5th Annual Workshop on Metabolomics

Sunday, July 16th - Friday July 21st, 2017

Welcome to the 5th 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.

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Overview

The themes in this fifth 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 16

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

Monday, July 17

Time Topics & Speakers Resources
7:30-8:00 am Breakfast - LRC 249  
8:00-8:15 am Introductions - LRC 249
Stephen Barnes, PhD/Hemant Tiwari, PhD, UAB

8:15-8:25 am Welcome to UAB - LRC 249
Christopher Brown, PhD, Vice-President for Research, UAB

8:25-9:05 am The Whys and Hows of Metabolomics - LRC 249
Stephen Barnes, PhD, UAB

9:05-9:10 am Questions  
9:10-9:45 am Designing a metabolomics experiment - LRC 249
Xiangqin Cui, PhD, UAB

9:45-10:00 am Questions  
10:00-10:20 am Break – LRC 249  
10:20-11:05 am Metabolite Extraction and Platforms - LRC 249
Andrew Patterson, PhD, Penn State University

11:05-11:15 am Questions  
11:15-11:50 am Choosing the Metabolomics Platform - LRC 249
Stephen Barnes, PhD, UAB

11:50-12 noon Questions  
12 noon Lunch – LRC 249  
12:15-12:55 Lunch speaker - LRC 249
Matthew Skaley, SciEx
 
1:15-3:00 pm Group 1 – NMR Metabolomics and Imaging-MS basics 101 - proceed to Chemistry Building

Basic

101
Group 2 – Targeted and Untargeted Metabolomics and Lipidomics training - proceed to McCallum Building
Chen

Jeevan

Taylor
3:15-5:00 pm Group 1 – Targeted and Untargeted Metabolomics and Lipidomics training - proceed to McCallum Building
Chen

Jeevan

Taylor
Group 2 – NMR Metabolomics and Imaging-MS basics 101 - proceed to Chemistry Building
Basic

101
Evening On your own - see LaShun Lanier about restaurant options – Dreamland (for the meat eaters) shouldn’t be missed. Surin up on Five Points (up the hill from the hotel) has good vegetarian options.  

Tuesday, July 18

Time Topics & Speakers Resources
7:30 am Breakfast - LRC 249  
8:00-8:15 am Questions  
8:15-8:30 am Attendee Presentation:
Urinary lipidomics in nephrotic syndrome - LRC 249
Dr. Elfin Erkan, University of Cincinnati

8:30-8:35 am Questions
8:35-9:10 am Introduction to MS data pre-processing - LRC 249
Xiuxia Du, PhD, UNC-Charlotte

9:10-9:15 am Questions
9:15-9:45 am Introduction to NMR data pre-processing - LRC 249
Delisha Stewart, PhD, UNC-CH

9:45-9:50 am Questions  
9:50-10:10 am Break - LRC 249  
10:30-11:30 am Plenary Lecture - Margaret Cameron Spain Auditorium
Metabolomics at the Single-Cell Level
Peter Nemes, PhD, George Washington University
Flyer, Abstract

11:30-11:45 am Questions  
12 noon - Lunch - LRC 249 and workshop photo
1:00-1:45 pm Setting up Single Cell Analysis and CE-MS - LRC 249
Peter Nemes, PhD, George Washington University

1:45-1:55 pm Questions - LRC 249
2:00-3:15 pm Group 1 - Inspecting NMR data - hands-on *Download ACD/NMR, TopSpin and Chenomix(trial) software prior to class - LRC 215
Delisha Stewart, PhD/Wimal Pathmasiri, PhD, UNC-CH

Group 2 - Hands-on data analysis with MZmine 2 – LRC 219
Xiuxia Du, PhD, UNC-Charlotte/Stephen Barnes, PhD, UAB

3:15-3:30 pm Break  
3:30-4:45 pm Group 1 - Hands-on data analysis with MZmine 2 – LRC 219
Xiuxia Du, PhD, UNC-Charlotte/Stephen Barnes, PhD, UAB

