Science Inventory

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Toxicological outcomes in vivo result from complex interactions among molecular, cellular and tissue-level damage responses which are difficult to recapitulate in vitro or extrapolate from data-based Machine Learning or molecular-level computer simulations. Mechani...

Background and Purpose: A virtual embryo may be conceptualized as a compendium of computational systems models that integrate biological systems information with chemical specific information to make predictions about developmental toxicity in a digital twin.  A challenge to...

Virtual models (vM) are mathematical representations of biological processes that are numerically solved computationally, and are used to investigate and predict system behaviors that cannot be predicted solely from studying the nature of the individual parts, or from the domain ...

Developmental hazard evaluation is an important part of assessing chemical risks during pregnancy. While New Approach Methods (NAM) based on in vitro chemical effects data offer alternatives to pregnant animal testing, adverse fetal outcomes in vivo result from complex interactio...

New Approach Methods (NAMs) refers to 21st-C testing strategies that rely on in vitro data and in silico models to predict human toxicity with less reliance on animal testing. Complex NAMs that accurately predict the potential for human developmental toxicity are needed to succee...

Identifying collections of reference chemicals for calibrating in vitro assays and in silico models is an important task in toxicological research.  A strong set of reference chemicals can bolster confidence in the accuracy and predictive value of new approach methods (NAMs)...

Modeling complex biological processes can require retrieving, organizing, and extracting entities and relationships from thousands of PubMed citations. The USEPA’s Center for Computational Toxicology and Exposure’s Virtual Tissue project team has developed an Excel-ba...

            New Approach Methods (NAMs) for assessing chemical effects on prenatal development with less reliance on animal testing is an important challenge for predictive toxicology at the USEPA [https://www.epa.gov/chemica...

For predictive toxicology, in vitro data and biological information must be organized and assimilated into computer models that bridge different levels of biological organization. This concept has been demonstrated with several virtual tissue model prototypes that predict adverse...

All-trans retinoic acid (ATRA) gradients determine skeletal patterning morphogenesis and can be disrupted by diverse genetic or environmental factors, leading to fetal skeleton malformations. Adverse Outcome Pathway (AOP) frameworks for ATRA metabolism, signaling, and homeostasis...

Summary: Congenital anomalies of the external genitalia (CAEG) are a prevalent and serious public health concern with lifelong impacts on the urinary function, sexual health, fertility, tumor development, and psychosocial wellbeing of affected individuals. Complications of treat...

This presentation will provide a general overview of the scientific rationale and main concepts behind single cell RNA profiling (scRNA-seq) for comprehensive interrogation of genomic function. scRNA-seq enables high-resolution cell lineage maps (continuum gene expression manifol...

Chemical toxicity testing is moving steadily toward a human cell and organoid-based in vitro approach for reasons including scientific relevancy, efficiency, cost, and ethical rightfulness. Inferring human health risk from chemical exposure based on in vitro testing data is a cha...

This joint American College of Toxicology/Teratology Society courseon Practical Reproductive and Developmental Toxicology is designed to provide a basic understanding in reproductive and developmental biology and principles of various testing approaches for reproductive and devel...

Cells in developing tissues must integrate and respond to highly dynamic information in the form of metabolic intermediates, genetic signals, and molecular gradients. Understanding the cellular decision-making process, and how these decisions may be perturbed by genetic errors or...

System biology models holistically describe, in a quantitative fashion, the relationships between different levels of a biologic system. Relationships between individual components of a system are delineated. System biology models describe how the components of the system inter...

Cleft palate (CP) is a common birth defect, occurring in an estimated 1 in 1000 births worldwide. The secondary palate is formed by paired palatal shelves that grow toward each other, appose, attach and fuse. CP can result from disruption of any of these processes. The palatal sh...

Organogenesis in the embryo involves cell differentiation and organization events that are unique to each tissue and organ and are susceptible to developmental toxicants. Animal models are the gold standard for identifying putative teratogens, but the limited throughput of develo...

Chemical regulation under the Frank R. Lautenberg Chemical Safety for the 21st Century Act of 2016 requires affirmation of ‘low’ and ‘high’ priority substances based on unreasonable risk to vulnerable subpopulations and lifestages. New approach methods (NAMs) based on in vitro da...

Presentation of the US EPA's Virtual Tissue Model project using agent-based models (ABMs). ABMs can execute simulations that self-organize cells into high levels of biological structure and function (emergent phenotypes), and simulate perturbations in the system-dose or stage res...

Virtual tissue models use new computational methods to construct advanced computer models capable of simulating how chemicals may affect human development. Virtual tissue models are some of the most advanced methods being developed today. The models will help reduce dependence on...

A major challenge to using in vitro high-throughput screening (HTS) data in risk assessment is the identification of toxicological “tipping points” between adaptation and adversity. Toxicological tipping points represent a systems threshold, or critical point, beyond which biolog...

Presentation at Brazialian Congress of Toxicology on Computational Modeling of Developmental Toxicity: Modeling with Human Pluripotent Stem Cells

Presentation at International Conference on Reproductive Biology and Toxicology Oct 2017 on Computational Biology

The Stemina devTOX quickPredict platform (STM) is a human pluripotent H9 stem cell-based assay that predicts developmental toxicants. Using the STM model, we screened 1065 ToxCast chemicals and entered the data into the ToxCast data analysis pipeline. Model performance was 83.3% ...