Faculty Publications

Selected Faculty Publications (2003-2014)

Mahdavian E, Marshall M, Martin PM, Cagle P, Salvatore BA, Quick QA. Caspase-dependent signaling underlies glioblastoma cell death in response to the fungal metabolite, fusarochromanone. Int J Mol Med. 2014 Sep;34(3):880-5. doi: 10.3892/ijmm.2014.1842. http://www.ncbi.nlm.nih.gov/pubmed/25016928

Hamilton JL, Brickman AM, Lang R, Byrd GS, Haines JL, Pericak-Vance MA, Manly JJ. Relationship Between Depressive Symptoms and Cognition in Older, Non-demented African Americans. J Int Neuropsychol Soc. 2014 Aug;20(7):756-63. http://www.ncbi.nlm.nih.gov/pubmed/24840093

Newman RH, Zhang J, Zhu H. Toward a systems-level view of dynamic phosphorylation networks. Front. Genet. 2014 Aug 15;5:263. http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00263/full

Wang Y, Liu Y, Tang F, Bernot KM, Schore R, Marcucci G, Caligiuri MA, Zheng P, Liu Y. Echinomycin protects mice against relapsed acute myeloid leukemia without adverse effect on hematopoietic stem cells. Blood. 2014 Aug 14;124(7):1127-35. http://www.ncbi.nlm.nih.gov/pubmed/24994068

Chapman S, Harrison SH, Bikdash M, KC Dukka. The Bustle of Bioinformatics: Cloudy with a Chance for Big Data. 2014 ASE BIGDATA/SOCIALCOM/CYBERSECURITY Conference, Stanford University, May 27-31, 2014 (review) http://www.ase360.org/handle/123456789/143

Lynch M, Bost D, Wilson S, Maruki T, Harrison SH. Population-genetic inference from pooled-sequencing data. Genome Biol Evol. 2014 Apr 30;6(5):1210-8. http://www.ncbi.nlm.nih.gov/pubmed/24787620

Harrison TM, Harrison SH, Sikarskie JG, Armstrong D. Humoral response to calicivirus in captive tigers given a dual-strain vaccine. J Zoo Wildl Med. 2014 Mar;45(1):23-8. http://www.ncbi.nlm.nih.gov/pubmed/24712158

Hu J, Rho HS, Newman RH, Hwang W, Neiswinger J, Zhu H, Zhang J, Qian J. Global analysis of phosphorylation networks in humans. Biochim Biophys Acta. 2014 Jan;1844(1 Pt B):224-31. http://www.ncbi.nlm.nih.gov/pubmed/23524292

Hu J, Rho HS, Newman RH, Zhang J, Zhu H, Qian J. PhosphoNetworks: a database for human phosphorylation networks. Bioinformatics. 2014 Jan 1;30(1):141-2. http://www.ncbi.nlm.nih.gov/pubmed/24227675

Bernot KM, Siebenaler RF, Whitman SP, Zorko NA, Marcucci GG, Santhanam R, Ahmed EH, Ngangana M, McConnell KK, Nemer JS, Brook DL, Kulp SK, Chen CS, Frankhouser D, Yan P, Bundschuh R, Zhang X, Dorrance AM, Dickerson KE, Jarjoura D, Blum W, Marcucci G, Caligiuri MA. Toward personalized therapy in AML: in vivo benefit of targeting aberrant epigenetics in MLL-PTD-associated AML. Leukemia. 2013 Dec;27(12):2379-82. http://www.ncbi.nlm.nih.gov/pubmed/23660685

Bernot KM, Nemer JS, Santhanam R, Liu S, Zorko NA, Whitman SP, Dickerson KE, Zhang M, Yang X, McConnell KK, Ahmed EH, Muñoz MR, Siebenaler RF, Marcucci GG, Mundy-Bosse BL, Brook DL, Garman S, Dorrance AM, Zhang X, Zhang J, Lee RJ, Blum W, Caligiuri MA, Marcucci G. Eradicating acute myeloid leukemia in a Mll(PTD/wt):Flt3(ITD/wt) murine model: a path to novel therapeutic approaches for human disease. Blood. 2013 Nov 28;122(23):3778-83. http://www.ncbi.nlm.nih.gov/pubmed/24085765

