John F. McDonald - Publications

Affiliations: 
Georgia Institute of Technology, Atlanta, GA 

125 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Housley SN, Nardelli P, Carrasco D, Rotterman TM, Pfahl E, Matyunina LV, McDonald JF, Cope TC. Cancer Exacerbates Chemotherapy-Induced Sensory Neuropathy. Cancer Research. PMID 32345673 DOI: 10.1158/0008-5472.CAN-19-2331  0.64
2020 Zhou H, Cao H, Matyunina L, Shelby M, Cassels L, McDonald JF, Skolnick J. MEDICASCY: A Machine Learning Approach for Predicting Small Molecule Drug Side Effects, Indications, Efficacy and Mode of Action. Molecular Pharmaceutics. PMID 32237745 DOI: 10.1021/acs.molpharmaceut.9b01248  0.32
2020 Zhang M, Wang Y, Matyunina LV, Akbar A, McDonald JF. The ability of miRNAs to induce mesenchymal-to-epithelial transition (MET) in cancer cells is highly dependent upon genetic background. Cancer Letters. PMID 32234315 DOI: 10.1016/j.canlet.2020.03.023  0.64
2020 Clayton EA, Rishishwar L, Huang TC, Gulati S, Ban D, McDonald JF, Jordan IK. An atlas of transposable element-derived alternative splicing in cancer. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 375: 20190342. PMID 32075558 DOI: 10.1098/rstb.2019.0342  0.48
2020 Clayton EA, Khalid S, Ban D, Wang L, Jordan IK, McDonald JF. Tumor suppressor genes and allele-specific expression: mechanisms and significance. Oncotarget. 11: 462-479. PMID 32064050 DOI: 10.18632/oncotarget.27468  0.48
2019 Zhang M, Jabbari N, Satpathy M, Matyunina LV, Wang Y, DeEtte McDonald L, McDonald JF. Sequence diverse miRNAs converge to induce mesenchymal-to-epithelial transition in ovarian cancer cells through direct and indirect regulatory controls. Cancer Letters. PMID 31163194 DOI: 10.1016/j.canlet.2019.05.039  0.64
2018 Huang C, Clayton EA, Matyunina LV, McDonald LD, Benigno BB, Vannberg F, McDonald JF. Machine learning predicts individual cancer patient responses to therapeutic drugs with high accuracy. Scientific Reports. 8: 16444. PMID 30401894 DOI: 10.1038/s41598-018-34753-5  0.64
2018 Lili LN, Huang AD, Zhang M, Wang L, DeEtte McDonald L, Matyunina LV, Satpathy M, McDonald JF. Time-course analysis of microRNA-induced mesenchymal-to-epithelial transition underscores the complexity of the underlying molecular processes. Cancer Letters. PMID 29733963 DOI: 10.1016/j.canlet.2018.05.001  0.64
2017 Huang C, Mezencev R, McDonald JF, Vannberg F. Open source machine-learning algorithms for the prediction of optimal cancer drug therapies. Plos One. 12: e0186906. PMID 29073279 DOI: 10.1371/journal.pone.0186906  0.44
2017 Zhang M, Matyunina LV, Walker LD, Chen W, Xiao H, Benigno BB, Wu R, McDonald JF. Evidence for the importance of post-transcriptional regulatory changes in ovarian cancer progression and the contribution of miRNAs. Scientific Reports. 7: 8171. PMID 28811560 DOI: 10.1038/s41598-017-08502-z  0.64
2017 Rishishwar L, Wang L, Clayton EA, Mariño-Ramírez L, McDonald JF, Jordan IK. Population and clinical genetics of human transposable elements in the (post) genomic era. Mobile Genetic Elements. 7: 1-20. PMID 28228978 DOI: 10.1080/2159256X.2017.1280116  0.68
2016 Clayton EA, Wang L, Rishishwar L, Wang J, McDonald JF, Jordan IK. Patterns of Transposable Element Expression and Insertion in Cancer. Frontiers in Molecular Biosciences. 3: 76. PMID 27900322 DOI: 10.3389/fmolb.2016.00076  0.48
2016 Satpathy M, Mezencev R, Wang L, McDonald JF. Targeted in vivo delivery of EGFR siRNA inhibits ovarian cancer growth and enhances drug sensitivity. Scientific Reports. 6: 36518. PMID 27819259 DOI: 10.1038/srep36518  0.44
2016 Mezencev R, Matyunina LV, Jabbari N, McDonald JF. 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. PMID 26988558 DOI: 10.1186/s12885-016-2274-5  0.64
