Current Graduate Student Publications
Jessica Apostol (Neal)
K McNally, JA Neal, TP McManus, McCormick, JJ, VM Maher: hRev7, putative subunit of hPol zeta, plays a critical role in survival, induction of mutations, and progression through S-phase, of UV(254nm)-irradiated human fibroblasts. DNA Repair ( APR 2 2008) 7 597-604.
Philip Bates
Bates, P. D., J. B. Ohlrogge, et al. (2007) Incorporation of newly synthesized fatty acids into cytosolic glycerolipids in pea leaves occurs via acyl editing. Journal of Biological Chemistry 282(43): 31206-31216.
Jian Chen
Zhang Z,* Chen J*, Guo F, He L, Wu Y, Zeng C, Xiao X, He D. (2008) A high-temporal resolution technology for dynamic proteomic analysis based on 35S labeling. PLoS ONE 3(8):e2991. (*These authors contributed equally to this paper.)
Hoo Sun Chung
Chung HS, Howe GA (2009) A critical role for the TIFY motif in repression of jasmonate signaling by a stabilized variant of the JASMONATE ZIM-domain protein JAZ10 in Arabidopsis. Plant Cell 21, 131-145.
Katsir L, Chung HS, Koo AJ, Howe GA (2008) Jasmonate signaling: a conserved mechanism of hormone sensing. Curr Opin Plant Biol. 11, 428-35.
Melotto M, Mecey C, Niu Y, Chung HS, Katsir L, Yao J, Zeng W, Thines B, Staswick P, Browse J, Howe GA, He SY (2008) A critical role of two positively charged amino acids in the Jas motif of Arabidopsis JAZ proteins in mediating coronatine- and jasmonoyl isoleucine-dependent interactions with the COI1 F-box protein. Plant J. 55, 979-88.
Chung HS, Koo AJ, Gao X, Jayanty S, Thines B, Jones AD, Howe GA (2008) Regulation and function of Arabidopsis JASMONATE ZIM-domain genes in response to wounding and herbivory. Plant Physiol. 146, 952-64.
Cho SK, Chung HS, Ryu MY, Park MJ, Lee MM, Bahk YY, Kim J, Pai HS, Kim WT (2006) Heterologous expression and molecular and cellular characterization of CaPUB1encoding a hot pepper U-Box E3 ubiquitin ligase homolog. Plant Physiol. 142, 1664-82.
Koo AJ, Chung HS, Kobayashi Y, Howe GA (2006) Identification of a peroxisomal acyl-activating enzyme involved in the biosynthesis of jasmonic acid in Arabidopsis. J Biol Chem. 281, 33511-20.
Adam Cornish
Xu C, Fan J, Cornish AJ, Benning C. (2008) Lipid trafficking between the endoplasmic reticulum and the plastid in Arabidopsis requires the extraplastidic TGD4 protein. Plant Cell. Aug;20(8):2190-204.
Edward Dere
Lee, K., Burgoon, L. D., Lamb, L., Dere, E., Zacharewski, T. R., Hogenesch, J. B. and LaPres, J. J. (2006). Identification and characterization of genes susceptible to transcriptional cross-talk between the hypoxia and dioxin signaling cascades. Chem Res Toxicol 19, 1284-93.
Dere, E., Boverhof, D. R., Burgoon, L. D. and Zacharewski, T. R. (2006). In vivo - in vitro toxicogenomic comparison of TCDD-elicited gene expression in Hepa1c1c7 mouse hepatoma cells and C57BL/6 hepatic tissue. BMC Genomics 7, 80.
Burgoon, L. D., Boutros, P. C., Dere, E. and Zacharewski, T. R. (2006). dbZach: A MIAME-compliant toxicogenomic supportive relational database. Toxicol Sci 90, 558-68.
Hye Jin Hwang
Hwang HJ, Kim EH, Cho YD. (2001) Isolation and properties of arginase from a shade plant, ginseng (Panax ginseng C.A. Meyer) roots. Phytochemistry. 58(7):1015-24.
James E. Johnson, Jr.
Hoogstraten, C.G. & Johnson, J.E., Jr. (2008) Metabolic Labeling: Taking Advantage of Bacterial Pathways to Prepare Spectroscopically Useful Isotope Patterns in Proteins and Nucleic Acids. Concepts Magn. Reson. Ser. A 32, 34-55.
Johnson JE Jr, Julien KR, Hoogstraten CG. (2006) Alternate-site isotopic labeling of ribonucleotides for NMR studies of ribose conformational dynamics in RNA. J Biomol NMR. 35(4):261-74.
Leron Katsir
Wu F, Katsir LJ, Seavy M, Gaffney BJ. (2003) Role of radical formation at tyrosine 193 in the allene oxide synthase domain of a lipoxygenase-AOS fusion protein from coral. Biochemistry 42(22):6871-6880.