Cagle P, Idassi O, Carpenter J, Minor R, Goktepe I, Martin P. Effect of Rosehip (Rosa canina) Extracts on Human Brain Tumor Cell Proliferation and Apoptosis. J Cancer Therapy. 2013 Oct;3(5):534-545. http://www.scirp.org/journal/PaperInformation.aspx?PaperID=23446

Woodard CL, Goodwin CR, Wan J, Xia S, Newman R, Hu J, Zhang J, Hayward SD, Qian J, Laterra J, Zhu H. Profiling the dynamics of a human phosphorylome reveals new components in HGF/c-Met signaling. PLoS One. 2013 Sep 2;8(9):e72671. http://www.ncbi.nlm.nih.gov/pubmed/24023761

Newman RH, Zhang J. The design and application of genetically encodable biosensors based on fluorescent proteins. Methods Mol Biol. 2013 Aug 12;1071:1-16. http://www.ncbi.nlm.nih.gov/pubmed/24052376

Xie Z, Harrison SH, Torti SV, Torti FM, Han J. Application of circuit simulation method for differential modeling of TIM-2 iron uptake and metabolism in mouse kidney cells. Front Physiol. 2013 Jun 7;4(136). http://www.ncbi.nlm.nih.gov/pubmed/23761763

Xu D, Cobb MG, Gavilano L, Witherspoon SM, Williams D, White CD, Taverna P, Bednarski BK, Kim HJ, Baldwin AS, Baines AT. Inhibition of oncogenic Pim-3 kinase
modulates transformed growth and chemosensitizes pancreatic cancer cells to gemcitabine. Cancer Biol Ther. 2013 Jun 1;14(6):492-501. http://www.ncbi.nlm.nih.gov/pubmed/23760491

Kohli MA, John-Williams K, Rajbhandary R, Naj A, Whitehead P, Hamilton K, Carney RM, Wright C, Crocco E, Gwirtzman HE, Lang R, Beecham G, Martin ER, Gilbert J, Benatar M, Small GW, Mash D, Byrd G, Haines JL, Pericak-Vance MA, Züchner S. Repeat expansions in the C9ORF72 gene contribute to Alzheimer's disease in Caucasians. Neurobiol Aging. 2013 May;34(5):1519.e5-12. http://www.ncbi.nlm.nih.gov/pubmed/23107433

Lang R, Kelkar VA, Byrd JR, Edwards CL, Pericak-Vance M, Byrd GS. African American participation in health-related research studies: indicators for effective recruitment. J Public Health Manag Pract. 2013 Mar-Apr;19(2):110-8. http://www.ncbi.nlm.nih.gov/pubmed/23358288

Hayes, R. The alien ecosystem project: An integrative and creative assignment for biology classes. EvoS J. 2013;5(1):61-80. http://evostudies.org/wp-content/uploads/2013/03/Hayes_Vol5Iss1.pdf

Reitz C, Jun G, Naj A, Rajbhandary R, Vardarajan BN, Wang LS, Valladares O, Lin CF, Larson EB, Graff-Radford NR, Evans D, De Jager PL, Crane PK, Buxbaum JD, Murrell JR, Raj T, Ertekin-Taner N, Logue M, Baldwin CT, Green RC, Barnes LL, Cantwell LB, Fallin MD, Go RC, Griffith P, Obisesan TO, Manly JJ, Lunetta KL, Kamboh MI, Lopez OL, Bennett DA, Hendrie H, Hall KS, Goate AM, Byrd GS, Kukull WA, Foroud TM, Haines JL, Farrer LA, Pericak-Vance MA, Schellenberg GD, Mayeux R. Alzheimer Disease Genetics Consortium. Variants in the ATP-binding cassette transporter (ABCA7), apolipoprotein E ϵ4,and the risk of late-onset Alzheimer disease in African Americans. JAMA. 2013 Apr 10;309(14):1483-92. http://www.ncbi.nlm.nih.gov/pubmed/23571587

