The Lemkin Group

Peter F. Lemkin, Ph.D.

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  1. Gibson F, Anderson L, (2008) Guidelines for reporting the use of gel electrophoresis in proteomics. Nature Biotechnology 26(8): 863-864. (PDF)
  2. Lemkin PF, Thornwall G, Evans J (2009) Comparing 2D Electrophoretic Gels Across Internet Databases. In J. Walker (ed), Protein Protocols Handbook, 3rd Edition. Humana Press, Totowa, NJ, Chapter 40, pp 409-441. ((working paper PDF)
  3. Medjahed D, Lemkin P (2005) Proteome knowledge bases in the context of cancer. In S. Srivastava (ed), Informatics In Proteomics, CRC Press, pp. 109-140. (PDF)
  4. Lemkin PF, Thornwall G, Evans J (2005) Comparing 2D Electrophoretic Gels Across Internet Databases. In J. Walker (ed), The Proteomics Protocols Handbook, 3rd Edition. Humana Press, Totowa, NJ. pp 279-306. (PDF) (12Mb)
  5. 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 (PDF)
  6. 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. (PDF)
  7. Lemkin PF, Thornwall G, Alvord WG, Lubomirski M, Sundaram(2003) Extending MicroArray Explorer with R Language Scripts. Poster: Frederick Bioinformatics Forum June 24, 2003. (PDF)
  8. Lemkin PF, Thornwall GC, Evans J (2003) Microarray Analysis using the MicroArray Explorer. In G. Parmigiani, E.S. Garrett, R.A. Irizarry, S.L. Zeger (eds) The Analysis of Gene Expression Data: Methods and Software, Springer-Verlag, New York, pp. 229-253. (PDF).
  9. Lemkin PF (2003) Reference Manual - MAExplorer Microarray Exploratory Data Analysis.(PDF).
  10. 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. (PDF)
  11. 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. (PDF)
  12. Lemkin PF, Thornwall G, Hennighausen L (2001) MicroArray Explorer - A Java-based Tool For Data Mining Microarrrays. Paper presented at the AMS-IMS-SIAM Summer Conference on Statistics in Functional Genomics, June 10-14, 2001. (PDF).
  13. 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)
  14. Lemkin PF, Thornwall G, Wagner U, Hennighausen L (1999) MAExplorer microarray exploratory data analysis, Nature Genetics 57 doi:10.1038/14346. (PDF)
  15. 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)
  16. 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. ((PDF))
  17. 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. (PDF)
  18. Lemkin PF (1997) 2DWG meta-database of 2D electrophoretic gel images on the Internet. Electrophoresis, 18, 2759-2773. (PDF)
  19. Lemkin PF (1997) Comparing Two-Dimensional electrophoretic gels across the Internet. Electrophoresis, 18, 461-470. (PDF)
  20. Lemkin PF (1997) Comparing 2D Electrophoretic gels across Internet databases. In Andrew Link (Ed) 2-D Protocols for Proteome Analysis, a book in Methods in Molecular Biology, Vol. 112, Humana Press, Totowa, NJ, pp 339-410.
  21. 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. (PDF)
  22. 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. (PDF)
  23. 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. (PDF)
  24. Lemkin PF, Orr G, Goldstein, MP, Creed J, Whitley E, Myrick JE, Merril CR (1995) The Protein Disease Database. Electrophoresis 16:1175. (PDF)
  25. 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. (PDF)
  26. Lemkin PF (1995) Representations of protein patterns from 2D gel electrophoresis databases. In: Pickover, C. (ed) Visualizing Biological Information, World Scientific Publishers, River Edge, New Jersey, pp 43-59.
  27. 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. Applied and Theoretical Electrophoresis 3, 335-346. (PDF)
  28. Wu Y, Lemkin PF, Upton K (1993) A fast spot segmentation algorithm for 2D electrophoresis analysis. Electrophoresis 14, 1350-1356. (PDF)
  29. 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. (PDF)
  30. Lemkin PF (1993) Xconf: a network-based image conferencing system. Comput. Biomed. Res. 26, 1-27. (PDF).
  31. Lemkin PF, Myrick J, Upton K (1993) Splitting merged spots in two-dimensional polyacrylamide gel electrophoresis gel images. Applied and Theoretical Electrophoresis 3, 163-172 (1993) (PDF).
  32. 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. (PDF)
  33. 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. (PDF)
  34. 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. (PDF)
  35. Lemkin PF, Rogan P (1991) Automatic detection of noisy spots in two-dimensional Southern blots. Applied and Theoretical Electrophoresis 2, 141-149 (PDF)
  36. 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. (PDF)
  37. 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. (PDF)
  38. 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.
  39. Lemkin PF (1988) PSAIL: A portable SAIL to C compiler - Description and tutorial. SIGPLAN Notices 13(10),149-169 PDF)
  40. 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. (PDF)
  41. 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. (PDF)
