Network-driven integrative analysis of multi-omics data using graphical models

To be described

Bioinformatic workflows for mass spectrometry-based metabolomics and lipidomics data

Untargeted workflows: In collaboration with SCIEX, we are actively developing a new bioinformatics tool, called MetaboKit, supporting robust metabolomics analysis from data dependent acquisition (DDA) and data independent acquisition (DIA) mass spectrometry. MetaboKit builds a spectral library from user’s own precursor and product ion spectra from DDA analysis, annotated with metabolite identities from external spectral libraries, adducts, dimers, in-source fragments (ISF) and retention time information unique to the chromatography system from the experiment. Using the customized library, the software performs targeted ion chromatogram extraction for precursor ions in DDA analysis and precursor and product ion chromatograms in DIA analysis. 

Targeted workflows: We are also working on a new tool MRMkit, a tool that can perform automated peak integration for a large number of samples. MRMkit scans thousands of MRM assay files with hundreds of transitions and provides first-pass extraction results with quality control measures in a matter of several hours. Users are prompted to inspect the ion chromatograms and provide further instructions to deal with transitions with interference or multi-modal shape, which undergo re-integration effort to address imperfect peak integration.  

Systems biology analysis of tissue fibrosis in metabolic diseases - NAFLD

To be described

Multi-tissue atlas of gene expression and metabolome 

To be described