Newman RH, Hu J, Rho HS, Xie Z, Woodard C, Neiswinger J, Cooper C, Shirley M, Clark HM, Hu S, Hwang W, Jeong JS, Wu G, Lin J, Gao X, Ni Q, Goel R, Xia S, Ji H, Dalby KN, Birnbaum MJ, Cole PA, Knapp S, Ryazanov AG, Zack DJ, Blackshaw S, Pawson T, Gingras AC, Desiderio S, Pandey A, Turk BE, Zhang J, Zhu H, Qian J. Construction of human activity-based phosphorylation networks. Mol Syst Biol. 2013 Feb;9:655. http://www.ncbi.nlm.nih.gov/pubmed/23549483

Fortune DA, Lang R, Cook S, Byrd GS. African Americans and Alzheimer's Disease: Role of Health Educators in Addressing this Silent Epidemic. American Journal of Health Studies. 2013;28(3). http://www.va-ajhs.com/28-3/index.aspx

Zorko NA*, Bernot KM*, Whitman SP*, Siebenaler RF, Ahmed EH, Marcucci GG, Yanes DA, McConnell KK, Mao C, Kalu C, Zhang X, Jarjoura D, Dorrance AM, Heerema NA, Lee BH, Huang G, Marcucci G, Caligiuri MA. Mll partial tandem duplication and Flt3 internal tandem duplication in a double knock-in mouse recapitulates features of counterpart human acute myeloid leukemias. Blood. 2012 Aug 2;120(5):1130-6. *co-1st authors. http://www.ncbi.nlm.nih.gov/pubmed/22674806

Zhang Y, Yan X, Sashida G, Zhao X, Rao Y, Goyama S, Whitman SP, Zorko N, Bernot K, Conway RM, Witte D, Wang QF, Tenen DG, Xiao Z, Marcucci G, Mulloy JC, Grimes HL, Caligiuri MA, Huang G. Stress hematopoiesis reveals abnormal control of self-renewal, lineage bias, and myeloid differentiation in Mll partial tandem duplication (Mll-PTD) hematopoietic stem/progenitor cells. Blood. 2012 Aug 2;120(5):1118-29. http://www.ncbi.nlm.nih.gov/pubmed/22740449

González IM, Martin PM, Burdsal C, Sloan JL, Mager S, Harris T, Sutherland AE. Leucine and arginine regulate trophoblast motility through mTOR-dependent and
independent pathways in the preimplantation mouse embryo. Dev Biol. 2012 Jan 15;361(2):286-300. http://www.ncbi.nlm.nih.gov/pubmed/22056783

Ongeri EM, Anyanwu O, Reeves WB, Bond JS. Villin and actin in the mouse kidney brush-border membrane bind to and are degraded by meprins, an interaction that
contributes to injury in ischemia-reperfusion. Am J Physiol Renal Physiol. 2011 Oct;301(4):F871-82. http://www.ncbi.nlm.nih.gov/pubmed/21795642

Byrd GS, Edwards CL, Kelkar VA, Phillips RG, Byrd JR, Pim-Pong DS, Starks TD, Taylor AL, Mckinley RE, Li YJ, Pericak-Vance M. Recruiting intergenerational
African American males for biomedical research Studies: a major research challenge. J Natl Med Assoc. 2011 Jun;103(6):480-7. http://www.ncbi.nlm.nih.gov/pubmed/21830630

