Advanced special topics course in metabolomics 2020
(GBSC 724)
Course will be held on Mondays, Wednesdays and Fridays 9-10:30 am in the SHELBY 1015
Schedule
| Date | Lecturer | Topic |
|---|---|---|
| Jan 13, Mon | S. Barnes | Transition from metabolism to metabolomics and targeted/untargeted approaches [PDF File] |
| Jan 15, Wed | S. Barnes | The extraordinary chemistry of the metabolome [PDF File] |
| Jan 17, Fri | H Tiwari | Designing a complex metabolomics experiment [PDF File] |
| Jan 20, Mon | Martin Luther King Holiday | |
| Jan 22, Wed | W. Placzek | The platform - fundamentals in NMR and metabolomics [PDF File] |
| Jan 24, Fri | J. Prasain | Extracting the metabolome (fluids, cells and tissues) [PDF File] |
| Jan 27, Mon | S. Barnes | The platform - GC- and LC-mass spectrometry [PDF File] |
| Jan 29, Wed | D. Sharer | Targeted metabolomics for congenital disease in children [PDF File] |
| Jan 31, Fri | S. Barnes | MZmine hands-on – bring PC [PDF File] |
| Feb 3, Mon | S. Barnes | Uploading GC-MS and LC-MS data to XCMSonline [PDF File] |
| Feb 5, Wed | S. Barnes | Evaluating XCMS analysis |
| Feb 7, Fri | S. Barnes | Output of XCMS features for univariate analysis [PDF File] |
| Feb 10, Mon | S. Barnes | Statistical analysis of XCMS data with MetaboAnalyst [PDF File] |
| Feb 12, Wed | W. Placzek | Processing NMR data [PDF File] |
| Feb 14, Fri | S. Barnes | Evaluation of MZmine, XCMS and MS-DIAL [PDF File 1] [PDF File 2] [Reference] |
| Feb 17, Mon | S. Barnes | The TMAO story and follow up [PDF File] |
| Feb 19, Wed | S. Barnes | Pathway databases [PDF File] |
| Feb 21, Fri | S. Barnes | The metabolomics workbench |
| Feb 24, Mon | No class | |
| Feb 26, Wed | S. Barnes | TBA |
| Feb 28, Fri | Student presentations | |
| Mar 2, Mon | J. Prasain | MSMS of small molecules - interpretation [PDF File] |
| Mar 4, Wed | J. Prasain | Validating metabolites [PDF File] |
| Mar 6, Fri | S. Barnes | Mummichog analysis of data |
| Mar 9, Mon | C. Beecher* | Isotope Ratio Outlier Analysis (IROA) |
| Mar 11, Wed | S. Barnes | Isotopes and pathway dynamics [PDF File] |
| Mar 13, Fri | Student presentations | |
| Mar 16, Mon | J. Prasain | SWATH-MS, Ion Mobility and LC-MS for lipidomics [PDF File] |
| Mar18, Wed | J. Prasain | Lipid maps database [PDF File] |
| Mar 20, Fri | J Kabarowski | Lipid imaging-mass spectrometry [PDF File] |
| Mar 23, Mon | J. Prasain | Novel prostanoid molecules [PDF File] |
| Mar 25, Wed | Student presentations | |
| Mar 27, Fri | N. Garg**** | Integrating the microbiome and metabolomics |
| Mar 30, Mon | S. Barnes | In situ lipidomics in the surgical suite [PDF File] |
| Apr 1, Wed | K. Uppal** | Integrating the metabolome with the genome, transcriptome and proteome [PDF File] |
| Apr 3, Fri | Jial Li | The drug exposome in a clinical trial
[PDF File]
[Reference 1] [Reference 2] [Presentation 1] [Presentation 2] |
| Apr 6, Mon | Student presentations | |
| Apr 8, Wed | Student presentations | |
| Apr 13, Mon | Dr. Tatiana Marquez-Lago | Machine learning in metabolomics (extra class ) FINAL exam due |
At this time, the standalone software we will use, ABC, MS-DIAL. MSConvert and MZmine, work only on a PC. MZmine used to be usable on a Mac, but new Mac OS (10.15.1 Catalina) has made it impossible due to security issues.
*IROA Technologies
** Emory University
**** Georgia Institute of Technology