Group 2 - Inspecting NMR data - hands-on *Download ACD/NMR, TopSpin and Chenomix(trial) software prior to class - LRC 215
Delisha Stewart, PhD/Wimal Pathmasiri, PhD, UNC-CH

4:45-6:15 pm Break
6:30-8:30 pm Workshop dinner – Hill Student Center - Ballroom D
History of Metabolomics Research
Speaker: Stephen Barnes, PhD, UAB

Wednesday, July 19

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Time Topics & Speakers Resources
7:30 am Breakfast - LRC 235  
8:00-8:15 am Questions  
8:15-8:30 am Short presentation by Subhash Rajpurohit, PhD, U. Pennsylvania
8:30-8:35 am Questions  
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
Xavi Domingo, PhD, Scripps

9:55-10:00 am Questions
10:00-10:20 am Break - LRC 235  
10:20-10:55 am Working with Metabolomics Data - LRC 235
Stephen Barnes, PhD, UAB

10:55-11:00 am Questions  
11:00-11:40 am Isotope Ratio Outlier Analysis
Chris Beecher, PhD, IROA Technologies

11:40-11:45 am Questions  
11:45-1:00 pm Lunch - LRC 215/219  
12:15-12:50 pm Fluxomics - By GoToMeeting - LRC 215
Teresa W.-M. Fan, PhD, University of Kentucky

1:00-2:15 pm
Group 1: Hands-on NMR data processing to Metaboanalyst - LRC 215
Delisha Stewart, PhD/Wimal Pathmasiri, PhD, UNC-CH

1.Metaboanalyst.csv
2.NoPools.csv
3.VehicleHighDose.csv
Group 2: Hands-on LC-MS data processing to Metaboanalyst - LRC 219
Xavi Domingo, PhD, Scripps/Stephen Barnes, PhD, UAB

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

Group 2: Hands-on NMR data processing to Metaboanalyst - LRC 215
Delisha Stewart, PhD/Wimal Pathmasiri, PhD, UNC-CH

1.Metaboanalyst.csv
2.NoPools.csv
3.VehicleHighDose.csv
3:50-4:00 pm Break/Questions  
4:00-4:25 pm Pathway Analysis with Metaboanalyst - LRC 215/219
Stephen Barnes, PhD, UAB
4:25-4:30 pm Questions  
4:30-4:55 pm Introducing MS-DIAL - LRC 215/219
Ivana Blazenovic, PhD, UC-Davis

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

Thursday, July 20

Time Topics & Speakers Resources
7:30 am Breakfast - LRC 249  
8:00-8:15 am Questions  
8:15-8:30 am Saliva Metabolomics - LRC 249
Short presentation by Yanhui Zhang, PhD, UTHSC, Memphis

8:30-8:35 am Questions
8:35-9:10 am Pathway and Network Analysis for Metabolomics – Mummichog - LRC 249
Shuzhao Li, PhD, Emory U

9:10-9:15 am Questions
9:15-9:55 am Group 1 - Metabolite databases - LRC 265
Xiuxia Du, PhD, UNC-Charlotte
Group 2 - Searching METLIN – hands-on - LRC 249
Jeevan Prasain, PhD, UAB
9:55-10:00 am Questions
10:00-10:20 am Break - LRC 249
10:20-11:05 am Group 1 - Searching METLIN – hands-on - LRC 249
Jeevan Prasain, PhD, UAB
Group 2 - Metabolite databases - LRC 265
Xiuxia Du, PhD, UNC-Charlotte
11:05-11:10 am Questions
11:10-11:50 am Introduction to imaging metabolomics - LRC 249
Janusz Kabarowski, PhD, UAB

