4th Annual Workshop on Metabolomics

Sunday, July 17th - Thursday July 21st, 2016

Welcome to the 4th 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.




The themes in this fourth 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 analysis, Ion mobility, Command line and R programs)
  10. Electives will allow attendees to fine tune their training experience

Tentative Agenda

Sunday, July 17

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

Monday, July 18

Time Topics & Speakers Resources
7:30 am Breakfast, VH 302
8:00 - 8:15 am Introductions (Steve Barnes/Hemant Tiwari) - VH 302
Schedule Video

Intro Video
8:15 - 8:20 am Richard Marchase, PhD, Vice-President Research - VH 302
Welcome to UAB
8:20 - 9:00 am Stephen Barnes, PhD, UAB – VH 302
Introduction to metabolomics research

9:00 - 9:10 am Questions  
9:10 - 9:50 am Xiangqin Cui, PhD, UAB - VH 302
Designing a metabolomics experiment

9:50 - 10:00 am Questions  
10:00 - 10:20 am Coffee Break  
10:20 - 10:45 am Pamela Bounelis, PhD, UAB - VH 302
Integrity in research

10:45 - 10:50 am Questions  
10:50 - 11:25 am Andrew Patterson, PhD, Penn State University - VH 302
Recovering metabolites from biological fluids and tissues

11:25 - 11:30 am Questions  
11:30 - 11:55 am Stephen Barnes, PhD, UAB - VH 302
Choosing the analysis platform

11:55 - 12 noon Questions  
12 noon Lunch  
12:25 - 12:55 Susan Sumner, PhD - VH 302
Regional Comprehensive Metabolomic Research Centers: the RTI experience

1:15 - 3:00 pm Group 1 – proceed to McCallum for MS training






Group 2 – proceed to Chemistry for NMR training



3:15 - 5:00 pm Group 1 – proceed to Chemistry for NMR training




Group 2 – proceed to McCallum for MS training





Evening On your own - see Lynn Waddell about restaurant options – Dreamland (for the meat eaters) shouldn’t be missed. Surin has good vegetarian options.  

Tuesday, July 19

Time Topics & Speakers Resources
7:30 am Breakfast
8:00 - 8:15 am Questions  
8:15 - 9:05 am Wimal Pathmasiri, PhD/Rod Snyder - VH 302
NMR data pre-processing

9:30 - 10:20 am James Kinross, PhD, Imperial College - Margaret Cameron Spain auditorium
The iKnife: Translational metabolic phenotyping for precision surgery

10:20 - 10:30 am Questions Q&A video
10:45 - 11:10 am Xiuxia Du, PhD, UNC-Charlotte - VH 302
LC-MS data pre-processing

11:10 - 11:15 am Questions  
11:15 - 12 noon Xiuxia Du, PhD/Stephen Barnes, PhD - VH 302
Hands-on data analysis with mzmine 2
(need write up on downloading mzmine)

Q&A Video
12 noon Lunch - VH 302  
12:20 - 1:00 pm James Kinross, PhD - VH 302
Open forum
1:00 - 1:55 pm Wimal Pathmasiri, PhD/Rod Snyder - VH 302
Introductions to NMR data analysis

1:55 - 2:00 pm Questions  
2:00 - 2:25 pm Paul Benton, PhD, Scripps Research Institute - VH 302
Introduction to XCMS

2:25 - 2:30 pm Questions  
2:30 - 2:55 pm Paul Benton, PhD - VH 302
Uploading data to XCMSonline

2:55 - 3:00 pm Questions  
3:00 pm Coffee break  
3:20 - 3:45 pm Paul Benton, PhD - VH 302
“The cloud plot”
3:45 - 3:50 pm Questions  
3:50 - 4:20 pm Paul Benton, PhD - VH 302
Online XCMS analysis and using your iPhone

4:20 - 4:25 pm Questions  
4:30 - 4:55 pm Stephen Barnes, PhD - VH 302
Preparing data for Metaboanalyst

