6th Annual Workshop on Metabolomics

Sunday, July 22nd - Friday July 27th, 2018

Welcome to the 6th Annual Workshop on Metabolomics. The course is jointly sponsored by the National Institute of General Medical Sciences (NIGMS) as part of the NIH Common Fund Metabolomics Initiative, and the Departments of Chemistry and Pharmacology and Toxicology at UAB.

 

Overview

The themes in this sixth year of the workshop are:

  1. Design of a metabolomics experiment
  2. Sample stability and extraction methods
  3. Analytical systems (nuclear magnetic resonance and gas- and liquid chromatography-mass spectrometry)
    1. Targeted metabolomics
    2. Untargeted metabolomics
    3. Quantitative metabolomics
  4. Pre-processing of analytical data (Mzmine 2 and XCMSonline and Chenomx)
  5. Statistical analysis of the data (MetaboAnalyst, Simca, SAS)
  6. Metabolite databases (METLIN, HMDB, LIPIDMAPS, PubChem, ChemSpider)
  7. Identification of metabolites (MetaboSearch, MSMS analysis)
  8. Metabolite pathway analysis (Mummichog, KEGG, GeneGo, Ingenuity)
  9. Advanced elective sessions (Imaging mass spectrometry, isotope ratio outlier analysis, Ion mobility, Command line and R programs)
  10. Electives will allow attendees to fine tune their training experience

Tentative Agenda

Sunday, July 22

Time Topics & Speakers Resources
5:00-8:00 pm Social at the Double Tree Hotel  

Monday, July 23

Time Topics & Speakers Resources
7:30 am Breakfast - VH 302  
8:00-8:15 am Introductions - VH 302
Stephen Barnes, PhD/Hemant Tiwari, PhD, UAB

Barnes-video

Tiwari-
video
8:15-8:25 am Welcome to UAB - VH 302
Christopher Brown, PhD, Vice-President for Research, UAB
 
8:25-9:05 am Why study Metabolomics - VH 302
Stephen Barnes, PhD, UAB

Video
9:05-9:10 am Questions Video
9:10-9:45 am Metabolism in the raw - the SeaHorse™, the modern version of the Warburg apparatus - VH 302
Jianhua Zhang PhD, UAB

Video
9:45-10:00 am Questions Video
10:00-10:20 am Break – VH 302  
10:20-11:05 am Metabolite Extraction and Platforms - VH 302
Stephen Barnes/Jeevan Prasain

Barnes-video
Prasain-video
11:05-11:15 am Questions Video
11:15-11:50 am Choosing the Metabolomics Platform - VH 302
Stephen Barnes, PhD, UAB

Video
11:50-12 noon Questions  
12 noon Lunch – VH 302  
12:15-12:55 Lunch speaker - VH 302
Paul Baker, PhD, Avanti
 
INSTRUMENT SESSIONS:
Group 1 1:15-2:15 pm – NMR Basics/Metabolomics 101 - Chemistry Bldg Part1-Video
Part2-Video
2:30-3:30 pm – Targeted and Untargeted Metabolomics - McCallum 427
Taylor-video

Landon-video
3:45-4:45 pm – Metabolism using the SeaHorse™ - BMR II, room 520 Video
Q&A-Video
Lab-Video
Group 2 1:15-2:15 pm – Targeted and Untargeted Metabolomics - McCallum 427
Taylor-video

Landon-video
2:30-3:30 pm – Metabolism using the SeaHorse™ - BMR II, room 520 Video
Q&A-Video
Lab-Video
3:45-4:45 pm – NMR Basics/Metabolomics 101 - Chemistry Bldg Part1-Video
Part2-Video
Group 3 1:15-2:15 pm – Metabolism using the SeaHorse™ - BMR II, room 520 Video
Q&A-Video
Lab-Video
2:30-3:30 pm – NMR Basics/Metabolomics 101 - Chemistry Bldg Part1-Video
Part2-Video
3:45-4:45 pm – Targeted and Untargeted Metabolomics - McCallum 427
Taylor-video

Landon-video

Evening
On your own –Dreamland Bar-B-Que on 14th Ave S. (for the meat eaters) shouldn’t be missed. Up the hill from the DoubleTree Hotel in the Five Points area: Surin West, Jim & Nick’s BBQ, Pho Pho Vietnamese & Sushi Bar, Black Market Bar & Grill, T’Bones Philly Shop, Original Pancake House, Makarios Kabobs, Little Italy’s Pizza & Pints

