2nd Annual Workshop on Metabolomics

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

Keith A. Baggerly, PhD

Dr. Baggerly is a Professor, Department of Bioinformatics and Computational Biology, Division of Quantitative Sciences, UT MD Anderson Cancer Center.

His research interests involve the analysis of high-throughput biological data, and centers on themes of experimental design and reproducible research. I am best known as a practitioner of "forensic bioinformatics," where raw data and reported results are used to reconstruct what the methods must have been.

Website: http://odin.mdacc.tmc.edu/~kabaggerly/

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.

Krista Casazza, PhD

Krista Casazza obtained her PhD from Florida International University in 2006, where her research focused on dietary and physical activity education interventions in adolescents. She received a postdoctoral fellowship on a T32 training grant at the University of Alabama at Birmingham (UAB) later that year under the mentorship of Drs. Jose Fernandez and Barbara Gower. During her training Dr. Casazza competed for and received an intramural pilot feasibility grant as well grant support from the Thrasher Research fund to investigate the effects of macronutrient modification (carbohydrate in particular) on reproductive hormones, insulin dynamics and body composition during a weight loss intervention in peri-pubertal African American girls. The data gathered from these studies were used in the submission of an NIH/NIDDK K99/R00 Transition to Independence Award which Dr. Casazza received in 2009. Working with the pediatric population, Dr. Casazza’s research interests have evolved into understanding the resource partitioning during critical periods of growth and development with primary focus on the bone fat interface. In addition to the R00 study, she is currently conducting an investigation of the contribution of bone marrow adipose tissue accrual to the bone-fat interface and the metabolic effects of this relationship in young children. During here four years as a postdoctoral fellow, Dr. Casazza has published 44 papers, 3 book chapters, presented numerous abstracts and invited talks at national and local meetings. She was promoted to Assistant Professor at UAB in February, 2011.

Xiuxia Du, PhD

Dr. Du received her Ph.D. in Systems Science and Mathematics from Washington University in St. Louis in 2005. She subsequently did a postdoc in Dr. Richard D. Smith's lab at the Pacific Northwest National Laboratory. Her postdoctoral research focused on development of computational algorithms for processing and analyzing mass spectrometry (MS)-based proteomics data. In 2008, Dr. Du joined the Department of Bioinformatics & Genomics at UNC-Charlotte as an assistant professor and expanded her research to include development of computational algorithms and visual analytics for MS-based metabolomics studies.

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

Jeffrey A. Engler, PhD

Dr. Engler is the Associate Dean for Academic Affairs in the UAB Graduate School and is the Director of the UAB PREP Scholars Program.  He completed undergraduate studies in chemistry at the University of California, Santa Barbara (B.S. 1971) and graduate studies in biochemistry at the University of Wisconsin (Ph.D. in 1977). His postdoctoral studies at Cold Spring Harbor Laboratory in Long Island, New York led to a staff appointment there in 1980. Dr. Engler joined the faculty at UAB in 1982, and he is a Professor of Biochemistry and Molecular Genetics. He was an Editor of Gene from 1986 through 2008. Over the past 12 years he has focused on ethics education for graduate students. Using funds awarded by the Council of Graduate Schools and the National Science Foundation, he helped develop online ethics education modules on avoiding plagiarism and on whistle blowing (http://www.uab.edu/graduate/rcr/index.html); these modules are used in both undergraduate and graduate education. With new funding from the Council of Graduate Schools and the Office of Research Integrity at the Department of Health and Human Services, teaching assistants are being trained to include ethics education in their undergraduate and graduate classes. He also organizes periodic surveys of graduate students, postdoctoral fellows and graduate faculty, to assess their perceptions of ethical conduct in research.

TE-mail address: engler@uab.edu

Stanley L. Hazen, MD, PhD

Dr Hazen received both his PhD in Biophysical Chemistry and Molecular Biology and medical degree at Washington University School of Medicine in St. Louis. He has been at the Cleveland Clinic since 1997, where he serves as the Faculty Director of Mass Spectrometry Services, and oversees a large NIH funded laboratory that heavily uses mass spectrometry based approaches to investigations, including both metabolomics and proteomics based studies. Dr. Hazen is Chair of the Department of Cellular and Molecular Medicine at the Cleveland Clinic’s Lerner Research Institute. He is also the Section Head of Preventive Cardiology & Rehabilitation at the Cleveland Clinic, and holds both the Jan Bleeksma Chair in Vascular Cell Biology and Atherosclerosis, and the Leonard Krieger Chair in Preventive Cardiology. Dr Hazen has published over 300 peer reviewed publications, including many in top tier clinical and basic science journals alike. He has been elected as member to honorary clinical and basic science societies including ASCI in 2003, the AAP in 2007, and in 2008 he was elected as a Fellow to the American Association for the Advancement of Science (AAAS). Dr. Hazen’s laboratory focuses on understanding mechanisms through which inflammation contributes to diseases such as atherosclerosis and asthma. Major research efforts include a focus on: the role of myeloperoxidase, a leukocyte heme protein, in promoting oxidant stress in vivo and its participation in cardiovascular diseases; HDL structure and function; the role of peroxidases in airway remodeling in asthma; and the role of intestinal microbiota in cardiometabolic diseases.