Newman RH, Fosbrink MD, Zhang J. Genetically encodable fluorescent biosensors for tracking signaling dynamics in living cells. Chem Rev. 2011 May 11;111(5):3614-66. http://www.ncbi.nlm.nih.gov/pubmed/21456512

Xu D, Allsop SA, Witherspoon SM, Snider JL, Yeh JJ, Fiordalisi JJ, White CD, Williams D, Cox AD, Baines AT. The oncogenic kinase Pim-1 is modulated by K-Ras
signaling and mediates transformed growth and radioresistance in human pancreatic ductal adenocarcinoma cells. Carcinogenesis. 2011 Apr;32(4):488-95. http://www.ncbi.nlm.nih.gov/pubmed/21262926

Luckie D, Harrison SH, Ebert-May D. Model-based reasoning: using visual tools to reveal student learning. Adv Physiol Educ. 2011 Mar;35(1):59-67. http://www.ncbi.nlm.nih.gov/pubmed/21386003

Rajendran S, Harrison SH, Thomas RA, Tucker JD. The role of mitochondria in the radiation-induced bystander effect in human lymphoblastoid cells. Radiat Res.
2011 Feb;175(2):159-71. http://www.ncbi.nlm.nih.gov/pubmed/21268709

Balagopalan L, Ashwell BA, Bernot KM, Akpan IO, Quasba N, Barr VA, Samelson LE. Enhanced T-cell signaling in cells bearing linker for activation of T-cell (LAT) molecules resistant to ubiquitylation. Proc Natl Acad Sci U S A. 2011 Feb 15;108(7):2885-90. http://www.ncbi.nlm.nih.gov/pubmed/21282648

Han J, Seaman WE, Di X, Wang W, Willingham M, Torti FM, Torti SV. Iron uptake mediated by binding of H-ferritin to the TIM-2 receptor in mouse cells. PLoS One.
2011;6(8):e23800. http://www.ncbi.nlm.nih.gov/pubmed/21886823

Goins G, Chen M, White C, Clemence D, Redd T, Kelkar V. An initiative to broaden diversity in undergraduate biomathematics training. CBE Life Sci Educ. 2010 Fall;9(3):241-7. http://www.ncbi.nlm.nih.gov/pubmed/20810956

Yadavilli S, Chen Z, Albrecht T, Muganda PM. Mechanism of diepoxybutane-induced p53 regulation in human cells. J Biochem Mol Toxicol. 2009 Nov-Dec;23(6):373-86. http://www.ncbi.nlm.nih.gov/pubmed/20024960

Barr VA, Bernot KM, Shaffer MH, Burkhardt JK, Samelson LE. Formation of STIM and Orai complexes: puncta and distal caps. Immunol Rev. 2009 Sep;231(1):148-59. http://www.ncbi.nlm.nih.gov/pubmed/19754895

Isikhuemhen OS, Mikiashvili NA, Kelkar V. Application of solid waste from anaerobic digestion of poultry litter in Agrocybe aegerita cultivation: mushroom
production, lignocellulolytic enzymes activity and substrate utilization. Biodegradation. 2009 Jun;20(3):351-61. http://www.ncbi.nlm.nih.gov/pubmed/18982415

Gordon EJ, Kelkar V. Natural killer T cell facilitated engraftment of rat skin but not islet xenografts in mice. Xenotransplantation. 2009 May-Jun;16(3):135-44. http://www.ncbi.nlm.nih.gov/pubmed/19566653

Saha S, Harrison SH, Chen JY. Dissecting the human plasma proteome and inflammatory response biomarkers. Proteomics. 2009 Jan;9(2):470-84. http://www.ncbi.nlm.nih.gov/pubmed/19105179

Huan T, Sivachenko AY, Harrison SH, Chen JY. ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining. BMC
Bioinformatics. 2008 Aug 12;9 Suppl 9:S5. http://www.ncbi.nlm.nih.gov/pubmed/18793469