The Birmingham Barons play the Tennessee Smokies at Region Field

Tuesday, July 24

Time Topics & Speakers Resources
7:30 am Breakfast - VH 302  
8:00-8:15 am Questions  
8:15-8:30 am Attendee Presentation: Casey M. Rebholz, PhD, MS, MNSP, MPH, , John Hopkins University - VH 302

8:30-8:35 am Questions  
8:35-9:10 am Introduction to Preprocessing of Untargeted Metabolomics Data - VH 302
Xiuxia Du, PhD, UNC-Charlotte

Video
9:10-9:15 am Questions Video
9:15-9:45 am Introduction to NMR Data Pre-Processing - VH 302
Nagana Gowda, PhD, UW-Seattle

Video
9:45-9:50 am Questions Video
9:50-10:10 am Break - VH 302  
10:30-11:30 am Plenary Lecture - Finley Conference Center in Kaul Building
Microbial Programming of the Tumor Microenvironment
George Miller, PhD, NYU School of Medicine
Abstract, Flyer

Intro-video

Lecture-video
11:30-11:45 am Questions Video
12 noon-1:00 pm Lunch - Finley Conference Center - George Miller Q&A Video
1:15-1:30 pm Proceed to Learning Resource Center (LRC) for Workshop Group Photo
1:30-2:45 pm
Group 1 - Inspecting NMR data - hands-on *Download ACD/NMR, TopSpin and Chenomix(trial) software prior to class - LRC 210A
Nagana Gowda, PhD, U Wash
Video
Group 2 - Hands-on data analysis with MZmine – LRC 235
Xiuxia Du, PhD, UNC-Charlotte/Stephen Barnes, PhD, UAB

Video
2:45-3:00 pm Break - LRC 235  
3:00-4:15 pm Group 1 - Hands-on data analysis with MZmine – LRC 235
Xiuxia Du, PhD, UNC-Charlotte/Stephen Barnes, PhD, UAB

Video
Group 2 - Inspecting NMR data - hands-on *Download ACD/NMR, TopSpin and Chenomix(trial) software prior to class - LRC 210A
Nagana Gowda, PhD, U Wash
Video
4:20-4:50 pm Preparing Metabolomics Data, LRC 235
Stephen Barnes, PhD, UAB

Video
4:50-5:00 pm
Questions
 
5:00-6:15 pm Break
6:30-8:30 pm Workshop Dinner – Edge of Chaos, Lister Hill Library – 4th Floor
Plotting Career Paths in Science
Speaker: Victor Darley-Usmar, PhD, UAB
Video
Q&A-Video

Wednesday, July 25

Time Topics & Speakers Resources
7:30 am Breakfast - LRC 235  
8:00-8:15 am Questions Video
8:15-8:30 am Attendee Presentation: Jai Woo Lee, Dartmouth College - LRC 235

Video
8:30-8:35 am Questions Video
8:35-9:10 am Introduction to XCMS in R - LRC 235
Xiuxia Du, PhD, UNC-Charlotte

9:10-9:15 am Questions
9:15-9:50 am Capabilities of XCMS Online - LRC 235
H. Paul Benton, PhD, Scripps

Video
9:55-10:00 am Questions
10:00-10:20 am Break - LRC 235  
10:20-10:55 am Experimental Design in Metabolomics - LRC 235
Hemant Tiwari, PhD, UAB

Video
10:55-11:00 am Questions Video
11:00-11:40 am Isotope Ratio Outlier Analysis and QA/QC - LRC 235
Chris Beecher, PhD, IROA Technologies

11:40-11:45 am Questions  
11:45-12:45 pm Lunch - LRC 235  
12:00-12:45 pm Introduction to Fluxomics (recorded talk)
Teresa Fan, PhD, U. Kentucky

HANDS-ON SESSIONS:
1:00-2:15 pm
Group 1 - Hands-on NMR data processing - Metaboanalyst - LRC 215
Nagana Gowda, PhD, U Wash
Video
Group 2 - Hands-on LC-MS data processing - Metaboanalyst - LRC 219
Stephen Barnes, PhD, UAB

2:30-3:45 pm
Group 1 - Hands-on LC-MS data processing - Metaboanalyst - LRC 219
Stephen Barnes, PhD, UAB

Group 2 - Hands-on NMR data processing - Metaboanalyst - LRC 215
Nagana Gowda, PhD, U Wash
Video
3:50-4:00 pm Break/Questions LRC 215/219  
4:00-4:25 pm Mapping to Pathways in Metaboanalyst - LRC 215/219
Stephen Barnes, PhD, UAB

