Publications

2021

Stone, N.E., Raj, A., Young, K.M. , DeLuca, A.P., Chrit, F.E., Tucker, B.A., Alexeev, A., McDonald J.F., Benigno, B.B., Sulchek, T. (2021). Label-free microfluidic enrichment of cancer cells from non-cancer cells in ascites. Sci Rep 11, 18032. https://doi.org/10.1038/s41598-021-96862-y.

2020

Clayton, E. A., Pujol, T. A., McDonald, JF., Qiu, P (2020). Leveraging TCGA gene expression data to build predictive models for cancer drug response. BMC Bioinformatics. https://doi.org/10.1186/s12859-020-03690-4

Housley, SN., Nardelli, P., Carrasco, D., Rotterman, TM., Pfahl, E., Matyunina, L., McDonald, JF., Cope, TC (2020). Cancer Exacerbates Chemotherapy-Induced Sensory Neuropathy. Cancer Res. https://doi.org/10.1158/0008-5472.CAN-19-2331

Zhou, H., Cao, H., Matyunina, L., Shelby, M., Cassels, L., McDonald, JF., & Skolnick, J. (2020). MEDICASCY: A Machine Learning Approach for Predicting Small-Molecule Drug Side Effects, Indications, Efficacy, and Modes of Action. Mol. Pharmaceutics. https://doi.org/10.1021/acs.molpharmaceut.9b01248

Zhang, M., Wang, Y., Matyunina, L., Akbar, A., McDonald, JF. (2020). The ability of miRNAs to induce mesenchymal-to-epithelial transition (MET) in cancer cells is highly dependent upon genetic background. Cancer Letters, 480, 15-23. DOI:10.1016/j.canlet.2020.03.023

Clayton, E. A., Rishishwar, L., Huang, T. C., Gulati, S., Ban, D., McDonald, J. F., & Jordan, I. K. (2020). An atlas of transposable element-derived alternative splicing in cancer. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 375(1795), 20190342.

Clayton, E. A., Khalid, S., Ban, D., Wang, L., Jordan, I. K., & McDonald, J. F. (2020). Tumor suppressor genes and allele-specific expression: mechanisms and significance. Oncotarget, 11(4), 462.

2019

Birmingham, KG., O’Melia, MJ., Ban, D., Mouw, J., Edwards, EE., Marcus, AI., McDonald, JF., Thomas SN. 2019. Analyzing Mechanisms of Metastatic Cancer Cell Adhesive Phenotype Leveraging Preparative Adhesion Chromatography Microfluidic. Advanced biosystems, 3(3), 1800328. DOI:10.1002/adbi.201800328.

Lopes, E., Paim, L. R., Matos-Souza, J. R., Calegari, D. R., Gorla, J. I., Cliquet, A., Jr, … Schreiber, R. 2019. Bioinformatics analysis of circulating miRNAs related to cancer following spinal cord injury. Bioscience reports, 39(9), BSR20190989. DOI:10.1042/BSR20190989

Chu, CH., Liu, R., Ozkaya-Ahmadov, T., Boya, M., Swain, BE., Owens, JM., Burentugs, E., Bilen, MA., McDonald, JF., Sarioglu, AF. 2019. Hybrid negative enrichment of circulating tumor cells from whole blood in a 3D-printed monolithic device. Lab Chip, 20, 3427-3437. DOI:10.1039/c9lc00575g.

Lopes, E., Paim, L. R., Matos-Souza, J. R., Calegari, D. R., Gorla, J. I., Cliquet, A., Jr, … Schreiber, R. 2019. Bioinformatics analysis of circulating miRNAs related to cancer following spinal cord injury. Bioscience reports, 39(9), BSR20190989. DOI:10.1042/BSR20190989

Zhang, M., Jabbari, N., Satpathy, M., Matyunina, L. V., Wang, Y., McDonald, L. D., & McDonald, J. F. 2019. Sequence diverse miRNAs converge to induce mesenchymal-to-epithelial transition in ovarian cancer cells through direct and indirect regulatory controls. Cancer letters, 449, 168-175. DOI: 10.1016/j.canlet.2019.05.039.

