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Blog posts : "toxpi"

ToxPi*GIS Toolkit: creating, viewing, and sharing integrative visualizations for geospatial data using ArcGIS (2022) J Expo Sci Environ Epidemiol.

Fleming J, Marvel SW, Supak S, Motsinger-Reif AA, Reif DM. ToxPi*GIS Toolkit: creating, viewing, and sharing integrative visualizations for geospatial data using ArcGIS. J Expo Sci Environ Epidemiol. 2022 Apr 26. doi: 10.1038/s41370-022-00433-w. Epub ahead of print. PMID: 35474345.

doi: 10.1038/s…

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Kirkwood et al. pub recognized as "NIEHS Paper of the Month"

https://factor.niehs.nih.gov/2022/4/papers/dert/index.htm

Pine needles work as passive samplers for PFAS

NIEHS-funded researchers showed that pine needles can be used as a tool to monitor the presence and distribution of per- and polyfluoroalkyl substances (PFAS) over time. The pine needle’s w…

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Utilizing Pine Needles to Temporally and Spatially Profile Per- and Polyfluoroalkyl Substances (2022) Environ Sci Technol.

Kirkwood KI, Fleming J, Nguyen H, Reif DM, Baker ES, Belcher SM. Utilizing Pine Needles to Temporally and Spatially Profile Per- and Polyfluoroalkyl Substances (PFAS). Environ Sci Technol. 2022 Feb 17. doi: 10.1021/acs.est.1c06483. Epub ahead of print. PMID: 35175744.

https://pubmed.ncbi.nlm.nih.…

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Collaborative paper featuring Jonathon's work highlighted in the news

https://news.ncsu.edu/2022/02/pine-needles-story-of-nc-pfas/

Pine Needles Tell the Story of PFAS in North Carolina

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toxpiR package posted on CRAN

An R package for the ToxPi framework has been assembled and posted to CRAN:

https://cran.r-project.org/web/packages/toxpiR/index.html

 

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Demonstrating a systems approach for integrating disparate data streams to inform decisions on children's environmental health (2022) BMC Public Health

Hubal EAC, DeLuca NM, Mullikin A, Slover R, Little JC, Reif DM. Demonstrating a systems approach for integrating disparate data streams to inform decisions on children's environmental health. BMC Public Health. 2022 Feb 15;22(1):313. doi: 10.1186/s12889-022-12682-3. PMID: 35168583; PMCID: PMC8845296…

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Using ToxPi to visualize baseball

In a very creative analysis, Benjamin Detringer and Stephen Detringer used ToxPi as a visual analytic for baseball statistics!

As new and complicated baseball statistics have proliferated, the authors used ToxPi to synthesize complex MLB player performance metrics into summary graphics and stati…

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The COVID-19 Pandemic Vulnerability Index (PVI) Dashboard: Monitoring County-Level Vulnerability Using Visualization, Statistical Modeling, and Machine Learning (2021) Environmental Health Perspectives

Marvel SW, House JS, Wheeler M, Song K, Zhou YH, Wright FA, Chiu WA, Rusyn I, Motsinger-Reif A, Reif DM. The COVID-19 Pandemic Vulnerability Index (PVI) Dashboard: Monitoring County-Level Vulnerability Using Visualization, Statistical Modeling, and Machine Learning. Environ Health Perspect. 2021 Jan…

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Fighting COVID-19 using data science

HGBEnviroScreen: Enabling Community Action through Data Integration in the Houston–Galveston– Brazoria Region (2020) International Journal of Environmental Research and Public Health

Sharmila Bhandari, P. Grace Tee Lewis, Elena Craft, Skylar W. Marvel, David M. Reif, and Weihsueh A. Chiu. HGBEnviroScreen: Enabling Community Action through Data Integration in the Houston–Galveston–Brazoria Region. Int. J. …

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Population-based toxicity screening in human induced pluripotent stem cell-derived cardiomyocytes (2019) Toxicol Appl Pharmacol

Burnett SD, Blanchette AD, Grimm FA, House JS, Reif DM, Wright FA, Chiu WA,
Rusyn I. Population-based toxicity screening in human induced pluripotent stem
cell-derived cardiomyocytes. Toxicol Appl Pharmacol. 2019 Aug 16;381:114711. doi:
10.1016/j.taap.2019.114711. [Epub ahead of print] PubMed P…

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ToxPi software updated (v2.2) @ www.toxpi.org

The complete .zip is available for free download at: www.toxpi.org

This update adds flexibility for setting weights, offers improved "zoom" capabilities, updates information included in the saved Results Table object, and fixes issues identified by users.

The updated manual includes a full …

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Updated ToxPi version (v 2.1) available at www.toxpi.org

A major update to the ToxPi interface (version 2.1) is now available at:

www.toxpi.org

This update includes major speed improvements (especially noticeable when clustering large datasets), the ability to zoom/pan on cluster dendrograms, as well as other refinements for GUI users. 

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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

 

Updated ToxPi version (20180329) available at www.toxpi.org

http://toxpi.org/

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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Incorporating ToxCast and Tox21 datasets to rank biological activity of chemicals at Superfund sites in North Carolina (2017) Environment International

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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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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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19 blog posts