4:25-4:30 pm Questions  
4:30-4:55 pm Capabilities of the Metabolomics Workbench (Zoom) - LRC 215/219
Eoin Fahy, PhD, DRCC, UCSD

Evening On your own – visit restaurants or Birmingham Barons at Regions Field (7:05 pm) versus the Tennessee Smokies

Thursday, July 26

Time Topics & Speakers Resources
7:30 am Breakfast - LRC 235  
8:00-8:15 am Questions  
8:15-8:30 am The UAB Precision Medicine Institute - LRC 235
Matthew Might, PhD

8:30-8:35 am Questions
8:35-9:10 am Pathway and Network Analysis for Metabolomics – Mummichog - LRC 235
Shuzhao Li, PhD, Emory U

9:10-9:15 am Questions
9:15-9:55 am Metabolite databases - LRC 235
Xiuxia Du, PhD, UNC-Charlotte

9:55-10:00 am Questions
10:00-10:20 am Break - LRC 235
10:20-11:05 am Searching METLIN – hands-on - LRC 235
Jeevan Prasain, PhD, UAB

11:05-11:10 am Questions
11:10-11:50 am Identifying adducts in metabolite ion data (Zoom) - LRC 235
Corey Broeckling, PhD, Colorado St

11:50-12:00 noon Questions
12 noon Lunch - LRC 235  
12:15-12:55 pm Research Integrity - LRC 235
Pam Bounelis, PhD, Asst. Vice President for Research, UAB
OPTION 1
1:15-3:00 pm 2D-NMR methods and metabolomics – LRC 215
Nagana Gowda, PhD, U Wash

3:15-5:00 pm Uploading and Processing data on the Metabolomics Workbench (Zoom) – LRC 215
Eoin Fahy, PhD, DRCC, UCSD

OPTION 2
1:15 - 3:00 pm Using XCMSonline – Hands-On – LRC 219
H. Paul Benton, PhD, Scripps

3:15-5:00 pm Using XCMS in R - LRC 219
Xiuxia Du, PhD, UNC-Charlotte

OPTION 3
1:15-3:00 pm ClusterFinder Software – Hands-On – LRC 255
Chris Beecher, PhD, IROA Technologies

3:15-5:00 pm Interpreting MSMS spectra – LRC 255
Jeevan Prasain, PhD, UAB

OPTION 4
1:15-3:00 pm RAMClustR - Hands-On (Zoom) – LRC 235
Corey Broeckling, PhD, Colorado State U

3:15-5:00 pm Mummichog - Hands-On – LRC 235
Shuzhao Li, PhD, Emory

Evening on your own – list of restaurants available

Friday, July 27

Time Topics & Speakers Resources
7:30-8:00 am Breakfast - VH 302  
8:00-8:15 am Questions  
8:15-8:55 am Transitioning from transcriptomics to metabolomics - VH 302
Jason Tennessen, PhD, Indiana

8:55-9:00 am Questions
9:00-9:40 am Hyperpolarized NMR – VH 302
Mukundan Ragavan, University of Florida

9:40-9:45 am Questions
9:45-10:00 am Break - VH 302
10:00-10:40 am Movie and Presentation: Ion mobility mass spectrometry - VH 302
Erin Baker, PhD, PNNL

10:40-10:45 am Questions
10:45-11:55 am Imaging metabolomics - VH 302
Janusz Kabarowski, PhD, UAB

11:55-12 noon Questions  
12 noon Lunch - VH 302
12:30-1:00 pm General Q&A
1:00-1:30 pm Evaluations
1:30-3:00 pm Consultations with UAB metabolomics faculty

Workshop Faculty

Stephen Barnes, PhD

Dr. Barnes, Director of the Metabolomics Workshop, is Professor of Pharmacology and Toxicology and has secondary appointments in five other departments.  He started his research career in the laboratory of A. T. (Tony) James, co-inventor of gas-liquid chromatography, studying fatty metabolism in green algae and did his PhD on the carbohydrate metabolism of the acellular slime mold Physarum polycephalum at Imperial College, University of London under the tutelage of Sir Ernst Boris Chain, 1945 Nobel Laureate for the discovery of penicillin. He began his long-standing interest in bile acid metabolism at the Royal Free Hospital with Dame Sheila Sherlock and Barbara Billing. After the winter of 1975 in Alan Hofmann’s lab at the Mayo Clinic in Rochester, he took up an offer to come to the University of Alabama at Birmingham (UAB) in 1977 where he has remained ever since. In the early 1980s he applied high field NMR using superconducting magnets to unravel the proton NMR spectrum of bile acids as well as to use pulse sequences to greatly simplify the process. In 1992 he took over the development of LC-mass spectrometry in biomedical research at UAB and was the Director of the UAB Comprehensive Cancer Center Mass Spectrometry Shared Facility from 1992 to 2009. In 2009 he was appointed as the Director of the Targeted Metabolomics and Proteomics Laboratory (TMPL).  He also was the Associate Director of the Purdue-UAB Botanicals Center for Age-related Disease from 2000-2011 and the Director of the UAB Center for Nutrient-Gene Interaction from 2002-2010. These latter roles provided critical experience in experimental design, statistical analysis of –Omics data and the important role of the diet in determining the outcome of experimental models of chronic diseases.

