Advanced special topics course in metabolomics 2021
(GBSC 724)
Course will be held on Mondays, Wednesdays and Fridays 9-10:30 am in the SHELBY 1015
Schedule
| Date | Lecturer | Topic |
|---|---|---|
| Jan 11, Mon | S. Barnes | Transition from metabolism to metabolomics and targeted/untargeted approaches [PDF File] |
| Jan 13, Wed | S. Barnes | The extraordinary chemistry of the metabolome [PDF File] |
| Jan 15, Fri | H Tiwari | Designing a complex metabolomics experiment [PDF File] |
| Jan 18, Mon | No class | Martin Luther King Holiday |
| Jan 20, Wed | J. Prasain | Extracting the metabolome (fluids, cells and tissues) [PDF File] |
| Jan 23, Fri | W. Placzek | The platform - fundamentals in NMR and metabolomics [PDF File] |
| Jan 25, Mon | S. Barnes | The platform – fundamentals in GC- and LC-mass spectrometry [PDF File] |
| Jan 27, Wed | D. Sharer | Targeted metabolomics for congenital disease in children [PDF File] |
| Jan 29, Fri | S. Barnes | MZmine 2.53 hands-on class exercise [Instruction] [PDF File] |
| Feb 1, Mon | S. Barnes | Peak detection and alignment - MZmine [PDF File] |
| Feb 3, Wed | S. Barnes | Uploading GC-MS and LC-MS data to XCMSonline [PDF File] |
| Feb 5, Fri | S. Barnes | Output of XCMS features for univariate analysis [PDF File] |
| Feb 8, Mon | S. Barnes | Statistical analysis of XCMS data with MetaboAnalyst 5.0 [PDF File] |
| Feb 10, Wed | W. Placzek | Processing NMR data [PDF File] |
| Feb 12, Fri | S. Barnes | The TMAO story and follow up – Students’ presentations |
| Feb 15, Mon | S. Barnes | MS-DIAL 4.48 – a comprehensive metabolomics tool – bring PC [PDF File] |
| Feb 17, Wed | S. Barnes | MS-DIAL 4.48 – and statistics [PDF File] |
| Feb 19, Fri | S. Barnes | No Class |
| Feb 22 Mon | S. Barnes | Pathway databases [PDF File] |
| Feb 24, Wed | S. Barnes | The metabolomics workbench [PDF File] |
| Feb 26, Fri | MANA symposium on single cell metabolomics [zip file] | |
| Mar 1, Mon | J. Prasain | MSMS of small molecules - interpretation [PDF File] |
| Mar 3, Wed | J. Prasain | Validating metabolites [PDF File] |
| Mar 5, Fri | S. Barnes | Peaks-to-pathways - Mummichog analysis of data [PDF File] |
| Mar 8, Mon | C. Beecher* | Isotope Ratio Outlier Analysis (IROA) [Video] |
| Mar 10, Wed | C. Beecher* | Building a metabolite standards database [Video] |
| Mar 12, Fri | Student presentations | |
| Mar 15, Mon | J. Prasain | SWATH-MS, Ion Mobility and LC-MS for lipidomics [PDF File] |
| Mar 17, Wed | J. Prasain | Lipid maps database [PDF File] |
| Mar 19, Fri | J Kabarowski | Lipid imaging-mass spectrometry [PDF File] |
| Mar 22, Mon | J. Prasain | Novel prostanoid molecules [PDF File] |
| Mar 24, Wed | S. Barnes | Isotopes and pathway dynamics [PDF File] |
| Mar 26, Fri | Student presentations | |
| Mar 29, Mon | Laura Reed (UA) | Integrating the metabolome with the genome and transcriptome in the context of environmental exposure in the fruit fly [PDF File] |
| Mar 31, Wed | T. Marquez-Lago | Machine learning and artificial intelligence and its application to metabolomics [Reference 1] [Reference 2] |
| Apr 2, Fri | S. Barnes | In situ lipidomics in the surgical suite [PDF File] |
| Apr 5, Mon | No class | |
| Apr 7, Wed | X. Hu** | Integration of -omics data [Presentation Video] [Q&A Video] |
| Apr 9, Fri | S. Barnes | Course review |
| Apr 12, Mon | FINAL exam due |
*At this time, the standalone software we will use, .abc generator, MS-DIAL and MSConvert, work only on a PC. Some software, e.g., Metaboanalyst 5.0, will be used with browsers and are platform-independent
**Xin Hu is from Emory University in Atlanta