Biology

John McDonald, Professor and Associate Dean for Biology Program Development

Ph.D., Genetics, University of California Davis, 1977
john.mcdonald@biology.gatech.edu
Phone: 404-894-3735, 404-385-6630
Fax: (404) 894-0519
Office: CE 201 / IBB 3314

Publications

2009

Guan W, Zhou M, Hampton CY, Benedict B, Walker D, Gray A, McDonald JF. and Facundo, FM. 2009. Ovarian Cancer Detection from Metabolomic Liquid Chromatography/Mass Spectrometry Data by Support Vector Machines. BMC Bioinformatics. Aug 2009, 10:259

Arora G, Polavarapu N, McDonald JF.2009. Did Natural Selection for Increased Cognitive Ability in Humans Lead to an Elevated Risk of Cancer? Med. Hypotheses Apr 29 [Epub ahead of print] .

Blackburn W, Dickerson E, Smith M, McDonald JF, Lyon A.2009. Peptide- Functionalized Nanogels for Targeted siRNA Delivery. Bioconjugate Chemistry, Apr 2 [Epub ahead of print].

Mezencev R, Kutschy P, Salayová A, Updegrove T, McDonald JF. 2009.The design, synthesis and anticancer activity of new nitrogen mustard derivatives of natural indole phytoalexin 1-methoxyspirobrassinol. Neoplasma, 56(4): 321-330.

Carpendo RL, Bratt-Leal AM, Marklein RA, Seamen SA, Bowen NJ, McDonald JF, McDevitt TC. 2009.Homogeneous and organized differentiation within embyoid bodies induced by microsphere-mediated delivery of small molecules. Biomaterials, 30(13) :2507-15.

2008

Scharer CD, Laycock N, Osunkoya AO, Logani S, McDonald JF, Benigno BB, Moreno CS. 2008. Aurora kinase inhibitors synergize with paclitaxel to induce apoptosis in ovarian cancer cells. J Transl Med, Dec 11.6:79.

Arakaki A, Skolnick J, McDonald JF. 2008.Marker metabolites can be thereapeutic as well. Nature, Nov 27. 456 (7221): 443

Dickerson, E.B., Dreaden, E.C, Huang, X.,  Chu, X.,  Pushpanketh, S.,  McDonald, J.F and El-Sayed, M.A.  2008.  Gold nanorod assisted near infrared plasmonic photothermal therapy (PPTT) of HSC-3 tumors in mice. Cancer Lett. Sep 28.269 (1): 57-66.

Mezencev, R., Kutschy,P.  Salayová, A.  Curillová, Z.,   Mojzis, J., Pilatová, M.  and  McDonald, J.F.  2008.  Anticancer properties of 2-piperidyl analogues of the natural indole phytoalexin 1-methoxyspirobrassinol. Chemotherapy, Sep 4. 54 (5) : 372-78

Scarberry, K., Dickerson,E.B.,  McDonald, J.F. and Zhang, Z.J.  2008.Targeting and extraction of cancer cells in vitro and in vivo using magnetic nanoparticle-peptide conjugates. J. Am. Chem. Soc., Aug 6; 130 (31):10258-62

Abbott K.L., Nairn, A.V., Hall, E.M., Horton, M.B., McDonald, J.F., Moremen, K.W. , Dinulescu, D.W.  and Pierce, M.  2008.  Focused glycomic analysis for the N-linked glycan biosynthetic pathway in ovarian cancer, Proteomics . Aug 2008; 8 (16): 3210-20

Navare  A, Zhou, M , McDonald  JF , Noriega  FG, Fernandez FM, Serum Biomarker profiling  by solid phase extraction with particle embedded micro tips and matrix assisted laser desorption/ ionization mass spectrometry,   Rapid Commun Mass Spectrom, Apr 15, 22: 997.

Huda A, Polavarapu  N, Jordan  IK and McDonald JF, Endogenous  Retroviruses of the Chicken Genome, Biology Direct Mar 24, 3:9

Polavarapu  N., Marino-Ramirez, L., Landsman, D., McDonald, J.F. and Jordan, I.K. 2008. Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA, BMC Genomics May 17, 9 : 226.

Matyunina, L.V., Bowen N.J. and  McDonald ,J.F.  2008.  LTR retrotransposons and dosage compensation in Drosophila. 2008 BMC Mol. Biol. Jun 2008 9:55.

Menendez L., Walker, L.D., Matyunina, L.V,  Totten, K.A.,  Benigno, B.B.,  and  McDonald, J.F.  2008.  Epigenetic changes within the promoter region of the HLA-G gene in ovarian tumors. Mol. Cancer  May 2008 ; 7:43.

