Literature DB >> 21177775

The evolution of bioinformatics in toxicology: advancing toxicogenomics.

Cynthia A Afshari1, Hisham K Hamadeh, Pierre R Bushel.   

Abstract

As one reflects back through the past 50 years of scientific research, a significant accomplishment was the advance into the genomic era. Basic research scientists have uncovered the genetic code and the foundation of the most fundamental building blocks for the molecular activity that supports biological structure and function. Accompanying these structural and functional discoveries is the advance of techniques and technologies to probe molecular events, in time, across environmental and chemical exposures, within individuals, and across species. The field of toxicology has kept pace with advances in molecular study, and the past 50 years recognizes significant growth and explosive understanding of the impact of the compounds and environment to basic cellular and molecular machinery. The advancement of molecular techniques applied in a whole-genomic capacity to the study of toxicant effects, toxicogenomics, is no doubt a significant milestone for toxicological research. Toxicogenomics has also provided an avenue for advancing a joining of multidisciplinary sciences including engineering and informatics in traditional toxicological research. This review will cover the evolution of the field of toxicogenomics in the context of informatics integration its current promise, and limitations.

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Year:  2010        PMID: 21177775      PMCID: PMC3145387          DOI: 10.1093/toxsci/kfq373

Source DB:  PubMed          Journal:  Toxicol Sci        ISSN: 1096-0929            Impact factor:   4.849


  76 in total

1.  Assessing gene significance from cDNA microarray expression data via mixed models.

Authors:  R D Wolfinger; G Gibson; E D Wolfinger; L Bennett; H Hamadeh; P Bushel; C Afshari; R S Paules
Journal:  J Comput Biol       Date:  2001       Impact factor: 1.479

2.  Detection of diluted gene expression alterations using cDNA microarrays.

Authors:  H K Hamadeh; P Bushel; C J Tucker; K Martin; R Paules; C A Afshari
Journal:  Biotechniques       Date:  2002-02       Impact factor: 1.993

3.  Exploration of low-dose estrogen effects: identification of No Observed Transcriptional Effect Level (NOTEL).

Authors:  Edward K Lobenhofer; Xiangqin Cui; Lee Bennett; P LouAnn Cable; B Alex Merrick; Gary A Churchill; Cynthia A Afshari
Journal:  Toxicol Pathol       Date:  2004 Jul-Aug       Impact factor: 1.902

4.  Validation of putative genomic biomarkers of nephrotoxicity in rats.

Authors:  Er-Jia Wang; Ronald D Snyder; Mark R Fielden; Roger J Smith; Yi-Zhong Gu
Journal:  Toxicology       Date:  2008-01-16       Impact factor: 4.221

5.  Cluster analysis and display of genome-wide expression patterns.

Authors:  M B Eisen; P T Spellman; P O Brown; D Botstein
Journal:  Proc Natl Acad Sci U S A       Date:  1998-12-08       Impact factor: 11.205

6.  Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization.

Authors:  P T Spellman; G Sherlock; M Q Zhang; V R Iyer; K Anders; M B Eisen; P O Brown; D Botstein; B Futcher
Journal:  Mol Biol Cell       Date:  1998-12       Impact factor: 4.138

Review 7.  The plasma proteome, adductome and idiosyncratic toxicity in toxicoproteomics research.

Authors:  B Alex Merrick
Journal:  Brief Funct Genomic Proteomic       Date:  2008-02-12

8.  Discernment of possible mechanisms of hepatotoxicity via biological processes over-represented by co-expressed genes.

Authors:  Jeff W Chou; Pierre R Bushel
Journal:  BMC Genomics       Date:  2009-06-18       Impact factor: 3.969

9.  Cytochrome c: a non-invasive biomarker of drug-induced liver injury.

Authors:  T J Miller; A Knapton; O Adeyemo; L Noory; J Weaver; J P Hanig
Journal:  J Appl Toxicol       Date:  2008-10       Impact factor: 3.446

10.  A prediction-based resampling method for estimating the number of clusters in a dataset.

Authors:  Sandrine Dudoit; Jane Fridlyand
Journal:  Genome Biol       Date:  2002-06-25       Impact factor: 13.583

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  34 in total

Review 1.  Back to the Future - Part 2. Post-mortem assessment and evolutionary role of the bio-medicolegal sciences.

