Search Results - "Kuo, Byron"

Comparison of toxicogenomics and traditional approaches to inform mode of action and points of departure in human health risk assessment of benzo[a]pyrene in drinking water by Moffat, Ivy, Chepelev, Nikolai L., Labib, Sarah, Bourdon-Lacombe, Julie, Kuo, Byron, Buick, Julie K., Lemieux, France, Williams, Andrew, Halappanavar, Sabina, Malik, Amal I, Luijten, Mirjam, Aubrecht, Jiri, Hyduke, Daniel R., Fornace, Albert J., Swartz, Carol D., Recio, Leslie, Yauk, Carole L.

“…Abstract Toxicogenomics is proposed to be a useful tool in human health risk assessment. However, a systematic comparison of traditional risk assessment…”
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Impact of Genomics Platform and Statistical Filtering on Transcriptional Benchmark Doses (BMD) and Multiple Approaches for Selection of Chemical Point of Departure (PoD) by Webster, A Francina, Chepelev, Nikolai, Gagné, Rémi, Kuo, Byron, Recio, Leslie, Williams, Andrew, Yauk, Carole L

“…Many regulatory agencies are exploring ways to integrate toxicogenomic data into their chemical risk assessments. The major challenge lies in determining how…”
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Transcriptional profiling of male F344 rats suggests the involvement of calcium signaling in the mode of action of acrylamide-induced thyroid cancer by Chepelev, Nikolai L., Gagné, Rémi, Maynor, Timothy, Kuo, Byron, Hobbs, Cheryl A., Recio, Leslie, Yauk, Carole L.

“…Acrylamide (AA) exposure in 2-year cancer bioassays leads to thyroid, but not liver, adenomas and adenocarcinomas in rats. Hypothesized modes of action (MOAs)…”
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Pulmonary gene and microRNA expression changes in mice exposed to benzo(a)pyrene by oral gavage by Halappanavar, Sabina, Wu, Dongmei, Williams, Andrew, Kuo, Byron, Godschalk, Roger W, Van Schooten, Frederik J, Yauk, Carole Lyn

“…Highlights ► The study examines pulmonary response in mice exposed to BaP by oral gavage. ► We examined pulmonary gene and miRNA expression changes and…”
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iHOPerator: user-scripting a personalized bioinformatics Web, starting with the iHOP website by Good, Benjamin M, Kawas, Edward A, Kuo, Byron Yu-Lin, Wilkinson, Mark D

“…User-scripts are programs stored in Web browsers that can manipulate the content of websites prior to display in the browser. They provide a novel mechanism by…”
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CGMIM: automated text-mining of Online Mendelian Inheritance in Man (OMIM) to identify genetically-associated cancers and candidate genes by Bajdik, Chris D, Kuo, Byron, Rusaw, Shawn, Jones, Steven, Brooks-Wilson, Angela

“…Online Mendelian Inheritance in Man (OMIM) is a computerized database of information about genes and heritable traits in human populations, based on…”
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SAGE2Splice: unmapped SAGE tags reveal novel splice junctions by Kuo, Byron Yu-Lin, Chen, Ying, Bohacec, Slavita, Johansson, Ojvind, Wasserman, Wyeth W, Simpson, Elizabeth M

“…Serial analysis of gene expression (SAGE) not only is a method for profiling the global expression of genes, but also offers the opportunity for the discovery…”
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A Mouse Atlas of Gene Expression: Large-Scale Digital Gene-Expression Profiles from Precisely Defined Developing C57BL/6J Mouse Tissues and Cells by Asim S. Siddiqui, Khattra, Jaswinder, Allen D. Delaney, Yongjun Zhao, Caroline Astell, Jennifer Asano, Ryan Babakaiff, Barber, Sarah, Jaclyn Beland, Slavita Bohacec, Mabel Brown-John, Steve Chand, David Charest, Anita M. Charters, Rebecca Cullum, Noreen Dhalla, Ruth Featherstone, Gerhard, Daniela S., Brad Hoffman, Holt, Robert A., Juan Hou, Byron Y. -L. Kuo, Lisa L. C. Lee, Stephanie Lee, Derek Leung, Kevin Ma, Corey Matsuo, Mayo, Michael, McDonald, Helen, Anna-Iiisa Prabhu, Pawan Pandoh, Riggins, Gregory J., Teresa Ruiz de Algara, James L. Rupert, Duane Smailus, Jeff Stott, Miranda Tsai, Richard Varhol, Pavle Vrljicak, Wong, David, Mona K. Wu, Yuan-Yun Xie, George Yang, Ida Zhang, Hirst, Martin, Steven J. M. Jones, Helgason, Cheryl D., Simpson, Elizabeth M., Pamela A. Hoodless, Marra, Marco A., Waterston, Robert H.

“…We analyzed 8.55 million LongSAGE tags generated from 72 libraries. Each LongSAGE library was prepared from a different mouse tissue. Analysis of the data…”
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BMDExpress 2: enhanced transcriptomic dose-response analysis workflow by Phillips, Jason R, Svoboda, Daniel L, Tandon, Arpit, Patel, Shyam, Sedykh, Alex, Mav, Deepak, Kuo, Byron, Yauk, Carole L, Yang, Longlong, Thomas, Russell S, Gift, Jeff S, Davis, J Allen, Olszyk, Louis, Merrick, B Alex, Paules, Richard S, Parham, Fred, Saddler, Trey, Shah, Ruchir R, Auerbach, Scott S

“…Abstract Summary A new version (version 2) of the genomic dose-response analysis software, BMDExpress, has been created. The software addresses the increasing…”
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Recommended approaches in the application of toxicogenomics to derive points of departure for chemical risk assessment by Farmahin, Reza, Williams, Andrew, Kuo, Byron, Chepelev, Nikolai L., Thomas, Russell S., Barton-Maclaren, Tara S., Curran, Ivan H., Nong, Andy, Wade, Michael G., Yauk, Carole L.

