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.
Blog posts : "toxpi"
David presents to Bioinformatics Users Group (BUGs) + toxpiR now available on High-Performance Computing Cluster
David presented on software options available for ToxPi to the university-wide Bioinformatics Users Group (BUGs). Thanks to Lisa Lowe for installing and documenting the new toxpiR package on the HPC cluster (Github link).
Links to all versions of ToxPi are available at https://toxpi.org
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…
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.…
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
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
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…
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…
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…
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. …
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…
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 …
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:
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.
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.
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…
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…
20 blog posts