2015 Gaul DA, Mezencev R, Long TQ, Jones CM, Benigno BB, Gray A, Fernández FM, McDonald JF. Highly-accurate metabolomic detection of early-stage ovarian cancer. Scientific Reports. 5: 16351. PMID 26573008 DOI: 10.1038/srep16351  1
2015 Sengupta A, Mezencev R, McDonald JF, Prausnitz MR. Delivery of siRNA to ovarian cancer cells using laser-activated carbon nanoparticles. Nanomedicine (London, England). 10: 1775-84. PMID 26080699 DOI: 10.2217/nnm.15.27  1
2015 Sodji QH, Kornacki JR, McDonald JF, Mrksich M, Oyelere AK. Design and structure activity relationship of tumor-homing histone deacetylase inhibitors conjugated to folic and pteroic acids. European Journal of Medicinal Chemistry. 96: 340-59. PMID 25899338 DOI: 10.1016/j.ejmech.2015.04.014  1
2015 Vermeersch KA, Wang L, Mezencev R, McDonald JF, Styczynski MP. OVCAR-3 spheroid-derived cells display distinct metabolic profiles. Plos One. 10: e0118262. PMID 25688563 DOI: 10.1371/journal.pone.0118262  1
2015 McGrail DJ, Mezencev R, Kieu QM, McDonald JF, Dawson MR. SNAIL-induced epithelial-to-mesenchymal transition produces concerted biophysical changes from altered cytoskeletal gene expression. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. 29: 1280-9. PMID 25491311 DOI: 10.1096/fj.14-257345  1
2015 Allam H, Aoki K, Benigno BB, McDonald JF, Mackintosh SG, Tiemeyer M, Abbott KL. Glycomic analysis of membrane glycoproteins with bisecting glycosylation from ovarian cancer tissues reveals novel structures and functions. Journal of Proteome Research. 14: 434-46. PMID 25437919 DOI: 10.1021/pr501174p  1
2015 Muniyan S, Chou YW, Tsai TJ, Thomes P, Veeramani S, Benigno BB, Walker LD, McDonald JF, Khan SA, Lin FF, Lele SM, Lin MF. p66Shc longevity protein regulates the proliferation of human ovarian cancer cells. Molecular Carcinogenesis. 54: 618-31. PMID 24395385 DOI: 10.1002/mc.22129  1
2014 Vermeersch KA, Wang L, McDonald JF, Styczynski MP. Distinct metabolic responses of an ovarian cancer stem cell line. Bmc Systems Biology. 8: 134. PMID 25518943 DOI: 10.1186/s12918-014-0134-y  1
2014 Hill CG, Jabbari N, Matyunina LV, McDonald JF. Functional and evolutionary significance of human microRNA seed region mutations. Plos One. 9: e115241. PMID 25501359 DOI: 10.1371/journal.pone.0115241  1
2014 Medrzycki M, Zhang Y, Zhang W, Cao K, Pan C, Lailler N, McDonald JF, Bouhassira EE, Fan Y. Histone h1.3 suppresses h19 noncoding RNA expression and cell growth of ovarian cancer cells. Cancer Research. 74: 6463-73. PMID 25205099 DOI: 10.1158/0008-5472.CAN-13-2922  1
2014 Zang X, Jones CM, Long TQ, Monge ME, Zhou M, Walker LD, Mezencev R, Gray A, McDonald JF, Fernández FM. Feasibility of detecting prostate cancer by ultraperformance liquid chromatography-mass spectrometry serum metabolomics. Journal of Proteome Research. 13: 3444-54. PMID 24922590 DOI: 10.1021/pr500409q  1
2014 Wang L, Mezencev R, Švajdler M, Benigno BB, McDonald JF. Ectopic over-expression of miR-429 induces mesenchymal-to-epithelial transition (MET) and increased drug sensitivity in metastasizing ovarian cancer cells. Gynecologic Oncology. 134: 96-103. PMID 24802724 DOI: 10.1016/j.ygyno.2014.04.055  1
2014 Hill CG, Matyunina LV, Walker D, Benigno BB, McDonald JF. Transcriptional override: a regulatory network model of indirect responses to modulations in microRNA expression. Bmc Systems Biology. 8: 36. PMID 24666724 DOI: 10.1186/1752-0509-8-36  1
2014 Lili LN, Matyunina LV, Walker LD, Daneker GW, McDonald JF. Evidence for the importance of personalized molecular profiling in pancreatic cancer. Pancreas. 43: 198-211. PMID 24518497 DOI: 10.1097/MPA.0000000000000020  1
2014 Jabbari N, Reavis AN, McDonald JF. 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. Journal of Ovarian Research. 7: 12. PMID 24447705 DOI: 10.1186/1757-2215-7-12  1