“…There is increasing interest in the use of quantitative transcriptomic data to determine benchmark dose (BMD) and estimate a point of departure (POD) for human…”
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Hepatic transcriptional dose-response analysis of male and female Fischer rats exposed to hexabromocyclododecane by Farmahin, Reza, Gannon, Anne Marie, Gagné, Rémi, Rowan-Carroll, Andrea, Kuo, Byron, Williams, Andrew, Curran, Ivan, Yauk, Carole L.

“…Hexabromocyclododecane (HBCD) is a brominated flame retardant found in the environment and human tissues. The toxicological effects of HBCD exposure are not…”
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Potency Ranking of Per- and Polyfluoroalkyl Substances Using High-Throughput Transcriptomic Analysis of Human Liver Spheroids by Reardon, Anthony J F, Rowan-Carroll, Andrea, Ferguson, Stephen S, Leingartner, Karen, Gagne, Remi, Kuo, Byron, Williams, Andrew, Lorusso, Luigi, Bourdon-Lacombe, Julie A, Carrier, Richard, Moffat, Ivy, Yauk, Carole L, Atlas, Ella

“…Abstract Per- and polyfluoroalkyl substances (PFAS) are some of the most prominent organic contaminants in human blood. Although the toxicological implications…”
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High-Throughput Transcriptomic Analysis of Human Primary Hepatocyte Spheroids Exposed to Per- and Polyfluoroalkyl Substances as a Platform for Relative Potency Characterization by Rowan-Carroll, Andrea, Reardon, Anthony, Leingartner, Karen, Gagné, Remi, Williams, Andrew, Meier, Matthew J, Kuo, Byron, Bourdon-Lacombe, Julie, Moffat, Ivy, Carrier, Richard, Nong, Andy, Lorusso, Luigi, Ferguson, Stephen S, Atlas, Ella, Yauk, Carole

“…Abstract Per- and poly-fluoroalkyl substances (PFAS) are widely found in the environment because of their extensive use and persistence. Although several PFAS…”
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Benchmark dose modeling of transcriptional data: a systematic approach to identify best practices for study designs used in radiation research by Stainforth, Robert, Vuong, Ngoc, Adam, Nadine, Kuo, Byron, Wilkins, Ruth C., Yauk, Carole, Beheshti, Afshin, Chauhan, Vinita

“…Benchmark dose (BMD) modeling is a method commonly used in chemical toxicology to identify the point of departure (POD) from a dose-response curve linked to a…”
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Evaluating the influences of confounding variables on benchmark dose using a case study in the field of ionizing radiation by Adam, Nadine, Vuong, Ngoc Q., Adams, Hailey, Kuo, Byron, Beheshti, Afshin, Yauk, Carole, Wilkins, Ruth, Chauhan, Vinita

“…A vast amount of data regarding the effects of radiation stressors on transcriptional changes has been produced over the past few decades. These data have…”
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Toxicogenomic assessment of liver responses following subchronic exposure to furan in Fischer F344 rats by Dong, Hongyan, Gill, Santokh, Curran, Ivan H., Williams, Andrew, Kuo, Byron, Wade, Michael G., Yauk, Carole L.

“…Furan is a widely used industrial chemical and a contaminant in heated foods. Chronic furan exposure causes cholangiocarcinoma and hepatocellular tumors in…”
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Comprehensive interpretation of in vitro micronucleus test results for 292 chemicals: from hazard identification to risk assessment application by Kuo, Byron, Beal, Marc A., Wills, John W., White, Paul A., Marchetti, Francesco, Nong, Andy, Barton-Maclaren, Tara S., Houck, Keith, Yauk, Carole L.

“…Risk assessments are increasingly reliant on information from in vitro assays. The in vitro micronucleus test (MNvit) is a genotoxicity test that detects…”
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Meta-analysis of transcriptomic datasets using benchmark dose modeling shows value in supporting radiation risk assessment by Chauhan, Vinita, Adam, Nadine, Kuo, Byron, Williams, Andrew, Yauk, Carole L., Wilkins, Ruth, Stainforth, Robert

“…Benchmark dose (BMD) modeling is used to determine the dose of a stressor at which a predefined increase in any biological effect above background occurs (e.g…”
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The use of in vitro transcriptional data to identify thresholds of effects in a human lens epithelial cell-line exposed to ionizing radiation by Chauhan, Vinita, Rowan-Carroll, Andrea, Gagné, Rémi, Kuo, Byron, Williams, Andrew, Yauk, Carole L.

“…Purpose: The International Commission on Radiological Protection (ICRP) recently recommended reducing the occupational equivalent dose limit for the lens of…”
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Transcriptomic pathway and benchmark dose analysis of Bisphenol A, Bisphenol S, Bisphenol F, and 3,3',5,5'-Tetrabromobisphenol A in H9 human embryonic stem cells by Peshdary, Vian, Hobbs, Cheryl A., Maynor, Timothy, Shepard, Kim, Gagné, Remi, Williams, Andrew, Kuo, Byron, Chepelev, Nikolai, Recio, Leslie, Yauk, Carole, Atlas, Ella

“…Bisphenol A (BPA) is a chemical used in the manufacturing of plastics to which human exposure is ubiquitous. Numerous studies have linked BPA exposure to many…”
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