More details about TMPL can be obtained at http://tmpl.uab.edu


Erin Baker, PhD

Dr. Erin Baker is a bioanalytical chemist with more than 16 years' experience utilizing ion mobility spectrometry in conjunction with mass spectrometry (IMS-MS) to study environmental and biological systems. In the last 10 years, she has worked primarily on IMS-MS applications in the field of proteomics and more recently she has worked to optimize IMS-MS metabolomic, glycomic and lipidomic separations. Her research involves the development and evaluation of high-throughput IMS-MS, SPE-IMS-MS and LC-IMS-MS analyses to quickly study numerous samples in a short time period without losing valuable biological information, as well as assessing the number and quality of features detected with IMS-MS for comparison with existing MS platforms. Dr. Baker is also presently working with the PNNL Informatics team to design and implement software tools that automatically analyze the complex multidimensional SPE-IMS-MS and LC-IMS-MS data.

PNNL Website


Paul Baker, PhD

Paul Baker received his PhD in Biochemistry from Wake Forest University School of Medicine, where he began his training in lipids with the study of the metabolism and signaling actions of ether-linked lipid mediators under the guidance of Robert Wykle. He did his post-doctoral work with Bruce Freeman at the University of Alabama at Birmingham where he helped lead the discovery of a novel class of anti-inflammatory lipid mediators—nitrated lipids. He continued his work on nitrated lipids as an assistant professor at the University of Pittsburgh School of Medicine until June of 2011 when he joined SCIEX. While at SCIEX, Paul was a senior applications manager and the global lead applications scientist for Lipidomics. Paul pioneered the use of differential Ion mobility spectrometry in the study of lipids, and worked to develop novel workflows to improve lipid analysis by mass spectrometry.

At Avanti, Paul will be responsible for leading and energizing our customer analytical services group and our GMP endeavors. We plan to dramatically increase the depth and quality of our lipid analysis services and develop a center of excellence in lipid analysis that focuses on quantitative rigor, molecular specificity, and quick sample turn around. In addition to lipid analysis, the center will promote education in this rapidly growing area of research. Our goal is to provide the highest quality data and services to our customers that matches the standard of excellence we and our customers expect from our synthetic lipid standards.

Website


Chris Beecher

IROA Technologies

Professor Chris Beecher is the Associate Director of the South-East Center for Integrated Metabolomics (SECIM) at the University of Florida, one of six NIH-funded Metabolomics Centers in the United States, and the Chief Science Officer for IROA Technologies (IROA).  The IROA protocols are a core technology within SECIM.  Professor Beecher had previously established the unbiased Metabolomics platforms at the University of Michigan (2007) in Ann Arbor, Michigan, and, prior to that, had developed the metabolomics platforms for Metabolon, a metabolomics-based company (2004), and Paradigm Genetics (1999) both in RTP, North Carolina.

Since 1999 Professor Beecher’s research focus has been on the continued development of the science of Metabolomics.  As the newest of the “Omics” sciences, establishing methods for higher sensitivity, resolution and reproducibility, and algorithms for data handling, and data generation are areas of ongoing exploration.  The Lab actively collaborates with diverse researchers to find experimental systems that benefit from a metabolomic analytical approach, and provide new avenues for metabolomic exploration.

The Beecher metabolomic platform is 1) a MS-based analytical component that is 2) well integrated into a 3) fully automated sample prep operation.  Integration requires that sample flow is directed by a LIMS system, and an automated informatics system for processing information generated within the platform.  Due to the high level of integration and automation one can put in place a relentless program for error reduction and improvement.

