Core Mentors

Devin Absher, Ph.D. 

Dr. Absher is a Faculty Investigator at the HudsonAlpha Institute for Biotechnology. His research work focuses on using high-throughput technologies to study the genetics of common diseases and traits. His studies include genome-wide association studies for a broad spectrum of chronic diseases, including cardiovascular disease, bipolar disorder, lupus, and rheumatoid arthritis. Dr. Absher has also performed a variety of studies on natural genetic variation in human populations that have enabled more detailed association studies. In addition, his laboratory has contributed to The Cancer Genome Atlas project, studying copy number variation in three types of cancer. Finally, he is also actively investigating the epigenetics of complex diseases, and used both microarrays and next-generation sequencing to assay DNA methylation patterns genome-wide. Collaborations (past or current): Drs. Tiwari, Zhi, West, Wang, Bridges, Arnett, Kimberly, Brown, Payami, Korf, Limdi, G. Cooper, Myers, and Barsh.

Scott Ballinger, Ph.D. 

Dr. Ballinger has broad experience in the field of cardiovascular and mitochondrial biology, especially regarding the influence of mitochondrial genetics, damage and dysfunction as it relates to disease development and susceptibility. His current research emphasis is the role of mitochondrial genetics and function on disease susceptibility and progression in both human and animal models, with particular interest upon the role of mtDNA haplotype background on influencing cellular function, nuclear gene expression, body composition, and bioenergetics (e.g. “Mito-Mendelian” genetics). Collaborations (past or current): Drs. Allison, Zhi, Sweatt, Tollefsbol, and Hartman.

David Bedwell, Ph.D.

A major goal of Dr. Bedwell’s lab is the development of nonsense suppression therapies, an approach designed to treat a range of genetic diseases caused by premature translation termination codons (PTCs). He is using a combination of genomics, genetics, biochemistry, and cell biology to better understand the molecular details of these processes and to develop PTC suppression as a viable therapeutic strategy. Dr. Bedwell has been working to optimize the suppression of PTCs that cause cystic fibrosis (CF) for almost 20 years. Roughly 10% of CF patients carry a premature stop mutation in the CFTR gene. His lab has identified drugs that suppress premature stop mutations in the CFTR gene in various experimental models, including cultured CF cells, transgenic and knock-in CF mice, and CF patients. Ultimately, this therapeutic approach could be used to treat a broad range of human genetic diseases caused by premature stop mutations. Collaborations (past or current): Drs. Korf and Hartman. 

S. Louis Bridges, M.D., Ph.D.

Dr. Bridges research includes lab-based research (immunoglobulin gene expression and autoantibodies in rheumatoid arthritis [RA]); observational clinical studies/clinical trials; genetics and pharmacogenetics; and biomarkers and biorepositories.  His research program focuses on pathogenesis and treatment of RA, including immunogenetics, autoantibodies, and biomarkers of treatment response.  Dr. Bridges has been the PI of UAB/NIH program grants such as the Multidisciplinary Clinical Research Center and the Center of Research Translation, and he currently serves as the Director of the Comprehensive Arthritis, Musculoskeletal, Bone, and Autoimmunity Center. Collaborations (past or current): Drs. Brown, Kimberly, Wang, Absher, and Myers.

Elizabeth Brown, Ph.D.

Dr. Brown is a molecular and genetic epidemiologist whose research work is targeted toward understanding aberrant immune function common to inflammatory-mediated chronic diseases, such as multiple myeloma (MM) and systemic lupus erythematosus (SLE). She uses a multidisciplinary approach to characterize pathways involved in plasma cell activation and homeostasis, chronic immune perturbation, and inflammation as modifiers of disease. The primary objective of her research is to identify and validate molecular biomarkers of relevant outcomes to target high‐risk populations in order to reduce disease burden or modify disease surveillance and therapeutic intervention. Dr. Brown’s experience as Principal Investigator of the Molecular and Genetic Epidemiology Study of Multiple Myeloma (iMAGE) and the PROFILE III Cohort Study laid the groundwork for the translational population-based component of the research. Collaborations (past or current): Drs. Bridges, Arnett, Kimberly, Absher, and Myers.

Jake Y. Chen, Ph.D.

