Principal Investigator/Program Director (Last, First, Middle


Wang, Binghe

Provide the following information for the key personnel and other significant contributors in the order listed on Form Page 2. Follow this format for each person. DO NOT EXCEED FOUR PAGES. NAME POSITION TITLE

McDonald, John F.

Professor and Chair

EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.) INSTITUTION AND LOCATION DEGREE (if applicable) YEAR(s) FIELD OF STUDY

Assumption College, Worcester, Massachusetts University of California, Davis, California,
University of California, San Diego (La Jolla)

B.A. Ph.D. NIH Fellow

1969 1977 1978-1980

Biology/Philosophy Genetics

A. Positions and Honors. List in chronological order previous positions, concluding with your present position. List
any honors. Include present membership on any Federal Government public advisory committee. Positions

1978.1980 1980.1982 1983.1984 1984-1985 1986-1990 1987 1989 1990-2004 1998-2004 2000-2002 2001-2002 2000.2002 2002-present 2004-present

NIH Post-Doctoral Fellow, UC San Diego Assistant Professor, Iowa State University Associate Professor, Iowa State University Visiting Professor, Waksman Institute, Rutgers University Associate Professor, University of Georgia Visiting Professor, University of Mainz, Mainz, Germany Visiting Professor, Columbia Medical School, Cancer Instituite Professor, University of Georgia Department Head, Genetics, University of Georgia Chairman, UGA Bioinformatics Committee Interim Director, Institute of Bioinformatics, University of Georgia UGA representative on the Georgia Research Alliance Bioinformatics Cluster Chief Scientific Officer, Ovarian Cancer Institute (Atlanta) Chair, School of Biology, Georgia Institute of Technology

Honors and recognitions


Elected Fellow, American Association for the Advancement of Science (AAAS)
Selected relevant publications since 2002 (in chronological order, out of 115).

Menendez, L., N. Bowen, E. Dickerson, L. Matyrunina 2006. Identification of candidate methylation-responsive genes in ovarian cancer (in press). McDonald, JF, C. Moreno, N. Bowen, E. Dickerson, N. Schubert, L. Matyrunina. 2006. Comparative gene expression analysis of ovarian cancer patients treated with neo-adjuvant chemotherapy (in press). Bowen NJ, Logani S, Dickerson EB, Akhtar M, Benigno BB, McDonald JF. Evidence of a Role for PAX8 in Ovarian Cancer. In Press. Polavarapu, N., N. Bowen and J. F. McDonald 2006. Characterization of nine newly identified human endogenous retroviruses.J. Virology 80: 4640-4642. Polavarapu, N., N. Bowen and J. F. McDonald 2006. Identification and characterization of chimpanzee LTR retrotransposons. J. Virology 80: 4640-4642. Genome Biol. 7:R51. Herrera, R. J., R. Lowery, A. Alfonso, J. F. McDonald and J. Luis (2006). Ancient retroviral insertions among human populations. J. Human Genetics 51: 353-362. Ganko, E., C. Greene, J. Lewis, V. Bhattacharjee and J. F. McDonald. (2006) LTR retrotransposon-gene associations in D. melanogaster. J Mol Evol. 62: 111-120.
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Biographical Sketch Format Page

Principal Investigator/Program Director (Last, First, Middle):