Q&A Video
6:00 - 8:00 pm Workshop dinner - Hill Student Center Ballroom C
Speaker: Gary Patti, PhD – "MythBusters: The Metabolomics Edition"

Wednesday, July 20

Time Topics & Speakers Resources
7:30 am Breakfast
8:00 - 8:15 am Questions  
8:15 - 8:55 am Xiangqin Cui, PhD - VH 302
Statistical analysis using Metaboanalyst

8:55 - 9:00 am Questions  
9:00 - 9:25 am Xiuxia Du, PhD/Stephen Barnes, PhD - VH 302
Metabolite databases

9:25 - 9:30 am Questions Q&A Video
9:30-9:55 am Gary Patti, PhD - VH 302
Bar coding tandem mass spectral data for metabolite identification
9:55-10:00 am Questions Q&A Video
10:00-10:20 am Coffee  
10:20-11:00 am Shuzhao Li, PhD, Emory U - VH 302
Pathway analysis using mummichog
11:00-11:05 am Questions  
11:05-11:25 Stephen Barnes, PhD - VH 302
Pathway analysis using Metaboanalyst

11:25 - 11:30 Questions  
11:30 - 11:55 pm Chris Beecher, PhD, IROA Technologies - VH 302
Isotopic signatures and identifying real metabolites

11:55 - 12 noon Questions Q&A Video
12 noon Lunch  
12:20 - 12:55 pm Jeremiah D. Tipton, PhD, SCIEX - VH 302
OMICS and Precision Medicine - Full Workflows for Lipidomic and Metabolic Profiling

12:55 - 1:00 pm Questions  
  Workshop hands-on electives 1:15-3:00 pm and 3:15-5:00 pm
1:15 - 3:00 pm
3:15 - 5:00 pm
  1. Using R in data analysis – up to 10 participants (both sessions) – Xiuxia Du - VH 302
  1. Mummichog software – up to 10 participants (both sessions) – Shuzhao Li - LRC 210
  1. IROA analysis – up to five participants (both sessions) – Chris Beecher - KAUL 737
  1. Differential Ion mobility – up to five participants (both sessions) – TMPL staff/Jeff Miller - McCallum 427
  1. Imaging metabolomics – preparation and data acquisition (up to five participants) – Janusz Kabarowski/Kelly Walters – Bevill 334 and Chemistry (this demo will last the whole afternoon)
  1. Advanced NMR – up to five participants (both sessions) - Wimal Patmasiri, Rod Snyder - Chemistry
Evening On your own – list of restaurants available
Birmingham Barons play Montgomery at Regions Field at 7:05 pm

Thursday, July 21

Time Topics & Speakers Resources
7:30 am Breakfast
8:00 - 8:15 am Questions  
8:15 - 9:00 am Adam Wende, PhD, UAB - VH 302
Metabolomics in diabetes

9:00 - 9:05 am Questions Q&A Video
9:05 - 9:55 am Karan Uppal, PhD, Emory U - VH 302
Integrating –omics data

9:55 - 10:00 am Questions Q&A Video
10:00 - 10:20 am Coffee  
10:20 - 10:55 am Hui Wu, PhD, UAB - VH 302
The role of the microbiome in metabolomics

10:55 – 11:00 am Questions Q&A Video
11:00 - 12 noon Workshop attendee presentations - VH 302 Video 1
Video 2
Video 3
12 noon Lunch  
12:20 - 12:55 pm Norton Kitagawa, PhD, Agilent - VH 302
An Integrated Workflow for Qualitative Flux Analysis by Accurate Mass LC/MS.

12:55 - 1:00 pm Questions Q&A Video
1:00 - 1:40 pm David Heywood, Waters - VH 302
The routine application of Ion Mobility in Metabolomics

1:45 - 1:50 pm Questions  
1:50 - 2:25 pm Stephen Barnes, PhD - VH 302
Future in metabolomics

2:25 - 2:30 pm Questions  
2:30 - 3:00 pm Open forum - VH 302  
3:00 - 5:00 pm Consulting with Workshop team  

Workshop Faculty

The bios are drafts.

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.

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.

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.