Dr. Jake Y. Chen is a Professor of Genetics and Computer Science, Chief Bioinformatics Officer of the newly established Informatics Institute, and Head of the Informatics Section of the Genetics Department at the University of Alabama at Birmingham. He holds a BS degree in Biochemistry and Molecular Biology from Peking University, and both MS and PhD degrees in Computer Science and Engineering from the University of Minnesota. He has more than 20 years of bioinformatics R&D experience, including biological data mining, computational systems biology, and translational bioinformatics, with more than 150 peer-reviewed publications. His research focuses on building quantitative biomolecular systems models from genomic and clinical big data, thus helping understand, simulate, and predict complex disease biology outcomes. Prior to join UAB, he holds tenured faculty positions at Indiana University School of Informatics and Computing and at Purdue University Computer and Information Science Department. He is also an entrepreneur who created several startup companies to make emerging biomedical data easy to interpret and use by growing Medicine 2.0 stakeholders.

Gregory Cooper, Ph.D.

Dr. Greg Cooper has been a Faculty Investigator at the HudsonAlpha Institute for Biotechnology since 2010. His research work is focused on using functional genomics and comparative sequence analysis to identify disease-causing mutations, building on both my postdoctoral and graduate research.  Towards that end, he works in several major areas, including expression genetics, analysis of transcriptional regulatory elements, and developing new genomic annotations to identify impactful genetic variants.  Dr. Cooper is also the leader, along with Dr. Rick Myers and Dr. Greg Barsh, of a clinical sequencing effort to find diagnostic mutations in children with intellectual disability, developmental delay, and related phenotypes.  In addition, he collaborates with Dr. Bruce Korf to use clinical sequencing for the diagnosis of rare diseases. Collaborations (past or current): Drs. Absher, S. Cooper, Myers, Tiwari, Korf, Hartman, Allison, Kimberly, Limdi, Payami, and Standaert.

Christopher A. Klug, Ph.D.

Christopher A. Klug, Ph.D., is a Professor in the Departments of Microbiology, Biochemistry and Molecular Genetics, and Pathology at UAB. Dr. Klug received his Ph.D. degree from the Department of Molecular Genetics and Cell Biology at the University of Chicago in 1993, where he worked on early lymphocyte development in the laboratory of Dr. Harinder Singh. While there, he was recognized with the Wayne C. Booth award for excellence in teaching, the University’s highest honor for teaching given to one student each year in the Biomedical Sciences Division. His Ph.D. work led to the discovery that Abelson virus can arrest B cell development and promote leukemia in progenitor B cells by inactivating the NF-kB signaling pathway. Dr. Klug’s postdoctoral research was in the laboratory of Dr. Irving Weissman at Stanford University, where he studied hematopoietic stem cell biology and acute myeloid leukemia (AML) as an Irvington Institute Fellow before coming to UAB as an Assistant Professor in 1997. He has been Co-Director of the Experimental Therapeutics Program at the UAB Comprehensive Cancer Center since 2006 and currently serves as Associate Director of the Immunology Graduate Program. His laboratory continues to study the underlying mechanisms regulating hematopoietic stem cell (HSC) self-renewal and how normal HSC developmental programs are subverted in the context of acute myeloid leukemia. Dr. Klug is also responsible for the design and implementation of a personalized medicine initiative in myeloid leukemia where state-of-the-art genomics tools are used for the evaluation of adult patients with myeloid malignancies. The project includes the development of a drug sensitivity assay where the entire FDA-approved compound library is screened for its ability to kill chemorefractory acute myeloid leukemia cells. This screen has led to the identification a number of novel drugs that can potentially be repurposed for treatment of AML. From 2006 to 2010, Dr. Klug served as a Regular Member of the NIH Hematopoiesis Study Section and from 2008 to 2013, served as a regular member of the Scientific Committee on Myeloid Biology for the American Society of Hematology, which organizes the program for the annual scientific meeting. Dr. Klug has been a Ph.D. thesis mentor for 14 students and has served on the thesis committees of another 60 students in the Ph.D. graduate program at UAB. 

Karin Hardiman, M.D., Ph.D.

Karin Hardiman, M.D., Ph.D., is an Associate Professor of Surgery in the UAB Division of Gastrointestinal Surgery. She was recruited from the University of Michigan in 2019 where she was in academic practice for eight years. Dr. Hardiman practices at the Birmingham VA and University Hospital. Her clinical interests are in colorectal cancer, anal cancer, inflammatory bowel disease and anorectal disease.  Dr. Hardiman’s primary research interests are in improving the treatment of colon and rectal cancer via basic and translational research. She has an NIH-funded laboratory studying the role of intra-tumor genetic heterogeneity in colorectal cancer metastasis and response to therapy. 

John L. Hartman, M.D.