Elliott, B., Millena, A. C., Matyunina, L., Zhang, M., Zou, J., Wang, G., Zhang, Q., Bowen, N., Eaton, V., Webb, G., Thompson, S., McDonald JF., Khan, S. 2019. Essential role of JunD in cell proliferation is mediated via MYC signaling in prostate cancer cells. Cancer letters, 448, 155-167. DOI: 10.1016/j.canlet.2019.02.005.

2018

Huang, C., Clayton, E. A., Matyunina, L. V., McDonald, L. D., Benigno, B. B., Vannberg, F., & McDonald, J. F. 2018. Machine learning predicts individual cancer patient responses to therapeutic drugs with high accuracy. Scientific reports, 8(1), 16444. DOI: 10.1038/s41598-018-34753-5.

Lili LN, Huang AD, Zhang M, Wang L, McDonald LD, Matyunina LV, Satpathy M, McDonald JF. 2018. Time-course analysis of microRNA-induced mesenchymal-to-epithelial transition underscores the complexity of the underlying molecular processes. Cancer Letters 428:184-191. DOI: 10.1016/j.canlet.2018.05.001

McDonald JF 2018. Back to the future- The integration of big data with machine learning is re-establishing the importance of predictive correlations in ovarian cancer diagnostics and therapeutics. Gynecologic Oncology 149(2): 230-231. DOI: 10.1016/j.ygyno.2018.03.053

2017

Huang C, Mezencev R, McDonald JF, Vannberg F. 2017. Open source machine-learning algorithms for the prediction of optimal cancer drug therapies. PLoS ONE 12(10): e0186906. DOI: 10.1371/journal.pone.0186906

Mittal, V. and McDonald, J.F. 2017. De novo assembly and characterization of breast cancer transcriptomes identifies large numbers of novel fusion-gene transcripts of potential functional significance. BMC Medical Genomics 10:53. DOI 10.1186/s12920-017-0289-7

Zhang, M., Matyunina, L.V., Walker, L.D,Weixuan, C, Haopeng, X., Benigno, B.B., Wu, R., and McDonald, J.F. 2017. Evidence for the importance of post-transcriptional regulatory changes in ovarian cancer progression and the contribution of miRNAs.Scientific Reports 7: 8171. DOI:10.1038/s41598-017-08502-z

Rishishwar, L., Wang, L., Clayton, E.A., Marino-Ramirez, L., McDonald, J.F. and Jordan I.K., 2017. Population and clinical genetics of human transposable elements in the (post) genomic era. Mobile Genetic Elements. 7: 1-20. DOI:10.1080/2159256X.2017.1280116

Waldetoft, K.W., McDonald, J.F. and Brown, S.P., 2017. Controlling Rogue Cells in Cancer and Bacterial Infections. In Ecology and Evolution of Cancer, B. Ujvari, B. Roche and F. Thomas, eds. (Elsiver, London)

2016

Clayton, E.A., Wang, L., Rishishwar, L., Wang, J., McDonald, J.F., and Jordan, I.K. 2016. Patterns of transposable element expression and insertion in cancer. Frontiers in Molecular Biosciences 3(76). doi: 10.3389/fmolb.2016.00076.

M. Satpathy, R. Mezencev, L. Wang, and J. F. McDonald. 2016. Targeted in vivo delivery of EGFR siRNA inhibits ovarian cancer growth and enhances drug sensitivity. Scientific Reports 6:36518.

Mezencev, R., Matyunina, L. V., Wagner, G. T., & McDonald, J. F. 2016. Acquired resistance of pancreatic cancer cells to cisplatin is multifactorial with cell context-dependent involvement of resistance genes. Cancer Gene Ther. doi:10.1038/cgt.2016.71

Mezencev, R, McDonald JF. 2016. Snail-induced epithelial-to-mesenchymal transition of MCF-7 breast cancer cells: systems analysis of molecular changes and their effect on radiation and drug sensitivity. BMC Cancer 16:236.

