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Grantee Research Project Results

Grantee Research Project Results

Publications Details for:

Estrogen Elicited Gene Expression Network Elucidation in the Rat Uterus
Grant Number R831847
RFA: Computational Toxicology and Endocrine Disruptors: Use of Systems Biology in Hazard Identification and Risk Assessment (2004)


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Book Chapter (1)
Journal Article (13)
Presentation (75)
Reference Type Citation Progress Report Year Document Sources
Book Chapter Kwekel JC, Burgoon LD, Zacharewski TR. Comparative toxicogenomics in mechanistic and predictive toxicology. In: Brown JR, ed. Comparative Genomics: Basic and Applied Research. Boca Raton, FL: CRC Press, Taylor & Francis Group, 2008, Chapter 16, pp. 299-320.
abstract available    
R831847 (2006)
Journal Article Kidambi S, Udpa N, Schroeder SA, Findlan R, Lee I, Chan C. Cell adhesion on polyelectrolyte multilayer coated polydimethylsiloxane surfaces with varying topographies. Tissue Engineering 2007;13(8):2105-2117.
abstract available    
R831847 (Final)
Journal Article Kidambi S, Sheng L, Yarmush ML, Toner M, Lee I, Chan C. Patterned co-culture of primary hepatocytes and fibroblasts using polyelectrolyte multilayer templates. Macromolecular Bioscience 2007;7(3):344-353.
abstract available     full text available
R831847 (Final)
Journal Article Kiyosawa N, Kwekel JC, Burgoon LD, Williams KJ, Tashiro C, Chittim B, Zacharewski TR. o,p'-DDT elicits PXR/CAR-, not ER-, mediated responses in the immature, ovariectomized rat liver. Toxicological Sciences 2008;101(2)350-363.
abstract available     full text available
R831847 (Final)
Journal Article 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. Physiological Genomics 2005;23(3):327-342.
abstract available     full text available
R831847 (2006)
R831847 (Final)
Journal Article Li Z, Shaw SM, Yedwabnick MJ, Chan C. Using a state-space model with hidden variables to infer transcription factor activities. Bioinformatics 2006;22(6):747-754.
abstract available     full text available
R831847 (Final)
Journal Article Li Z, Srivastava S, Mittal S, Yang X, Sheng L, Chan C. A three stage integrative pathway search (TIPS©) framework to identify toxicity relevant genes and pathways. BMC Bioinformatics 2007;8:202.
abstract available     full text available
R831847 (Final)
Journal Article Li Z, Srivastava S, Yang X, Mittal S, Norton P, Resau J, Haab B, Chan C. A hierarchical approach employing metabolic and gene expression profiles to identify the pathways that confer cytotoxicity in HepG2 cells. BMC Systems Biology 2007;1:21.
abstract available     full text available
R831847 (Final)
Journal Article Li Z, Srivastava S, Findlan R, Chan C. Using dynamic gene module map analysis to identify targets that modulate free fatty acid induced cytotoxicity. Biotechnology Progress 2008;24(1):29-37.
abstract available     full text available
R831847 (Final)
Journal Article Patil S, Melrose J, Chan C. Involvement of astroglial ceramide in palmitic acid-induced Alzheimer-like changes in primary neurons. European Journal of Neuroscience 2007;26(8):2131-2141.
abstract available    
R831847 (Final)
Journal Article Srivastava S, Chan C. Hydrogen peroxide and hydroxyl radicals mediate palmitate-induced cytotoxicity to hepatoma cells:relation to mitochondrial permeability transition. Free Radical Research 2007;41(1):38-49.
abstract available    
R831847 (Final)
Journal Article Srivastava S, Li Z, Yang X, Yedwabnick M, Shaw S, Chan C. Identification of genes that regulate multiple cellular processes/responses in the context of lipotoxicity to hepatoma cells. BMC Genomics 2007;8:364.
abstract available     full text available
R831847 (Final)
Journal Article Srivastava S, Chan C. Application of metabolic flux analysis to identify the mechanisms of free fatty acid toxicity to human hepatoma cell line. Biotechnology and Bioengineering 2008;99(2):399-410.
abstract available    
R831847 (Final)
Journal Article Yang X, Chan C. Repression of PKR mediates palmitate-induced apoptosis in HepG2 cells through regulation of Bcl-2. Cell Research 2009;19(4):469-486.
abstract available     full text available
R831847 (Final)
Presentation Burgoon LD, Hung S, Kwekel JC, Boverhof DR, Dere E, Fong CJ, Lang W, Zacharewski TR. Novel analytical methods for toxicogenomics. Presented at the Empowering Environmental Health Sciences Research with New Technologies: A Conference on Omics Applications in the Environmental Health Sciences, Chapel Hill, NC, December 4-6, 2006.