  42. Lemkin PF (1985) PSAIL- A portable SAIL compiled translator for C environments. Computer Languages 2, 39-45. ()
  43. 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. (PDF)
  44. 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.
  45. Lester EP, Lemkin PF, Lipkin LE (1984) Protein indexing in leukemias and lymphomas. Ann. N. Y. Acad. Sci. 428, 158-172.
  46. Howard RJ, Aley SB, Lemkin PF (1983) High resolution comparison of clones of different variant antigen phenotypes by two-dimensional gel electrophoresis and computer analysis. Electrophoresis 4 420-427. (PDF)
  47. 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. (PDF)
  48. Lemkin PF, Lipkin LE (1983) 2D Electrophoresis gel data base analysis: Aspects of data structures and search strategies in GELLAB. Electrophoresis 4, 71-81. (PDF)
  49. 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. (PDF)
  50. Lemkin PF (1982) Some extensions to the GELLAB two-dimensional electrophoretic gel analysis system. Clin. Chem. 28, 840-849. (PDF)
  51. 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.
  52. Lester EP, Lemkin PF, Lowery JF, Lipkin LE (1982) Human leukemias: a preliminary 2D electrophoretic analysis. Electrophoresis 3, 364-375. (PDF)
  53. 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)
  54. 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.
  55. 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. (PDF)
  56. Lemkin PF, Lipkin LE (1981) GELLAB: A computer system for 2D gel electrophoresis analysis. II. Pairing spots. Comput. Biomed. Res. 14, 355-380. (PDF)
  57. 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. (PDF)
  58. 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.
  59. Lester EP, Lemkin PF, Lipkin LE (1981) New Dimensions in Protein Anallysis. Analytical Chem. 53,290A. (PDF)
  60. 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)
  61. Lipkin LE, Lemkin PF (1980) Data-base techniques for multiple two-dimensional polyacrylamide gel electrophoresis analyses. Clin. Chem. 26, 1403-1412. (PDF)
  62. Lemkin PF, Lipkin L (1980) BMON2 - a distributed monitor system for biological image processing. Comput Programs Biomed 11, 21-42. (PDF). Here is more discussion and the BMON2 source code.
  63. Lemkin PF (1976) Buffer memory monitor system for interactive image processing. NCI/IP TR-21, 3-31-1976. NTIS Accession No. PB261536/AS, Springfield, VA, 26 pp. (PDF)
  64. Lemkin PF, Lipkin L, Merril C, Shiffrin S (1980) Protein abnormalities in macrophages bearing asbestos. Environ. Health Perspect. 34, 75-89. (PDF)
  65. 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. (PDF)
  66. 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. (PDF)
  67. 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. (PDF)
  68. 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. (PDF)
  69. Lemkin PF (1979) An approach to region splitting. Comput. Graph. Image Process. 10, 281-288. (PDF)
  70. Lemkin PF (1979) Splitting touching nuclei in clusters of bone marrow smear cell images. Anal. Quant. Cytol..
  71. Lemkin PF (1979) The boundary trace transform: an edge and region enhancement transform. Comput. Graph. Image Process. 9, 150-165.
  72. Lemkin PF (1978) Bone marrow smear image analysis. College Park, MD, University of Maryland Computer Science Center TR-653, April, 1978, 156 pp. (PDF)
  73. 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)
  74. 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)
  75. Lemkin PF (1977) Real Time Picture Processor: Description and specification. TR-7a, 6-23-1977. NTIS Accession No. PB269600/AS, Springfield, VA, 1977, 185 pp. (PDF TR-7a)
  76. 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. NTIS Accession No. PB252268/AS, Springfield, VA, 139 pp. (PDF)
  77. 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)
  78. 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)
  79. 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)
  80. 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)
  81. 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)
  82. Shapiro B, Lemkin P, Lipkin L, (1974) The application of artificial intelligence techniques to biologic cell identification. J. Histochem. Cytochem. 22, 741-750. (PDF)
  83. Schultz ML, Lipkin LE, Wade MJ, Lemkin PF, Carman GM (1974) High resolution shading correction. J. Histochem. Cytochem. 22, 751-754. (PDF)
  84. Lipkin LE, Lemkin PF, Carman G (1974) Automated autoradiographic grain counting in human determined context. J. Histochem. Cytochem. 22, 755-765. (PDF)
  85. Shapiro H, Bryan S, Lipkin L, Stein P, Lemkin PF (1971) Computer-aided microspectrophotometry of biological specimens. Exp. Cell Res. 67, 81-89. (PDF)
  86. Lemkin PF (1967) Theoretically unlimited band width frequency divider. Proc. IEEE.55(9),1645-1646. (PDF) [circuit]

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Revised: Feb 16, 2024
Note: Some of the links have changed over time and were corrected as of 9/23/2023.