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Publications

2015

2014

2013

2012

2011

  • Angrish, Michelle M., A.D. Jones, Jack R. Harkema, and Timothy R. Zacharewski. 2011. Aryl hydrocarbon receptor-mediated induction of stearoyl-CoA desaturase 1 alters hepatic fatty acid composition in TCDD-elicited steatosis. Toxicological Sciences .  124(2):299-310. doi:10.1093/toxsci/kfr226
  • Bhattacharya, Sudin, Qiang Zhang, and Melvin E. Andersen. 2011. Double-negative feedback loops as a common design motif in the transcriptional networks regulating cell fate. International Journal of Design Engineering4:41-57. doi:10.1504/IJDE.2011.041408
  • Boyd, Stephen A., Cliff T. Johnston, Thomas J. Pinnavaia, Norbert Kaminski, Brian J. Teppen, Robert B. Crawford, Natalia Kovalova, Seong Su Kim, H. Shao, Chen Gu, Barbra LF Kaplan, Bushra Khan, and Hui Li. 2011. Suppression of humoral immune responses by 2,3,7,8-tetrachlorodibenzo-p-dioxin intercalated in smectite clay. Environmental Toxicology and Chemistry .  30:2748-2755. doi:10.1002/etc.701
  • De Abrew, K.N., Ashwini S. Phadnis, Robert B. Crawford, Norbert Kaminski, and Russell S. Thomas. 2011. Regulation of Bach2 by the aryl hydrocarbon receptor as a mechanism for suppression of B-cell differentiation by 2,3,7,8-tetrachlorodibenzo-p-dioxin. Toxicology and Applied Pharmacology .  252(2):150-158. doi:10.1016/j.taap.2011.01.020
  • Dere, Edward, Agnes L. Forgacs, Timothy R. Zacharewski, and Lyle D. Burgoon. 2011. Genome-Wide Computational Analysis of Dioxin Response Element Location and Distribution in the Human, Mouse, and Rat Genomes. Chemical Research in Toxicology .  24:494-504. doi:10.1021/tx100328r
  • Dere, Edward, Andrea W. Lee, Lyle D. Burgoon, and Timothy R. Zacharewski. 2011. Differences in TCDD-elicited gene expression profiles in human HepG2, mouse Hepa1c1c7 and rat H4IIE hepatoma cells. BMC Genomics .  12:doi:10.1186/1471-2164-12-193
  • Dere, Edward, Raymond Lo, Trine Celius, Jason Matthews, and Timothy R. Zacharewski. 2011. Integration of Genome-Wide Computation DRE Search, AhR ChIP-chip and Gene Expression Analyses of TCDD-Elicited Responses in the Mouse Liver. BMC Genomics .  12:365. doi:10.1186/1471-2164-12-365
  • Gu, Chen, Cun Liu, Yunjie Ding, Hui Li, Brian J. Teppen, Cliff T. Johnston, and Stephen A. Boyd. 2011. Clay mediated route to natural formation of polychlorodibenzo-p-dioxins. Environmental Science & Technology .  45(8):3445-3451. doi:10.1021/es104225d  PMID:21434682
  • Gu, Chen, Cun Liu, Cliff T. Johnston, Brian J. Teppen, H. Li, and Stephen A. Boyd. 2011. Pentachlorophenol Radical Cations Generated on Fe(III)-Montmorillonite Initiate Octachlorodibenzo-p-dioxin Formation in Clays: Density Functional Theory and Fourier Transform Infrared Studies. Environmental Science & Technology .  45:1399-1406. doi:10.1021/es103324z
  • Iwai, Shoko, Timothy A. Johnson, Benli Chai, Syed A. Hashsham, and James M. Tiedje. 2011. Comparison of the Specificities and Efficacies of Primers for Aromatic Dioxygenase Gene Analysis of Environmental Samples. Applied and Environmental Microbiology .  77:3551-3557.doi:10.1128/aem.00331-11