Dr. Hartman’s research is focused on understanding the fundamental contribution of gene-gene, gene-environment and gene-drug interaction in phenotypic expression and disease. For most of his work, he utilizes S. cerevisiae to study gene interaction on a genome-wide scale using genomic collection of yeast gene knockout and knockdown (YKO/KD) strains. To study gene interaction systematically, comprehensively, and quantitatively, his laboratory has developed quantitative high throughput cell array phenotyping (Q-HTCP) to leverage use of the YKO/KD library to experimentally derive quantitative gene interaction networks. For example, he is using Q-HTCP technology to understand the gene interaction landscape modulating the biogenesis of CFTR-ΔF508, the most common mutation causing cystic fibrosis disease, and is applying this methodology to identify genetic networks underlying biological processes such as cellular aging, through analysis of chronological lifespan. Collaborations (past or current): Allison, Ballinger, Bedwell, Sweatt, Tollefsbol, Korf, West, S. Cooper, and G. Cooper.

Robert Kimberly, MD.

Dr. Kimberly’s work is dedicated to the study of human biology and pathophysiology and its translation to clinical application. Through his training in translational investigation and therapeutic trials in SLE at the NIH, he developed adept skills in team science to build nationally and internationally-based collaborative consortia, which have explored the genetic architecture of risk for autoimmune disease. His laboratory is focused on molecular immunology, and through their work they have identified functionally critical genetically encoded variants of human antibody receptors that have created the foundation for SLE and RA disease risk, the pharmacogenomics of responses to therapeutic monoclonal antibodies, and the pathophysiology of ANCA antibodies in vasculitis. Collaborations (past or current): Drs. Allison, Tiwari, Arnett, Brown, Sweatt, Bridges, Liu, Absher, Myers, and Levy.

Nita Limdi, MSPH, PharmD, Ph.D.

Dr. Limdi’s primary research focus is on pharmacogenomics, specifically on genomic predictors of drug efficacy and safety. Her current NIH-sponsored projects aim to define the influence of genomic and environmental factors on warfarin dose, anticoagulation control and risk of hemorrhagic complications and to develop and validate dosing algorithms for European Americans and African Americans. She is also interested in cardiovascular epidemiology and pharmacoepidemiology. Currently through collaborative efforts, Dr. Limdi is working to identify critical knowledge gaps in atrial-fibrillation and stroke, target strategies to mitigate stroke severity, and assess the effects of antiplatelet, anticoagulant, and statin therapy. Also as part of the CHARGE consortium, she is aiming to identify genetic susceptibility to adverse reactions, thereby selecting other medications for patients who are genetically likely to benefit. Collaborations (past or current): Drs. Allison, Tiwari, Zhi, Arnett, Absher, G. Cooper, Myers and Levy.

Gang Liu, Ph.D.

Dr. Liu's research involves identifying the roles of non-coding RNAs (ncRNAs), including microRNAs and long non-coding RNAs in pulmonary inflammation, injury, and repair. His laboratory is focused on determining the specific ncRNAs that are involved in these pathological pulmonary conditions, as well as characterizing their functions in the regulation of macrophage activation.  In addition, he is actively exploring the therapeutic potential of specific pathological targets in treating pulmonary diseases. Collaborations (past or current): Drs. Zhi, Kimberly, and Wang. 

Richard Myers, Ph.D.

Dr. Myers is the President and a Faculty Investigator of the HudsonAlpha Institute for Biotechnology. He has more than 35 years of experience studying the regulation of gene expression, human genetics, cancer genetics and genomics. He directed one of the first U.S. genome centers, and has been involved in developing and applying functional genomics and genetics approaches to understand how genes and regulatory regions contribute to basic biology, human diseases, including cancer, childhood genetic disorders, psychiatric and neurological disorders, responses to environment, and population genetics. His laboratory uses DNA sequencing and other high-throughput methods to identify genetic variants and to measure gene expression, binding of transcription factors, and epigenetic variation on a comprehensive, genome-wide level to study these problems.  For decades, a significant fraction of his research has been in large collaborations of genomics and genetics work, including the Human Genome Project, the ENCODE Project, The Cancer Genome Atlas, and the Pritzker Neuropsychiatric Consortium, and he has served as PI and coordinator for our portions of these projects.  In addition, his laboratory does directed biological research on human diseases and basic problems in gene regulation. Collaborations (past or current): Drs. Townes, Payami, Limdi, Kimberly, Tiwari, Allison, Payami, Bridges, Arnett, Brown, Standaert, Barsh, S. Cooper, G. Cooper, Absher, and Levy.

Haydeh Payami, Ph.D.