R831847 (Final)
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Presentation Chan C. Integrating multi-source biological data. Presented at Rice University, Houston, TX, November 2004.
R831847 (Final)
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Presentation Chan C. A systems biology approach to reconstructing networks. Presented at the University of Michigan, MI, April 2005.
R831847 (Final)
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Presentation Chan C. Reconstructing biological networks from gene expression and phenotypic data. Presented at the Oklahoma State University, Stillwater, OK, November 2005.
R831847 (Final)
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Presentation Chan C. Reconstructing cellular networks from multi-level data. Presented at Virginia Tech, Blacksburg, VA, October 2005.
R831847 (Final)
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Presentation Chan C. TIPS© for reconstructing signaling networks from high-throughput data. Presented at the Science at the Edge Seminar Series, Michigan State University, MI, October 2005.
R831847 (Final)
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Presentation Chan C. Integration of micro-array and metabolic data. Presented at the 2006 Mathematical Modeling in Nutrition and the Health Sciences, Roanoke, VA, August 15-17, 2006.
R831847 (Final)
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Presentation Chan C. Reconstructing cellular networks from high throughput data. Presented at the University of Virginia, VA, December 2006.
R831847 (Final)
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Presentation Chan C. Using graphical models to infer pathways and networks from gene expression data. Presented at the University at Buffalo, Buffalo, NY, March 2006.
R831847 (Final)
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Presentation Chan C. Using graphical models to infer transcription activities to networks. Presented at the Biochemistry and Molecular Biology Department, Michigan State University, MI, March 2006.
R831847 (Final)
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Presentation Chan C. Methods that integrate domain knowledge with gene expression data to identify physiologically relevant discriminating genes. Presented at the Genetics Forum, Michigan State University, MI, April 30, 2007.
R831847 (Final)
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Presentation Chan C. Chemical engineering as preparation for systems biology. Presented at the 2007 AIChE Annual Fall Meeting, Salt Lake City, UT, November 4-9, 2007.
R831847 (Final)
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Presentation Chan C. Does domain knowledge contribute to the robustness of the network reconstructed from expression data? Presented at the 2007 BMES Annual Fall Meeting, Los Angeles, CA, September 26-29, 2007.
R831847 (Final)
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Presentation Forgacs A, Kwekel J, Burgoon L, Zacharewski TR. Comparative analysis of temporal gene expression, morphometry and utertrophy in o,p-DDT and ethynyl estradiol treated rats. Presented at the 46th Annual Meeting of the Society of Toxicology, Charlotte, NC, March 25-29, 2007.
R831847 (2006)
R831847 (Final)
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Presentation Jin R, Si L, Srivastava S, Li Z, Chan C. A knowledge driven regression model for gene expression and microarray analysis. Presented at the 28th Annual International Conference IEEE Engineering in Medicine and Biology Society (EMBS), New York City, NY, August 30-September 3, 2006.
R831847 (Final)
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Presentation Kidambi S, Lee I, Chan C. Polyelectrolyte multilayer as bioactive surfaces for cell co-culture. Presented at the Polymers for Bioactive Surfaces Session of the 230th ACS National Meeting, Washington, DC, August 28-September 1, 2005 (won Best Paper award).
R831847 (Final)
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Presentation Kidambi S, Lee I, Chan C. Patterns of aptamers on polyelectrolyte multilayers. Presented at the 2005 AIChE Annual Meeting, Cincinnati, OH, 2005.
R831847 (Final)
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Presentation Kidambi S, Chan C, Lee I. pH and salt responsive PEG SAMs on polyelectrolyte multilayer. Presented at the 2005 AIChE Annual Meeting, Cincinnati, OH, 2005.