Xiangqin Cui, PhD

I was initially trained as a lab/field geneticist and later on moved into statistical genetics through my postdoctoral training. After joining the UAB Department of Biostatistics, I have been conducting research in genome-wide studies, such as gene expression (both arrays and next-generation sequencing), next generation sequencing, DNA methylation, metabolomics, and microbiome with more than 50 publications in these areas. I have served as a Co-investigator/Biostatistician for statistical data analyses in multiple funded grants involving omics studies. RNAseq analysis specifically, I have published several papers listed below and taught this topic in national short courses many times. The current application is well-suited to my background and I am enthusiastic to help.

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.

David Heywood

Senior Manager -Omics Business Development

As a graduate of Salford University (UK) in Electronics and Computer Systems, David joined Fisons Instruments in November 1992 as a test and installation engineer for LC and GC triple and single quad products being manufactured in Altricham, UK. He emigrated to Canada in January 1995 to join Fisons Canada as field service engineer supporting all LC-MS quadrupole mass spectrometers. After moving into sales with Micromass covering Western Canada, David then supported both sales staff and customers with a focus on -Omics informatics tools. This role expanded from a purely Canadian perspective to a number of years in the Americas Field Marketing organization, responsible for -Omics technologies and specifically Metabolomics and Lipidomics in all of the Americas. In 2015, he moved into his current role with the Health Sciences global marketing and business development group for -Omics applications.

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.

James Kinross, PhD

James Kinross is a Senior Lecturer in Colorectal Surgery and a Consultant Surgeon at Imperial College London. His clinical interest is in minimally invasive surgery for colorectal cancer, and the prevention, diagnosis and treatment of early rectal cancer. He also has an interest in surgical nutrition and modulation of the gut microbiota for improved operative outcomes. He was trained in Northwest London, and he was an NIHR Clinical Lecturer in Surgery and an Ethicon Laparoscopic Fellow in Colorectal Surgery. He was awarded a Royal College of Surgeons of England training fellowship during his PhD and he was funded by the Academy of Medical Sciences as an early stage lecturer. He is a visiting Professor at the Royal College of Surgeons of Ireland. He is currently funded by Bowel and Cancer research and the Imperial BRC. He performs clinical research at Imperial College London and at the Royal Marsden Hospital. He collaborates internationally with researchers in the USA and across Europe.

Mr Kinross performs translational research into computational and systems biology in surgery. He worked as part of the team that developed and delivered the world’s first clinical phenome centre (CPC). Specifically, he is involved in clinical trials using intra-operative mass spectrometry (known as Rapid Evaporative Electrospray Ionisation Mass Spectrometry or REIMS) and mass spectrometry imaging technologies for augmented histology. This technology is also known as the iknife, and he is developing both surgical and endoscopic applications. A complementary component of his analysis is the study of the gut microbiome in the aetiology of gut inflammation and colon cancer. He has published over 60 peer reviewed papers and numerous book chapters.

Norton Kitagawa, PhD

Norton Kitagawa has worked in mass spectrometry for over 18 years and Windows software engineering for 17. He received his doctorate in Cell, Molecular & Developmental Biology from UC Riverside, where he used stable isotope label protein quantitation to solve a subunit stoichiometry problem in the vacuolar ATPase. Norton has worked at Agilent Technologies for over eight years as a software engineer, an R&D scientist and most recently as an R&D software manager. His team develops software workflows that integrate genomics, metabolomics and proteomics data in context of statistical profiling, biological pathway analysis and metabolic flux analysis.

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.

Jeffrey D. Miller, PhD

Current Employer: SCIEX
Current Title: Senior Support Scientist, Global Metabolomics.

Previous Titles/positions:
ABSciex/Life Technologies/Applied Biosystems/PE Biosystems, Wilton, CT & Framingham, MA. Senior Manager, Product Demonstration & Applications Lab, April 2005 – 2015.
Pharma/Small Molecule Field Support Manager, N.A., February 2010 – 2015.
Group Leader, Small Molecule Applications, September 2001 - March 2005.
Applications Specialist for the LC/MS products division of Applied Biosystems/MDS Sciex (January 1998 - March 2005).

