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


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 [ (895Mb)] [Coke vs Pepsi.tsv]
Please bring your computer.
Feb 9, Mon X. Cui Statistical analysis with MetaboAnalyst [] [] [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