MicroArray Explorer - A Java-based Tool For Data Mining Microarrays. Paper presented at the AMS-IMS-SIAM Summer Conference on Statistics in Functional Genomics, June 10-14, 2001. (PDF).
9. Lemkin PF, Thornwall G, Walton K, Hennighausen L (2000) The Microarray Explorer tool for data mining of cDNA microarrays - application for the mammary gland, Nucleic Acids Research 20(22) 4452-4459. (PDF)
10. Lemkin PF, Myrick JM, Lakshmanan Y, Shue MJ, Patrick JL, Hornbeck PV, Thornwall G, Partin AW (1999) Exploratory data analysis groupware for qualitative and quantitative electrophoretic gel analysis over the Internet-WebGel. Electrophoresis 20(18) 3492-507. ( PDF)
11. Pannek J, Lakshmanan Y, Pound CR, Lemkin PF, Epstein JI, Partin AW (1999) Nuclear Shape and nuclear matrix protein composition in prostate and seminal vesicles. Urology 54(5) 934-939.
12. Lemkin PF, Thornwall G (1999) Flicker image comparison of 2-D gel images for putative protein identification using the 2DWG meta-database. Molecular Biotechnology 12(2) 159-172.
13. Lemkin PF (1997) 2DWG meta-database of 2D electrophoretic gel images on the Internet. Electrophoresis, 18, 2759-2773. [Extended paper]
14. Lemkin PF (1997) Comparing Two-Dimensional electrophoretic gels across the Internet. Electrophoresis, 18, 461-470. [Extended paper]
15. Lemkin PF (1997) Comparing 2D Electrophoretic gels across Internet databases. In 2-D Protocols for Proteome Analysis , Andrew Link (Ed), a book in Methods in Molecular Biology, Vol. 112, Humana Press, Totowa, NJ, pp 339-410.
16. Lemkin PF, Chipperfield M, Merril C, Zullo S (1996) A World Wide Web (WWW) server database engine for an organelle database, MitoDat. Electrophoresis 17(2), 556-572.
17. Merril C, Goldstein M, Myrick J, Creed, J. and Lemkin PF (1995) The protein disease database of human body fluids: I. Information management needs and fundamental design considerations. Applied and Theoretical Electrophoresis 5(2), 49-54. [Paper], and (PDF)
18. Lemkin PF, Orr GA, Goldstein M, Creed J, Myrick J, and Merril, C. (1995) The protein disease database of human body fluids: II. Computer methods and data issues. Applied and Theoretical Electrophoresis 5(2), 55-72.[Paper], and (PDF)
19. Lemkin PF, Orr G, Goldstein, MP, Creed J, Whitley E, Myrick JE, Merril CR (1995) The Protein Disease Database. Electrophoresis 16:1175.
20. Robinson MK, Myrick JE, Henderson LO, Coles CD, Powell MK, Orr GA, Lemkin PF (1995) Two-dimensional protein electrophoresis and multiple hypothesis testing to detect potential serum protein biomarkers in children with fetal alcohol syndrome. Electrophoresis 16, 1176-1183.
21. Lemkin PF (1995) Representations of protein patterns from 2D gel electrophoresis databases. In: Pickover, C., (Ed) The Visual Display of Biological Information, World Scientific Publishers, River Edge, New Jersey, pp 43-59.
22. Myrick JE, Lemkin PF, Robinson MK, Upton KM (1993) Comparison of the Bio Image VisageTM 2,000 and the GELLAB-II two-dimensional electrophoretic analysis systems. Appl. Theor. Electrophor. 3, 335-346.
23. Wu Y, Lemkin PF, Upton K (1993) A fast spot segmentation algorithm for 2D electrophoresis analysis. Electrophoresis 14, 1350-1356.
24. Lemkin PF, Wu Y, Upton K (1993) An efficient disk based data structure for rapid searching of quantitative two-dimensional gel databases. Electrophoresis 14, 1341-1350.