ABC Labs, Columbia, MO, Research Scientist. June 1997 – December 1997.
Butler County Community College, El Dorado, KS, Adjunct Professor, Chemistry. 1996 – 1997.

Wichita State University, Wichita, KS, Consultant/Graduate Research/Teaching Assistant. 1991 – 1997. Consultant for Boeing-Wichita

Wimal Pathmasiri, PhD

Wimal Pathmasiri, PhD, is currently a research biochemist in the Systems and Translational Sciences Center at RTI International. Dr. Pathmasiri is a team member of the NIH Eastern Regional Comprehensive Metabolomics Resource Core (RTI RCMRC). His experience includes high-resolution nuclear magnetic resonance (NMR) spectroscopy, gas chromatography-mass spectrometry (GC-MS), liquid chromatography-mass spectrometry (LC-MS), medicinal chemistry, structural biology, and molecular biological and bio analytical methods.

Dr. Pathmasiri has expertise in metabolomics in a wide range of research areas including cancer research, disease phenotypes, drug-induced liver injury, energy metabolism, gut microbiome, toxicology, environmental exposure, and immune response to vaccines involving analysis of cells, biological fluids and tissue extracts obtained from animal models and human subjects studies. He has provided leadership for NMR and GC-MS core activities in the RTI RCMRC by optimizing the NMR and GCMS metabolomics pipeline, developing quality control procedures, evaluating software, and setting up center specific protocols for sample preparation, data acquisition, and data analysis.

Andrew Patterson, PhD

Penn State University

I have a broad background in molecular biology, biochemistry, and metabolism and am well versed in using cutting edge approaches including mass spectrometry-based metabolomics and gut microbial community analysis. As a research fellow in the Laboratory of Metabolism of the National Cancer Institute, I was an integral and productive member of the metabolomics program and applied my experience to study nuclear receptor dynamics, drug metabolism, and diseases related to metabolic syndrome and cancer. My efforts greatly promoted the development and identification of translational biomarkers using cutting-edge metabolomics platforms, including liquid chromatography and gas chromatography coupled with mass spectrometry and nuclear magnetic resonance spectroscopy. I have significant and continued record of important and novel findings (Google Scholar h-index = 29) in the field of metabolomics and biomedicine in the form of papers published in numerous journals including Analytical Chemistry, Cell Metabolism, Environmental Health Perspectives, Environmental Science and Technology, Hepatology, Journal of Biological Chemistry, Journal of Clinical Investigation, Journal of Proteome Research, Nature Communications, and Radiation Research; invited review articles, in such publications as in Nature Reviews Cancer, Mass Spectrometry Reviews and Chemical Research in Toxicology; a book chapter published in General and Applied Toxicology; and seminars and lectures presented at numerous local, national, and international meetings, including Metabomeeting in the UK (2014, 2015), Microsomes and Drug Oxidations in China (2010) and Germany (2014), and Society of Toxicology (2015).

Gary Patti, PhD

Gary Patti is an associate professor in the Department of Chemistry and the Department of Medicine at Washington University. His research focuses on applying both NMR- and mass spectrometry-based metabolomic technologies to understand regulatory phenomena in basic mammalian metabolism.

Rodney Snyder, MS

Rodney Snyder is a research chemist in Discovery Sciences Division at RTI. He has conducted studies involving metabolism, pharmacokinetics, and adduct analysis. Mr. Snyder's experience includes all aspects of conducting absorption, distribution, metabolism, and excretion (ADME) studies in rodents using oral, dermal, and intravenous exposure routes. He has 20 years of experience in conducting ADME and pharmacokinetic studies. Mr. Snyder has worked extensively on the development of high-performance liquid chromatography (HPLC) and HPLC-mass spectrometry methods for the identification and quantitation of xenobiotics and their metabolites in biological media and the analysis of hemoglobin and DNA adducts. Much of his research has involved the conduct of studies to help understand metabolism, and the effects of dose and exposure route, and extrapolation between species. Mr. Snyder has also developed methods to conduct metabolomics analysis of endogenous metabolites in biofluids, as well as using innovative software tools to interpret the data. Mr. Snyder is also part of the RTI Regional Comprehensive Metabolomics Resource Core (RCMRC) directed by Susan Sumner which is one of three Cooperative Agreement centers that are funded to work in a U24 consortium to establish our national standards for metabolomics research and reporting, to facilitate translational and clinical research using metabolomics, and to train and educate future researchers.