2014 Bongiorno T, Kazlow J, Mezencev R, Griffiths S, Olivares-Navarrete R, McDonald JF, Schwartz Z, Boyan BD, McDevitt TC, Sulchek T. Mechanical stiffness as an improved single-cell indicator of osteoblastic human mesenchymal stem cell differentiation. Journal of Biomechanics. 47: 2197-204. PMID 24296276 DOI: 10.1016/j.jbiomech.2013.11.017  1
2014 Ghosh D, Lili L, McGrail DJ, Matyunina LV, McDonald JF, Dawson MR. Integral role of platelet-derived growth factor in mediating transforming growth factor-β1-dependent mesenchymal stem cell stiffening. Stem Cells and Development. 23: 245-61. PMID 24093435 DOI: 10.1089/scd.2013.0240  1
2013 Lili LN, Matyunina LV, Walker LD, Wells SL, Benigno BB, McDonald JF. Molecular profiling supports the role of epithelial-to-mesenchymal transition (EMT) in ovarian cancer metastasis. Journal of Ovarian Research. 6: 49. PMID 23837907 DOI: 10.1186/1757-2215-6-49  1
2013 Lili LN, Matyunina LV, Walker LD, Benigno BB, McDonald JF. Molecular profiling predicts the existence of two functionally distinct classes of ovarian cancer stroma. Biomed Research International. 2013: 846387. PMID 23762861 DOI: 10.1155/2013/846387  1
2013 Mezencev R, Wang L, Xu W, Kim B, Sulchek TA, Daneker GW, McDonald JF. Molecular analysis of the inhibitory effect of N-acetyl-L-cysteine on the proliferation and invasiveness of pancreatic cancer cells. Anti-Cancer Drugs. 24: 504-18. PMID 23511429 DOI: 10.1097/CAD.0b013e32836009d7  1
2012 Mezencev R, Wang L, McDonald JF. Identification of inhibitors of ovarian cancer stem-like cells by high-throughput screening. Journal of Ovarian Research. 5: 30. PMID 23078816 DOI: 10.1186/1757-2215-5-30  1
2012 Xu W, Mezencev R, Kim B, Wang L, McDonald J, Sulchek T. Cell Stiffness Is a Biomarker of the Metastatic Potential of Ovarian Cancer Cells Plos One. 7. PMID 23056368 DOI: 10.1371/journal.pone.0046609  1
2012 Arora G, Mezencev R, McDonald JF. Human cells display reduced apoptotic function relative to chimpanzee cells. Plos One. 7: e46182. PMID 23029431 DOI: 10.1371/journal.pone.0046182  1
2012 Shahab SW, Matyunina LV, Hill CG, Wang L, Mezencev R, Walker LD, McDonald JF. The effects of MicroRNA transfections on global patterns of gene expression in ovarian cancer cells are functionally coordinated. Bmc Medical Genomics. 5: 33. PMID 22853714 DOI: 10.1186/1755-8794-5-33  1
2012 Nakamura T, Jing C, Xinhua Y, Li J, Chen JP, King SB, Chronos N, McDonald JF, Hou D. Vasomotor function and molecular responses following drug-eluting stent in a porcine coronary model. International Journal of Cardiology. 160: 210-2. PMID 22727460 DOI: 10.1016/j.ijcard.2012.06.018  1
2012 Liu Y, Bowen NJ, Matyunina L, McDonald J, Prausnitz MR. Gene transfection enhanced by ultrasound exposure combined with drug treatment guided by gene chip analysis International Journal of Hyperthermia. 28: 349-361. PMID 22621736 DOI: 10.3109/02656736.2012.669513  1
2012 Mittal VK, McDonald JF. R-SAP: a multi-threading computational pipeline for the characterization of high-throughput RNA-sequencing data. Nucleic Acids Research. 40: e67. PMID 22287631 DOI: 10.1093/nar/gks047  1
2012 Medrzycki M, Zhang Y, McDonald JF, Fan Y. Profiling of linker histone variants in ovarian cancer. Frontiers in Bioscience (Landmark Edition). 17: 396-406. PMID 22201751 DOI: 10.2741/3934  1
2012 Wang L, Mezencev R, Bowen NJ, Matyunina LV, McDonald JF. Isolation and characterization of stem-like cells from a human ovarian cancer cell line. Molecular and Cellular Biochemistry. 363: 257-68. PMID 22160925 DOI: 10.1007/s11010-011-1178-6  1
2012 Xu W, Mezencev R, Kim B, Wang L, McDonald J, Sulchek T. Ovarian cancer cell invasiveness correlates with increased cell deformability Asme 2012 Summer Bioengineering Conference, Sbc 2012. 1161-1162. DOI: 10.1115/SBC2012-80624  1
