ArticleBioinformatics (Oxford, England)2005
SPLINDID: a semi-parametric, model-based method for obtaining transcription rates and gene regulation parameters from genomic and proteomic expression profiles.
Article in Bioinformatics (Oxford, England), 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Integrated Dissection of Cysteine Oxidative Post-translational Modification Proteome During Cardiac Hypertrophy.Journal of proteome research · 2018Article
- Modeling transitions in body composition: the approach to steady state for anthropometric measures and physiological functions in the Minnesota human starvation study.Dynamic medicine : DM · 2008Article
- Analysis of gene coexpression by B-spline based CoD estimation.EURASIP journal on bioinformatics & systems biology · 2007Article
- Application of SPLINDID, a semiparametric, model-based method for pharmacogenomic modeling of mRNA dynamics.Pharmaceutical research · 2006Article
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Authors and funding
3 authors.
Funding
Abstract
purposeTo evaluate a semi-parametric, model-based approach for obtaining transcription rates from mRNA and protein expression.
methodsThe transcription profile input was modeled using an exponential function of a cubic spline and the dynamics of translation; mRNA and protein degradation were modeled using the Hargrove-Schmidt model. The transcription rate profile and the translation, and mRNA and protein degradation rate constants were estimated by the maximum likelihood method.
resultsSimulated datasets generated from the stochastic, transit compartment and dispersion signaling models were used to test the approach. The approach satisfactorily fit the mRNA and protein data, and accurately recapitulated the parameter and the normalized transcription rate profile values. The approach was successfully used to model published data on tyrosine aminotransferase pharmacodynamics.
conclusionsThe semi-parametric approach is effective and could be useful for delineating the genomic effects of drugs. AVAILABILITY: Code suitable for use with the ADAPT software program is available from the corresponding author. CONTACT: murali@acsu.buffalo.edu.
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