A5025230517- Genetics, Bioinformatics, and Biomedical Research
- Metabolomics and Mass Spectrometry Studies
- Bioinformatics and Genomic Networks
- Cell Image Analysis Techniques
- Protein Structure and Dynamics
- Scientific Computing and Data Management
- Medical Imaging Techniques and Applications
- Cardiac Imaging and Diagnostics
- Nuclear Physics and Applications
- Advanced NMR Techniques and Applications
- Machine Learning in Bioinformatics
- Enzyme Structure and Function
- NMR spectroscopy and applications
- Research Data Management Practices
- Microfluidic and Capillary Electrophoresis Applications
- Advanced Database Systems and Queries
- Distributed and Parallel Computing Systems
- Constraint Satisfaction and Optimization
University of Kentucky
2018-2019
University of Louisville
2017
Traditional Protein NMR Referencing workflow leads to “chicken-egg dilemma” vs. proposed automatic Bayesian Model Optimized Reference Correction approach
The Biological Magnetic Resonance Data Bank (BMRB) is a public repository of Nuclear (NMR) spectroscopic data biological macromolecules. It an important resource for many researchers using NMR to study structural, biophysical, and biochemical properties primarily maintained accessed in flat file ASCII format known as NMR-STAR. While the human readable, size most BMRB entries makes computer readability explicit representation practical requirement almost any rigorous systematic analysis. To...
We describe BaMORC, a software package that performs 13C chemical shifts reference correction for either assigned or unassigned peak lists derived from protein NMR spectra. BaMORC provides an intuitive command line interface allows non-NMR experts to detect and correct shift referencing errors of at the very beginning data analysis, further lowering bar expertise required effective analysis. Furthermore, application programming integration into sophisticated analysis pipelines, both before...
The Metabolomics Workbench Data Repository is a public repository of mass spectrometry and nuclear magnetic resonance data metadata derived from wide variety metabolomics studies. for each study deposited, stored, accessed via files in the domain-specific 'mwTab' flat file format. In order to improve accessibility, reusability, interoperability stored formatted files, we implemented Python library package. This package, named 'mwtab', parser format, which provides facilities reading,...
Peak lists derived from nuclear magnetic resonance (NMR) spectra are commonly used as input data for a variety of computer assisted and automated analyses. These include protein assignment structure calculation software tools. Prior to these analyses, peak must be aligned each other sets related peaks grouped based on common chemical shift dimensions. Even when programs can perform grouping, they require the user provide uniform match tolerances or use default values. However, grouping is...
Poor chemical shift referencing, especially for 13C in protein Nuclear Magnetic Resonance (NMR) experiments, fundamentally limits and even prevents effective study of biomacromolecules via NMR, including structure determination analysis dynamics. To solve this problem, we constructed a Bayesian probabilistic framework that circumvents the limitations previous reference correction methods required resonance assignment and/or three-dimensional structure. Our algorithm named Model Optimized...