25. Lemkin PF (1993) Xconf: a network-based image conferencing system. Comput. Biomed. Res. 26, 1-27.
26. Lemkin PF, Myrick J, Upton K (1993) Splitting merged spots in two-dimensional polyacrylamide gel electrophoresis gel images. Appl. Theor. Electrophor. 3, 163-172 (1993)
27. Amberger A, Lemkin PF, Sonderegger P, Bauer HC (1993) ECGF and heparin determine differentiation of cloned cerebral endothelial cells in vitro. Molecular and Chemical Neuropathology 20, 33-43.
28. Amberger A, Tontsch U, Lemkin PF, Gabbiani G, Baueer HC (1992) Two cloned cerebral endothelial cell phenotypes: an in vitro model for angiogenesis. EXS 61, 244-249.
29. Rogan P, Lemkin PF, Klar A, Singh J, Strathern J (1991) Two-dimensional agarose gel electrophoresis of restriction-digested genomic DNA. Methods: A Companion to Methods Enzymol. 3(2), 91-97.
30. Lemkin PF, Rogan P (1991) Automatic detection of noisy spots in two-dimensional Southern blots. Appl. Theor. Electrophor. 2, 141-149.
31. Stoeckli ET, Lemkin PF, Kuhn TB, Ruegg MA, Heller M, Sonderegger P (1989) Identification of proteins secreted from axons of embryonic dorsal-root-ganglia neurons. Eur. J. Biochem. 180, 249-258.
32. Lemkin PF, Lester EP (1989) Database and search techniques for two-dimensional gel protein data: a comparison of paradigms for exploratory data analysis and prospects for biological modeling. Electrophoresis 10, 122-140.
33. Lemkin PF (1989) GELLAB-II, A workstation based 2D electrophoresis gel analysis system. In: Endler, T. and Hanash, S. (Eds) Proceedings of 2D Electrophoresis. Vienna Austria, Nov. 8-11, 1988, West Germany: VCH Press, pp 52-57.
34. Lemkin PF (1988) PSAIL: A portable SAIL to C compiler - Description and tutorial. SIGPLAN Notices 13(10), 149-169.
35. Sonderegger P, Lemkin PF, Lipkin L, Nelson P (1986) Coordinate regulation of the expression of axonal proteins by the axonal microenvironment. Dev. Biol. 118, 222-232.
36. Sonderegger P, Lemkin PF, Lipkin L, Nelson P (1985) Differential modulation of the expression of axonal proteins by non-neuronal cells of the peripheral and central nervous system. EMBO J. 4, 1395-1401.
37. Lemkin PF (1985) PSAIL- A portable SAIL compiled translator for C environments. Comput. Lang. 2, 39-45.
38. Lester EP, Lemkin, PF (1984) A 'GELLAB' computer assisted 2D gel analysis of states of differentiation in hematopoietic cells. In: Neuhoff, V. (Ed) Electrophoresis '84, Springer-Verlag Chemie, Basel, pp 309-311.
39. Lemkin PF, Sonderegger P, Lipkin L (1984) Identification of coordinate pairs of polypeptides: A technique for screening of putative precursor product pairs in 2D gels. Clin. Chem. 30, 1965-1971.
40. Lester EP, Lemkin PF, Lipkin LE (1984) Protein indexing in leukemias and lymphomas. Ann. N. Y. Acad. Sci. 428, 158-172.
41. Lemkin PF, Lipkin LE (1983) Database techniques for 2D electrophoretic gel analysis. In: Geisow, M. and Barrett, A. (Eds) Computing in Biological Science. Elsevier/North-Holland, pp 181-226.
42. Lemkin PF, Lipkin LE (1983) 2D Electrophoresis gel data base analysis: Aspects of data structures and search strategies in GELLAB. Electrophoresis 4, 71-81.
43. Lester, E.P., Lemkin, P.F., and Lipkin, L.E. (1983) States of differentiation in leukemias: A 2D gel analysis. In: Proceedings of 5th Annual Bristol Myers Symposium on Cancer Research. Chromosomes and Cancer: From Molecules to Man, Academic Press, pp 226-245.