2011 Polavarapu N, Arora G, Mittal VK, McDonald JF. Characterization and potential functional significance of human-chimpanzee large INDEL variation. Mobile Dna. 2: 13. PMID 22024410 DOI: 10.1186/1759-8753-2-13  1
2011 Shahab SW, Matyunina LV, Mezencev R, Walker LD, Bowen NJ, Benigno BB, McDonald JF. Evidence for the complexity of microRNA-mediated regulation in ovarian cancer: a systems approach. Plos One. 6: e22508. PMID 21811625 DOI: 10.1371/journal.pone.0022508  1
2011 Mezencev R, McDonald JF. Subcutenous xenografts of human T-lineage acute lymphoblastic leukemia Jurkat cells in nude mice. In Vivo (Athens, Greece). 25: 603-7. PMID 21709003  1
2011 McDonald JF. Integrated cancer systems biology: current progress and future promise. Future Oncology (London, England). 7: 599-601. PMID 21568674 DOI: 10.2217/fon.11.33  1
2011 Khogali SE, Davies DA, Donnan PT, Gray A, Harden RM, McDonald J, Pippard MJ, Pringle SD, Yu N. Integration of e-learning resources into a medical school curriculum. Medical Teacher. 33: 311-8. PMID 21456989 DOI: 10.3109/0142159X.2011.540270  1
2011 Mezencev R, Updegrove T, Kutschy P, Repovská M, McDonald JF. Camalexin induces apoptosis in T-leukemia Jurkat cells by increased concentration of reactive oxygen species and activation of caspase-8 and caspase-9. Journal of Natural Medicines. 65: 488-99. PMID 21424253 DOI: 10.1007/s11418-011-0526-x  1
2011 Chen J, Wang L, Matyunina LV, Hill CG, McDonald JF. Overexpression of miR-429 induces mesenchymal-to-epithelial transition (MET) in metastatic ovarian cancer cells. Gynecologic Oncology. 121: 200-5. PMID 21277012 DOI: 10.1016/j.ygyno.2010.12.339  1
2011 Scarberry KE, Mezencev R, McDonald JF. Targeted removal of migratory tumor cells by functionalized magnetic nanoparticles impedes metastasis and tumor progression. Nanomedicine (London, England). 6: 69-78. PMID 21182419 DOI: 10.2217/nnm.10.103  1
2010 Zhou M, Guan W, Walker LD, Mezencev R, Benigno BB, Gray A, Fernández FM, McDonald JF. Rapid mass spectrometric metabolic profiling of blood sera detects ovarian cancer with high accuracy. Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association For Cancer Research, Cosponsored by the American Society of Preventive Oncology. 19: 2262-71. PMID 20699376 DOI: 10.1158/1055-9965.EPI-10-0126  1
2010 Liu Y, Chen Y, Momin A, Shaner R, Wang E, Bowen NJ, Matyunina LV, Walker LD, McDonald JF, Sullards MC, Merrill AH. Elevation of sulfatides in ovarian cancer: an integrated transcriptomic and lipidomic analysis including tissue-imaging mass spectrometry. Molecular Cancer. 9: 186. PMID 20624317 DOI: 10.1186/1476-4598-9-186  1
2010 Dickerson EB, Blackburn WH, Smith MH, Kapa LB, Lyon LA, McDonald JF. Chemosensitization of cancer cells by siRNA using targeted nanogel delivery. Bmc Cancer. 10: 10. PMID 20064265 DOI: 10.1186/1471-2407-10-10  1
2010 Scarberry KE, Dickerson EB, Zhang ZJ, Benigno BB, McDonald JF. Selective removal of ovarian cancer cells from human ascites fluid using magnetic nanoparticles. Nanomedicine : Nanotechnology, Biology, and Medicine. 6: 399-408. PMID 19969103 DOI: 10.1016/j.nano.2009.11.003  1
2010 Abbott KL, Lim JM, Wells L, Benigno BB, McDonald JF, Pierce M. Identification of candidate biomarkers with cancer-specific glycosylation in the tissue and serum of endometrioid ovarian cancer patients by glycoproteomic analysis. Proteomics. 10: 470-81. PMID 19953551 DOI: 10.1002/pmic.200900537  1
2010 Zhou M, McDonald JF, Fernández FM. Optimization of a direct analysis in real time/time-of-flight mass spectrometry method for rapid serum metabolomic fingerprinting. Journal of the American Society For Mass Spectrometry. 21: 68-75. PMID 19819164 DOI: 10.1016/j.jasms.2009.09.004  1
