3rd 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.

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.

Richard M. Caprioli, PhD

Richard M. Caprioli is the Stanford Moore Chair in Biochemistry and Director of the Mass Spectrometry Research Center at Vanderbilt University School of Medicine. He is also currently Professor in the Departments of Chemistry, Medicine and Pharmacology at Vanderbilt University. Professor Caprioli is interested in the use of mass spectrometry for the analysis of compounds in biological systems. Current work includes the use of electrospray and laser desorption ionization methods with biological tissues and samples. Applications have focused on the development of this instrumentation and associated methodologies to achieve ultra-high sensitivity detection of endogenous compounds (e.g., neuropeptides) in live animal systems. Recent work involves the development of Imaging Mass Spectrometry, a technique whereby molecular images of peptides, proteins, drugs and other compounds are localized in tissue sections with molecular weight specificity. This method involves molecular mapping of animal tissue through the production of ion images obtained from the analysis of mammalian tissue. Applications to specific research areas involve questions about certain spatial distributions of molecules within specific tissues, e.g., mapping proteins in cancer tissue. Specific applications include human glioblastomas, breast cancer, colorectal cancer and lung cancer.

Sara Cooper, PhD

HudsonAlpha

I have been working as a Faculty Investigator at the HudsonAlpha Institute for Biotechnology for four years. The institute is focused on high throughput sequencing and functional genomics. My area of expertise lies at the intersection of metabolomics and genomics. My graduate work focused on genomics, genetics, gene regulation, and development of high-throughput assays and data analysis pipelines for the large datasets. As a post-doctoral fellow with Stan Fields, I applied this experience to the new and growing field of metabolomics. My work there began with the development of a high-throughput technique for quantification of amine-containing compounds and continued on using two-dimensional gas chromatography with mass spectrometry for analysis of yeast extracts. I have since established an independent lab initially focusing on metabolomics and evolving to integrate high-throughput sequencing based data. My research projects include metabolomics-based methods for biomarker identification in pancreatic cancer, characterization of heritability of metabolite levels in yeast and human populations, and the use of yeast and human cell culture models to understand metabolic changes in human disease.

Xiangqin Cui, PhD

Dr. Cui received her Ph.D in Genetics at Iowa State University in 2001. She then took her 3-year postdoctoral training in statistical genetics at the Jackson Laboratory. Dr. Cui joined SSG in Aug 2004 as an Assistant Professor with a joint appointment in the Biostatistics Department and the Department of Medicine (Division of Genetic and Translational Medicine). Her research interest includes statistical genetics/genomics, epigenomics, and high throughput experimental design and data analyses.

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 ofGenefrom 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; 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.

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.

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.

Robert Mohney, PhD

Dr. Mohney is a diversely trained biologist with expertise in metabolomics and a background in neuroscience, cell biology, and drug discovery. He received his PhD in Neurosciences from Case Western Reserve University and continued his scientific training as a Pharmacology Research Associate Fellow at the NIH. Subsequently, he joined a Research Triangle Park-based screening/drug discovery company characterizing enzyme-small molecule inhibitor interactions and led several key oncology and inflammation programs for the company. Dr. Mohney joined Metabolon in 2006, analyzing and interpreting discovery metabolomics data for the company’s pharmaceutical and biotechnology clients before taking a leadership role to establish Metabolon’s academic metabolomics business. Dr. Mohney leads a team of very talented PhD-level scientists and biochemical support personnel that function as the primary scientific and technical liaisons for academic and government metabolomics projects. He is the author and co-author of >40 peer-reviewed publications, including a 2014 Nature Genetics article exploring genetic influences on human metabolism through an integration of comprehensive metabolomic profiling with genomics.

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.

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.

RTI Intl Regional Comprehensive Metabolomics Research Center

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.

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.

RTI Intl Regional Comprehensive Metabolomics Research Center

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.

Jeremiah Tipton, PhD

Sciex, Advanced Workflows Specialist in OMICS

Jeremiah Tipton received his Ph.D. in Analytical Chemistry (LC/MS) from the University of Florida in 2005 and has over 10 years of experience in OMICS research. Jeremiah has worked on general LC/MS Platform Design and Method Development for Proteomics and Metabolomics Workflows. He has over 19 co-authored publications while performing research at: University of Florida; Scripps Florida; National High Magnetic Field Laboratory-FSU; Northwestern University; and the Center for Drug Discovery and Innovation-USF. Jeremiah now supports full LC/MS workflow integration (Sample preparation to Data Interpretation) to aid researchers in obtaining valuable information from challenging biological problems.

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.

David Wishart, PhD

Dr. David Wishart (PhD Yale, 1991) is a Professor in the Departments of Biological Sciences and Computing Science at the University of Alberta. He is also a senior research officer and the director of the Nano Life Science program at the NRC’s National Institute for Nanotechnology (NINT). He has been with the University of Alberta since 1995. Dr. Wishart has active research programs in structural biology, nanobiology, synthetic biology, prion biology, bioinformatics and metabolomics. From 2006-2009, Dr. Wishart led the Human Metabolome Project (HMP), a multi-university, multi-investigator project that catalogued all of the known metabolites in human tissues and biofluids. Using advanced methods in NMR spectroscopy, mass spectrometry, multi-dimensional chromatography and machine learning Dr. Wishart and his colleagues identified or found evidence for more than 8000 endogenous metabolites. This information has been archived on a freely accessible web-resource called the Human Metabolome Database (HMP). The methods and ideas developed for the HMP have helped lay the foundation for a number of other metabolomic databases (DrugBank, T3DB, FooDB) and metabolomic software tools (MetaboAnalyst, MetPA). They have also led to the development of a number of interesting clinical metabolomics projects and collaborations. These include studies of several cancer biomarkers, the identification of organ transplant biomarkers, and exploring wound healing mechanisms.

Lodging

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

DoubleTree by Hilton Hotel Birmingham
808 South 20th Street
Birmingham, Alabama , 35205, USA
TEL: 1-205-933-9000
FAX: 1-205-933-0920

Additional Lodging Options:

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 (2015 Workshop)

To apply, please perform the following tasks by your sending materials to mammadu@uab.edu

1. Complete application form (Word file or PDF file) . Only fully completed application forms will be considered.
2. Your current curriculum vitae.
3. 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 (for administrative questions about the Workshop, please contact Lynn Waddell – mammadu@uab.edu).
4. Letters of recommendation (minimum of two).

Attendance is limited to 40 for this course. Please apply prior to to Friday, March 27th, 2015. Accepted applicants will be notified by Fri, April 10th, 2015, with registration fee due by May 1st, 2015.

Women, members of underrepresented 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 towards registration, 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

For enquiries please contact

Stephen Barnes 205-934-7117 sbarnes@uab.edu

Lynn Waddell 205-934-4579 mammadu@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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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. David Graves, PhD (Chair Department of Chemistry)
4. UAB School of Medicine
5. Comprehensive Cancer Center
6. Office of the UAB Vice-President for Research
7. UAB-UCSD O’Brien Acute Kidney Injury Center
8. Diabetes Research Center & Comprehensive Diabetes Center
9. Center for Free Radical Biology
10. Metabolon, SCIEX and Waters