Dr. Beecher holds a B.A. in Anthropology (New York University), M.S. Biology (New York University), and a Ph.D. in Pharmaceutical Sciences / Natural products Chemistry (University of Connecticut).  He began his research into the high-throughput chemical characterization of complex mixtures while on the faculty of the University of Illinois, College of Pharmacy (1985) where he held the position of Associate Professor.  He was the editor of the NAPRALERT database from 1990 to 1998, Editor-in-Chief of the International Journal of Pharmacognosy, and served as a founding member of the Functional Foods Program of the University of Illinois.

In 1997 he was invited to continue this research in the laboratories of Bristol-Myers Squibb, and Ancile Pharmaceuticals.  His focus shifted from secondary metabolism to primary metabolism with the establishment of the first Metabolomics platform in America at Paradigm Genetics from 1999 to 2002, and in 2003 founded of two Metabolomics-based companies; Metabolon, Inc. (focused on human healthcare.) and Metabolic Analyses, Inc. (focused on the informatics issues associated with Metabolomics.)  Dr. Beecher compiled the first human metabolome in 2002 at Metabolic Analyses, and has been working toward the integration of metabolomic, proteomic, transcriptomic and genomic data.

Website


Paul Benton, PhD

Dr. Benton started working with metabolomics datasets in 2006 when he joined Prof. Gary Siuzdak’s lab as a Research Tech. Working with XCMS and METLIN, he developed and published a tandem mass spectra extension to XCMS called XCMS2. He gained a valuable understanding of mass spectrometry methods and the need for computational developments in the field. Working with Dr. Timothy MD Ebbels & Prof. Jeremy Nicholson while studying for his Ph.D at Imperial College London, he developed methods to increase the reproducibility of metabolic profiling experiments and two novel methods for temporal metabolite profiling. Since receiving his Ph. D in August 2013 he has returned to Prof. Siuzdak’s lab at The Scripps Research Institute to develop Online XCMS and the labs many other metabolomics toolset.


Pam Bounelis, PhD

Pam Bounelis, PhD, serves as the Research Integrity Officer (RIO) and Assistant Vice President for Research at the University of Alabama at Birmingham (UAB). She is also the Assistant Dean for Biomedical Research in the UAB School of Medicine and associate professor in the Department of Cell, Developmental, and Integrative Biology. She received her PhD in anatomy from the University of Illinois in Chicago (1985) and was recruited to UAB shortly thereafter. In her role as RIO, Dr. Bounelis has responsibility for the research misconduct process. She has more than 15 years of experience in space programming and planning. She has been the lead or substantially‐contributing author on many extramural proposals that have resulted in nearly $90 million of extramural support to UAB for capital projects and equipment acquisition. She has served on four NIH special emphasis panel/scientific review groups. She is an active member of the American Association of Medical Colleges Group on Institutional Planning and is currently service as the National Chair.


Corey Broeckling, PhD

Dr. Corey Broeckling is a trained biologist, with a B.S in Environmental Science from Quincy University, an M.S. in Entomology from Virginia Tech, and a PhD in Cell and Molecular Biology from Colorado State University. This disparate educational background is bound by a common theme – the use of analytical chemistry in support of his research. He applies his biological knowledge and extensive analytical experience in his current role as the Director of the Proteomics and Metabolomics Facility at Colorado State University, and has developed a publication record describing his continuing interest in furthering the fields of analytical mass spectrometry and non-targeted metabolomics.


Christopher S. Brown, PhD

Chris Brown is the Vice President for Research at UAB and a tenured professor in the Department of Biology. He received his B.S. degree from the University of North Carolina at Chapel Hill and his M.S. and Ph.D. from North Carolina State University (NCSU). After a postdoctoral fellowship in biochemistry at the University of Missouri-Columbia and seven years running the space biology laboratories at NASA's Kennedy Space Center in Florida, he returned to NCSU where he took a faculty position in the Department of Plant and Microbial Biology. Prior to arriving at UAB, he served as Associate Vice Chancellor for Research Development at NCSU and later as the Vice President for Research at the 16-campus University of North Carolina System.

For many years, his research focused on the effects of spaceflight – that is, altered gravity and lighting conditions relative to earth – on plant growth and development. He led and or participated in numerous projects on the Space Shuttle and the International Space Station. He served as the President of the American Society for Gravitational and Space Biology and as a board member for Research Triangle International, the North Carolina Biotechnology Center, and the UNC Coastal Studies Institute. He currently serves on the boards of the Innovation Depot, the MS/AL Sea Grant Consortium, the Alabama EPSCoR steering committee, the Economic Development Foundation of Alabama, and as a member of the executive committee of the Association of Public and Land Grant Universities' Council on Research.