2010 Ravindran R, Sadie JA, Scarberry KE, Yang HS, Bakir MS, McDonald JF, Meindl JD. Biochemical sensing with an arrayed silicon nanowire platform Proceedings - Electronic Components and Technology Conference. 1015-1020. DOI: 10.1109/ECTC.2010.5490826  1
2009 Bowen NJ, Walker LD, Matyunina LV, Logani S, Totten KA, Benigno BB, McDonald JF. Gene expression profiling supports the hypothesis that human ovarian surface epithelia are multipotent and capable of serving as ovarian cancer initiating cells. Bmc Medical Genomics. 2: 71. PMID 20040092 DOI: 10.1186/1755-8794-2-71  1
2009 Guan W, Zhou M, Hampton CY, Benigno BB, Walker LD, Gray A, McDonald JF, Fernández FM. Ovarian cancer detection from metabolomic liquid chromatography/mass spectrometry data by support vector machines. Bmc Bioinformatics. 10: 259. PMID 19698113 DOI: 10.1186/1471-2105-10-259  1
2009 Mezencev R, Kutschy P, Salayova A, Updegrove T, McDonald JF. The design, synthesis and anticancer activity of new nitrogen mustard derivatives of natural indole phytoalexin 1-methoxyspirobrassinol. Neoplasma. 56: 321-30. PMID 19473057 DOI: 10.4149/neo_2009_04_321  1
2009 Arora G, Polavarapu N, McDonald JF. Did natural selection for increased cognitive ability in humans lead to an elevated risk of cancer? Medical Hypotheses. 73: 453-6. PMID 19409719 DOI: 10.1016/j.mehy.2009.03.035  1
2009 Blackburn WH, Dickerson EB, Smith MH, McDonald JF, Lyon LA. Peptide-functionalized nanogels for targeted siRNA delivery. Bioconjugate Chemistry. 20: 960-8. PMID 19341276 DOI: 10.1021/bc800547c  1
2009 Carpenedo RL, Bratt-Leal AM, Marklein RA, Seaman SA, Bowen NJ, McDonald JF, McDevitt TC. Homogeneous and organized differentiation within embryoid bodies induced by microsphere-mediated delivery of small molecules. Biomaterials. 30: 2507-15. PMID 19162317 DOI: 10.1016/j.biomaterials.2009.01.007  1
2008 Scharer CD, Laycock N, Osunkoya AO, Logani S, McDonald JF, Benigno BB, Moreno CS. Aurora kinase inhibitors synergize with paclitaxel to induce apoptosis in ovarian cancer cells. Journal of Translational Medicine. 6: 79. PMID 19077237 DOI: 10.1186/1479-5876-6-79  1
2008 Arakaki AK, Skolnick J, McDonald JF. Marker metabolites can be therapeutic targets as well. Nature. 456: 443. PMID 19037294 DOI: 10.1038/456443c  1
2008 Mezencev R, Kutschy P, Salayová A, Čurillová Z, Mojžiš J, Pilátová M, McDonald J. Anticancer properties of 2-piperidyl analogues of the natural indole phytoalexin 1-methoxyspirobrassinol Chemotherapy. 54: 372-378. PMID 18769026 DOI: 10.1159/000152027  1
2008 Abbott KL, Nairn AV, Hall EM, Horton MB, McDonald JF, Moremen KW, Dinulescu DM, Pierce M. Focused glycomic analysis of the N-linked glycan biosynthetic pathway in ovarian cancer. Proteomics. 8: 3210-20. PMID 18690643 DOI: 10.1002/pmic.200800157  1
2008 Scarberry KE, Dickerson EB, McDonald JF, Zhang ZJ. Magnetic nanoparticle-peptide conjugates for in vitro and in vivo targeting and extraction of cancer cells. Journal of the American Chemical Society. 130: 10258-62. PMID 18611005 DOI: 10.1021/ja801969b  1
2008 Arakaki AK, Mezencev R, Bowen NJ, Huang Y, McDonald JF, Skolnick J. Identification of metabolites with anticancer properties by computational metabolomics. Molecular Cancer. 7: 57. PMID 18559081 DOI: 10.1186/1476-4598-7-57  1
2008 Dickerson EB, Dreaden EC, Huang X, El-Sayed IH, Chu H, Pushpanketh S, McDonald JF, El-Sayed MA. Gold nanorod assisted near-infrared plasmonic photothermal therapy (PPTT) of squamous cell carcinoma in mice. Cancer Letters. 269: 57-66. PMID 18541363 DOI: 10.1016/j.canlet.2008.04.026  1