Newman RH, Zhang J. Small molecules and chemical tools at the interface. Nat Chem Biol. 2008 Jul;4(7):382-6. http://www.ncbi.nlm.nih.gov/pubmed/18560425

Barr VA, Bernot KM, Srikanth S, Gwack Y, Balagopalan L, Regan CK, Helman DJ, Sommers CL, Oh-Hora M, Rao A, Samelson LE. Dynamic movement of the calcium sensor STIM1 and the calcium channel Orai1 in activated T-cells: puncta and distal caps. Mol Biol Cell. 2008 Jul;19(7):2802-17. http://www.ncbi.nlm.nih.gov/pubmed/18448669

Patino-Lopez G, Dong X, Ben-Aissa K, Bernot KM, Itoh T, Fukuda M, Kruhlak MJ, Samelson LE, Shaw S. Rab35 and its GAP EPI64C in T cells regulate receptor recycling and immunological synapse formation. J Biol Chem. 2008 Jun 27;283(26):18323-30. http://www.ncbi.nlm.nih.gov/pubmed/18450757

Saha S, Harrison SH, Shen C, Tang H, Radivojac P, Arnold RJ, Zhang X, Chen JY. HIP2: an online database of human plasma proteins from healthy individuals.
BMC Med Genomics. 2008 Apr 25;1:12. http://www.ncbi.nlm.nih.gov/pubmed/18439290

Yadavilli S, Martinez-Ceballos E, Snowden-Aikens J, Hurst A, Joseph T, Albrecht T, Muganda PM. Diepoxybutane activates the mitochondrial apoptotic
pathway and mediates apoptosis in human lymphoblasts through oxidative stress. Toxicol In Vitro. 2007 Dec;21(8):1429-41. http://www.ncbi.nlm.nih.gov/pubmed/17693053

Ongeri EM, Verderame MF, Hammond JM. The TATA binding protein associated factor 4b (TAF4b) mediates FSH stimulation of the IGFBP-3 promoter in cultured
porcine ovarian granulosa cells. Mol Cell Endocrinol. 2007 Nov 15;278(1-2):29-35. Epub 2007 Aug 19. http://www.ncbi.nlm.nih.gov/pubmed/17888567

Hayes RD, Merigan WH. Mechanisms of Sensitivity Loss due to Visual Cortex Lesions in Humans and Macaques. Cereb Cortex. 2007 May;17(5):1117-28. http://www.ncbi.nlm.nih.gov/pubmed/16769744

Saxena A, Rorie CJ, Dimitrova D, Daniely Y, Borowiec JA. Nucleolin inhibits Hdm2 by multiple pathways leading to p53 stabilization. Oncogene. 2006 Nov 23;25(55):7274-88. http://www.ncbi.nlm.nih.gov/pubmed/16751805

Barr VA, Balagopalan L, Barda-Saad M, Polishchuk R, Boukari H, Bunnell SC, Bernot KM, Toda Y, Nossal R, Samelson LE. T-cell antigen receptor-induced signaling complexes: internalization via a cholesterol-dependent endocytic pathway. Traffic. 2006 Sep;7(9):1143-62. http://www.ncbi.nlm.nih.gov/pubmed/16919152

Lilburn TG, Harrison SH, Cole JR, Garrity GM. Computational aspects of systematic biology. Brief Bioinform. 2006 Jun;7(2):186-95. Epub 2006 Apr 24.
Review. http://www.ncbi.nlm.nih.gov/pubmed/16772262

Ongeri EM, Verderame MF, Hammond JM. Follicle-stimulating hormone induction of ovarian insulin-like growth factor-binding protein-3 transcription requires a
TATA box-binding protein and the protein kinase A and phosphatidylinositol-3 kinase pathways. Mol Endocrinol. 2005 Jul;19(7):1837-48. http://www.ncbi.nlm.nih.gov/pubmed/15718291