Schreiber, R., R. Mezencev, L.V. Matyunina, and J.F. McDonald. 2016. Evidence for the role of miRNA 374b in acquired cisplatin resistance in pancreatic cancer. Cancer Gene Ther May 27. doi: 10.1038/cgt.2016.23. [Epub 2016 May 27]

Hill, C.G. and McDonald J.F. 2016. Evidence and potential clinical significance of changes in gene network interactions in ovarian cancer. J Biomedical Engineering and Informatics 2(1):1-12.

2015

Gaul DA, Mezencev R, Long TQ, Jones CM, Benigno BB, Gray A, Fernandez FM, McDonald JF. 2015. Highly-accurate metabolomics detection of early-stage ovarian cancer. Sci Reports (Nature pub) Nov 17; 5:16351. Doi 10,1038/srep16351

Sodji, Q.H., J.R. Kornacki, J.F. McDonald, M. Mrksich and A.K. Oyelere. 2015. Design and structure activity relationship of tumor-homing histone deacetylase inhibitors conjugated to folic and pteroic acids. Eur J Med Chem 96:340-359. PubMed

Mittal, V.K. and McDonald, J.F. 2015.Integrated sequence and expression analysis of ovarian cancer structural variants underscores the importance of gene fusion regulation. BMC Med Genomics 8:40. PubMed

Sengupta, A, R. Mezencev, J. F. McDonald, and M. R. Prausnitz. 2015.  Delivery of siRNA to ovarian cancer cells using laser-activated carbon nanoparticles. Nanomedicine 10:1775-1784. PubMed

Vermeersch KA, Wang L, Mezencev R, McDonald JF, Styczynski MP. 2015. OVCAR-3 spheroid-derived cells display distinct metabolic profiles. PLoS One 10:e0118262. PubMed

Allam, H., K. Aiok, B.B. Benigno, J.F. McDonald, S.G. Mackintosh, M. Tiemeyer, and K.L. Abbott. 2015. Glycomic analysis of membrane glycoproteins with bisecting glycosylation from ovarian cancer tissues reveals novel structures and functions. J Proteome Res 14:434-446.PubMed

McGrail, D.J., R. Meznecev, Q.M.N. Kieu, J.F. McDonald, and M.R. Dawson. 2015. SNAIL-induced epithelial-to-mesenchymal transition produces concerted biophysical changes from altered cytoskeletal gene expression. FASEB J 29:1280-1289. PubMed

Muniyan, S., Y-W. Chou, T-J. Tsai, P. Thomes, S. Veeramani, B.B. Benigno, L.D. Walker, J. F. McDonald, S.A. Khan, F-F. Lin, S.M. Lele, and M-F. Lin. 2015. P66Shc longevity protein regulates the proliferation of human ovarian cancer cells. Mol Carcinog. 54(8):618-631. PubMed

2014

Vermeersch, K.A., L. Wang, J.F. McDonald, M.P. Styczynski. 2014. Distinct metabolic responses of an ovarian cancer stem cell line. BMC Syst Biol 8:134. PubMed

Hill, C.G., N. Jabbari, L.V. Matyunina and J.F. McDonald. 2014. Functional and evolutionary significance of human microRNA seed region mutations. PLos One, 9(12): e115241. PubMed

Medrzycki, M., Zhang, Y., Zhang, W., Cao, K., Pan, C., Lailler, N., McDonald, J.F., Bouhassira, E.E., Fan, Y. 2014. Histone H1.3 suppresses H19 noncoding RNA expression and cell growth of ovarian cancer cells. Cancer Res 74:6463-6473. PubMed

Zang, X., C. Jones, T. Long, M. Monge, M. Zhou, Manshui, L.D.Walker, R. Mezencev, A. Gray, J. F. McDonald, and F. Fernandez. 2014. Feasibility of detecting prostate cancer by ultra performance liquid chromatography−mass spectrometry serum metabolomics. J Proteome Res 13:3444-3454. PubMed

