Scholars@Duke
Dayne Filer

Selected Publications

Noninvasive prenatal exome sequencing diagnostic utility limited by sequencing depth and fetal fraction.

Journal Article Prenatal diagnosis · May 2022 Featured Publication ObjectiveSequencing cell-free DNA now allows detection of large chromosomal abnormalities and dominant Mendelian disorders in the prenatal period. Improving upon these methods would allow newborn screening programs to begin with prenatal genetics, ... Full text Cite

On the Utility of ToxCast-Based Predictive Models to Evaluate Potential Metabolic Disruption by Environmental Chemicals.

Journal Article Environmental health perspectives · May 2022 Featured Publication BackgroundResearch suggests environmental contaminants can impact metabolic health; however, high costs prohibit in vivo screening of putative metabolic disruptors. High-throughput screening programs, such as ToxCast, hold promise to reduce ... Full text Cite

Pre-capture multiplexing provides additional power to detect copy number variation in exome sequencing.

Journal Article BMC bioinformatics · July 2021 Featured Publication BackgroundAs exome sequencing (ES) integrates into clinical practice, we should make every effort to utilize all information generated. Copy-number variation can lead to Mendelian disorders, but small copy-number variants (CNVs) often get overlook ... Full text Cite

Projected t-SNE for batch correction.

Journal Article Bioinformatics (Oxford, England) · June 2020 MotivationLow-dimensional representations of high-dimensional data are routinely employed in biomedical research to visualize, interpret and communicate results from different pipelines. In this article, we propose a novel procedure to directly es ... Full text Cite

Falciparum malaria from coastal Tanzania and Zanzibar remains highly connected despite effective control efforts on the archipelago.

Journal Article Malaria journal · January 2020 BackgroundTanzania's Zanzibar archipelago has made significant gains in malaria control over the last decade and is a target for malaria elimination. Despite consistent implementation of effective tools since 2002, elimination has not been achieve ... Full text Cite

Curation of food-relevant chemicals in ToxCast.

Journal Article Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association · May 2017 High-throughput in vitro assays and exposure prediction efforts are paving the way for modeling chemical risk; however, the utility of such extensive datasets can be limited or misleading when annotation fails to capture current chemical usage. To address ... Full text Cite

tcpl: the ToxCast pipeline for high-throughput screening data.

Journal Article Bioinformatics (Oxford, England) · February 2017 Featured Publication MotivationLarge high-throughput screening (HTS) efforts are widely used in drug development and chemical toxicity screening. Wide use and integration of these data can benefit from an efficient, transparent and reproducible data pipeline. Summary: ... Full text Cite

Editor's Highlight: Analysis of the Effects of Cell Stress and Cytotoxicity on In Vitro Assay Activity Across a Diverse Chemical and Assay Space.

Journal Article Toxicological sciences : an official journal of the Society of Toxicology · August 2016 Chemical toxicity can arise from disruption of specific biomolecular functions or through more generalized cell stress and cytotoxicity-mediated processes. Here, responses of 1060 chemicals including pharmaceuticals, natural products, pesticidals, consumer ... Full text Cite

Prioritizing Environmental Chemicals for Obesity and Diabetes Outcomes Research: A Screening Approach Using ToxCast™ High-Throughput Data.

Journal Article Environmental health perspectives · August 2016 BackgroundDiabetes and obesity are major threats to public health in the United States and abroad. Understanding the role that chemicals in our environment play in the development of these conditions is an emerging issue in environmental health, a ... Full text Cite

Evaluation of food-relevant chemicals in the ToxCast high-throughput screening program.

Journal Article Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association · June 2016 Thousands of chemicals are directly added to or come in contact with food, many of which have undergone little to no toxicological evaluation. The landscape of the food-relevant chemical universe was evaluated using cheminformatics, and subsequently the bi ... Full text Cite

High-Throughput Screening of Chemical Effects on Steroidogenesis Using H295R Human Adrenocortical Carcinoma Cells.

Journal Article Toxicological sciences : an official journal of the Society of Toxicology · April 2016 Disruption of steroidogenesis by environmental chemicals can result in altered hormone levels causing adverse reproductive and developmental effects. A high-throughput assay using H295R human adrenocortical carcinoma cells was used to evaluate the effect o ... Full text Cite

Integrated Model of Chemical Perturbations of a Biological Pathway Using 18 In Vitro High-Throughput Screening Assays for the Estrogen Receptor.

Journal Article Toxicological sciences : an official journal of the Society of Toxicology · November 2015 We demonstrate a computational network model that integrates 18 in vitro, high-throughput screening assays measuring estrogen receptor (ER) binding, dimerization, chromatin binding, transcriptional activation, and ER-dependent cell proliferation. The netwo ... Full text Cite

Test driving ToxCast: endocrine profiling for 1858 chemicals included in phase II.

Journal Article Current opinion in pharmacology · December 2014 Identifying chemicals, beyond those already implicated, to test for potential endocrine disruption is a challenge and high throughput approaches have emerged as a potential tool for this type of screening. This review focused the Environmental Protection A ... Full text Cite

Predictive endocrine testing in the 21st century using in vitro assays of estrogen receptor signaling responses.

Journal Article Environmental science & technology · January 2014 Thousands of environmental chemicals are subject to regulatory review for their potential to be endocrine disruptors (ED). In vitro high-throughput screening (HTS) assays have emerged as a potential tool for prioritizing chemicals for ED-related whole-anim ... Full text Cite

Cross-species analysis of thyroperoxidase inhibition by xenobiotics demonstrates conservation of response between pig and rat.

Journal Article Toxicology · October 2013 Thyroperoxidase (TPO), the enzyme that catalyzes the synthesis of thyroid hormone, is a known target for thyroid-disrupting chemicals. In vivo toxicological evidence supporting TPO-inhibition as one molecular-initiating event that leads to thyroid disrupti ... Full text Cite