Literature DB >> 27797781

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

Dayne L Filer1, Parth Kothiya1, R Woodrow Setzer2, Richard S Judson2, Matthew T Martin2.   

Abstract

Motivation: Large 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: The tcpl R package and its associated MySQL database provide a generalized platform for efficiently storing, normalizing and dose-response modeling of large high-throughput and high-content chemical screening data. The novel dose-response modeling algorithm has been tested against millions of diverse dose-response series, and robustly fits data with outliers and cytotoxicity-related signal loss. Availability and Implementation: tcpl is freely available on the Comprehensive R Archive Network under the GPL-2 license. Contact: martin.matt@epa.gov. Published by Oxford University Press 2016. This work is written by US Government employees and is in the public domain in the US.

Entities:  

Mesh：

Year:  2017        PMID： 27797781     DOI： 10.1093/bioinformatics/btw680

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  53 in total

Review 1.  Progress in data interoperability to support computational toxicology and chemical safety evaluation.

Authors:  Sean Watford; Stephen Edwards; Michelle Angrish; Richard S Judson; Katie Paul Friedman
Journal:  Toxicol Appl Pharmacol       Date:  2019-08-09       Impact factor: 4.219

2.  Screening the ToxCast Phase 1, Phase 2, and e1k Chemical Libraries for Inhibitors of Iodothyronine Deiodinases.

Authors:  Jennifer H Olker; Joseph J Korte; Jeffrey S Denny; Phillip C Hartig; Mary C Cardon; Carsten N Knutsen; Paige M Kent; Jessica P Christensen; Sigmund J Degitz; Michael W Hornung
Journal:  Toxicol Sci       Date:  2019-04-01       Impact factor: 4.849

Review 3.  In vitro to in vivo extrapolation for high throughput prioritization and decision making.

Authors:  Shannon M Bell; Xiaoqing Chang; John F Wambaugh; David G Allen; Mike Bartels; Kim L R Brouwer; Warren M Casey; Neepa Choksi; Stephen S Ferguson; Grazyna Fraczkiewicz; Annie M Jarabek; Alice Ke; Annie Lumen; Scott G Lynn; Alicia Paini; Paul S Price; Caroline Ring; Ted W Simon; Nisha S Sipes; Catherine S Sprankle; Judy Strickland; John Troutman; Barbara A Wetmore; Nicole C Kleinstreuer
Journal:  Toxicol In Vitro       Date:  2017-12-05       Impact factor: 3.500

4.  The Next Generation Blueprint of Computational Toxicology at the U.S. Environmental Protection Agency.

Authors:  Russell S Thomas; Tina Bahadori; Timothy J Buckley; John Cowden; Chad Deisenroth; Kathie L Dionisio; Jeffrey B Frithsen; Christopher M Grulke; Maureen R Gwinn; Joshua A Harrill; Mark Higuchi; Keith A Houck; Michael F Hughes; E Sidney Hunter; Kristin K Isaacs; Richard S Judson; Thomas B Knudsen; Jason C Lambert; Monica Linnenbrink; Todd M Martin; Seth R Newton; Stephanie Padilla; Grace Patlewicz; Katie Paul-Friedman; Katherine A Phillips; Ann M Richard; Reeder Sams; Timothy J Shafer; R Woodrow Setzer; Imran Shah; Jane E Simmons; Steven O Simmons; Amar Singh; Jon R Sobus; Mark Strynar; Adam Swank; Rogelio Tornero-Valez; Elin M Ulrich; Daniel L Villeneuve; John F Wambaugh; Barbara A Wetmore; Antony J Williams
Journal:  Toxicol Sci       Date:  2019-06-01       Impact factor: 4.849

5.  The Tox21 10K Compound Library: Collaborative Chemistry Advancing Toxicology.

Authors:  Ann M Richard; Ruili Huang; Suramya Waidyanatha; Paul Shinn; Bradley J Collins; Inthirany Thillainadarajah; Christopher M Grulke; Antony J Williams; Ryan R Lougee; Richard S Judson; Keith A Houck; Mahmoud Shobair; Chihae Yang; James F Rathman; Adam Yasgar; Suzanne C Fitzpatrick; Anton Simeonov; Russell S Thomas; Kevin M Crofton; Richard S Paules; John R Bucher; Christopher P Austin; Robert J Kavlock; Raymond R Tice
Journal:  Chem Res Toxicol       Date:  2020-11-03       Impact factor: 3.739

6.  An "EAR" on Environmental Surveillance and Monitoring: A Case Study on the Use of Exposure-Activity Ratios (EARs) to Prioritize Sites, Chemicals, and Bioactivities of Concern in Great Lakes Waters.

Authors:  Brett R Blackwell; Gerald T Ankley; Steven R Corsi; Laura A DeCicco; Keith A Houck; Richard S Judson; Shibin Li; Matthew T Martin; Elizabeth Murphy; Anthony L Schroeder; Edwin R Smith; Joe Swintek; Daniel L Villeneuve
Journal:  Environ Sci Technol       Date:  2017-07-18       Impact factor: 9.028

7.  Contaminants in bald eagles of the upper Midwestern U.S.: A framework for prioritizing future research based on in-vitro bioassays.

Authors:  Sarah M Elliott; William T Route; Laura A DeCicco; David D VanderMeulen; Steven R Corsi; Brett R Blackwell
Journal:  Environ Pollut       Date:  2018-10-24       Impact factor: 8.071

8.  Differentiating Pathway-Specific From Nonspecific Effects in High-Throughput Toxicity Data: A Foundation for Prioritizing Adverse Outcome Pathway Development.

Authors:  Kellie A Fay; Daniel L Villeneuve; Joe Swintek; Stephen W Edwards; Mark D Nelms; Brett R Blackwell; Gerald T Ankley
Journal:  Toxicol Sci       Date:  2018-06-01       Impact factor: 4.849

9.  ToxRefDB version 2.0: Improved utility for predictive and retrospective toxicology analyses.

Authors:  Sean Watford; Ly Ly Pham; Jessica Wignall; Robert Shin; Matthew T Martin; Katie Paul Friedman
Journal:  Reprod Toxicol       Date:  2019-07-21       Impact factor: 3.143

10.  Channel Interactions and Robust Inference for Ratiometric β-lactamase Assay Data: a Tox21 Library Analysis.

Authors:  Fjodor Melnikov; Jui-Hua Hsieh; Nisha S Sipes; Paul T Anastas
Journal:  ACS Sustain Chem Eng       Date:  2018-01-15       Impact factor: 8.198
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