Dean P. Jones, PhD

Dr. Jones is a Professor in the Department of Medicine (Pulmonary Division) at Emory University, Atlanta, GA. He received a Ph.D in Biochemistry from Oregon Health Sciences Univ., Portland, in 1976. He studied nutritional biochemistry at Cornell University and molecular toxicology at the Karolinska Institute as a post-doctoral fellow. He joined Emory University as an Assistant Professor of Biochemistry in 1979, was subsequently promoted to Assoc. Prof in 1985 and Professor of Biochemistry in 1990. He became Professor of Medicine in 2003. His central research focus is on redox mechanisms of oxidative stress. He currently directs the Emory Clinical Biomarkers Laboratory, which is focused on oxidative stress biomarkers and applications of 1H-NMR spectroscopy and Fourier-transform mass spectrometry for high-throughput clinical metabolomic analyses of nutritional and environmental factors in human health and disease.

Website: http://medicine.emory.edu/pulmonary-allergy-critical-care/faculty-directory/jones-dean-p.html

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.

Grier P. Page, PhD

Grier Page is a Senior Statistical Geneticist at RTI International. For the past 15 years he has been developing statistical methods and distributable web-based tools for the analysis of high dimensional biological data and genomic data, such as metabolomic, metagenomics, microarray, proteomics, next generation sequencing, linkage, association, and genome wide association studies. His particular are of emphasis is on methods for the valid and robust design and conduct high dimensional biological studies. He has over 100 peer review publications in various aspects of statistical genetics and the analysis of expression data. He is active involved in a number of projects including the HIV GWA studies, Heroine GWA studies, Recipient Donor Epidemiology Study (REDS-III), Stillbirth Collaborative Research Network (SCRN), Neonatal Research Network (NRN), NuMoms2B, Obstetric Pharmaceutical Research Network, and LungMap.

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

Wimal Pathmasiri, PhD

RTI Intl Regional Comprehensive Metabolomics Research Center

Website

Matthew B. Renfrow, PhD

Dr. Renfrow is an Assistant Professor of Biochemistry and Molecular Genetics at UAB. He received his PhD training in Biochemistry at the University of Georgia. As a postgraduate fellow, he was trained by Dr. Alan Marshall at the National High Magnet Field Laboratory at Florida State University. His major research interests are in applying high-resolution mass spectrometry to explore solution structure of protein-ligand complexes with hydrogen-deuterium exchange and the study of oxidative and O-glycosylated posttranslational modifications. He is the Director of the Biomedical FT-ICR MS Laboratory at UAB.

Website: http://www.uab.edu/BiomedFTICR/renfrow/

Rodney Snyder, MS

RTI Intl Regional Comprehensive Metabolomics Research Center

Website

Kathleen Stringer, PharmD

Dr. Stringer is professor of clinical pharmacy at the College of Pharmacy, University of Michigan, in Ann Arbor, Michigan. She is also an affiliate member in the Department of Computational Medicine and Informatics and a member of the University of Michigan’s Cancer Center.  Dr. Stringer received her PharmD from the University of Michigan, completed a residency in clinical pharmacy at the University of Illinois Chicago and did her post-doctoral research training at the University of Buffalo.  Until 2007, Dr. Stringer served on the faculty of the School of Pharmacy, University of Colorado Health Sciences Center (CU), Denver, Colorado. That is where her work in metabolomics began in collaboration with Dr. Natalie Serkova.  Since leaving CU, Dr. Stringer metabolomics studies have translated to the clinic and are aimed at identifying metabolites associated with sepsis and acute lung injury.  In particular, she is applying metabolomics to both clinical and experimental models to search for potential candidate biomarkers of disease severity and drug target opportunities in these critical illnesses. She is accomplishing this by using complementary nuclear magnetic resonance (NMR) and liquid chromatography (LC)- mass spectrometry (MS) platforms and computational analyses.

Website: http://sitemaker.umich.edu/stringek/home

 

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

Sean Wilkinson

Sean earned his Bachelor of Arts degree from Rice University in 2008 with a triple-major in Computational and Applied Mathematics, Statistics, and Mathematics. At the University of Texas at Austin, where he was a PhD student and fellowship recipient in the Institute for Computational Engineering and Sciences, exposure to the field of uncertainty quantification inspired him to leave the program to pursue dedicated statistical training. As a PhD student in Statistics at Rice University, he joined the lab of Jonas Almeida, who was then at the MD Anderson Cancer Center; they have since joined the Pathology Department at the University of Alabama at Birmingham. Sean is currently a PhD student in Biomedical Engineering, and his research into distributed computing combines his unique experiences in high performance computing and statistics with cloud computing and bioinformatics.

Email address: Wilkinson@uab.edu

For enquiries please contact

Stephen Barnes 205 934-7117 sbarnes@uab.edu

Jennifer Spears 205 934-4579 jspears@uab.edu

Map

Volker Hall - 1670 University Blvd‎

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Chemistry Building - 901 14th Street South

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McCallum Basic Health Sciences Bldg - 1918 University Blvd

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Acknowledgements

The primary support for this workshop comes from a grant from the National Institute for the General Medical Sciences (R25 GM103798-01). We are also indebted to the Departments of Chemistry and Pharmacology and Toxicology and the UAB School of Medicine for use of laboratory, and computing space.

In addition, the following Centers at UAB have provided support for this workshop and the 2012 UAB Metabolomics Symposium:

• Center for Free Radical Biology
• Center for Diabetes Research
• Comprehensive Cancer Center
• Comprehensive Cardiovascular Center
• Comprehensive Diabetes Center
• Lung Health Center
• Nutrition and Obesity Research Center
• O’Brien UAB-UCSD Acute Kidney Injury Center

We also acknowledge the unrestricted financial and material support from the following companies:

• AB Sciex (Danaher)
• Avanti Polar Lipids
• Bruker Daltonik GmbH
• Non-Linear Dynamics
• Waters