ArticleBioinformatics (Oxford, England)2019
BMDExpress 2: enhanced transcriptomic dose-response analysis workflow.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 113 papers.
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Who cites it
113 citing papers in PubMed.
- Using MetaboAnalyst 6.0 for exposomics data analysis-from LC-MS2 spectra processing to dose-response modeling and causal inference.Nature protocols · 2026Review
- Exposure Duration Shapes the Hepatic Response to GenX: Divergent Acute and Chronic Transcriptomic Profiles Reveal Non-Monotonic Dose Effects and Increased Sensitivity in Human Liver Spheroids.bioRxiv : the preprint server for biology · 2026Article
- Systematic comparison of temporal hepatotoxicant-induced gene network responses across 3 liver test systems.Toxicological sciences : an official journal of the Society of Toxicology · 2026Article
- PFOS and PFOA exposure induces liver injury and sex-dependent immune effects in C57BL/6 mice.iScience · 2026Article
- Review on Predictive Models and Integration Strategies for Holistic Impact Assessment of Chemicals and Materials.Environmental science & technology · 2026Review
- Challenging Additivity: Comparing Predicted and Observed AhR Activity of Polycyclic Aromatic Compound (PAC) Mixtures Containing Active and Inactive Constituents.Environmental science & technology · 2026Article
- ARACRA: Automated RNA-seq Analysis for Chemical Risk Assessment.Computational and structural biotechnology journal · 2026Article
- An AOP-guidedNAM journal · 2026Article
- Article
- Zebrafish cell lines and high-throughput transcriptomics: advancing in vitro and bioinformatics methods for supporting environmental risk assessment.Toxicological sciences : an official journal of the Society of Toxicology · 2025Article
- Transcriptomic dose response assessment of PFAS chemicals 3:3 fluorotelomer carboxylic acid, 7:3 fluorotelomer alcohol, and perfluorohexanesulfonamide.Toxicology · 2025Article
- Testing the effects of two different zebrafish exposure paradigms on transcriptomic-based chemical risk assessment using the flame retardant triphenyl phosphate.Toxicological sciences : an official journal of the Society of Toxicology · 2025Article
- Environmentally relevant lead exposure impacts gene expression in SH-SY5Y cells throughout neuronal differentiation.Toxicological sciences : an official journal of the Society of Toxicology · 2025Article
- Identification of four mechanisms of toxicity for per- and polyfluoroalkyl substances through transcriptomic profiling in human liver spheroids exposed to 24 PFAS.Toxicological sciences : an official journal of the Society of Toxicology · 2025Article
- Comprehensive analysis of high-throughput transcriptomics to distinguish drug-induced liver injury (DILI) phenotypes.Archives of toxicology · 2025Review
- Article
- Shift in the urinary metabolome associated with 2,3,7,8-tetrachlorodibenzo-p-dioxin activation of the hepatic aryl hydrocarbon receptor.Scientific reports · 2025Article
- Profiling the cytotoxic effects of naled and other pesticides in primary human placental cytotrophoblasts.Toxicological sciences : an official journal of the Society of Toxicology · 2025Article
- bmdrc: Python package for quantifying phenotypes from chemical exposures with benchmark dose modeling.PLoS computational biology · 2025Article
- Comparison of phenotypic and transcriptomic profiles between HFPO-DA and prototypical PPARα, PPARγ, and cytotoxic agents in wild-type and Ppara-null mouse livers.Toxicological sciences : an official journal of the Society of Toxicology · 2025Article
53 more citing papers are in PubMed but not listed here.
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Authors and funding
19 authors.
Funding
Abstract
summaryA new version (version 2) of the genomic dose-response analysis software, BMDExpress, has been created. The software addresses the increasing use of transcriptomic dose-response data in toxicology, drug design, risk assessment and translational research. In this new version, we have implemented additional statistical filtering options (e.g. Williams' trend test), curve fitting models, Linux and Macintosh compatibility and support for additional transcriptomic platforms with up-to-date gene annotations. Furthermore, we have implemented extensive data visualizations, on-the-fly data filtering, and a batch-wise analysis workflow. We have also significantly re-engineered the code base to reflect contemporary software engineering practices and streamline future development. The first version of BMDExpress was developed in 2007 to meet an unmet demand for easy-to-use transcriptomic dose-response analysis software. Since its original release, however, transcriptomic platforms, technologies, pathway annotations and quantitative methods for data analysis have undergone a large change necessitating a significant re-development of BMDExpress. To that end, as of 2016, the National Toxicology Program assumed stewardship of BMDExpress. The result is a modernized and updated BMDExpress 2 that addresses the needs of the growing toxicogenomics user community. AVAILABILITY AND IMPLEMENTATION: BMDExpress 2 is available at https://github.com/auerbachs/BMDExpress-2/releases. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.