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Blog posts : "computational toxicology"

Characterizing the effects of missing data and evaluating imputation methods for chemical prioritization applications using ToxPi (2018) BioData Mining

Kimberly T. To, Rebecca C. Fry, David M. Reif. Characterizing the effects of missing data and evaluating imputation methods for chemical prioritization applications using ToxPi. BioData Mining. 2018. 

https://rdcu.be/XYtJ

 

Confirmation of high-throughput screening data and novel mechanistic insights into VDR-xenobiotic interactions by orthogonal assays (2018) Scientific Reports

Mahapatra D, Franzosa JA, Roell K, Kuenemann MA, Houck KA, Reif DM, Fourches
D, Kullman SW. Confirmation of high-throughput screening data and novel
mechanistic insights into VDR-xenobiotic interactions by orthogonal assays. Sci
Rep. 2018 Jun 11;8(1):8883. doi: 10.1038/s41598-018-27055-3. PubMe…

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ToxPi Graphical User Interface 2.0: Dynamic exploration, visualization, and sharing of integrated data models (2018) BMC Bioinformatics

Marvel SW, To K, Grimm FA, Wright FA, Rusyn I, Reif DM. ToxPi Graphical User Interface 2.0: Dynamic exploration, visualization, and sharing of integrated data models. BMC Bioinformatics. 2018 Mar 5;19(1):80. doi: 10.1186/s12859-018-2089-2. PubMed PMID: 29506467.

 

https://bmcbioinformatics.bi…

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Reif presents at OpenTox conference

David Reif presented at the 2017 OpenTox USA meeting. Thanks to Barry Hardy and Noffisat Oki for the invitation to speak! 

His seminar was entitled "Implications of Population Genetic Diversity for Safety Assessment."  

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An introduction to terminology and methodology of chemical synergy -perspectives from across disciplines (2017) Frontiers in Pharmacology

Reif presents in Systematic Evaluation of the Application of Zebrafish in Toxicology (SEAZIT) series

David Reif presented as part of the ongoing Systematic Evaluation of the Application of Zebrafish in Toxicology (SEAZIT) webinar series. 

A New Statistical Approach to Characterize Chemical-Elicited Behavioral Effects in High-Throughput Studies Using Zebrafish (2017) PLoS One

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A data-driven weighting scheme for multivariate phenotypic endpoints recapitulates zebrafish developmental cascades (2016) TAAP

Zhang G, Roell KR, Truong L, Tanguay RL, Reif DM. A data-driven weighting
scheme for multivariate phenotypic endpoints recapitulates zebrafish
developmental cascades. Toxicol Appl Pharmacol. 2016 Nov 21. pii:
S0041-008X(16)30365-9. doi: 10.1016/j.taap.2016.11.010. [Epub ahead of print]
PubMed …

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Article featured as Editor's Highlight in Toxicological Sciences

Judson R, Houck K, Martin M, Richard AM, Knudsen TB, Shah I, Little S,
Wambaugh J, Woodrow Setzer R, Kothya P, Phuong J, Filer D, Smith D, Reif D,
Rotroff D, Kleinstreuer N, Sipes N, Xia M, Huang R, Crofton K, Thomas RS.
Editor's Highlight: Analysis of the Effects of Cell Stress and Cytotoxicit…

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Analysis of the Effects of Cell Stress and Cytotoxicity on In Vitro Assay Activity Across a Diverse Chemical and Assay Space (2016) Toxicological Sciences

Judson R, Houck K, Martin M, Richard AM, Knudsen TB, Shah I, Little S,
Wambaugh J, Woodrow Setzer R, Kothya P, Phuong J, Filer D, Smith D, Reif D,
Rotroff D, Kleinstreuer N, Sipes N, Xia M, Huang R, Crofton K, Thomas RS.
Analysis of the Effects of Cell Stress and Cytotoxicity on In Vitro Assay
…

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A chemical-biological similarity-based grouping of complex substances as a prototype approach for evaluating chemical alternatives (2016) Green Chemistry

F. A. Grimm, Y. Iwata, O. Sirenko, G. A. Chappell, F. A. Wright, D. M. Reif, J. Braisted, D. L. Gerhold, J. M. Yeakley, P. Shepard, B. Seligmann, T. Roy, P. J. Boogaard, H. B. Ketelslegers, A. M. Rohde and I. Rusyn, Green Chem., 2016, DOI: 10.1039/C6GC01147K.

