BMDExpress specifications

Information


Unique identifier OMICS_15711
Name BMDExpress
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Windows
License MIT License
Computer skills Medium
Version 1.4
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Russell Thomas <>

Publication for BMDExpress

BMDExpress in publications

 (8)
PMCID: 5837509
PMID: 28472532
DOI: 10.1093/toxsci/kfx085

[…] polymerase chain reaction (qrt-pcr) results in the previously published analyses ()., dose–response modeling of the degs associated with cr(vi) exposure in the mouse duodenum was conducted with bmdexpress v1.4 using methods previously detailed (; ). briefly, analyses were carried out on the lists of degs (represented by their respective microarray probesets) against cr(vi) dose (mg sdd/l) […]

PMCID: 5399047
PMID: 27928627
DOI: 10.1007/s00204-016-1886-5

[…] within the same rodent models. to do this, we leveraged published affymetrix microarray data on well-designed dose–response studies in rats with matching (derived from the same rats) apical data. bmdexpress (yang et al. ) was used to derive bmd and lower confidence limit benchmark dose (bmdl) values for gene expression. eleven approaches to select groups of genes and molecular pathways […]

PMCID: 5489644
PMID: 27858113
DOI: 10.1007/s00204-016-1891-8

[…] labib et al. (). since our previous studies (labib et al. , , ) focussed on carcinogenic effects of pahs, pathways pertinent to cancer formation were the focus of the analysis in the present study., bmdexpress version 1.4.1 (yang et al. ) was used to perform bmd analysis on the transcriptomic data. only genes that had “present” calls in at least one dose group (i.e., 4 out of 5 biological […]

PMCID: 4915531
PMID: 27195522
DOI: 10.1002/em.22020

[…] data, normalized log2‐transformed expression values for individual genes were fit as continuous data to a series of four dose‐response models (hill, power, linear, and second degree polynomial) by bmdexpress software [yang et al., ]. each model was run assuming constant variance, with maximum iterations of 250, benchmark response (bmr) factor of 1.349, confidence level of 0.95, and power […]

PMCID: 4551741
PMID: 26313361
DOI: 10.1371/journal.pone.0136764

[…] were at least 0.5 counts per million (cpm) in at least 3 of 4 samples, in at least one dose group (and were called ‘absent’ if they did not pass this filter). tmm normalization was applied before bmdexpress analysis. the dataset is publically available through the gene expression omnibus (geo, http://www.ncbi.nlm.nih.gov/geo/): gse64371., the microarray experimental design and analysis […]


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BMDExpress institution(s)
The Hamner Institutes for Health Sciences, Research Triangle Park, NC, USA; Bruce Allen Consulting, Chapel Hill, NC, USA
BMDExpress funding source(s)
This work was supported by a grant from the American Chemistry Council's Long Range Initiative and a Superfund Program Project Grant (2 P42 ES004911-17).

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