Anna Kopec
Wei-Chun Wei, Anna K Kopec and Ming-Jer Tang, "Requirement of focal adhesion kinase in branching tubulogenesis", Journal of Biomedical Sciences, 2009 Jan 12; 16(1):5. Link to publication
Anna K. Kopec , Darrell R. Boverhof , Lyle D. Burgoon , Daher Ibrahim-Aibo, Jack R. Harkema , Colleen Tashiro, Brock Chittim and Timothy R. Zacharewski, "Comparative Toxicogenomic Examination of the Hepatic Effects of PCB126 and TCDD in Immature, Ovariectomized C57BL/6 Mice", Toxicological Sciences 2008 102(1):61-75. Link to "About the Cover"
Joshua Kwekel
Boverhof DR, Kwekel JC, Humes DG, Burgoon LD, Zacharewski TR. Dioxin induces an estrogen-like, estrogen receptor dependent gene expression response in the murine uterus. Mol Pharmacol. 2006 Feb 8; [Epub ahead of print]
Kwekel JC, Burgoon LD, Burt JW, Harkema JR, Zacharewski TR. A cross-species analysis of the rodent uterotrophic program: elucidation of conserved responses and targets of estrogen signaling. Physiol Genomics. 2005 Nov 17;23(3):327-42. [Epub 2005 Sep 20]
Sean Law
Mukherjee S, Law SM, Feig M. Deciphering the mismatch recognition cycle in MutS and MSH2-MSH6 using normal-mode analysis. Biophys J. 2009 Mar 4;96(5):1707-20.
Law, S. M. and M. Feig (2008). Applications of a Novel Biasing Potential to Study DNA Translocation and DNA Base Flipping. From Computational Biophysics to Systems Biology (CBSB08), Forschungszentrum, Julich, Germany, NIC Series, Vol. 40.
Feig, M., S. Tanizaki, et al. (2008). Simulating Biomolecules in Cellular Environments. From Computational Biophysics to Systems Biology (CBSB08), Forschungszentrum, Julich, Germany, NIC Series, Vol. 40.
Chin-Mei Lee
Lin HJ, Lee CM, Luo CW, Chen YH. (2005) Functional preservation of duplicated pair for RSVS III gene in the REST locus of rat 3q42. Biochem Biophys Res Commun. Vol. 326(2) p.355-63.
Chih-Shia Lee
Jou YS, Lee CS, Chang YH, Hsiao CF, Chen CF, Chao CC, Wu LS, Yeh SH, Chen DS, Chen PJ. Clustering of minimal deleted regions reveals distinct genetic pathways of human hepatocellular carcinoma. Cancer Res. 2004 May 1;64(9):3030-6.
Ziru Li
J. Lyew, Z. Li, L.C. Yuan, Y.B. Luo, T.L. Sage. (2007) Pollen tube growth in association with a dry-type stigmatic transmitting tissue and extragynoecial compitum in the basal angiosperm Kadsura longipedunculata (Schisandraceae). American Journal of Botany 94:1170 - 1182.
Binbin Lu
Lu B, Xu C, Awai K, Jones AD, Benning C. (2007) A small ATPase protein of Arabidopsis, TGD3, involved in chloroplast lipid import. J. Biol. Chem., 282(49): 35945-35953.
Awai K, Xu C, Lu B, Benning C. (2006) Lipid trafficking between the endoplasmic reticulum and the chloroplast. Biochem Soc Trans. 34(Pt 3):395-398.
Bryan Mets
Lito P, Mets BD, Kleff S, O'Reilly S, Maher VM, McCormick JJ. (2008) Evidence That Sprouty 2 Is Necessary for Sarcoma Formation by H-Ras Oncogene-transformed Human Fibroblasts. J Biol Chem. Jan 25;283(4):2002-9.
Patrick Ochieng
BenA-tez JJ, Keller AM, Ochieng P, Yatsunyk LA, Huffman DL, Rosenzweig AC, Chen P. Probing Transient Copper Chaperone-Wilson Disease Protein Interactions at the Single-Molecule Level with Nanovesicle Trapping. J Am Chem Soc. 2008 Feb 5 [Epub ahead of print]
Jennifer Phillips
Phillips, J. M., and Goodman, J. I. (2008) Identification of Genes that May Play Critical Roles in Phenobarbital (PB)-induced Liver Tumorigenesis Due to Altered DNA Methylation. Toxicol. Sci. 104, 86-99. Link to "About the Cover"
Phillips, J. M., Yamamoto, Y., Negishi, M., Maronpot, R. R., and Goodman, J. I. (2006) Orphan Nuclear Receptor Constitutive Active/Androstane Receptor (CAR)-mediated Alterations in DNA Methylation during Phenobarbital (PB) Promotion of Liver Tumorigenesis. Toxicol. Sci. Mar;96(1):72-82.
Bachman, A. N., Phillips, J. M., and Goodman, J. I. (2006) Phenobarbital induces progressive patterns of GC-rich and gene-specific altered DNA methylation in the liver of tumor-prone B6C3F1 mice. Toxicol. Sci. 91, 393-405.
Vengellur, A., Phillips, J.M., Hogenesch J.B., and LaPres, J.J. (2005) Gene expression profiling of hypoxia signaling in human hepatocellular carcinoma cells. Physiol. Genomics 22, 308-18.