R831847 (Final)
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Presentation Kidambi S, Lee I, Chan C. Salt tunable m-dPEG acid patterns on polyelectrolyte multilayers-templates for directed deposition of macromolecules. Presented at the Excellence in Graduate Polymer Research Symposium at the 231st ACS National Meeting, Atlanta, GA, March 26-30, 2006.
R831847 (Final)
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Presentation Kidambi S, Lee I, Chan C. Engineering aptamer and siRNA based drug delivery systems using polyelectrolyte multilayer films. Presented at the 2006 AIChE Annual Meeting in San Francisco, CA, October 30-November 4, 2006.
R831847 (Final)
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Presentation Kwekel JC, Dalgleish HA, Burgoon LD, Harkema JR, Zacharewski TR. Analysis of gene expression during uterine induction and regression in immature, ovariectomized rats following treatment with ethynyl estradiol. Toxicogenomics. Presented at the Gordon Research Conference, Colby-Sawyer College, New London, NH, June 5-10, 2005.
R831847 (2006)
R831847 (Final)
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Presentation Kwekel JC, Dalgleish HA, Burgoon LD, Harkema JR, Zacharewski TR. Analysis of gene expression during uterine induction and regression in immature, ovariectomized rats following treatment with ethynyl estradiol. Presented at the 44th Annual Meeting of the Society of Toxicology, New Orleans, LA, March 6-10, 2005.
R831847 (2006)
R831847 (Final)
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Presentation Kwekel JC, Fong CJ, Forgacs AL, Burgoon LD, Zacharewski TR. Comparative analysis of temporal gene expression, morphometry and uterotrophy in ethynylestradiol and tamoxifen treated rats. Presented at the Society of Toxicology Annual Meeting, San Diego, CA, March 5-9, 2006.
R831847 (Final)
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Presentation Kwekel J, Fong C, Burgoon L, Zacharewski TR. Species-specific, compound-conserved gene expression of estrogen receptor ligands during uterotrophy. Presented at the ENDO ’07 Endocrine Society Annual Meeting, Toronto, Ontario, Canada, June 1-6, 2007.
R831847 (Final)
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Presentation Kwekel J, Fong C, Burgoon LB, Zacharewski TR. Cross-species comparison of Tamoxifen and estrogen induced uterotrophy in rodents. Presented at the 46th Annual Meeting of the Society of Toxicology, Charlotte, NC, March 25-29, 2007.
R831847 (2006)
R831847 (Final)
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Presentation Kwekel J, Fong C, Burgoon L, Zacharewski TR. Species-specific, compound-conserved gene expression of estrogen receptor ligands during uterotrophy. Presented at the EPA Computational Toxicology Forum, Research Triangle Park, NC, May 21-23, 2007.
R831847 (Final)
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Presentation Li Z, Chan C. Systems approach based upon feature selection, Bayesian network and independent component analysis to integrate gene expression and metabolic profiles. Presented at the Systems Engineering of System Biology Session of the 2004 American Controls Conference, Boston, MA, 2004.
R831847 (Final)
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Presentation Li Z, Srivastava S, Yang X, Chan C. Reconstructing gene regulatory and signaling pathways from high throughput data. Presented at the 2005 Biochemical Engineering XIV Conference, Harrison Hot Springs, British Columbia, Canada, July 10-14, 2005.
R831847 (Final)
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Presentation Li Z, Srivastava S, Yang X, Chan C. Integrating gene expression and metabolic profiles to infer pathways and networks that confer palmitate induced cytotoxicity in HepG2 cells. Presented at the 2005 Summer Bioengineering Conference, Vail, CO, June 22-26, 2005.
R831847 (Final)
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Presentation Li Z, Srivastava S, Chan C. Integrating gene expression and metabolic profiles to identify genes that confer cytotoxicity in HepG2 cells. Presented at the 229th ACS National Meeting, San Diego, CA, March 13-17, 2005.
R831847 (Final)
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Presentation Li Z, Srivastava S, Yang X, Chan C. A systems approach to reconstructing pathways by integrating gene expression and metabolic profiles. Presented at the 2005 BMES Annual Meeting, Baltimore, MD.