Schmiederer M, Knutson E, Muganda P, Albrecht T. Acute exposure of human lung cells to 1,3-butadiene diepoxide results in G1 and G2 cell cycle arrest. Environ
Mol Mutagen. 2005 May;45(4):354-64. http://www.ncbi.nlm.nih.gov/pubmed/15688362

Martin PM, Hussaini IM. PKC eta as a therapeutic target in glioblastoma multiforme. Expert Opin Ther Targets. 2005 Apr;9(2):299-313. Review. http://www.ncbi.nlm.nih.gov/pubmed/15934917

Bernot KM, Lee CH, Coulombe PA. A small surface hydrophobic stripe in the coiled-coil domain of type I keratins mediates tetramer stability. J Cell Biol. 2005 Mar 14;168(6):965-74. http://www.ncbi.nlm.nih.gov/pubmed/15767464

Amos S, Martin PM, Polar GA, Parsons SJ, Hussaini IM. Phorbol 12-myristate 13-acetate induces epidermal growth factor receptor transactivation via protein kinase Cdelta/c-Src pathways in glioblastoma cells. J Biol Chem. 2005 Mar 4;280(9):7729-38. http://www.ncbi.nlm.nih.gov/pubmed/15618223

Hayes RD, Byrne JH, Cox, SJ, Baxter, DA. Estimation of single-neuron model parameters from spike train data. Neurocomputing. 2005;65:517-529.
http://www.sciencedirect.com/science/article/pii/S0925231204004242

Aeder SE, Martin PM, Soh JW, Hussaini IM. PKC-eta mediates glioblastoma cell proliferation through the Akt and mTOR signaling pathways. Oncogene. 2004 Dec 2;23(56):9062-9. http://www.ncbi.nlm.nih.gov/pubmed/15489897

Rorie CJ, Weissman BE. The Ews/Fli-1 fusion gene changes the status of p53 in neuroblastoma tumor cell lines. Cancer Res. 2004 Oct 15;64(20):7288-95. http://www.ncbi.nlm.nih.gov/pubmed/15492248

Yadavilli S, Muganda PM. Diepoxybutane induces caspase and p53-mediated apoptosis in human lymphoblasts. Toxicol Appl Pharmacol. 2004 Mar 1;195(2):154-65. http://www.ncbi.nlm.nih.gov/pubmed/14998682

Rorie CJ, Thomas VD, Chen P, Pierce HH, O'Bryan JP, Weissman BE. The Ews/Fli-1 fusion gene switches the differentiation program of neuroblastomas to Ewing sarcoma/peripheral primitive neuroectodermal tumors. Cancer Res. 2004 Feb 15;64(4):1266-77. http://www.ncbi.nlm.nih.gov/pubmed/14973077

Bernot KM, Coulombe PA, Wong P. Skin: an ideal model system to study keratin genes and proteins. Methods Cell Biol. 2004;78:453-87. http://www.ncbi.nlm.nih.gov/pubmed/15646628

Coulombe PA and Bernot KM. "Keratins and the Skin" in Encyclopedia of Biological Chemistry. eds. W.J. Lennarz & M.D. Lane. 2004. Elsevier, Oxford. Vol. 2. pp. 497-504.

Bernot KM and Coulombe PA. “Intermediate Filaments” in Encyclopedia of Biological Chemistry. eds. W.J. Lennarz & M.D. Lane.  Elsevier, Oxford. 2004 Vol. 2. pp. 468-464.

Martin PM, Sutherland AE, Van Winkle LJ. Amino acid transport regulates blastocyst implantation. Biol Reprod. 2003 Oct;69(4):1101-8. http://www.ncbi.nlm.nih.gov/pubmed/12801981

Han J, Day JR, Connor JR, Beard JL. Gene expression of transferrin and transferrin receptor in brains of control vs. iron-deficient rats. Nutr Neurosci. 2003 Feb;6(1):1-10. http://www.ncbi.nlm.nih.gov/pubmed/12608731