Wang, L., R. Mezencev, M. Svajdler, B.B. Benigno, and J.F. McDonald. 2014. Ectopic over-expression of miR-429 induces mesenchymal-to-epithelial transition (MET) and increased drug sensitivity in metastasizing ovarian cancer cells. Gyn Oncol 134:96-103. PubMed

Hill, C.G., L.V. Matyunina, L.D. Walker, B.B. Benigno, and J.F. McDonald. 2014. Transcriptional override: a network model of indirect responses to modulations in microRNA expression. BMC Syst Biol 8:36-44. PubMed

Lili, L.N., L.V. Matyunina, L.D. Walker, G.W. Daneker, and J.F. McDonald. 2014. Evidence for the importance of personalized molecular profiling in pancreatic cancer. Pancreas 43 (2):198-211. PubMed

Jabbari, N., A.N. Reavis and J.F. McDonald. 2014. Sequence variation among members of the miR-200 microRNA family is correlated with variation in the ability to induce hallmarks of mesenchymal-epithelial transition in ovarian cancer cells. J Ovarian Res 7:12. PubMed

Ghosh, D., Lilli, L., McGrail, D.J., Matyunina, L.V., McDonald, J.F., Dawson, M.R. 2014. Integral role of platelet derived growth factor in mediating transforming growth factor-β1 dependent mesenchymal stem cell stiffening. Stem Cells Dev 23:245-61. PubMed

Bongiorno T, Kazlow J, Mezencev R, Griffiths S, Olivares-Navarrete R, McDonald JF, Schwartz Z, Boyan BD, McDevitt TC, Sulchek T. 2014. Mechanical stiffness as an improved single-cell Indicator of osteoblastic human mesenchymal stem cell differentiation. J Biomechanics 47:2197-2204. PubMed

2013

Lili L, Matyunina L, Walker LD, Wells S, Benigno B, McDonald JF. 2013. Molecular profiling supports the role of epithelial-to-mesenchymal transition (EMT) in ovarian cancer metastasis. Journal of Ovarian Research. Jul 10;6(1):49.Pubmed / Journal

Lili L, Matyunina L, Walker LD, Benigno B, McDonald JF. 2013. Molecular profiling predicts the existence of two functionally distinct classes of ovarian cancer stroma. BioMed Research International. Vol. 2013, Article ID 846387.Pubmed / Journal

Mezencev R, Wang L, Xu W, Kim B, Sulchek TA, Daneker GW , McDonald JF. 2013. Molecular analysis of the inhibitory effect of N-acetyl-L-cysteine on the proliferation and invasiveness of pancreatic cancer cells.Anti-Cancer Drugs Jun;24(5):504-18. Pubmed / Journal

2012

Mezencev R, Wang L, McDonald JF. 2012. Identification of inhibitors of ovarian cancer stem-like cells by high-throughput screening. Journal of Ovarian Research; Oct 18;5(1).Pubmed / Journal

Xu W., Mezencev R., Kim B., Wang L., McDonald JF., Sulchek T. 2012. Cell stiffness is a biomarker of the metastatic potential of ovarian cancer cells. PLoS ONE 7(10).Pubmed / Journal

Arora G, Mezencev R, McDonald JF. 2012. Human cells display reduced apoptotic function relative to chimpanzee cells. PLoS ONE 2012;7(9)Pubmed / Journal

Shahab SW, Matyunina LV, Hill CG, Wang L, Mezencev R, Walker LD, McDonald JF. 2012. The effects of microRNA transfections on global patterns of gene expression in ovarian cancer cells are functionally coordinated.BMC Medical Genomics Aug 1 5:33 Pubmed / Journal

Nakamura T, Jing C, Xinhua Y, Li J, Chen JP, King SB 3rd, Chronos N, McDonald JF, Hou D. 2012. Vasomotor function and molecular responses following drug-eluting stent in a porcine coronary model. International Journal of Cardiology June: 21; DOI:10.1016/j.bbr.2011.03.031Pubmed / Journal

Liu Y, Bowen NJ, Matyunina LV, McDonald JF, Prausnitz MR. 2012. Gene transfection enhanced by ultrasound exposure combined with drug treatment guided by gene chip analysis. International Journal of Hyperthermia June;28(9):349-61.Pubmed / Journal