  • Jia, Hanzhong, Chen Gu, Stephen A. Boyd, Brian J. Teppen, Cliff T. Johnston, Hui Li, and Cunyi Song. 2011. Comparison of Reactivity of Nanoscaled Zero-Valent Iron Formed on Clay Surfaces. Soil Science Society of America Journal .  75(2):357-364. doi:10.2136/sssaj2010.0080nps
  • Kaplan, Barbra LF, Robert B. Crawford, Natalia Kovalova, Amaya Arencibia, Seong Su Kim, Thomas J. Pinnavaia, Stephen A. Boyd, Brian J. Teppen, and Norbert Kaminski. 2011. TCDD adsorbed on silica as a model for TCDD contaminated soils: Evidence for suppression of humoral immunity in mice. Toxicology . 282(3):82-87. doi:10.1016/j.tox.2011.01.013
  • Kim, D., Miyoun Yoo, Ki Young Choi, Beom S. Kang, T.K. Kim, S.G. Hong, Gerben J. Zylstra, and Eungbin Kim. 2011. Differential Degradation of Bicyclics with Aromatic and Alicyclic Rings by Rhodococcus sp Strain DK17. Applied and Environmental Microbiology .  77:8280-8287. doi:10.1128/AEM.06359-11
  • Kopec, Anna K., Michelle L. D'Souza, Bryan D. Mets, Lyle D. Burgoon, Sarah E. Reese, Kellie J. Archer, Dave Potter, Colleen Tashiro, Bonnie Sharratt, Jack R. Harkema, and Timothy R. Zacharewski. 2011. Non-additive hepatic gene expression elicited by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and 2,2 ',4,4 ',5,5 '-hexachlorobiphenyl (PCB153) co-treatment in C57BL/6 mice. Toxicology and Applied Pharmacology . 256:154-167. doi:10.1016/j.taap.2011.08.002
  • Lee, Tae K., Jaejin Lee, Woo Jun Sul, Shoko Iwai, Benli Chai, James M. Tiedje, and Joonhong Park. 2011. Novel Biphenyl-Oxidizing Bacteria and Dioxygenase Genes from a Korean Tidal Mudflat. Applied and Environmental Microbiology .  77:3888-3891. doi:10.1128/aem.00023-11
  • Lo, Raymond, Trine Celius, Edward Dere, L. MacPherson, Patricia A. Harper, Timothy R. Zacharewski, and Jason Matthews. 2011. Identification of aryl hydrocarbon receptor binding targets in mouse hepatic tissue treated with 2,3,7,8-tetrachlorodibenzo-p-dioxin. Toxicology and Applied Pharmacology .  257:38-47.doi:10.1016/j.taap.2011.08.016
  • Lu, Haitian, Robert B. Crawford, Barbra LF Kaplan, and Norbert Kaminski. 2011. 2,3,7,8-Tetrachlorodibenzo-p-dioxin-mediated disruption of the CD40 ligand-induced activation of primary human B cells. Toxicology and Applied Pharmacology .  255:251-260. doi:10.1016/j.taap.2011.06.026
  • McClure, Emily A., Colin M. North, Norbert Kaminski, and Jay I. Goodman. 2011. Changes in DNA Methylation and Gene Expression during 2,3,7,8-Tetrachlorodibenzo-p-dioxin-Induced Suppression of the Lipopolysaccharide-Stimulated IgM Response in Splenocytes. Toxicological Sciences .  120(2):339-348.doi:10.1093/toxsci/kfq396
  • Olivero-Verbal, Jesus, Robert A. Roth, and Patricia E. Ganey. 2011. Dioxin alters inflammatory responses to lipopolysaccharide. Toxicological & Environmental Chemistry .  93:1180-1194.doi:10.1080/02772248.2011.577554
  • Sulentic, Courtney E W and Norbert Kaminski. 2011. The long winding road toward understanding the molecular mechanisms for B cell suppression by 2,3,7,8-Tetrachlorodibenzo-p-dioxin. Toxicological Sciences .  120(suppl1):S171-S191. doi:10.1093/toxsci/kfq324
  • Yoo, Miyoun, Gerben J. Zylstra, Dockyu Kim, Beom S. Kang, and Eungbin Kim. 2011. Biphenyl hydroxylation enhanced by an engineered o-xylene dioxygenase from Rhodococcus sp strain DK17.Research in Microbiology .  162:724-728. doi:10.1016/j.resmic.2011.04.013