44. Lemkin PF (1982) Some extensions to the GELLAB two-dimensional electrophoretic gel analysis system. Clin. Chem. 28, 840-849.
45. Lester EP, Lemkin PF, Lipkin LE (1982) A two-dimensional gel analysis of autologous T and B lymphoblastoid cell lines. Clin. Chem. 28, 828-839.
46. Lester EP, Lemkin PF, Lowery JF, Lipkin LE (1982) Human leukemias: a preliminary 2D electrophoretic analysis. Electrophoresis 3, 364-375.
47. Lester EP, Lemkin PF, Lipkin LE (1981) New dimensions in protein analysis - 2D gels coming of age through Image Processing. Analyt. Chem. 53, 390A-397A. (PDF)

48. Lemkin PF, Lipkin LE (1981) GELLAB: Multiple 2D electrophoretic gel analysis. In: Allen, R. and Arnaud (Eds) Electrophoresis '81. New York, W. De Gruyter. pp 401-411.
49. Lemkin PF, Lipkin LE (1981) GELLAB: a computer system for two-dimensional gel electrophoresis analysis. III. Multiple two-dimensional gel analysis. Comput. Biomed. Res. 14, 407-446.
50. Lemkin PF, Lipkin LE (1981) GELLAB: A computer system for 2D gel electrophoresis analysis. II. Pairing spots. Comput. Biomed. Res. 14, 355-380.
51. Lemkin PF, Lipkin LE (1981) GELLAB: a computer system for 2D gel electrophoresis analysis I. Segmentation of spots and system preliminaries. Comput. Biomed. Res. 14, 272-297.
52. Lester EP, Lemkin PF, Lipkin LE, Cooper HL (1981) A two-dimensional electrophoretic analysis of protein synthesis in resting and growing lymphocytes in vitro. J. Immunol. 126, 1428-1434.
53. Lester EP, Lemkin PF, Cooper HL, Lipkin LE (1980) Computer-assisted analysis of two-dimensional electrophoresis of human peripheral blood lymphocytes. Clin. Chem. 26, 1392-1402. (PDF)
54. Lipkin LE, Lemkin PF (1980) Data-base techniques for multiple two-dimensional polyacrylamide gel electrophoresis analyses. Clin. Chem. 26, 1403-1412. (PDF)
55. Lemkin PF, Lipkin L (1980) BMON2 - a distributed monitor system for biological image processing. Comput Programs Biomed 11, 21-42.
56. Lemkin PF, Lipkin L, Merril C, Shiffrin S (1980) Protein abnormalities in macrophages bearing asbestos. Environ. Health Perspect. 34, 75-89. (PDF)
57. Lemkin PF, Merril C, Lipkin L, Van Keuren, M, Oertel W, Shapiro B, Wade M, Schultz M, Smith E (1979) Software aids for the analysis of 2D gel electrophoresis images. Comput. Biomed. Res. 12, 517-544.
58. Lemkin PF, Shapiro B, Lipkin L, Maizel J, Sklansky J, Schultz M (1979) Preprocessing of electron micrographs of nucleic acid molecules for automatic analysis by computer. II. Noise removal and gap filling. Comput. Biomed. Res. 12, 615-630.
59. Lipkin L, Lemkin PF, Shapiro B, Sklansky J, (1979) Preprocessing of electron micrographs of nucleic acid molecules for automatic analysis by computer. Comput. Biomed. Res. 12, 279-289.
60. Lemkin PF, Lipkin L (1979) Use of the positive difference transform for RBC elimination in bone marrow smear images. Anal Quant Cytol 1, 67-76.
61. Lemkin PF (1979) An approach to region splitting. Comput. Graph. Image Process. 10, 281-288.
62. Lemkin PF (1979) Splitting touching nuclei in clusters of bone marrow smear cell images. Anal. Quant. Cytol..
63. Lemkin PF (1979) The boundary trace transform: an edge and region enhancement transform. Comput. Graph. Image Process. 9, 150-165.