In his current position, Dr. Brown and his team work with stakeholders to broaden and enhance UAB's >$500M research portfolio, strengthen research support operations, and raise the stature, visibility, and support of the UAB research enterprise nationally and internationally.

Website


Victor Darley-Usmar, PhD

Dr. Darley-Usmar is the UAB Endowed Professor in Mitochondrial Medicine and Pathology. He serves as Associate Dean for Research for the School of Medicine at UAB. His research program focuses on redox cell signaling and molecular bioenergetics in the pathogenesis of human disease. He received his Ph.D. training from Dr. M.T. Wilson at the University of Essex which was to define the structure and function of cytochrome c oxidase. This involved defining whether the monomer or dimer of the enzyme was active and applying the then new techniques of SDS-polyacrylamide gel electrophoresis to membrane proteins. He continued to pursue his interest in mitochondrial proteins with Dr. R. A. Capaldi at the University of Oregon and was one of the first to use Western Blotting to understand the molecular pathology of a mitochondrial myopathy. On returning to the UK after two years as an Assistant Professor in Japan he first became interested in the area of nitric oxide research in industry as a Research Scientist at Wellcome Research Laboratories. Over a ten year period there he worked on the interactions of nitric oxide with reactive oxygen species and mitochondria. Working with Salvador Moncada and Tony Schapira (Royal Free Hospital) he was one of the first to discover that nitric oxide can interact reversibly with cytochrome c oxidase and so control respiration. He left the UK in 1995 to join the Free Radical group and Department of Pathology at UAB led by Bruce Freeman. Currently he is developing novel methods to assess the measurement of bioenergetic health in human populations.

Website


Xiuxia Du, PhD

Dr. Du is an Associate Professor of Bioinformatics at the Department of Bioinformatics and Genomics, University of North Carolina at Charlotte. She received her Ph.D. in Systems Science and Mathematics from Washington University in St. Louis. Subsequently, she did a postdoc at the Pacific Northwest National Laboratory. She joined the University of North Carolina at Charlotte in 2008 as an assistant professor. The research of her group has been focusing on the development of computational algorithms for mass spectrometry-based proteomics and metabolomics research.

Website: http://www.du-lab.org


Eoin Fahy, DRCC, UCSD


Whei-Mei Teresa Fan, PhD

Dr. Teresa Fan, Professor of Toxicology and faculty member of the Markey Cancer Center and Center for Environmental Systems Biochemistry at the University of Kentucky, is one of the leaders of the Resource Center for Stable Isotope-Resolved Metabolomics. Dr. Fan uses metabolomics to study cell metabolism in lung cancer. Using special molecular tools called stable isotope tracers, she can label certain types of metabolites and watch as they move through the complicated and interconnected network of biological reactions that contribute to cell metabolism. This kind of technique is like “tracing breadcrumbs in the forest,” says Dr. Fan. She traces her metabolite “breadcrumbs” through a “forest” of cancer cells grown in the laboratory, tumors in animals, and in human patients with lung cancer. Dr. Fan and her research team systematically probe the metabolic network of cancer in these systems to identify new cell processes that could be targeted with drugs and discover diagnostic markers for early-stage lung cancer. With a research grant from the NIH Common Fund Metabolomics program, Dr. Fan and her colleagues are developing ways to treat samples before analyzing them to increase sensitivity and stability. They are making chemical agents that can modify particular parts of certain metabolites, making them easier to detect. This approach could also enhance a researcher’s ability to identify previously unknown metabolites.


Nagana Gowda , PhD

Dr. Nagana Gowda is the Associate Director for the Northwest Metabolomics Research Center and Research Assistant Professor, Mitochondria and Metabolism Center, Anesthesiology and Pain Medicine, University of Washington, Seattle. He has more than 30 years of experience working with NMR spectroscopy techniques. Since more than 15 years, he is working in the area of NMR based metabolomics. His research interests in the metabolomics field are focused on methods development as well as applications focusing investigation of human diseases. As a part of methods development, he has utilized a variety of 1D and 2D NMR techniques to identify unknown metabolites and quantify them accurately. To date, he has developed a large number of NMR methods for quantitation of expanded pool of metabolites in biological specimens such as blood, urine, bile, tissue and cell lines. Most recently, he has shown identification and quantitation of nearly 80 blood metabolites including the redox coenzymes (NAD+, NADH, NADP+, NADPH), energy coenzymes (ATP, ADP, AMP) and antioxidants (reduced and oxidized glutathione: GSH, GSSG), most of which are unstable and previously inaccessible to NMR, using a simple 1D NMR experiment.


