Advanced Graduate Course in Metabolomics 2015
(GBS 748)
Course will be held on Mondays, Wednesdays and Fridays 9 – 10:30 am in the Cudworth Hall, room 307
Schedule
| Date | Lecturer | Topic |
|---|---|---|
| Basics Course | ||
| Jan 5, Mon | S. Barnes | Transition from metabolism to metabolomics and targeted/untargeted approaches [PDF File] |
| Jan 7, Wed | X. Cui | Designing a complex - omics experiment [PDF File] |
| Jan 9, Fri | S. Barnes | The chemistry of the metabolome [PDF File] |
| Jan 12, Mon | A. Patterson* | Extracting the metabolome (fluids, cells and tissues) [PDF File] |
| Jan 14, Wed | S. Barnes | Choosing the platform for metabolomics [PDF File] |
| Jan 16, Fri | R. Krishna | Fundamentals in NMR and metabolomics [PDF File] |
| Jan 19, Mon | Martin Luther King Holiday | |
| Jan 21, Wed | S. Barnes | Liquid chromatography-mass spectrometry [PDF File] |
| Jan 23, Fri | S. Cooper** | Gas chromatography-mass spectrometry [PDF File] |
| Jan 26, Mon | M. Renfrow | Mass accuracy and absolute mass [PDF File] [Reference 1: doi:10.1021/ac500951v] [Reference 2: doi:10.1021/ac5014767] [Reference 3: doi:10.1002/mas.21401] |
| Jan 28, Wed | S. Barnes | The TMAO story [PDF File 1] [PDF File 2] [Video] [Reference 1: doi:10.1016/j.celrep.2014.12.036] [Reference 2: doi:10.1056/NEJMoa1109400] [Reference 3: doi:10.1038/nm.3145] [Reference 4: doi:10.1038/nature09922] |
| Jan 30, Fri | First exam | |
| Feb 2, Mon | S. Barnes | Uploading GC-MS and LC-MS data to XCMSonline [PDF File] [Instruction] |
| Feb 4, Wed | P. Benton*** | Output of XCMS (1) [PDF File] |
| Feb 6, Fri | S. Barnes | Output of XCMS (2) – univariate analysis [coke_pepsi_x_10_mzXML.zip (895Mb)] [Coke vs Pepsi.tsv] Please bring your computer. |
| Feb 9, Mon | X. Cui | Statistical analysis with MetaboAnalyst [Diet_IR.zip] [Diet_NR.zip] [Analysis_Report.pdf] |
| Feb 11, Wed | S. Barnes | Pathway databases - MetaboSearch The students should download the software at the Ressom Lab web site. Note: It will run as a Java program. It’s possible that your computer software will ask questions about the safety of running this program. |
| Feb 13, Fri | W Pathmasiri | 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 16, Mon | Student presentations Cancelled | |
| Feb 18, Wed | J. Prasain | MSMS of small molecules - interpretation [PDF File] |
| Feb 20, Fri | J. Prasain | Validating metabolites [PDF File] |
| Feb 23, Mon | Student presentations [PDF File 1] [PDF File 2] | |
| Feb 25, Wed | S. Barnes |
canceled due to wintry weather |
| Feb 27, Fri | Student presentations [PDF File 1] [PDF File 2] | |
| Mar 2, Mon | S. Barnes | Isotopes and pathway dynamics [PDF File] |
| Mar 4, Wed | S. Barnes | Analysis of lipids [PDF File] |
| Mar 6, Fri | J. Prasain | Lipid maps database [PDF File] |
| Mar 9, Mon | J Kabarowski | Lipid imaging-mass spectrometry [PDF File] [PPT File] |
| Mar 11, Wed | A. Wende | Metabolomics in models of cardiovascular disease [PDF File] |
| Mar 13, Fri | J. Prasain | Novel prostanoid molecules [PDF File] |
| Mar16, Mon | Student presentations | |
| Mar18, Wed | R. Krishna | NMR and magic angle spectroscopy [PDF File] [Reference: doi:10.1002/cmr.a.20068] |
| Mar 20, Fri | S. Barnes | In situ lipidomics in the surgical suite [PDF File] |
| Mar23, Mon | H. Wu | The microbiome and metabolomics [PDF File] |
| Mar27, Fri | FINAL exam due |
*Dr. Patterson is from Penn St University and will present his material by Skype at 9:30 am
** Dr. Cooper is from HudsonAlpha
*** Dr. Benton is from Scripps Res Inst, La Jolla and will present his material by Skype