Open Access / Freely-available:

ht…

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Advancing Exposure Science through Chemical Data Curation and Integration in the Comparative Toxicogenomics Database (2016) Environmental Health Perspectives

Grondin CJ, Davis AP, Wiegers TC, King BL, Wiegers JA, Reif DM, Hoppin JA,
Mattingly CJ. Advancing Exposure Science through Chemical Data Curation and
Integration in the Comparative Toxicogenomics Database. Environ Health Perspect. 
2016 May 12. [Epub ahead of print] PubMed PMID: 27170236.

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Aggregate entropy scoring for quantifying activity across endpoints with irregular correlation structure (2016) Reproductive Toxicology

Zhang G, Marvel S, Truong L, Tanguay RL, Reif DM. Aggregate entropy scoring
for quantifying activity across endpoints with irregular correlation structure.
Reprod Toxicol. 2016 Apr 27;62:92-99. doi: 10.1016/j.reprotox.2016.04.012. [Epub 
ahead of print] PubMed PMID: 27132190.

Selected as cov…

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European Chemicals Agency workshop on "New Approach Methodologies in Regulatory Science"

David Reif presented at an invited workshop from the European Chemicals Agency (ECHA) in Helsinki, Finland on "New Approach Methodologies in Regulatory Science".

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Prioritizing Environmental Chemicals for Obesity and Diabetes Outcomes Research: A Screening Approach Using ToxCast High Throughput Data (2016) Environmental Health Perspectives

Auerbach S, Filer D, Reif D, Walker V, Holloway AC, Schlezinger J, Srinivasan 
S, Svoboda D, Judson R, Bucher JR, Thayer KA. Prioritizing Environmental
Chemicals for Obesity and Diabetes Outcomes Research: A Screening Approach Using 
ToxCast High Throughput Data. Environ Health Perspect. 2016 M…

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Reif co-authors National Academy of Sciences (NAS) report "Application of Modern Toxicology Approaches for Predicting Acute Toxicity for Chemical Defense"

David Reif served as a member of an expert committee that authored the report "Application of Modern Toxicology Approaches for Predicting Acute Toxicity for Chemical Defense". 

The official citation is:

National Academies of Sciences, Engineering, and Medicine. Application of Modern Toxicolo…

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Reif part of multi-institute research team awarded EPA grant

The Environmental Protection Agency (EPA) has awarded a $6 million grant to fund a multi-institutional collaboration between the Texas A&M College of Veterinary Medicine & Biomedical Sciences and the Bioinformatics Research Center at NCSU. 

More information is available from the BRC and from Tex…

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Toxicity testing in the 21st century beyond environmental chemicals (2015) Altex

Costanza Rovida, Shoji Asakura, Mardas Daneshian, Hana Hofman-Huether, Marcel Leist, Leo Meunier, David Reif, Anna Rossi, Markus Schmutz, Jean-Pierre Valentin, Joanne Zurlo, Thomas Hartung.Toxicity testing in the 21st century beyond environmental chemicals. (2015) Altex 32 (3), 171-181.

http://w…

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High-throughput characterization of chemical-associated embryonic behavioral changes predicts teratogenic outcomes (2015) Archives of Toxicology

High-throughput characterization of chemical-associated embryonic behavioral changes predicts teratogenic outcomes (2015) Archives of Toxicology

http://www.ncbi.nlm.nih.gov/pubmed/26126630

(NOTE: Full-text available for free via link above or here)

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Computational Methods Used in Systems Biology (2015) Systems Biology in Toxicology and Environmental Health

Michele Meisner, David M Reif. "Computational Methods Used in Systems Biology" Systems Biology in Toxicology and Environmental Health: From the Genome to the Epigenome. Chapter 5, Pages 85-115. Elsevier.

http://store.elsevier.com/Systems-Biology-in-Toxicology-and-Environmental-Health/R…

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20 blog posts