Janusz Kabarowski, PhD

Janusz Kabarowski, PhD, Associate Professor of Microbiology. Dr. Kabarowski obtained his PhD in the field of hematopoiesis and leukemia at University College, London and did his postdoctoral training in immunology with Dr. Owen Witte at UCLA. His expertise is in the study of lipids in inflammation and immunity. He has applied this expertise to studies of lipid mediated mechanisms controlling inflammation and autoimmunity using mouse models of atherosclerosis, Lupus and tissue/organ injury. He is currently investigating approaches by which potential anti-inflammatory and immunosuppressive properties of HDL (linked to its ability to regulate cholesterol homeostasis and remove pro-inflammatory and oxidized lipids) may be harnessed to treat autoimmune diseases like Lupus. During the course of these studies, he has developed expertise in the study of lipid and lipoprotein based mechanisms regulating inflammation and immunity, as well as the necessary preparative methods for mass spectrometry lipidomic analyses during a long-standing collaborative relationship with Dr. Steve Barnes. More recently, Dr. Kabarowski has established a method for lipid imaging in cryosections by MALDI-Imaging Mass Spectrometry using vacuum sublimation for matrix application. This technology is being applied to a number of areas, including identifying lipids with roles in modulating inflammatory processes in response to acute kidney injury, autoimmunity and kidney disease in Lupus, as well as those involved in the deterioration of ocular function with ageing.

Website


Shuzhao Li, PhD

Assistant Professor, Associate Director of Clinical Biomarkers Laboratory, Department of Medicine, Emory University

Dr. Li was trained in bioinformatics, and he has been combining computational developments with metabolomics and systems biology. His work in human immunology applied large-scale data integration and network modeling to delineate transcriptomic programs for antibody response induced by several vaccines. These are early steps towards quantitative and systems modeling of human immunity, which is an integral part of most human diseases. His mummichog software brought genome-scale metabolic models into the field of high throughput metabolomics, and enabled pathway/network analysis for untargeted metabolomics. He strives to bring these scientific developments to personalized and precision medicine.

http://clinicalmetabolomics.org/


Matthew E. Merritt, PhD

Matthew Merritt received his PhD in physical chemistry in the lab of Dr. Jacob Schaefer at Washington University in St. Louis, MO (1996). His dissertation focused on determining 3D structures in condensed solids, including polymers and biopolymers, using solid state NMR distance measurements. He then joined the lab of Dr. Gary Drobny at the University of Washington in Seattle. For his post-doctoral research at UW, he determined structural constraints in DNA using 31P-19F REDOR solid state NMR. In the year 2000, he joined the staff of the Radiological Sciences Department at the University of Texas Southwestern Medical Center in Dallas, Texas. In 2004 he was promoted to research faculty, and in 2008 to tenure track faculty as an assistant professor. In 2015 he was promoted to Associate Professor of Radiology at UTSW. In September of 2015 he joined the UF faculty as an associate professor of Biochemistry and Molecular Biology.

Website


George Miller, MD

H.L. Pachter Professor
Departments of Surgery and Cell Biology
Leader, Cancer Immunology Program
New York University School of Medicine

Lab Website


Matthew Might, PhD


The UAB Precision Medicine Institute


Jeevan Prasain, PhD

Dr. Prasain is an Associate Professor of Pharmacology and Toxicology at UAB. He received his undergraduate and master’s training (Chemistry) at Tribhuvan University, Nepal and his Ph.D. at Toyama Medical & Pharmaceutical University, Japan. His expertise is in the use of NMR and LC-MS/MS for the identification of metabolites. Dr. Prasain's current research interests include delineation of the Cox-independent Prostaglandin synthesis, mass spectrometry based metabolomics/lipidomics, oxidized lipids, metabolisms and bioavailability of dietary botanicals and medicinal herbs in vitro and in vivo.

Website


Jason Tennessen – Indiana

Website


Hemant Tiwari, PhD

Dr. Tiwari is the Co-Director of the Metabolomics Workshop. He received his Ph.D. in mathematics from the University of Notre Dame, South Bend, Indiana. While being a faculty at the University of Maine, he got interested in statistical genetics, and completed a post-doctoral fellowship in Statistical Genetics under Prof. Robert Elston in the Department of Biometry and Genetics at Louisiana State University Medical Center, New Orleans and at the Case Western Reserve University in Cleveland. Subsequently, he worked as a faculty member in the Department of Epidemiology and Biostatistics at Case Western Reserve University. In January 2002, he joined UAB as a faculty in the Department of Biostatistics (Section on Statistical Genetics). His research interests include Genetic Linkage Analysis, Disequilibrium Mapping, Population Genetics, Molecular Evolution, Bioinformatics, and Genetics of Infectious Diseases. Currently, he is involved in gene mapping studies of epilepsy, SLE, phonological disorders, and dental traits. He is the Head of the Section on Statistical Genetics, the William “Student” Sealy Gosset Professor, Director of the Biostatistics Pre-Doctoral NHLBI Training Program and Director of the Post-Doctoral NHLBI Training Program in Statistical Genetics. He also is the Director of the NIGMS-funded National Short Course in Statistical Genetics and Genomics.