11:50-12:00 noon Questions
12 noon Lunch - LRC 249  
12:15-12:55 pm Research Integrity - LRC 249
Pam Bounelis, PhD, Asst. Vice President for Research, UAB
OPTION 1
1:15-3:00 pm Preparing samples for imaging MS - Bevill 334
Janusz Kabarowski, PhD, UAB

3:15-5:00 pm Collecting and processing imaging data - Chemistry
Kelly Waters, BS, UAB

OPTION 2
1:15 - 3:00 pm 2D-NMR methods and metabolomics - LRC 215
Delisha Stewart, PhD/Wimal Pathmasiri, PhD

3:15-5:00 pm Using MS-DIAL – hands-on – LRC 215
Ivana Blazenovic, PhD, UC-Davis

OPTION 3
1:15-3:00 pm Using Mummichog – hands-on – LRC 219
Shuzhao Li, PhD, Emory

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

OPTION 4
1:15-3:00 pm Interpretation of MSMS data and advanced nanoLC-MS – MCLM 427/459
Landon Wilson, BS, UAB and Jeevan Prasain, PhD, UAB

3:15-5:00 pm ClusterFinder Software – Hands-On – 7th Floor Kaul Building
Chris Beecher, PhD, IROA Technologies

Evening On your own – list of restaurants available  

Friday, July 21

Time Topics & Speakers Resources
7:30-8:00 am Breakfast - LRC 249  
8:00-8:15 am Questions  
8:15-8:55 am Microbiome and metabolomics - LRC 249
Hui Wu, PhD, UAB

8:55-9:00 am Questions
9:00-9:40 am Integration of metabolomics with other –omics – LRC 249
Karan Uppal, PhD, Emory
9:40-9:45 am Questions
9:45-10:00 am Break - LRC 249
10:00-10:40 am Movie and Presentation: Ion mobility mass spectrometry - LRC 249
Erin Baker, PhD, PNNL

10:40-10:45 am Questions
10:45-11:55 am Integration of –omics data – hands-on session LRC 249
Karan Uppal, PhD, Emory
11:55-12 noon Questions
12 noon Lunch - LRC 249
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


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


Ivana Blazenovic, PhD

Dr. Ivana Blazenovic is currently a post doctoral scholar in the Fiehn lab at UC Davis working on multiple pilot projects with focus on

• structure elucidation of small molecules
• LC-MS and IM-QTOF data analysis and interpretation
• statistical data analysis
• method development and validation

She has obtained her phD at TU Braunschweig, Germany in the field of Metabolomics and Microbiology and her MSc at University of Zagreb, Croatia in the field of Biotechnology.

Metabolomics Fiehn Lab


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.

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


Xavi Domingo, PhD

Dr. Domingo-Almenara obtained his PhD in Bioengineering at the University Rovira i Virgili (Catalonia, Spain), where he researched on automated methods for the processing of mass spectrometry untargeted metabolomics data. As a bioinformatician, he has developed different free and open source computational tools for processing of GC and LC-MS data, including the R package eRah. In 2017 he moved into the Scripps Research Center for Metabolomics in La Jolla, California, where he serves as a postdoctoral fellow with Prof. Gary Siuzdak. His research focuses on evolving towards advanced computational workflows to streamline targeted and untargeted analysis in metabolomics, systems biology and -omic integration.


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.

Web Site: http://www.du-lab.org


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.


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/


Peter Nemes, PhD

Peter Nemes is an Assistant Professor of Chemistry (2013–present) at the George Washington University (GWU), whence he obtained a PhD in chemistry in 2009 (advisor: Prof. Akos Vertes). He completed postdoctoral training in analytical neuroscience at the University of Illinois—Urbana-Champaign (mentor: Prof. Jonathan V. Sweedler). After serving as a Laboratory Leader and Staff Fellow at the US Food and Drug Administration between 2011–2013, Dr. Nemes joined the faculty of the GWU Department of Chemistry.