R831847 (Final)
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Presentation Li Z, Srivastava S, Yang, X, Chan C. A systems approach to reconstructing pathways to connect genes with metabolites. Presented at the 2005 AIChE Annual Meeting, Cincinnati, OH, 2005.
R831847 (Final)
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Presentation Li Z, Shaw SM, Yedwabnick MJ, Chan C. Inferring transcription factor activities with a probabilistic framework of Hidden Markov Model. Presented at the 2005 AIChE Annual Meeting, Cincinnati, OH, 2005.
R831847 (Final)
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Presentation Li Z, Srivastava S, Chan C. Network reconstruction to identify molecular targets of toxicity. Presented at the 2006 BMES Annual Meeting, Chicago, IL, October 11-14, 2006.
R831847 (Final)
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Presentation Li Z, Srivastava S, Chan C. A hierarchical approach to identify phenotype relevant pathways. Presented at the 2006 AIChE Annual Meeting in San Francisco, CA, October 30-November 4, 2006.
R831847 (Final)
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Presentation Li Z, Srivastava S, Chan C. Dynamic model integrating gene expression and metabolite profiles to identify lipotoxic pathways. Presented at the 232nd ACS National Meeting and Exposition, San Francisco, CA, September 10-14, 2006.
R831847 (Final)
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Presentation Li Z, Srivastava S, Findlan R, Chan C. Identifying toxicity pathways through analysis of global transcriptional dynamics. Presented at the 234th National Meeting and Exposition, Boston, MA, August 19-23, 2007.
R831847 (Final)
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Presentation Li Z, Srivastava S, Finland R, Chan C. Using dynamic analysis of module mapping to identify targets that modulate free fatty acid and tumor necrosis factor (TNF)-α induced cytotoxicity. Presented at the Society for Biological Engineering’s (SBE) 1st International Conference on Biomolecular Engineering, Coronado, CA, January 14-18, 2007.
R831847 (Final)
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Presentation Li Z, Srivastava S, Findlan R, Chan C. A study of the transcriptional dynamics of free fatty acids in liver cells. Presented at the Biochemical Engineering XV: Engineering Biology from Biomolecules to Complex Systems, Quebec City, PQ, Canada, July 15-19, 2007.
R831847 (Final)
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Presentation Li Z, Zhou Y, Srivastava S, Jin R, Chan C. Knowledge driven matrix factorization to reconstruct modular gene regulatory network. Presented at the 2007 AIChE Annual Fall Meeting, Salt Lake City, UT, November 4-9, 2007.
R831847 (Final)
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Presentation Li Z, Srivastava S, Zhang L, Jin R, Chan C. Identifying pathophysiology relevant pathways by integrating gene expression, metabolic profile with a priori knowledge. Presented at the 2007 BMES Annual Fall Meeting, Los Angeles, CA, September 26-29, 2007.
R831847 (Final)
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Presentation Mehrotra S, Lee I, Chan C. Three-dimensional (3-D) cellular assembly using self-standing composite polyelectrolyte multilayers. Presented at the 2007 AIChE Annual Fall Meeting, Salt Lake City, UT, November 4-9, 2007.
R831847 (Final)
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Presentation Patil S, Chan C. Involvement of saturated fatty acids in the pathogenesis of Alzheimer’s disease. Presented at the 2005 AIChE Annual Meeting, Cincinnati, OH, 2005 (won Best Poster award).
R831847 (Final)
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Presentation Patil S, Chan C. Involvement of saturated fatty acids in the pathogenesis of Alzheimer’s disease. Presented at the 2006 Experimental Biology Meeting in San Francisco, CA, April 1-5, 2006.
R831847 (Final)
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Presentation Patil S, Chan C. Involvement of saturated fatty acids in the pathogenesis of Alzheimer's disease. Presented at the 2006 10th International Conference on Alzheimer's Disease and Related Disorders, Madrid, Spain, July 15-20, 2006.
R831847 (Final)
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Presentation Patil S, Chan C. Astroglia-mediated involvement of saturated fatty acids in the pathogenesis of Alzheimer's disease. Presented at the 2006 Midwest Quantitative Biology Conference, Mackinac Island, MI, September 29-October 1, 2006.
