Office of Research and Development Publications

Records 1 to 25 of 1008

Understanding the Biology and Technology of ToxCast and Tox21 Assays (PRESENTATION)
The ToxCast high-throughput toxicity (HTT) testing methods have been developed to evaluate the hazard potential of diverse environmental, industrial and consumer product chemicals. The main goal is prioritizing the compounds of greatest concern for more detailed toxicological stu...
Curating and sharing structures and spectra for the environmental community (PRESENTATION)
The increasing popularity of high mass accuracy non-target mass spectrometry methods has yielded extensive identification efforts based on spectral and chemical compound databases in the environmental community and beyond. Increasingly, new methods are relying on open data resour...
Prediction Of pKa From Chemical Structure Using Free And Open-Source Tools (PRESENTATION)
The ionization state of a chemical, reflected in pKa values, affects lipophilicity, solubility, protein binding and the ability of a chemical to cross the plasma membrane. These properties govern the pharmacokinetic parameters such as absorption, distribution, metabolism, excreti...
Sharing chemical structures with peer-reviewed publications. Are we there yet? (PRESENTATION)
In the domain of chemistry one of the greatest benefits to publishing research is that data are shared. Unfortunately, the vast majority of chemical structure data remain locked up in document form, primarily as PDF files. Despite the explosive growth of online chemical databases...
Structure identification by Mass Spectrometry Non-Targeted Analysis using the US EPA’s CompTox Chemistry Dashboard (PRESENTATION)
Identification of unknowns in mass spectrometry based non-targeted analyses (NTA) requires the integration of complementary pieces of data to arrive at a confident, consensus structure. Researchers use chemical reference databases, spectral matching, fragment prediction tools, r...
Automated workflows for data curation and standardization of chemical structures for QSAR modeling (PRESENTATION)
Large collections of chemical structures and associated experimental data are publicly available, and can be used to build robust QSAR models for applications in different fields. One common concern is the quality of both the chemical structure information and associated experime...
Development of a Tool for Systematic Integration of Traditional and New Approach Methods for Prioritizing Chemical Lists (PRESENTATION)
Multiple chemical regulatory bodies (US EPA, ECHA, OECD, Health Canada) are currently tasked with prioritizing chemicals for in-depth risk assessments. These prioritization efforts are driven by the fact that there are many chemicals in commerce, or in the environment for which d...
Differential Gene Expression and Concentration-Response Modeling Workflow for High-Throughput Transcriptomic (HTTr) Data: Results From MCF7 Cells (PRESENTATION)
Increasing efficiency and declining cost of generating whole transcriptome profiles has made high-throughput transcriptomics a practical option for chemical bioactivity screening. The resulting data output provides information on the expression of thousands of genes and is amenab...
EPA’s Non-Targeted Analysis Research Program: Expanding public data resources in support of exposure science (PRESENTATION)
Suspect screening (SSA) and non-targeted analysis (NTA) methods using high-resolution mass spectrometry (HRMS) offer new approaches to efficiently generate exposure data for chemicals in a variety of environmental and biological media. These techniques aid characterization of the...
High Throughput Transcriptomics: From screening to pathways (PRESENTATION)
The EPA ToxCast effort has screened thousands of chemicals across hundreds of high-throughput in vitro screening assays. The project is now leveraging high-throughput transcriptomic (HTTr) technologies to substantially expand its coverage of biological pathways. The first HTTr sc...
Resources and Alternative Publication Streams for Big Data (PRESENTATION)
The volume of data and associated myriad of data analyses conducted to support toxicological research studies has been expanding for years and there is little indication that it will be slowing. Traditional publication methods offer, at best, a summary of the data underlying a re...
Screening the 10K Tox21 chemical library for thyroid hormone receptor modulators (PRESENTATION)
Few ligands for the thyroid hormone receptor (TR) have been identified outside of endogenous ligands and pharmaceuticals, which suggests that TR is a very selective nuclear receptor (NR). However, large and diverse chemical libraries, particularly of environmental chemicals, have...