Authors:  Santo Davide Ferrara; Giovanni Cecchetto; Rossana Cecchi; Donata Favretto; Silke Grabherr; Takaki Ishikawa; Toshikazu Kondo; Massimo Montisci; Heidi Pfeiffer; Maurizio Rippa Bonati; Dina Shokry; Marielle Vennemann; Thomas Bajanowski
Journal:  Int J Legal Med       Date:  2017-04-25       Impact factor: 2.686

2.  Toxicogenomic module associations with pathogenesis: a network-based approach to understanding drug toxicity.

Authors:  J J Sutherland; Y W Webster; J A Willy; G H Searfoss; K M Goldstein; A R Irizarry; D G Hall; J L Stevens
Journal:  Pharmacogenomics J       Date:  2017-04-25       Impact factor: 3.550

3.  Application of epigenetic data in human health risk assessment.

Authors:  Ila L Cote; Shaun D McCullough; Ronald N Hines; John J Vandenberg
Journal:  Curr Opin Toxicol       Date:  2017-11-06

4.  Multi-walled carbon nanotube-induced gene expression in the mouse lung: association with lung pathology.

Authors:  M Pacurari; Y Qian; D W Porter; M Wolfarth; Y Wan; D Luo; M Ding; V Castranova; N L Guo
Journal:  Toxicol Appl Pharmacol       Date:  2011-05-23       Impact factor: 4.219

5.  Multiwalled carbon nanotube-induced gene signatures in the mouse lung: potential predictive value for human lung cancer risk and prognosis.

Authors:  Nancy L Guo; Ying-Wooi Wan; James Denvir; Dale W Porter; Maricica Pacurari; Michael G Wolfarth; Vincent Castranova; Yong Qian
Journal:  J Toxicol Environ Health A       Date:  2012

6.  Systems Approach to Identifying Relevant Pathways from Phenotype Information in Dose-Dependent Time Series Microarray Data.

Authors:  Julian Dymacek; Nancy Lan Guo
Journal:  Proceedings (IEEE Int Conf Bioinformatics Biomed)       Date:  2011-11

7.  Multi-walled carbon nanotube-induced gene expression in vitro: concordance with in vivo studies.

Authors:  Brandi N Snyder-Talkington; Chunlin Dong; Xiangyi Zhao; Julian Dymacek; Dale W Porter; Michael G Wolfarth; Vincent Castranova; Yong Qian; Nancy L Guo
Journal:  Toxicology       Date:  2014-12-13       Impact factor: 4.221

Review 8.  Integrative approaches for predicting in vivo effects of chemicals from their structural descriptors and the results of short-term biological assays.

Authors:  Yen Sia Low; Alexander Yeugenyevich Sedykh; Ivan Rusyn; Alexander Tropsha
Journal:  Curr Top Med Chem       Date:  2014       Impact factor: 3.295

9.  New perspectives for in vitro risk assessment of multiwalled carbon nanotubes: application of coculture and bioinformatics.

Authors:  Brandi N Snyder-Talkington; Yong Qian; Vincent Castranova; Nancy L Guo
Journal:  J Toxicol Environ Health B Crit Rev       Date:  2012       Impact factor: 6.393

Review 10.  Recent advances in 2D and 3D in vitro systems using primary hepatocytes, alternative hepatocyte sources and non-parenchymal liver cells and their use in investigating mechanisms of hepatotoxicity, cell signaling and ADME.

Authors:  Patricio Godoy; Nicola J Hewitt; Ute Albrecht; Melvin E Andersen; Nariman Ansari; Sudin Bhattacharya; Johannes Georg Bode; Jennifer Bolleyn; Christoph Borner; Jan Böttger; Albert Braeuning; Robert A Budinsky; Britta Burkhardt; Neil R Cameron; Giovanni Camussi; Chong-Su Cho; Yun-Jaie Choi; J Craig Rowlands; Uta Dahmen; Georg Damm; Olaf Dirsch; María Teresa Donato; Jian Dong; Steven Dooley; Dirk Drasdo; Rowena Eakins; Karine Sá Ferreira; Valentina Fonsato; Joanna Fraczek; Rolf Gebhardt; Andrew Gibson; Matthias Glanemann; Chris E P Goldring; María José Gómez-Lechón; Geny M M Groothuis; Lena Gustavsson; Christelle Guyot; David Hallifax; Seddik Hammad; Adam Hayward; Dieter Häussinger; Claus Hellerbrand; Philip Hewitt; Stefan Hoehme; Hermann-Georg Holzhütter; J Brian Houston; Jens Hrach; Kiyomi Ito; Hartmut Jaeschke; Verena Keitel; Jens M Kelm; B Kevin Park; Claus Kordes; Gerd A Kullak-Ublick; Edward L LeCluyse; Peng Lu; Jennifer Luebke-Wheeler; Anna Lutz; Daniel J Maltman; Madlen Matz-Soja; Patrick McMullen; Irmgard Merfort; Simon Messner; Christoph Meyer; Jessica Mwinyi; Dean J Naisbitt; Andreas K Nussler; Peter Olinga; Francesco Pampaloni; Jingbo Pi; Linda Pluta; Stefan A Przyborski; Anup Ramachandran; Vera Rogiers; Cliff Rowe; Celine Schelcher; Kathrin Schmich; Michael Schwarz; Bijay Singh; Ernst H K Stelzer; Bruno Stieger; Regina Stöber; Yuichi Sugiyama; Ciro Tetta; Wolfgang E Thasler; Tamara Vanhaecke; Mathieu Vinken; Thomas S Weiss; Agata Widera; Courtney G Woods; Jinghai James Xu; Kathy M Yarborough; Jan G Hengstler
Journal:  Arch Toxicol       Date:  2013-08-23       Impact factor: 5.153

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