R831847 (Final)
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Presentation Patil S, Chan C. Role of astroglial fatty acid metabolism in the pathogenesis of Alzheimer's disease: a metabolic flux analysis (MFA) study. Presented at the 234th National Meeting and Exposition, Boston, MA, August 19-23, 2007.
R831847 (Final)
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Presentation Srivastava S, Chan C. Application of metabolic flux analysis to identify the pathways of free fatty acid toxicity to liver cells. Presented at the 2005 Biochemical Engineering XIV Conference, Harrison Hot Springs, British Columbia, Canada, July 10-14, 2005.
R831847 (Final)
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Presentation Srivastava S, Chan C. Integration of genetic and metabolic information to identify the mechanism of fatty acid toxicity. Presented at the 2005 BMES Annual Meeting, Baltimore, MD, 2005.
R831847 (Final)
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Presentation Srivastava S, Chan C. Knowledge-based integration of metabolic and genetic information to identify targets of fatty acid toxicity. Presented at the 2005 AIChE Annual Meeting, Cincinnati, OH, 2005.
R831847 (Final)
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Presentation Srivastava S, Zhang L, Jin R, Chan C. Unsupervised classification and identification of physiologically relevant features by integrating ontology information and expression data using Bayesian regression mixture models. Presented at the 234th National Meeting and Exposition, Boston, MA, August 19-23, 2007.
R831847 (Final)
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Presentation Srivastava S, Jin R, Chan C. A novel feature selection method which incorporates ontology information to identify functionally relevant genes regulating processes of interest. Presented at the Biochemical Engineering XV:Engineering Biology from Biomolecules to Complex Systems, Quebec City, PQ, Canada, July 15-19, 2007.
R831847 (Final)
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Presentation Srivastava S, Chan C. Application of metabolic flux analysis to identify the mechanisms of free fatty acid toxicity to human hepatoma cell line. Presented at the 2007 AIChE Annual Fall Meeting, Salt Lake City, UT, November 4-9, 2007.
R831847 (Final)
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Presentation Srivatsan K, Lee I, Chan C. Aptamer incorporated polyelectroyte multilayer films targeting influenza virus hemagglutinin. Presented at the 234th National Meeting and Exposition, Boston, MA, August 19-23, 2007.
R831847 (Final)
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Presentation Srivatsan K, Mehrotra S, Gredell J, Walton SP, Lee I, Chan C. Polyelectrolyte multilayer films as platforms for efficient siRNA delivery. Presented at the 234th National Meeting and Exposition, Boston, MA, August 19-23, 2007.
R831847 (Final)
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Presentation Wu Y, Leekumjorn S, Sum AK, Chan C. Experimental and computational investigation of trehalose protection from Palmitate induced toxicity of HepG2 cells. Presented at the 2007 AIChE Annual Fall Meeting, Salt Lake City, UT, November 4-9, 2007.
R831847 (Final)
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Presentation Yang X, Li Z, Srivastava S, Chan C. Regulation of apoptosis by free fatty acids and TNF-α: role of double-stranded RNA-dependent protein kinase (PKR). Presented at the 2005 AIChE Annual Meeting, Cincinnati, OH, 2005.
R831847 (Final)
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Presentation Yang X, Chan C. Connecting PKR and Bcl-2: a candidate mechanism for palmitate-induced apoptosis of human liver cells. Presented at the 2006 AIChE Annual Meeting in San Francisco, CA, October 30-November 4, 2006.
R831847 (Final)
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Presentation Yang X, Chan C. Suppression of PKR activity mediates the apoptosis induced by palmitic acid and TNF-α in HepG2 cells. Presented at the 234th National Meeting and Exposition, Boston, MA, August 19-23, 2007.
R831847 (Final)
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Presentation Yang X, Chan C. Regulation of cellular apoptosis by palmitic acid:involvement of signal transduction pathways from PKR to Bcl-2. Presented at the Society for Biological Engineering’s (SBE) 1st International Conference on Biomolecular Engineering, Coronado, CA, January 14-18, 2007.
R831847 (Final)
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Presentation Yang X, Chan C. PKR is involved in regulating both insulin signaling and hepatocellular apoptosis pathways. Presented at the 2007 AIChE Annual Fall Meeting, Salt Lake City, UT, November 4-9, 2007.