Susan Sumner, PhD

Susan Sumner is working to make personalized medicine, and personalized nutrition, a reality. Using metabolomics, the unique chemical fingerprints that cellular processes leave behind, Sumner assesses differences in the metabotype of individuals that correlate with states of wellness or disease. Her team is identifying biomarkers for the early detection and diagnosis of disease to monitor therapeutic treatments and to provide insights into biological mechanisms. Dr. Sumner is the director of the Systems and Translational Sciences Center in the Discovery Sciences Division at RTI, and director of the NIH Eastern Regional Comprehensive Metabolomics Resource Core (RTI RCMRC). The RTI RCMRC works with the NIH Common Fund Metabolomics Consortium to establish nationwide standards that provide consistency in metabolomics data collection and provide quality data for storage in a central data repository and coordinating center. Dr. Sumner serves on the editorial boards for Metabolomics, the Journal of Applied Toxicology, the Journal of Toxicology, and is an Associate Editor for Environmental Health Perspectives. She is an adjunct professor in the Brody School of Medicine at East Carolina University, and the Department of Nutrition at the University of North Carolina at Chapel Hill.

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.

Karan Uppal, PhD

My research focuses on computational metabolomics, integrative -omics, and development of machine learning techniques for analyzing and extracting knowledge and information from “BIG” omics data, clinical text, and biomedical literature. I have a formal training in Bioinformatics with a focus on the development and application of statistical and machine learning techniques for analyzing high-throughput -omics data and biomedical/clinical text. I have experience in analyzing and developing computational pipelines for metabolomics, epigenomics, proteomics, and transcriptomics data. I also have experience in developing tools (https://sourceforge.net/u/kuppal2/profile/) and algorithms for network based annotation of high-resolution mass spectrometry data, predicting protein-protein interactions, and integrative analysis of –omics data. I developed xMSanalyzer that optimizes the performance of existing LC/MS data processing software such as apLCMS and XCMS for improved feature detection. The software allows detection of quantitatively reliable low abundance and variable chemicals and chemicals that are present in only small subset of samples. I have developed MetabNet for metabolome-wide association studies and algorithms for computational prediction of metabolite identity. I have also developed R packages for supervised and unsupervised analysis of metabolomics data and for identifying metabolic biomarkers using univariate and multivariate feature selection techniques such as PLSDA. I also have the expertise to integrate heterogeneous data (metabolomics and gene expression; metabolomics and proteomics) and identify the network structure or modules of co-regulating metabolites, which would assist in characterizing the association of the unknown chemicals with respect to diseases, clinical traits, and biological pathways. I have experience in developing literature mining tools and algorithms for automated summarization and knowledge discovery from clinical and biomedical text. I am proficient in R, Java, Perl, Python, C++, Flex, PHP, ActionScript, JavaScript, MySQL, and database and web-application development.