2008 Matyunina LV, Bowen NJ, McDonald JF. LTR retrotransposons and the evolution of dosage compensation in Drosophila. Bmc Molecular Biology. 9: 55. PMID 18533037 DOI: 10.1186/1471-2199-9-55  1
2008 Menendez L, Walker LD, Matyunina LV, Totten KA, Benigno BB, McDonald JF. Epigenetic changes within the promoter region of the HLA-G gene in ovarian tumors. Molecular Cancer. 7: 43. PMID 18498645 DOI: 10.1186/1476-4598-7-43  1
2008 Polavarapu N, Mariño-Ramírez L, Landsman D, McDonald JF, Jordan IK. Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA. Bmc Genomics. 9: 226. PMID 18485226 DOI: 10.1186/1471-2164-9-226  1
2008 Huda A, Polavarapu N, Jordan IK, McDonald JF. Endogenous retroviruses of the chicken genome. Biology Direct. 3: 9. PMID 18361801 DOI: 10.1186/1745-6150-3-9  1
2008 Navare A, Zhou M, McDonald J, Noriega FG, Sullards MC, Fernandez FM. Serum biomarker profiling by solid-phase extraction with particle-embedded micro tips and matrix-assisted laser desorption/ionization mass spectrometry. Rapid Communications in Mass Spectrometry : Rcm. 22: 997-1008. PMID 18320548 DOI: 10.1002/rcm.3462  1
2007 Piriyapongsa J, Polavarapu N, Borodovsky M, McDonald J. Exonization of the LTR transposable elements in human genome. Bmc Genomics. 8: 291. PMID 17725822 DOI: 10.1186/1471-2164-8-291  1
2007 Moreno CS, Matyunina L, Dickerson EB, Schubert N, Bowen NJ, Logani S, Benigno BB, McDonald JF. Evidence that p53-mediated cell-cycle-arrest inhibits chemotherapeutic treatment of ovarian carcinomas. Plos One. 2: e441. PMID 17505532 DOI: 10.1371/journal.pone.0000441  1
2007 Menendez L, Walker D, Matyunina LV, Dickerson EB, Bowen NJ, Polavarapu N, Benigno BB, McDonald JF. Identification of candidate methylation-responsive genes in ovarian cancer. Molecular Cancer. 6: 10. PMID 17254359 DOI: 10.1186/1476-4598-6-10  1
2007 Bowen NJ, Logani S, Dickerson EB, Kapa LB, Akhtar M, Benigno BB, McDonald JF. Emerging roles for PAX8 in ovarian cancer and endosalpingeal development. Gynecologic Oncology. 104: 331-7. PMID 17064757 DOI: 10.1016/j.ygyno.2006.08.052  1
2007 Guan W, Bowen N, Gray A, McDonald J, Navathe S, Matyunina L. Discovering ovarian cancer biomarkers using gene ontology based microarray analysis Proceedings of the Acm Sigkdd International Conference On Knowledge Discovery and Data Mining. 78-87.  1
2006 Polavarapu N, Bowen NJ, McDonald JF. Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses. Genome Biology. 7: R51. PMID 16805923 DOI: 10.1186/gb-2006-7-6-r51  1
2006 Fablet M, McDonald JF, Biémont C, Vieira C. Ongoing loss of the tirant transposable element in natural populations of Drosophila simulans. Gene. 375: 54-62. PMID 16626897 DOI: 10.1016/j.gene.2006.02.008  1
2006 Polavarapu N, Bowen NJ, McDonald JF. Newly identified families of human endogenous retroviruses. Journal of Virology. 80: 4640-2. PMID 16611924 DOI: 10.1128/JVI.80.9.4640-4642.2006  1
2006 Herrera RJ, Lowery RK, Alfonso A, McDonald JF, Luis JR. Ancient retroviral insertions among human populations. Journal of Human Genetics. 51: 353-62. PMID 16518567 DOI: 10.1007/s10038-006-0370-0  1
2006 Ganko EW, Greene CS, Lewis JA, Bhattacharjee V, McDonald JF. LTR retrotransposon-gene associations in Drosophila melanogaster. Journal of Molecular Evolution. 62: 111-20. PMID 16408244 DOI: 10.1007/s00239-004-0312-4  1
2006 DeBarry JD, Ganko EW, McCarthy EM, McDonald JF. The contribution of LTR retrotransposon sequences to gene evolution in Mus musculus. Molecular Biology and Evolution. 23: 479-81. PMID 16368779 DOI: 10.1093/molbev/msj076  1
2005 McDonald JF, Matzke MA, Matzke AJ. Host defenses to transposable elements and the evolution of genomic imprinting. Cytogenetic and Genome Research. 110: 242-9. PMID 16093678 DOI: 10.1159/000084958  1