Shahab S, Matyunina LV, Mittal VK, Wang L, Hill CG, Walker LD, McDonald JF. 2012. MicroRNAs indirectly regulate other microRNAs in ovarian cancer cells. British Journal of Medicine and Medical Research Feb 22;2(2):172-194. Journal

Mittal VK, McDonald JF. 2012. R-SAP: a multi-threading computational pipeline for the characterization of high-throughput RNA-sequencing data. Nucleic Acid Reseaech. Jan. 28;Pubmed / Journal

Medrzycki M, Zhang Y, McDonald JF and Fan Y. 2012. Profiling of linker histone variants in Ovarian Cancer. Front. Biosci. Jan 1;17:396-406.Pubmed / Journal

2011

Wang L, Mezencev R, Bowen NJ, Matyunina LV, McDonald JF. 2011. Isolation and characterization of stem-like cells from a human ovarian cancer cell line. Mol Cell Biochem Dec 9.Pubmed / Journal

Polavarapu N, Arora G, Mittal VK, McDonald JF. 2011. Characterization and potential functional significance of human-chimpanzee large INDEL variation. Mob DNAOct 25;2(1):13.Pubmed / Journal

Mezencev R and McDonald JF. 2011. Subcutaneous xenografts of human T-lineage acute lymphoblastic leukemia Jurkat cells in nude mice. In Vivo Jul-Aug;25(4):603-7.Pubmed / Journal

Shahab S, Matyunina L, Mezencev R, Walker LD, Bowen NJ, Benigno BB, McDonald JF. 2011. Evidence for the complexity of microRNA-mediated regulation in ovarian cancer: a systems approach. PLoS ONE July;6(7):e22508.Pubmed / Journal

McDonald, JF. 2011. Integrated cancer systems biology: current progress and future promise. Future Oncology May; 7(5):599-601. Pubmed / Journal

Chen, J., A. Huang, T. Nakamura, L. Matyunina, J. Yu, J. Li, J. Singh, J.F. McDonald, N. Chronos, and D. Hou. 2011. Microarray gene expression profiling identifies pathophysiological vascular responses to implantation of overlapping drug-eluting stents into porcine coronary arteries. J Amer. College Cardio. 57:e1693. Journal

Mezencev R, Updegrove T, Kutschy P, Repovská M and McDonald JF.2011. Camalexin induces apoptosis in Jurkat T-leukemia cells by increased concentration of reactive oxygen species and activation of caspases-8 and -9. J Nat. Med. Mar 19. Pubmed/ Journal

Chen J, Wang L, Matyunina LV, Hill CG and McDonald JF. 2011.Overexpression of miR-429 induces mesenchymal-to-epithelial transition (MET) in metastatic ovarian cancer cells. Gynecol. Oncol. Apr; 121(1): 200-5. Jan 28. Pubmed / Journal

Scarberry KE, Mezencev R and McDonald JF. 2011. Targeted removal of migratory tumor cells by functionalized magnetic nanoparticles impedes metastasis and tumor progression. Nanomedicine (Lond.) Jan; 6 (1) :69-78 . Pubmed / Journal

2010

Zhou M, Guan W, Walker LD, Mezencev R, Benigno BB, Gray A, Fernandez FM and McDonald JF. 2010. Rapid Mass Spectrometric Metabolic Profiling of Blood Sera detects Ovarian Cancer with High Accuracy. Cancer Epidemiology, Biomarkers and Prevention Sep; 19(9) :2262-71 . Pubmed / Journal

Liu Y, Chen Y, Momin A, Shaner R, Wang E, Bowen NJ, Matyunina L, Walker LD, McDonald JF, Sullards CM and Merrill AH Jr. 2010. Elevation of sulfatides in ovarian cancer: An integrated transcriptomic and lipidomic analysis including tissue-imaging mass spectrometry. Molecular Cancer Jul 12; 9: 186. Pubmed / Journal