Use of ToxPrint chemotypes for exploring chemical feature enrichments across the ToxCast chemical-assay landscape (PRESENTATION)
EPA’s ToxCast chemical library spans diverse chemical use-types, functionalities, structures and features potentially relevant to toxicity and environmental exposure. However, this structural diversity, along with assay noise and low average hit rates across the varied ToxCast h...
Variability of LD50 Values from Rat Oral Acute Toxicity Studies: Implications for Alternative Model Development (PRESENTATION)
Alternative models developed for estimating acute systemic toxicity are generally evaluated using in vivo LD50 values. However, in vivo acute systemic toxicity studies can produce variable results, even when conducted according to accepted test guidelines. This variability can ma...
Applying a High-Throughput PBTK Model for IVIVE (PRESENTATION)
The ability to link in vitro and in vivo toxicity enables the use of high-throughput in vitro assays as an alternative to resource intensive animal studies. Toxicokinetics (TK) should help describe this link, but prior work found weak correlation when using a TK model for in vitr...
Building scientific confidence in metabolic similarity in read-across through the use of in vitro, in silico and analytical data (PRESENTATION)
The underlying principle of read-across is that the biological activity of a chemical is inherent in its molecular structure. Analogues are typically identified by structural similarity then evaluated on the basis of their bioavailability, reactivity and metabolic similarity. Whi...
Deep Water Horizon Oil Spill: Lessons learned in applying novel assessment methodologies in emergency response (PRESENTATION)
Overview of the EPA's involvement in the Deep Water Horizon Oil Spill. This drives the need for rapid “screening-level” risk assessments using “New Approach Methods” (NAM).
Universal LD50 predictions using deep learning (PRESENTATION)
NICEATM Predictive Models for Acute Oral Systemic Toxicity LD50 entry Risa R. Sayre (sayre.risa@epa.gov) & Christopher M. Grulke Our approach uses an ensemble of multilayer perceptron regressions to predict rat acute oral LD50 values from chemical features. Features were genera...
OPERA: A free and open source QSAR tool for predicting physicochemical properties and environmental fate endpoints (PRESENTATION)
Collecting the chemical structures and data for necessary QSAR modeling is facilitated by available public databases and open data. However, QSAR model performance is dependent on the quality of data and modeling methodology used. This study developed robust QSAR models for physi...
The US EPA CompTox Chemistry Dashboard as a source of data to fill data gaps for chemical sources of risk (PRESENTATION)
Chemical risk assessment is both time-consuming and difficult because it requires the assembly of data for chemicals generally distributed across multiple sources. The US EPA CompTox Chemistry Dashboard is a publicly accessible web-based application providing access to various da...
New developments in delivering public access to data from the National Center for Computational Toxicology at the EPA (PRESENTATION)
Researchers at EPA’s National Center for Computational Toxicology integrate advances in biology, chemistry, and computer science to examine the toxicity of chemicals and help prioritize chemicals for further research based on potential human health risks. The goal of this researc...
Overview of open resources to support automated structure verification and elucidation (PRESENTATION)
Cheminformatics methods form an essential basis for providing analytical scientists with access to data, algorithms and workflows. There are an increasing number of free online databases (compound databases, spectral libraries, data repositories) and a rich collection of software...
Automated Structure Annotation and Curation for MassBank: Potential and Pitfalls (PRESENTATION)
The European MassBank server (www.massbank.eu) was founded in 2012 by the NORMAN Network (www.norman-network.net) to provide open access to mass spectra of substances of environmental interest contributed by NORMAN members. The automated workflow RMassBank was developed as a part...
Literature-based cheminformatics for research in chemical toxicity (PRESENTATION)
PubMed is the largest freely available source of published literature available online with access to 27 million citations (as of October 2017). Contained within the literature is an abundance of information about the activity of chemicals in biological systems. Literature inform...
20170918 - A New Tox21 Strategic and Operational Plan (SACATM Meeting) (PRESENTATION)
Presentation at Scientific Advisory Committee On Alternative Toxicological Methods (SACATM) Sep 2017