2004 Warrenfeltz S, Pavlik S, Datta S, Kraemer ET, Benigno B, McDonald JF. Gene expression profiling of epithelial ovarian tumours correlated with malignant potential. Molecular Cancer. 3: 27. PMID 15471544 DOI: 10.1186/1476-4598-3-27  1
2004 Calhoun JD, Rao RR, Warrenfeltz S, Rekaya R, Dalton S, McDonald J, Stice SL. Transcriptional profiling of initial differentiation events in human embryonic stem cells. Biochemical and Biophysical Research Communications. 323: 453-64. PMID 15369773 DOI: 10.1016/j.bbrc.2004.08.117  1
2004 Menendez L, Benigno BB, McDonald JF. L1 and HERV-W retrotransposons are hypomethylated in human ovarian carcinomas. Molecular Cancer. 3: 12. PMID 15109395 DOI: 10.1186/1476-4598-3-12  1
2004 Gao L, McCarthy EM, Ganko EW, McDonald JF. Evolutionary history of Oryza sativa LTR retrotransposons: a preliminary survey of the rice genome sequences. Bmc Genomics. 5: 18. PMID 15040813 DOI: 10.1186/1471-2164-5-18  1
2004 Franchini LF, Ganko EW, McDonald JF. Retrotransposon-gene associations are widespread among D. melanogaster populations. Molecular Biology and Evolution. 21: 1323-31. PMID 15014149 DOI: 10.1093/molbev/msh116  1
2004 McCarthy EM, McDonald JF. Long terminal repeat retrotransposons of Mus musculus. Genome Biology. 5: R14. PMID 15003117 DOI: 10.1186/gb-2004-5-3-r14  1
2004 McDonald JF, Zheleznyak A, Frazier WA. Cholesterol-independent interactions with CD47 enhance alphavbeta3 avidity. The Journal of Biological Chemistry. 279: 17301-11. PMID 14966135 DOI: 10.1074/jbc.M312782200  1
2003 McDonald JF, Dimitry JM, Frazier WA. An amyloid-like C-terminal domain of thrombospondin-1 displays CD47 agonist activity requiring both VVM motifs. Biochemistry. 42: 10001-11. PMID 12924949 DOI: 10.1021/bi0341408  1
2003 Ganko EW, Bhattacharjee V, Schliekelman P, McDonald JF. Evidence for the contribution of LTR retrotransposons to C. elegans gene evolution. Molecular Biology and Evolution. 20: 1925-31. PMID 12885961 DOI: 10.1093/molbev/msg200  1
2003 Panda K, Adak S, Aulak KS, Santolini J, McDonald JF, Stuehr DJ. Distinct influence of N-terminal elements on neuronal nitric-oxide synthase structure and catalysis. The Journal of Biological Chemistry. 278: 37122-31. PMID 12847099 DOI: 10.1074/jbc.M304456200  1
2003 McCarthy EM, McDonald JF. LTR_STRUC: a novel search and identification program for LTR retrotransposons. Bioinformatics (Oxford, England). 19: 362-7. PMID 12584121 DOI: 10.1093/bioinformatics/btf878  1
2002 McCarthy EM, Liu J, Lizhi G, McDonald JF. Long terminal repeat retrotransposons of Oryza sativa. Genome Biology. 3: RESEARCH0053. PMID 12372141  1
2002 Wei CC, Wang ZQ, Meade AL, McDonald JF, Stuehr DJ. Why do nitric oxide synthases use tetrahydrobiopterin? Journal of Inorganic Biochemistry. 91: 618-24. PMID 12237227 DOI: 10.1016/S0162-0134(02)00432-4  1
2002 McCollum AM, Ganko EW, Barrass PA, Rodriguez JM, McDonald JF. Evidence for the adaptive significance of an LTR retrotransposon sequence in a Drosophila heterochromatic gene. Bmc Evolutionary Biology. 2: 5. PMID 11914129 DOI: 10.1186/1471-2148-2-5  1
2002 Adak S, Bilwes AM, Panda K, Hosfield D, Aulak KS, McDonald JF, Tainer JA, Getzoff ED, Crane BR, Stuehr DJ. Cloning, expression, and characterization of a nitric oxide synthase protein from Deinococcus radiodurans. Proceedings of the National Academy of Sciences of the United States of America. 99: 107-12. PMID 11756668 DOI: 10.1073/pnas.012470099  1
2001 Ganko EW, Fielman KT, McDonald JF. Evolutionary history of Cer elements and their impact on the C. elegans genome. Genome Research. 11: 2066-74. PMID 11731497 DOI: 10.1101/gr.196201  1
2001 Bowen NJ, McDonald JF. Drosophila euchromatic LTR retrotransposons are much younger than the host species in which they reside. Genome Research. 11: 1527-40. PMID 11544196 DOI: 10.1101/gr.164201  1