Dickerson EB, Blackburn WH, Smith MH, Kapa LB, Lyon LA and McDonald JF 2010. Chemosensitization of cancer cells by siRNA using targeted nanogel delivery. BMC Cancer Jan 11;10: 10. Pubmed/ Journal

Scarberry KE, Dickerson EB, Zhang ZJ, Benigno BB and McDonald JF.2010.Selective removal of ovarian cancer cells from human ascites fluid using magnetic nanoparticles.Nanomedicine Jun; 6(3):399-408. Epub 2009 Dec 5 Pubmed / Journal

Abbott KL, Lim JM, Wells L, Benigno BB, McDonald JF and Pierce M. 2010.Identification of candidate biomarkers with cancer-specific glycosylation in the tissue and serum of endometrioid ovarian cancer patients by glycoproteomic analysis. Proteomics Feb; 10(3):470-811.Pubmed/Journal

Zhou M, McDonald JF and Fernandez FM. 2010. Optimization of a direct analysis in real time/time-of-flight mass spectrometry method for rapid serum metabolic fingerprinting. J. Am. Soc. Mass Spectrom 21:68-75.Pubmed/Journal

2009

Bowen NJ, Walker LD, Matyunina LV, Logani S, Totten KA, Benigno BB and McDonald JF.2009. Gene expression profiling supports the hypothesis that human ovarian surface epithelia are multipotent and capable of serving as ovarian cancer initiating cells.BMC Med Genomics. Dec 29;2(1):71Pubmed/Journal

Guan W, Zhou M, Hampton CY, Benigno BB, Walker D, Gray A, McDonald JF. and Fernandez, FM. 2009. Ovarian Cancer Detection from Metabolomic Liquid Chromatography/Mass Spectrometry Data by Support Vector Machines.BMC Bioinformatics. Aug 2009, 10:259-274.Pubmed/Journal

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 , Sep; 73(3):453-456 May 5Pubmed / Journal

Blackburn W, Dickerson E, Smith M, McDonald JF, Lyon A.2009. Peptide-Functionalized Nanogels for Targeted siRNA Delivery. Bioconjugate Chemistry. May 20; 20 (5): 960-8.Pubmed / Journal

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.Pubmed/ Journal

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, May 2009.30(13) :2507-15Pubmed/Journal

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.Pubmed/ Journal

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

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. Pubmed / Journal

Mezencev R, Kutschy P,  Salayova A,  Curillov�,Z, Mojzis J, Pilatov�, 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. Pubmed/ Journal

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.Pubmed / Journal

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. Pubmed / Journal

Navare A, Zhou M, McDonald JF, Noriega FG, Sullards C and Fernandez FM. 2008. 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. Pubmed/ Journal

Huda A, Polavarapu N, Jordan IK and McDonald JF. 2008. Endogenous retroviruses of the chicken genome. Biology Direct Mar 24, 3:9 PubMed/ Journal

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. Pubmed/Journal

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

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. Pubmed/ Journal

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. Pubmed / Journal

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. PubMed/ Journal

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. PubMed / Journal Website

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. PubMed / Journal

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. PubMed / Journal

2006

Dickerson, E.B., M. Akhtar, L.B. Kapa, N.J. Bowen, K.D. Clark, and J.F. McDonald. 2006. Peptide targeting of EphA2 in epithelial ovarian cancer. J Immunotherapy 29:672-673. Journal

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

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. PubMed / Journal

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

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. PubMed / Journal

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. PubMed /Journal Website

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. PubMed /Journal

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. PubMed /Journal Website

2004

Calhoun, J.D., R. Rao, S.W. Warrenfeltz, R. Rekaya, S. Dalton, J.F. McDonald, and S.L. Stice. 2004. Transcriptional profiling of initial differentiation events in human embryonic stem cells. Biochem. Biophys. Tes. Comm. 323:453-464. Pubmed / Journal

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. PubMed /Journal

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. PubMed / Journal Website

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. PubMed / Journal Website

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.PubMed / Journal Website

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

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. PubMed / Journal Supplemental Data

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

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. PubMed / Journal

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

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. PubMed / Journal