2010

  • Andersen, Melvin E., Qiang Zhang, and Sudin Bhattacharya. 2010. Modeling Gene and Protein Expression - Nested Motifs in Cellular and Tissue Response Networks. Chapter 10 in: Quantitative Modeling in Toxicology . John Wiley & Sons, Hoboken, NJ.
  • Bhattacharya, Sudin, Rory B. Conolly, Norbert Kaminski, Russell S. Thomas, Melvin E. Andersen, and Qiang Zhang. 2010. A bistable switch underlying B-cell differentiation and its disruption by the environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin. Toxicological Sciences .  115(1):51-65.doi:10.1093/toxsci/kfq035
  • Bhattacharya, Sudin, Qiang Zhang, and Melvin E. Andersen. 2010. Bistable Signaling Motifs and Cell Fate Decisions. Chapter 8 in: Quantitative Modeling in Toxicology . John Wiley & Sons, Hoboken, NJ.
  • Boyd, Stephen A., Cliff T. Johnston, D.A. Laird, Brian J. Teppen, and H. Li. 2010. Comprehensive Study of Organic Contaminant Adsorption by Clays: Methodologies, Mechanisms and Environmental Implications. In: Volume 3, Biophysico-Chemical Processes of Anthropogenic Organic Compounds in Environmental Systems. Wiley, New York, NY.
  • Chang, Hung-Kuang and Gerben J. Zylstra. 2010. Xanthomonads. In: Handbook of Hydrocarbon and Lipid Microbiology. Springer Verlag GmbH, Heidelberg, Germany. pp.1805-1811.
  • Crawford, Robert B., Norbert Kaminski, Haitian Lu, and Colin M. North. 2010. 2,3,7,8-Tetrachlorodibenzo-p-dioxin-Mediated Suppression of Toll-Like Receptor Stimulated B-Lymphocyte Activation and Initiation of Plasmacytic Differentiation. Toxicological Sciences .  116:99-112. doi:10.1093/toxsci/kfq095
  • Cummings, J.A., Lynwood G. Clemens, and Antonio A. Nunez. 2010. Mother counts: how effects of environmental contaminants on maternal care could affect the offspring and future generations. Frontiers in Neuroendocrinology31:440-451. doi:10.1016/j.yfrne.2010.05.004
  • De Abrew, K.N., Norbert Kaminski, and R.S. Thomas. 2010. An Integrated Genomic Analysis of Aryl Hydrocarbon Receptor-Mediated Inhibition of B-Cell Differentiation. Toxicological Sciences .  118(2):454-469. doi:10.1093/toxsci/kfq265
  • De Abrew, K.N., Norbert Kaminski, and R.S. Thomas. 2010. Identification of direct AhR-regulated genes involved in B cell differentiation. The Toxicologist 99 (Abst. 1195). .
  • Forgacs, Agnes L., Lyle D. Burgoon, Scott G. Lynn, John J. LaPres, and Timothy R. Zacharewski. 2010. Effects of TCDD on the expression of nuclear encoded mitochondrial genes. Toxicology and Applied Pharmacology .  246:58-65. doi:10.1016/j.taap.2010.04.006
  • Gu, Chen, Houli Jiang, Hui Li, Brian J. Teppen, and Stephen A. Boyd. 2010. Synthesis of Highly Reactive Subnano-Sized Zero-Valent Iron Using Smectite Clay Templates. Environmental Science & Technology . 44:4258-4263. doi:10.1021/es903801r
  • Iwai, Shoko, Benli Chai, Woo Jun Sul, James R. Cole, Syed A. Hashsham, and James M. Tiedje. 2010. Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment. The ISME Journal: Multidisciplinary Journal of Microbial Ecology .  4(2):279-285.doi:10.1038/ismej.2009.104
  • Johnston, Cliff T. 2010. Probing the Nanoscale Architecture of Clay Minerals. Clays and Clay Minerals . 45:245-279. doi:10.1180/claymin.2010.045.3.245
  • Kline, D.E., Q. Zhang, Sudin Bhattacharya, Melvin E. Andersen, Rory B. Conolly, Robert B. Crawford, and Norbert Kaminski. 2010. 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) Suppresses LPS-activated Binary Switching of B Cells to Plasma Cells. .
  • Kopec, A.K., Lyle D. Burgoon, Daher Ibrahim-Aibo, A.R. Burg, Andrea W. Lee, Colleen Tashiro, Bonnie Sharratt, Jack R. Harkema, Craig Rowlands, R. Budinsky, and Timothy R. Zacharewski. 2010. Automated Dose-Response Analysis and Comparative Toxicogenomic Evaluation of the Hepatic Effects Elicited by TCDD, TCDF, and PCB126 in C57BL/6 Mice. Toxicological Sciences .  118(1):286-297.doi:10.1093/toxsci/kfq236
  • Kopec, A.K., Lyle D. Burgoon, Daher Ibrahim-Aibo, Bryan D. Mets, Colleen Tashiro, Dave Potter, Bonnie Sharratt, Jack R. Harkema, and Timothy R. Zacharewski. 2010. PCB153-elicited hepatic responses in the immature, ovariectomized C57BL/6 mice: Comparative toxicogenomic effects of dioxin and non-dioxin-like ligands. Toxicology and Applied Pharmacology .  243(3):359-71. doi:10.1016/j.taap.2009.12.003