Website: http://www.soph.uab.edu/ssg/people/tiwari


Mukundan Ragavan, PhD

University of Florida


Landon Shay Wilson

http://www.uab.edu/proteomics/massspec/personnel/wilson.php


Jianhua Zhang, PhD

Our long-term research interests are to understand the cellular and molecular mechanisms responsible for autophagy, cellular bioenergetics, oxidative stress and cell death, in the context of human diseases. We use transgenic and conditional knockout mouse models, cell differentiation models to dissect mechanisms and pathways. Autophagy regulation is important for healthy aging, combating neurodegenerative, cardiovascular, liver and metabolic diseases.

Website

Lodging

Hotel options will be distributed to attendees once they have been selected to attend the workshop.

Apply (2018 Workshop)

To apply, please perform the following tasks.

  1. Complete on-line application form at https://goo.gl/forms/io74DK2rrY29D1Ad2. Only fully completed application form will be considered.
  2. Send your current curriculum vitae to metabolomicsws@uab.edu.
  3. Send letters of recommendation (minimum of two) to metabolomicsws@uab.edu.

Please apply prior to Friday, May 25, 2018. Accepted applicants will be notified by Friday, June 8th, with registration fee due by Friday, June 22nd.

Women, members of under-represented minority groups, and individuals with disabilities are strongly encouraged to apply.

There will be 20 fellowships for graduate students and postdoctoral fellows attending the workshop. The fellowships will provide up to $500 of travel and hotel expenses. Selection will be based on information provided by the applicants.

Upon Acceptance, the fee for attendees is:
$300 – for graduate students and postdoctoral fellows
$750 – for faculty at academic, government, and non-profit organizations
$1,500 – for-profit organizations

The fee includes course tuition and syllabus, breakfast, lunch and refreshment breaks and the Workshop dinner. Hotel accommodation and travel will be the attendees’ responsibility.

The fee will be payable upon acceptance into the course.

Need more information? Contact LaShun Lanier at 205 934-4579/metabolomicsws@uab.edu

Refund and Cancellation Policy: Attendee substitutions are allowed, but notification must be made in writing by Friday, June 1st and sent to metabolomicsws@uab.edu or by fax at 205.934.8240. After this date no substitutions will be granted. UAB reserves the right to cancel this conference, in which case a full refund of your registration fee will be provided. We are unable to refund any travel costs (flight, hotel, etc.) in the case of UAB’s cancellation.

Recording and Photography Clause: UAB reserves exclusive rights to record (audio and video) and/or photograph all conference proceedings for use in marketing materials, presentations and course content sales.

The fee will be payable upon acceptance into the course.

Need more information?  Contact LaShun Lanier at 205 934-4579/metabolomicsws@uab.edu

For enquiries please contact

Stephen Barnes
205-934-7117
sbarnes@uab.edu
  LaShun Lanier
205-934-4579
metabolomicsws@uab.edu
 

Map

Volker Hall - 1670 University Blvd‎



Chemistry Building - 901 14th Street South



McCallum Basic Health Sciences Bldg - 1918 University Blvd



LRC - 1714 9th Avenue South



Bevill Biomedical Ssciences - 845 19th Street South

Acknowledgements

Many thanks to

  1. NIH Common Fund R25 GM103798-03
  2. Mary-Ann Bjornsti, PhD (Chair, Pharmacology & Toxicology)
  3. Richard A Dluhy, PhD (Chair Department of Chemistry)
  4. UAB School of Medicine
  5. Comprehensive Cancer Center
  6. Comprehensive Cardiovascular Center (CCVC)
  7. Office of the UAB Vice-President for Research
  8. UAB-UCSD O’Brien Acute Kidney Injury Center
  9. Diabetes Research Center & Comprehensive Diabetes Center
  10. Center for Free Radical Biology
  11. Agilent
  12. Sciex
  13. Waters

Workshops

Seminar

About Metabolomics