Steven Proper
Leonard, S. S., Keil, D., Mehlman, T., Proper, S., Shi, X., and Harris, G. K. (2006). Essiac tea: scavenging of reactive oxygen species and effects on DNA damage. J Ethnopharmacol 103, 288-296.
Ham, J.E., Proper, S.P., Wells, J.R. (2006). Gas-phase chemistry of citronellol with ozone and OH radical: Rate constants and products. Atmospheric Environment. 40(4):726-735.
Michael Ruckle
Ruckle, M.E., and Larkin, R.M. (2009) Plastid signals that affect photomorphogenesis in Arabidopsis thaliana are dependent on GENOMES UNCOUPLED 1 and cryptochrome 1. New Phytologist 182: 367-379. Selected for commentary: Steering the solar panel: plastids influence development by Lopez-Juez, E.
Larkin, R.M., and Ruckle, M.E. (2008) Integration of light and plastid signals. Current Opinions in Plant Biology 11: 593-599.
ME Ruckle, SM DeMarco, RM Larkin.(2007) Plastid signals remodel light signaling networks and are essential for efficient chloroplast biogenesis in Arabidopsis Plant Cell ( 19 3944-3960.
Goffman FD, Ruckle M, Ohlrogge J, Shachar-Hill Y. (2004) Carbon dioxide concentrations are very high in developing oilseeds. Plant Physiology and Biochemistry 42 (9): 703-708.
Riekhof WR, Ruckle ME, Lydic TA, Sears BB, Benning C. (2003) The sulfolipids 2 '-O-acyl-sulfoquinovosyldiacylglycerol and sulfoquinovosyldiacylglycerol are absent from a Chlamydomonas reinhardtii mutant deleted in SQD1. Plant Physiology 133 (2): 864-874.
Juliana Sacoman
Sacoman, J.L., Monteiro, K.M., Possenti, A. et al. Cytotoxicity and antitumoral activity of dichloromethane extract and its fractions from Pothomorphe umbellata. Braz J Med Biol Res, May 2008, vol.41, no.5, p.411-415. ISSN 0100-879X.
Figueiredo, IM, Santos, LV, Carvalho, JE, Sacoman, JL, Kohn, LK, Costa, WF, Silva, CC, Sarragiotto, MH (2006). Antiproliferative Activity of New Limonene Derivatives with a Substituted Thiourea Moiety. Journal of the Brazilian Chemical Society, 17: 954-960.
Jana Simmons
Simmons JM, Müller TA, Hausinger RP. Fe(II)/alpha-ketoglutarate hydroxylases involved in nucleobase, nucleoside, nucleotide, and chromatin metabolism. Dalton Trans. 2008 Oct 14;(38):5132-42.
Jifeng Wang
Liu A, Lu Z, Wang J, Yao L, Li Y, Yan H. (2008) NMR detection of bifurcated hydrogen bonds in large proteins. J Am Chem Soc. 130(8):2428-9.
Wang JF, Zhou H, Han LY, Kong CY, Cao ZW, Chen X, and Chen YZ. (2005) TCM-ID: Traditional Chinese Medicine information database. Clinical Pharmacology and Therapeutics. 78(1):92-93.
Wang JF, Li ZR,Cai CZ, and Chen YZ. (2005) Assessment of approximate string matching in a biomedical text retrieval problem. Computers in Biology & Medicine. 35(8):717-724.
Torres J, Wang J, Parthasarathy K, Liu DX. (2005) The transmembrane oligomers of coronavirus protein E. Biophys J. 88(2):1283-90. (Co-first Author with Dr. Torres)
Wang JF, Cai CZ, Kong CY, Cao ZW, and Chen YZ. (2005) A Computer Method for Validating Traditional Chinese Medicine Herbal Prescriptions. Am. J. Chin. Med. 3(2):281-297.
Xue Y, Yap CW, Sun LZ, Cao ZW, Wang JF and Chen YZ. (2004) Prediction of p-glycoprotein substrates by support vector machine approach. J.Chem. Inf. Comput. Sci. 44(4), 1497-505.
Ji ZL, Sun LZ, Chen X, Zheng CJ, Yao LX, Han LY, Cao ZW, Wang JF, Yeo WK, Cai CZ, Chen YZ. (2003) Internet resources for proteins associated with drug therapeutic effects, adverse reactions and ADME. Drug Discov. Today. 8(12):526-9.
Sun LZ, Ji ZL, Chen X, Wang JF, Chen YZ. (2002) Absorption, distribution, metabolism, and excretion-associated protein database. Clin. Pharmacol. Ther. 71(5):405.
Sun LZ, Ji ZL, Chen X, Wang JF, Chen YZ. (2002) ADME-AP: a database of ADME associated proteins. Bioinformatics. 18(12):1699-1700.
Wang JF et al. (2001) Antioxidant effects of proanthocyanidins from the fruits of hawthorn. Natural product research and development. 2:46-49.
Fei Zheng
Qin S, Zheng F, Chen GH, Fang H, Wang XM, Zhou JN. (2005) Variable alternative spliced exon (VASE)-containing and VASE-lacking neural cell adhesion molecule in the dorsal and ventral hippocampus of SAMP8 mice.J Neurosci Res. Jun 15;80(6):838-44.
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