Adam Wende, PhD

In August of 2013 I started my independent laboratory at the University of Alabama at Birmingham, and have focused my training and research for the past 16 years to expand our understanding of the molecular pathways in control of mitochondrial function of striated muscle. During my thesis training I focused on how exercise alters skeletal muscle metabolism and glycogen turnover through the regulation of gene expression by the transcriptional co-activator PGC-1α. My postdoctoral training expanded these interests to include studies of how heart function, directly related to diabetic complications versus exercise, is influenced by insulin signaling and glucose utilization. By combining the gained expertise in transcriptional biology and cellular signaling I have concentrated on a mission to decipher the cardiometabolic regulation of cellular function in normal physiology and disease. This work has two primary goals: 1) to determine the role of metabolic substrate switching in heart disease, and 2) to define the posttranslational regulation of mitochondrial enzyme activity and epigenetic regulation of gene expression that together may lead to the development of muscular energetic dysfunction. I have begun to explore multiple aspects of metabolic control in a systems biology approach. Current animal model work in the laboratory, supported by an NIH R00 Pathway to Independence award (R00 HL111322), is focused on changes in DNA methylation and protein O-GlcNAcylation that may impact gene expression, protein function, and mitochondrial capacity in the hearts of diabetics. One of my primary reasons for starting my independent career at UAB is the strength of their Center for Free Radical Biology, Comprehensive Cardiovascular Center, and Diabetes Research Center. As an investigator at the intersection of these various fields the environment is perfect. In my short time at UAB I have contributed to collaborations while increasing the funding for my independent work. Specifically, as a collaboration we have obtained NIH funding to explore the role of circadian rhythm in regulating insulin signaling with Dr. Martin Young (R01 HL123574) and relevant to my participation of this workshop is an Administrative Supplement to examine metabolomics in the diabetic mouse heart (R00 HL111322-04S1). Most recently I have expanded this animal model studies to examine DNA methylation and RNA-sequencing in diabetic human heart failure samples (U24 DK076169; CHAAMPS; and CCTS). I have found my participation in this workshop to be both educational and critical to integrating different omics data with the focus on understanding diabetic complications and potential molecular mechanisms to treat them.

Hui Wu, PhD

Dr. Wu is a Professor in the Departments of Pediatric Dentistry and Microbiology. Dr. Wu received his Ph.D. degree in Cell and Molecular Biology in 1999 at the University of Vermont. After he completed his postdoctoral training there, Dr. Wu joined the UAB faculty as an Assistant Professor in 2004. Dr. Wu was promoted to full Professor in 2012. He was a recipient of NIH/NIHDCR Scholar and Faculty Transition Award in 2004. In 2011 he received IADR/GSK Innovation in Oral Care Award and was recently selected as a recipient for 2014 UAB Graduate Dean’s Award for Excellence in Mentoring.


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

  • SpringHill Suites
    2024 4th Avenue South Birmingham AL 35233, Phone 205-322-8600
  • Cobb Lane Bed and Breakfast
    1309 19th Avenue South Birmingham, AL 35205, Phone 205-918-9090

Additional Lodging Options:

  • DoubleTree by Hilton Hotel Birmingham: 808 South 20th Street, Birmingham, AL 35205, USA, Phone 1-205-933-9000, Fax: 1-205-933-0920
  • The Hotel Highland: 1023 20th St S Birmingham, AL 35205, Phone 205-933-9555
  • Courtyard by Marriott Birmingham: 1820 5th Ave S Birmingham, AL 35233, Phone 205- 254-0004
  • Residence Inn Birmingham Downtown at UAB: 821 20th Street South Birmingham AL 35205, Phone205-731-9595

Apply (2016 Workshop)

To apply, please perform the following tasks.

  1. Complete on-line application form at http://goo.gl/forms/DHLelzRnyO. Only fully completed application form will be considered.
  2. Send your current curriculum vitae to mammadu@uab.edu.
  3. Send letters of recommendation (minimum of two) to mammadu@uab.edu.
  4. Send a proposal to mammadu@uab.edu. Using a one-page proposal, describe why learning about metabolomics and its methodology would help your current research and/or influence your research career plans. If you have questions about the proposal, please contact Dr. Stephen Barnes – sbarnes@uab.edu

Attendance is limited to 40 for this course. Please apply prior to Friday, April 29, 2016. Accepted applicants will be notified by Friday, May 12th, with registration fee due by May 26th.

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 $1200 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 Lynn Waddell at 205 934-4579/mammadu@uab.edu

Refund and Cancellation Policy: Attendee substitutions are allowed, but notification must be made in writing by Friday, May 26th and sent to mammadu@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 Lynn Waddell at 205 934-4579/mammadu@uab.edu

For enquiries please contact

Stephen Barnes
Lynn Waddell


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


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, Sciex and Waters



About Metabolomics