Arakaki, A.K., R. Mezencev, N.J. Bowen, Y. Huang, J.F. McDonald and J. Skolnick.  2008.  Identification of metabolites with anticancer properties by computational metabolomics. Mol. Cancer  Jun 2008; 7:57.

2007

Piriyapongsa J, Polavarapu N, Borodovsky M, McDonald J.2007. Exonization of the LTR transposable elements in human genome. BMC Genomics. Aug 28; 8(1); 291.

Moreno CS, Matyunina L, Dickerson EB, Schubert N, Bowen NJ, Logani S, Benigno BB, McDonald JF.2007.Evidence that p53-Mediated Cell-Cycle-Arrest Inhibits Chemotherapeutic Treatment of Ovarian Carcinomas. PLoS ONE. May 16;2:e441.

Menendez L, Walker D, Matyunina L.V., Dickerson E.B., Bowen N.J., Polavarapu N., Benigno B.B, McDonald J.F.2007.Identification of candidate methylation-responsive genes in ovarian cancer. Mol Cancer. Jan 25;6:10.

Bowen N.J., Logani S, Dickerson E.B., Kapa L.B., Akhtar M, Benigno B.B.,, McDonald J.F.2007. Emerging roles for PAX8 in ovarian cancer and endosalpingeal development. Gynecol Oncol..Feb;104(2):331-7.

2006

Polavarapu N., Bowen N.J., McDonald J.F.2006. Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses. Genome Biol.7(6):R51.

Fablet M., McDonald J.F., Biemont C., Vieira C.2006. Ongoing loss of the tirant transposable element in natural populations of Drosophila simulans. Gene. Jun 21;375:54-62.

Polavarapu N, Bowen N.J., McDonald J.F.2006. Newly identified families of human endogenous retroviruses. J Virol.May;80(9):4640-2.

Herrera RJ, Lowery R.K, Alfonso A, McDonald J.F, Luis JR.2006.Ancient retroviral insertions among human populations.J Hum Genet. 51(4):353-62

Ganko E.W., Greene C.S., Lewis J.A., Bhattacharjee V, McDonald J.F.2006.LTR retrotransposon-gene associations in Drosophila melanogaster.J Mol Evol. Jan; 62(1):111-20.

DeBarry J.D,, Ganko E.W., McCarthy E.M., McDonald J.F. 2006.The contribution of LTR retrotransposon sequences to gene evolution in Mus musculus. Mol Biol Evol. Mar; 23(3):479-81

2005

McDonald J.F., Matzke M.A., Matzke A.J. 2005. Host defenses to transposable elements and the evolution of genomic imprinting. Cytogenet Genome Res. ,2005; 110(1-4):242-9.

2004

Warrenfeltz S, Pavlik S, Datta S, Kraemer ET, Benigno B, McDonald JF. 2004. Gene expression profiling of epithelial ovarian tumours correlated with malignant potential. Mol Cancer., Oct 7;3:27.

Franchini, L.F., E.W. Ganko, J.F. McDonald. 2004. Retrotransposon-gene associations are wide-spread among D.melanogaster populations. Mol. Biol. Evol., Jul;21(7):1323-31.

Menendez L, Benigno BB, McDonald JF. 2004. L1 and HERV-W retrotransposons are hypomethylated in human ovarian carcinomas. Mol Cancer., Apr 26;3(1):12.

Gao, L, McCarthy EM, Ganko EW, McDonald JF. 2004. Evolutionary history of Oryza sativa LTR retrotransposons: a preliminary survey of the rice genome sequences. BMC Genomics, 5:18.

McCarthy, E.M., and J.F. McDonald. 2004. LTR Retrotransposons of Mus musculus. Genome Biology, 5:R14.

2003

Ganko, E.W., V. Bhattacharjee, P.Schliekelman, and J.F. McDonald. 2003. Evidence for the contribution of LTR retrotransposons to C.elegans gene evolution. Mol. Biol. Evol., 20(11):1925-1931.

McCarthy, E.M., and J.F. McDonald. 2003. LTR_STRUC: A novel search and identification program for LTR retrotransposons. Bioinformatics 19: 362-367.

2002  

Jordan, I.K., and J.F. McDonald. 2002. A biologically active family of human endogenous retroviruses (HERVs) evolved from an ancient inactive lineage. Genome Letters 1(2):105-109

McCarthy E.M., J Liu, G Lizhi, McDonald JF. 2002. The LTR retrotransposons of Oryza sativa. Genome Biology 3:10

McCollum, A., E.W. Ganko, P. Barrass, J. Rodriguez, and J.F. McDonald. 2002. Evidence for the adaptive significance of an LTR retrotransposon sequence in a Drosophila heterochromatic gene. BMC Evolutionary Biology 2 No. 5: 1-7.