Research in the Nemes Laboratory develops ultrasensitive and microanalytical platforms for high-resolution mass spectrometry to study how metabolic and proteomic processes orchestrate normal cell heterogeneity during early development of the vertebrate embryo and the central nervous system. Using these custom-built single-cell mass spectrometry systems, the Nemes Research Group has uncovered previously unknown molecular differences between single embryonic cells that give rise to different types of tissues during vertebrate development. Furthermore, the group has discovered small molecules that are able to alter the normal developmental fate of these embryonic cells. These results challenge our basic understanding of molecular processes that are necessary for normal embryonic development.

Prof. Nemes has authored 36 peer-reviewed publications, 6 book chapters, and 110+ presentations. He is co-inventor of the patented and licensed LAESI mass spectrometry technology. In 2015, Prof. Nemes was named a Beckman Young Investigator by the Arnold and Mabel Beckman Foundation, and also received the 2016 Arthur F. Findeis Award for Achievements by a Young Analytical Chemist by the Division of Analytical Chemistry of the American Chemical Society. In 2017, Prof. Nemes received the DuPont Young Professor Award and the Robert J. Cotter New Investigator Award by the US Human Proteome Organization.


Wimal Pathmasiri, PhD

Wimal Pathmasiri, Ph.D. joined the University of North Carolina at Chapel Hill Nutrition Research Institute in March 2017 as a Research Assistant Professor. Dr. Pathmasiri is interested in identifying biomarkers for the early detection of disease, and monitoring nutritional intervention. His efforts at UNC NRI will focus on understanding the impact of diet and naturally occurring molecules in diet on gut microbiome related metabolism.

Dr. Pathmasiri earned his B.Sc. and M.Phil. from the University of Colombo, Sri Lanka, and a Licentiate of Philosophy from the Uppsala University, Sweden. He received his Ph.D. in Chemistry from Uppsala University and conducted postdoctoral research at the UNC Chapel Hill, and at RTI International.

Dr. Pathmasiri is an active member of the NIH Common Fund Eastern Regional Comprehensive Metabolomics Resource Core (ERCMRC), where he has served as a research biochemist for the past 5 years. As a metabolomics scientist, he has contributed to research in the areas of cancer, childhood obesity, early life exposure to antibiotics, environmental exposure, kidney disease, osteoarthritis, rare diseases, and toxicology.

Website


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).

Website


Jeevan Prasain, PhD

Dr. Prasain is an Assistant 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 for the discovery and identification of natural products. He will be demonstrating the use of LC-MS methods for the analysis of metabolite classes.

Website


Delisha Stewart, PhD

Dr. Delisha Stewart received her Ph.D. in Biochemistry from the University of Alabama at Birmingham (UAB). Following postdoctoral fellowships at the University of Delaware, UAB and UNC-Chapel Hill, she completed her training with the NIH Eastern Regional Comprehensive Metabolomics Resource Core (ERCMRC) at RTI International to learn metabolomics. She uses genomics, metabolomics and high-throughput molecular bioassays to study metabolic dysfunction in cancer and immunological diseases, most interested in the interplay between the immune system and malignancy. In March 2017, she joined the Department of Nutrition at UNC-Chapel Hill as a Research Assistant Professor, relocating with the ERCMRC to the Nutrition Research Institute. She continues to lead all cancer and immunology-focused studies, with an additional focus on the influence of nutrition on cancer health disparities. Her research aims to better characterize etiological and progressive microenvironments of breast and other types of hormonally-associated cancers, identify diagnostically and therapeutically relevant biomarkers and determine the role of altered nutritional states on disparate treatment outcomes.

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


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.


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.

Website

Lodging

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

Apply (2017 Workshop)

To apply, please perform the following tasks.

  1. Complete on-line application form at https://goo.gl/forms/yD7O1qChkEb9Mff22. 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.
  4. Send a proposal to metabolomicsws@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 28, 2017. Accepted applicants will be notified by Friday, May 12th, with registration fee due by Friday, 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 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, May 26th 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