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Blog posts : "computational toxicology"

Principles of Toxicology: Environmental and Industrial Applications, 4th Edition

Principles of Toxicology: Environmental and Industrial Applications, 4th Edition. Stephen M. Roberts (Editor), Robert C. James (Editor), Phillip L. Williams (Editor). ISBN: 978-1-119-63516-1.

David Reif co-authored Chapter 6 "Computational Toxicology", with Richard S. Judson, David M. Reif, Keit…

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Multiomic Big Data Analysis Challenges: Increasing Confidence in the Interpretation of Artificial Intelligence Assessments (2021) Analytical Chemistry

Odenkirk MT, Reif DM, Baker ES. Multiomic Big Data Analysis Challenges: Increasing Confidence in the Interpretation of Artificial Intelligence Assessments. Anal Chem. 2021 May 24. doi: 10.1021/acs.analchem.0c04850. Epub ahead of print. PMID: 34029068.

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Concentration-response evaluation of ToxCast compounds for multivariate activity patterns of neural network function (2019) Arch Toxicol

Kosnik MB, Strickland JD, Marvel SW, Wallis DJ, Wallace K, Richard AM, Reif
DM, Shafer TJ. Concentration-response evaluation of ToxCast compounds for
multivariate activity patterns of neural network function. Arch Toxicol. 2019 Dec
10. doi: 10.1007/s00204-019-02636-x. [Epub ahead of print] PubM…

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Determination of chemical-disease risk values to prioritize connections between environmental factors, genetic variants, and human diseases (2019) Toxicology and Applied Pharmacology

Kosnik MB, Reif DM. Determination of chemical-disease risk values to
prioritize connections between environmental factors, genetic variants, and human
diseases. Toxicol Appl Pharmacol. 2019 Jul 16:114674. doi:
10.1016/j.taap.2019.114674. [Epub ahead of print] PubMed PMID: 31323264.

Integration of curated and high-throughput screening data to elucidate environmental influences on disease pathways (2019) Computational Toxicology

Reif gives invited seminar at Paris symposium

The workshop, "Fish and amphibian embryos as alternative models in toxicology and teratology" was organized by the Helmholtz Centre for Environmental Research and hosted at L'Oréal headquarters in Paris, France. 

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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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20 blog posts