1999 Miller WJ, McDonald JF, Nouaud D, Anxolabéhère D. Molecular domestication--more than a sporadic episode in evolution. Genetica. 107: 197-207. PMID 10952213  1
1999 Jordan IK, McDonald JF. Comparative genomics and evolutionary dynamics of Saccharomyces cerevisiae Ty elements. Genetica. 107: 3-13. PMID 10952193  1
1999 Jordan IK, Matyunina LV, McDonald JF. Evidence for the recent horizontal transfer of long terminal repeat retrotransposon. Proceedings of the National Academy of Sciences of the United States of America. 96: 12621-5. PMID 10535972 DOI: 10.1073/pnas.96.22.12621  1
1999 Bowen NJ, McDonald JF. Genomic analysis of Caenorhabditis elegans reveals ancient families of retroviral-like elements. Genome Research. 9: 924-35. PMID 10523521 DOI: 10.1101/gr.9.10.924  1
1999 Jordan IK, McDonald JF. The role of interelement selection in Saccharomyces cerevisiae Ty element evolution. Journal of Molecular Evolution. 49: 352-7. PMID 10473776 DOI: 10.1007/PL00006558  1
1999 Promislow DE, Jordan IK, McDonald JF. Genomic demography: a life-history analysis of transposable element evolution. Proceedings. Biological Sciences / the Royal Society. 266: 1555-60. PMID 10467744 DOI: 10.1098/rspb.1999.0815  1
1999 Jordan IK, McDonald JF. Phylogenetic perspective reveals abundant Ty1/Ty2 hybrid elements in the Saccharomyces cerevisiae genome. Molecular Biology and Evolution. 16: 419-22. PMID 10331268  0.48
1999 Jordan IK, McDonald JF. Tempo and mode of Ty element evolution in Saccharomyces cerevisiae. Genetics. 151: 1341-51. PMID 10101161  0.48
1998 McDonald JF. Transposable elements, gene silencing and macroevolution. Trends in Ecology & Evolution. 13: 94-5. PMID 21238218 DOI: 10.1016/S0169-5347(97)01282-2  1
1998 Jordan IK, McDonald JF. Interelement selection in the regulatory region of the copia retrotransposon. Journal of Molecular Evolution. 47: 670-6. PMID 9847408  0.48
1998 Jordan IK, McDonald JF. Evolution of the copia retrotransposon in the Drosophila melanogaster species subgroup. Molecular Biology and Evolution. 15: 1160-71. PMID 9729880  0.48
1998 Jordan IK, McDonald JF. Evidence for the role of recombination in the regulatory evolution of Saccharomyces cerevisiae Ty elements. Journal of Molecular Evolution. 47: 14-20. PMID 9664692  0.48
1998 Wilson S, Matyunina LV, McDonald JF. An enhancer region within the copia untranslated leader contains binding sites for Drosophila regulatory proteins. Gene. 209: 239-46. PMID 9524274  0.64
1997 McDonald JF, Matyunina LV, Wilson S, Jordan IK, Bowen NJ, Miller WJ. LTR retrotransposons and the evolution of eukaryotic enhancers. Genetica. 100: 3-13. PMID 9440254  0.92
1997 McDonald JF, Shah AM, Schwalbe RA, Kisiel W, Dahlbäck B, Nelsestuen GL. Comparison of naturally occurring vitamin K-dependent proteins: correlation of amino acid sequences and membrane binding properties suggests a membrane contact site. Biochemistry. 36: 5120-7. PMID 9136872 DOI: 10.1021/bi9626160  1
1996 Matyunina LV, Jordan IK, McDonald JF. Naturally occurring variation in copia expression is due to both element (cis) and host (trans) regulatory variation. Proceedings of the National Academy of Sciences of the United States of America. 93: 7097-102. PMID 8692951  0.64
1995 Csink AK, McDonald JF. Analysis of copia sequence variation within and between Drosophila species. Molecular Biology and Evolution. 12: 83-93. PMID 7877499  1
1990 Csink AK, McDonald JF. copia expression is variable among natural populations of Drosophila. Genetics. 126: 375-85. PMID 1700962  1
1980 Marks RW, Brittnacher JG, McDonald JF, Prout T, Ayala FJ. Wineries, drosophila, alcohol, and Adh. Oecologia. 47: 141-144. PMID 28309643 DOI: 10.1007/BF00541790  0.48
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