Selected Faculty Publications (2003-2014)

Newman RH, Zhang J. The design and application of genetically encodable biosensors based on fluorescent proteins. Methods Mol Biol. 2014;1071:1-16. http://www.ncbi.nlm.nih.gov/pubmed/24052376

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. Epub 2013 Nov 13. http://www.ncbi.nlm.nih.gov/pubmed/24227675

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. Epub 2013 Mar 21. http://www.ncbi.nlm.nih.gov/pubmed/23524292

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

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

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

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

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

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

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

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

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

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

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