De Barry. J., E. Ganko and J. F. McDonald. (2006). The contribution of LTR retrotransposons sequences to gene evolution in Mus musculus. Mol Biol Evol . 23: 479-481. McDonald, J.F., Matzke, M.A. and A.J. Matzke. (2005). Host defenses to transposable elements and the evolution of genomic imprinting. Cytogenet Genome Res. 110: 242-249. Warrenfeltz, S., Pavlik, S. Datta, S., Kraemer, E. Benigni, B. and J. F. McDonald (2005).Gene expression profiling of epithelial ovarian tumours correlated with malignant potential. Molecular Cancer 3:27-44.. Menendez, L., Benigno, B. and J. F. McDonald. 2004. L1 and HERV-W retrotransposons are hypomethylated in human ovarian carcinomas. Molecular Cancer 3:12-17. Calhoun, J., Rao, R., Warrenfeltz, S., Rekaya, R, Dalton, S., McDonald, J and S. Stice. 2004. Transcriptional profiling of initial differentiation events in human embryonic stem cells. Bichem Biophys Tes Comm 323: 453-464. Franchini, L.F., Ganko, E. W. and J.F. McDonald. (2004). Retrotransposon-gene associations are widespread among D. melanogaster populations. Mol Biol Evol. 21: 1323-1331. Gao, L., McCarthy,E., Ganko, E. and J.F. McDonald. (2004). Evolutionary history of O. sativa LTR retrotransposons: a preliminary survey of the rice genome sequences. BMC Genomics 5:18-36. Ganko, E.W., Bhattacharjee, V., Schliekelman, P. and J.F. McDonald. (2003). Evidence for the contribution of LTR retrotransposons to C. elegans gene evolution. Mol Biol Evol 20: 1925-1931. McCarthy, E.M., and J. F. McDonald (2003). A new search program for the identification of LTR retrotransposons from large genomic databases. BioInformatics19:362-367. McCarthy, E.M., J. Liu, J., L. Gao, and J. F. McDonald (2002). Long terminal repeat retrotransposons of Oryza sativa. Genome Biology, September 2002. Jordan, I.K., and J.F. McDonald (2002). A biologically active family of human endogenous retroviruses evolved from an ancient inactive lineage. Genome Letters 1:105-109. McCollum, A., Ganko, E., Barrass, P., Rodriguez, J., and McDonald, J.F. (2002). Evidence for the adaptive significance of an LTR retrotransposon sequence in a Drosophila heterochromatic gene. Bio Med Central (Evolutionary Biology) 2:5 ( Bowen, N. and J. F. McDonald (2001). Drosophila LTR retrotransposons are much younger than the host species in which they reside. Genome Research 11:1527-1540. Ganko, E., K. Fielman, K. and J.F. McDonald (2001). Genomic analysis of C. elegans retroviral elements. Genome Research 11: 2066-2074. Jordan, I.K. and J. F. McDonald, (2000). Comparative genomics and evolutionary dynamics of Saccharomyces cerevisiae Ty elements. Genetica 107: 3-14. Miller, W. and J. F. McDonald, (2000). Enhancer of P-element mobility: Functional studies on a domesticated TE-derived neogene in Drosophila. Genetica 107: 197-208. McDonald, J. F. (1999). Genomic imprinting as a co-opted evolutionary character. Trends. Ecol. Evol. 13: 94-95. Bowen, N. and J. F. McDonald, (1999). Genomic analysis of Caenorhadditis elegans reveals ancient families of retroviral-like elements. Genome Research 9: 924-935. Jordan, I. K. and J.F. McDonald. (1999). Evidence for the recent horizontal transfer of an LTR retrotransposon. Proc. Natl. Acad. Sci., USA. 96: 12621-12625. Jordan, I.K. and J.F. McDonald. (1999). Phylogenetic perspective reveals abundant Ty1/Ty2 hybrid elements in the Saccharomyces cerevisiae genome. Mol. Biol. Evol. 16: 419-422. Jordan, I.K. and J.F. McDonald. (1999). Tempo and mode of yeast retrotransposon evolution. Genetics 151: 1341-1351. Jordan, I.K. and J.F. McDonald, (1999). The role of interelement selection in Saccharomyces cerevisiae Ty element evolution. J. Mol. Evol. 49: 352-357. Promislow, D. L., I. K. Jordan and J. F. McDonald, (1999). Genome demography: a life-history analysis of transposable element evolution. Proc. R. Soc. Lond. B. 266: 1555-1560. Jordan, I. K. and J. F. McDonald, (1998). Evidence for the role of recombination in the regulatory evolution of Saccharomyces cerevisiae Ty elements. J. Mol. Evol. 47: 14-20. Jordan, I. K. and J. F. McDonald, 1998. Inter-element selection in the regulatory region of the copia retrotransposon. J. Mol. Evol. 47: 670-676. Jordan, K. and J. McDonald, 1998.Evolution of the copia retrotransposon in the Drosophila melanogaster species subgroup. Mol. Bio. and Evol. 15: 1160-1171. McDonald, J. 1998. Transposable elements, gene silencing and macroevolution. Trends Ecol. Evol. 13: 94-95. Wilson, S., L. Matyunina and J. McDonald, 1998. An enhancer region within the copia untranslated leader which is variable in natural populations contains binding sites for Drosophila regulatory proteins. Gene 209:239-246.
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Principal Investigator/Program Director (Last, First, Middle):

McDonald, J., 1997. LTR retrotransposons and the evolution of eukaryotic enhancers. In Transposable Elements and Evolution (P. Capy, ed.), Kluwer Press. Matyunina, L., K. Jordan and J.F. McDonald. 1996. Naturally occurring variability in copia expression is due to both element (cis-) and host (trans-) genetic variation. Proc. Natl. Acad. Sci., USA, Vol. 93, p. 7097-7102. BOOKS: 1. Lambert, ME, JF McDonald and IB Weinstein. 1988. Eukaryotic Transposable Elements as Mutagenic Agents. Cold Spring Harbor Press. 2. McDonald, J. 1993. Transposable Elements and Evolution, Kluwer Press, Dordrecht Holland. 3. Atherly, A., Gurdon, J. and McDonald, J. 1999. The Science of Genetics, (Introductory Genetics text) Saunders Press, Philadelphia. 4. McDonald, J. 2000. Georgia Genetics Review, Vol I. Transposable Elements and Genome Evolution., Kluwer Press, Dordrecht, Holland. PATENTS: 1. 2004. Global analysis of transposable elements as molecular markers of the developmental potential of stem cells. (# 60/466,801) 2. 2004 Global analysis of transposable elements as molecular markers of cancer. (#60/466,798).

1. of an Oligonucleotide Microarray for Human Retrotransposon. J. McDonald & N. Schubert (PIs). DOD. $ $257,054 (DC). 3. RetroChip - Development of a novel oligonucleotide microarray for human retrotransposons" $274,847 (direct costs)

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