Advanced special topics course in metabolomics 2016
(GBSC 724)
Course will be held on Mondays, Wednesdays and Fridays 11:00 am to 12:30 pm in the SHELBY 515
Schedule
| Date | Lecturer | Topic |
|---|---|---|
| Basics Course | ||
| Jan 4, Mon | S. Barnes | Transition from metabolism to metabolomics and targeted/untargeted approaches [PDF File] |
| Jan 6, Wed | X. Cui | Designing a complex –omics experiment [PDF File] |
| Jan 8, Fri | S. Barnes | The chemistry of the metabolome [PDF File] |
| Jan 11, Mon | A. Patterson* | Extracting the metabolome (fluids, cells and tissues) [PDF File] [Reference 1] [Reference 2] [Reference 3] [Reference 4] |
| Jan 13, Wed | S. Barnes | Choosing the platform for metabolomics [PDF File] [Reference 1] |
| Jan 15, Fri | R. Krishna | Fundamentals in NMR and metabolomics [PDF File] |
| Jan 18, Mon | Martin Luther King Holiday | |
| Jan 20, Wed | S. Cooper** | Gas chromatography-mass spectrometry [PDF File] |
| Jan 21, Thu | S. Barnes | Liquid chromatography-mass spectrometry (452 McCallum Bldg at noon) [PDF File] |
| Jan 25, Mon | M. Renfrow | Mass accuracy and absolute mass [PDF File] [Reference 1] [Reference 2] [Reference 3] |
| Jan 27, Wed | S. Barnes | The TMAO story [PDF File] [Reference 1] [Reference 2] |
| Jan 29, Fri | First exam | |
| Feb 1, Mon | S. Barnes | Uploading GC-MS and LC-MS data to XCMSonline [PDF File] |
| Feb 3, Wed | P. Benton*** | Output of XCMS (1) [PDF File] |
| Feb 5, Fri | S. Barnes | Output of XCMS (2) – univariate analysis [PDF File] |
| Feb 8, Mon | X. Cui | Statistical analysis with MetaboAnalyst |
| Feb 10, Wed | S. Barnes | Pathway databases - MetaboSearch [PDF File] [peak_normalized_rt_mz.csv] |
| Feb 12, Fri | RTI Intl team | Processing NMR data [PDF File] [1. UAB_RFA_Metaboanalyst.csv] [2. UAB_RFA_Metaboanalyst_D14_NoPools.csv] [3. UAB_RFA_Metaboanalyst_D14_Vehicle_vs_HighDose.csv] |
| Feb 15, Mon | Student presentations Cancelled | |
| Feb 17, Wed | S. Barnes | Isotopically labeled precursors to identify pathways [PDF File] |
| Feb 19, Fri | S. Barnes | Isotopes and pathway dynamics [PDF File] |
| Feb 22, Mon | J. Prasain | MSMS of small molecules - interpretation [PDF File] |
| Feb 24, Wed | J. Prasain |
Validating metabolites [PDF File] |
| Feb 26, Fri | Student presentations | |
| Feb 29, Mon | S. Barnes | Mummichog analysis of data [PDF File] [peak_normalized_rt_mz_2.csv] |
| Mar 2, Wed | S. Barnes | SWATH-MS, Ion Mobility and LC-MS for lipidomics [PDF File] |
| Mar 4, Fri | J. Prasain | Lipid maps database [PDF File] |
| Mar 7, Mon | J Kabarowski | Lipid imaging-mass spectrometry [PDF File] [PPT File] |
| Mar 9, Wed | A. Wende | Metabolomics in models of cardiovascular disease [PDF File] |
| Mar 11, Fri | J. Prasain | Novel prostanoid molecules [PDF File] |
| Mar14, Mon | Student presentations | |
| Mar16, Wed | R. Krishna | NMR and magic angle spectroscopy [PDF File] |
| Mar 18, Fri | S. Barnes | In situ lipidomics in the surgical suite (finish at 9:55 am) [PDF File] |
| Mar 21, Mon | H. Wu | The microbiome and metabolomics [PDF File] |
| Mar 25, Fri | FINAL exam due |
*Dr. Patterson is from Penn St University and will present his material by Skype
** Dr. Cooper is from HudsonAlpha
*** Dr. Benton is from Scripps Res Inst, La Jolla and will present his material by Skype
An alternate meeting place will be used on January 22 and February 19.