64. Lemkin PF (1978) Bone marrow smear image analysis. College Park, MD, University of Maryland Computer Science Center TR-653, April, 1978, 156 pp. (PDF)
65. Lemkin, PF (1978) The run length map: A representation of contours and regions for efficient search and low level semantic encoding. College Park, MD, University of Maryland Computer Science Center TR-655, April, 1978, 60 pp. (PDF)
66. Shapiro B, Lemkin PF (1977) PRDL - Procedural Description Language. NCI/IP TR-15, 10-10-1977. NTIS Accession No. PB273112/AS Springfield, Va., 1977, 23 pp. (PDF)<
67. Carman G, Lemkin, PF, Schultz M, Lipkin L, Shapiro B (1977) Microprogram control architecture for the General Picture Processor. NCI/IP TR-22, 4-22-1977. NTIS Accession No. PB269762/AS, Springfield, VA, 1977, 35 pp. (PDF)
68. Lemkin PF (1976) BMOMNI - Fortran interface program for the RTPP buffer memory, Quantimet and control desk. NCI/IP TR-23, 12-14-1976. NTIS Accession No. PB261538/AS, Springfield, VA, 1976, 10 pp. (PDF)
69. Lemkin PF, Shapiro B, Schultz M, Lipkin L, Carman G (1976) GPPASM - A PDP8e assembler for the General Picture Processor. NCI/IP TR-16, 12-15-1976. NTIS Accession No. PB261537/AS, Springfield, VA, 1976, 45 pp. (PDF)
70. Lemkin PF (1976) Buffer memory monitor system for interactive image processing. NCI/IP TR-21, 3-31-1976, and TR-21b, 3-17-1978. NTIS Accession No. PB261536/AS, Springfield, VA, 26 pp. (PDF TR-21), and (PDF TR-21b)
71. Lemkin PF, Carman G, Lipkin L, Shapiro B, Schultz, M (1976) Real time picture processor: Description and specification. NCI/IP TR-7, 2-31-1976, and TR-7a, 6-23-1977. NTIS Accession No. PB252268/AS, Springfield, VA, 139 pp. (PDF), and (PDF TR-7a)
72. Lemkin PF (1976) DDTG - Functional specification for the RTPP monitor. NCI/IP TR-2, 2-5-1976. NTIS Accession No. PB250726/AS, Springfield, VA, 1976, 90 pp. (Also in DECUS No. 8-823). (PDF)
73. Lemkin, PF, Shapiro B, Gordon R, Lipkin L (1976) PROC10 - An image processing system for the PDP10: Description and specification. NCI/IP TR-8, 12-16-1976. NTIS Accession No. PB261535/AS. Springfield, Va., 1976, 53 pp. (Also in DECUS No. 10-270). (PDF)
74. Carman G, Lemkin PF, Lipkin L, Shapiro, B, Schultz M, Kaiser P (1974) A real time picture processor for use in biologic cell identification. II. Hardware implementation. J. Histochem. Cytochem. 22, 732-740. (PDF)
75. Lemkin PF, Carman G, Lipkin L, Shapiro B, Schultz M, Kaiser P (1974) A real time picture processor for use in biologic cell identification. I. System design. J. Histochem. Cytochem. 22, 725-731. (PDF)
76. Shapiro B, Lemkin P, Lipkin L, (1974) The application of artificial intelligence techniques to biologic cell identification. J. Histochem. Cytochem. 22, 741-750. (PDF)
77. Schultz ML, Lipkin LE, Wade MJ, Lemkin PF, Carman GM (1974) High resolution shading correction. J. Histochem. Cytochem. 22, 751-754. (PDF)
78. Lipkin LE, Lemkin PF, Carman G (1974) Automated autoradiographic grain counting in human determined context. J. Histochem. Cytochem. 22, 755-765. (PDF)
79. Shapiro H, Bryan S, Lipkin L, Stein P, Lemkin PF (1971) Computer-aided microspectrophotometry of biological specimens. Exp. Cell Res. 67, 81-89.
80. Lemkin PF (1967) Theoretically unlimited band width frequency divider. Proc. IEEE 1645-1646.