  • Lu, Haitian, Robert B. Crawford, J. Suarez-Martinez, Barbra LF Kaplan, and Norbert Kaminski. 2010. Induction of the Aryl Hydrocarbon Receptor-Responsive Genes and Modulation of the Immunoglobulin M Response by 2,3,7,8-Tetrachlorodibenzo-p-Dioxin in Primary Human B Cells. Toxicological Sciences . 118(1):86-97. doi:10.1093/toxsci/kfq234
  • Lu, Hatian, Barbra LF Kaplan, Robert B. Crawford, and Norbert Kaminski. 2010. Characterization of 2,3,7,8-tetrachlorodibenzo-pdioxin Effect on the CD40L-Induced IgM Antibody Responses in Primary Mouse and Human B Lymphocytes. The Toxicologist 99 (Abst. 1533). .
  • Ni Chadhain, Sinead M. and Gerben J. Zylstra. 2010. Functional Gene Diversity, Biogeography, and Dynamics. In: Handbook of Hydrocarbon and Lipid Microbiology. Springer Verlag GmbH, Heidelberg, Germany. pp.2413-2422.
  • North, Colin M., Robert B. Crawford, Hatian Lu, and Norbert Kaminski. 2010. Multiparametric single cell analysis of toll-like receptor activated kinase phosphorylation alteration by 2,3,7,8-Tetrachlorodibenzo-p-dioxin. The Toxicologist 99 (Abst. 632). .
  • Parnell, J.Jacob, Vincent J. Denef, Joonhong Park, Tamara V. Tsoi, and James M. Tiedje. 2010. Environmentally relevant parameters affecting PCB degradation: carbon source- and growth phase-mitigated effects of the expression of the biphenyl pathway and associated genes in Burkholderia xenovorans LB400. Biodegradation .  21(1):147-156. doi:10.1007/s10532-009-9289-4
  • Phadnis, Ashwini S., Maria A. Manzan, R.A. Thomas, and Norbert Kaminski. 2010. Direct regulation of Bach2 by 2,3,7,8- Tetrachlorodibenzo-p-dioxin in B lymphoma CH12.LX. The Toxicologist 99 (Abst. 73). .
  • Saini, Yogesh, K. Greenwood, C. Merrill, Kyung Y. Kim, S. Patial, N. Parameswaran, Jack R. Harkema, and John J. LaPres. 2010. Acute Cobalt-Induced Lung Injury and the Role of Hypoxia-Inducible Factor 1 alpha in Modulating Inflammation. Toxicological Sciences .  116:673-681. doi:10.1093/toxsci/kfq155
  • Saini, Yogesh, Ryan Lewandowski, Lori Bramble, Jack R. Harkema, John J. LaPres, and Kyung Y. Kim. 2010. The Role of Hypoxia Inducible Factor l ± (HIFI±) in Modulating Cobalt-Induced Lung Inflammation.American Journal of Physiology - Lung Cellular and Molecular Physiology .  298(2):L139-L147.doi:10.1152/ajplung.00252.2009
  • Shao, H. and Thomas J. Pinnavaia. 2010. Synthesis and properties of nanoparticle forms saponite clay, cancrinite zeolite and phase mixtures thereof. Microporous and Mesoporous Materials .  133:10-17.doi:10.1016/j.micromeso.2010.04.002
  • Thiex, Natalie W., Mark C. Chames, and Rita Loch-Caruso. 2010. Tissue-specific induction of COX-2 and prostaglandins in lipopolysaccharide-stimulated extraplacental human gestational membranes in a 2-chamber transwell culture system. Reproductive Sciences .  17(12):1120-1129.doi:10.1177/1933719110378344
  • Trosko, James E. and Brad L. Upham. 2010. A Paradigm Shift is Required for the Risk Assessment of Potential Human Health After Exposure to Low Level Chemical Exposures - A Response to the Toxicity Testing in the 21st Century Report. International Journal of Toxicology29(4):344-357.doi:10.1177/1091581810371384
  • Xue, Siqi and Thomas J. Pinnavaia. 2010. Methylene-functionalized saponite: A new type of organoclay with CH2 groups substituting for bridging oxygen centers in the tetrahedral sheet. Applied Clay Science . 48(1-2):60-66. doi:10.1016/j.clay.2009.11.006
  • Zhang, Qiang, Sudin Bhattacharya, Melvin E. Andersen, and Rory B. Conolly. 2010. Computational systems biology and dose-response modeling in relation to new directions in toxicity testing. Journal of Environmental Science and Health, Part B .  13(2-4):253-76. doi:10.1080/10937404.2010.483943
  • Zhang, Qiang, Sudin Bhattacharya, D.E. Kline, Robert B. Crawford, R.S. Thomas, Norbert Kaminski, Melvin E. Andersen, and Rory B. Conolly. 2010. Stochastic modeling of B lymphocyte terminal differentiation and its suppression by dioxin. BMC Systems Biology .  4(40):doi:10.1186/1752-0509-4-40
  • Zhang, Qiang, Sudin Bhattacharya, Courtney G. Woods, and Melvin E. Andersen. 2010. Ultrasensitive Response Motifs in Biochemical Networks. Chapter 9 in: Quantitative Modeling in Toxicology . John Wiley & Sons, Hoboken, NJ. pp.199-218.