R831847 (Final)
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Presentation Yang X, Chan C. PKR is involved in regulating both insulin signaling and hepatocellular apoptosis pathways. Presented at the 2007 BMES Annual Fall Meeting, Los Angeles, CA, September 26-29, 2007.
R831847 (Final)
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Presentation Zacharewski TR. Computational and empirical investigation of estrogen and dioxin elicited effects:a comparative analysis. Cross-species Toxicology in the Age of Genomics Symposium. Presented at the 44th Annual Meeting of the Society of Toxicology, New Orleans, LA, March 6-10, 2005.
R831847 (2006)
R831847 (Final)
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Presentation Zacharewski TR. Incorporation of toxicogenomics into quantitative risk assessment. Presented at the "Omics Technologies-Current and Future Applications to Environmental Toxicology" Session of the 2005 Annual Meeting of the Society of Environmental Toxicology and Chemistry, Baltimore, MD, November 15, 2005.
abstract available    
R831847 (2006)
R831847 (Final)
Presentation Zacharewski TR. Identification of early biomarkers of toxicity for the development of high throughput screening assays using comparative toxicogenomics. Presented at the NIH Roadmap Meeting on Predictive Models for Drug Safety Assessment, Lister Hill Auditorium, NIH, August 15-16, 2006.
R831847 (2006)
R831847 (Final)
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Presentation Zacharewski TR. Comparative analysis of the rodent uterotropic response:identification of conserved responses and mechanisms of action. Advancing Toxicology by Improving Linkage of Traditional Toxicity and Pathology Endpoints with Toxicogenomics. Presented at the 45th Annual Meeting of the Society of Toxicology, San Diego, CA, March 5-9, 2006.
R831847 (2006)
R831847 (Final)
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Presentation Zacharewski TR. Comparative toxicogenomic analysis of the hepatotoxic effects of TCDD. Presented at the Department of Biochemistry Seminar Series, Wright State University, Dayton, OH, November 3, 2006.
R831847 (Final)
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Presentation Zacharewski TR. Comparative toxicogenomic analysis of the hepatotoxic effects of TCDD. Presented at the Arkansas Children’s Nutrition Center, University of Arkansas, Little Rock, AR, November 9, 2006.
R831847 (Final)
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Presentation Zacharewski TR. Toxicogenomic assessment of endocrine disruptors. Presented at the Mountain West Chapter of the Society of Toxicology Regional Meeting, Phoenix, AZ, September 8-9, 2006.
R831847 (2006)
R831847 (Final)
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Presentation Zacharewski TR. Toxicogenomics: what have we learned about mechanisms of toxicity? Presented at the Eleventh International Congress of Toxicology (ICTXI), Montreal, Quebec, Canada, July 17, 2007 (keynote lecture).
R831847 (2006)
R831847 (Final)
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Presentation Zhang L, Howes T, Wright NT, Chan C. Studying the regulation of mesenchymal stem cell proliferation versus differentiation by cAMP signaling. Presented at the 2006 AIChE Annual Meeting, San Francisco, CA, October 30-November 4, 2006.
R831847 (Final)
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Presentation Zhang L, Chan C. cAMP induced neural differentiation of mesenchymal stem cells: real differentiation or pseudo-differentiation? Presented at the 234th National Meeting and Exposition, Boston, MA, August 19-23, 2007.
R831847 (Final)
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Presentation Zhang L, Howes T, Wright NT, Chan C. Studying the regulation of mesenchymal stem cell proliferation versus differentiation by cAMP signaling. Presented at the Society for Biological Engineering’s (SBE) 1st International Conference on Biomolecular Engineering, Coronado, CA, January 14-18, 2007.
R831847 (Final)
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Presentation Zhang L, Chan C. cAMP signaling caused apoptosis in Palmitate conditioned HepG2 cells. Presented at the 2007 AIChE Annual Fall Meeting, Salt Lake City, UT, November 4-9, 2007.
R831847 (Final)
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Presentation Zhang L, Chan C. cAMP induced both differentiation and apoptosis of mesenchymal stem cells. Presented at the 2007 BMES Annual Fall Meeting, Los Angeles, CA, September 26-29, 2007.
R831847 (Final)
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The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Conclusions drawn by the principal investigators have not been reviewed by the Agency.

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