Dr. Payami investigates neurodegenerative disorders, with a current emphasis on Parkinson’s disease. Much of her career has been applied and translational research. She has pioneered genome-wide gene-environment interaction studies, and has so far discovered, through hypotheses free experiments, HLA as a susceptibility locus for PD, GRIN2A as a genetic modulator of risk reduction by caffeine, and SV2C as a genetic basis for the variable effect of nicotine on PD risk.  She leads the NeuroGenetics Research Consortium, an international collaboration that has amassed full genome and key environmental data on 2,000 persons with PD and 2,000 control subjects. With her recent move to UAB, NGRC sample size is anticipated to double to 4,000 cases and 4,000 controls by 2019. Dr. Payami has a dual appointment at UAB and the HudsonAlpha Institute for Biotechnology. Collaborations (past or current): Drs. Myers, Absher, G. Cooper, Standaert, West. 

Keshav K. Singh, Ph.D

Dr. Singh studies the genetics of mitochondrial energy metabolism and aims to understand the role of mitochondria in aging, energetics, oncogenesis, and other diseases. His work focuses on identifying the genes that are involved in monitoring the functional state of mitochondria and transducing signals from dysfunctional mitochondria to the nucleus (mitocheckpoint) using human cell culture, mouse, and a unicellular eukaryote yeast Saccharomyces cerevisiae as model systems to study these processes. Dr. Singh’s laboratory uses molecular and genetic methods in concert: molecular assays detect and characterize genes of interest, and in vivo functions of the proteins are assessed by genetic and other analyses. They are also investigating the role of mitochondria regulated oncogene(s) and tumor suppressor(s) in the development of cancer. Knowledge gained by using different approaches and model systems is applied to population studies to understand the mechanisms of tumorigenesis and other pathologies in humans. Collaborations (past or current): Drs. Tiwari, Tollefsbol, Korf, Wang, and Hartman. 

David Standaert, M.D., Ph.D.

Dr. Standaert is a physician-scientist with a long-standing interest in the basic and clinical aspects of neurodegenerative diseases, especially Parkinson’s disease and dystonia. His laboratory is engaged in a variety of studies relevant to this program, including evaluation of novel therapeutics in animal model systems, genetic and genomic studies, identification of biomarkers, and human clinical trials. In addition to his research activities, Dr. Standaert is a practicing neurologist, and brings an important clinical perspective to the program. He is also the Program Director of an NIH R25 program for residents in Neurology, Neurosurgery, and Neuropathology. Collaborations (past or current): Drs. Olsen, Payami, West, Sweatt, Lubin, G. Cooper, and Myers.

Hemant Tiwari, Ph.D.

Dr. Tiwari has extensive experience in developing and applying statistical methods for biomedical research. His research interests include genetic linkage analysis, disequilibrium mapping, Genome-Wide Association Studies, structural variations and epigenetics, pharmacogenetics/pharmacogenomics, gene expression, exome sequencing, bioinformatics, and metabolomics. He has strong expertise in statistical genetics software programs and developing new methods for genomics data. In addition, Dr. Tiwari is also interested in developing methods for next generation sequencing technology including exome sequencing, genome-wide methylation, metabolomics, and RNA-Seq data types. Collaborations (past or current): Drs. Allison, Zhi, Arnett, Limdi, Kimberly, Singh, Absher, Barsh, Levy, G. Cooper, and Myers.

Trygve Tollefsbol, Ph.D.

Dr. Tollefsbol's research is primarily involved with cancer and aging epigenetics. This work has also involved translational research on breast cancer, prostate cancer and ovarian cancer as well as other cancers. In addition, he is interested in discovering novel approaches for modifying epigenetic gene expression in cancers and aging, as well as the translational potential of epigenetic-modulating nutritional compounds in inhibiting these processes. His laboratory is using or has plans to use many cutting-edge technological developments in cancer and aging genetics and translational research such as RNA interference (RNAi), chromatin immunoprecipitation assays, and microarray analysis, as well as proteomics and metabolomics. Currently, he serves as an Associate Editor for Frontiers in Epigenomics and serves as Series Editor for Translational Epigenetics by Elsevier. Collaborations (past or current): Allison, Ballinger, Singh, and Hartman. 

Tim Townes, Ph.D.

Dr. Townes is Director of the UAB Stem Cell Institute and Chairman of the Department of Biochemistry and Molecular Genetics. The major research interest of his laboratory is the regulation of gene expression during development. He studies the human hemoglobin genes as a model system and translates the understanding of basic mechanisms of globin gene regulation into strategies to correct hemoglobinopathies such as sickle cell disease. A report from his laboratory in collaboration with Rudolf Jaenisch demonstrated the conversion of skin cells into induced pluripotent stem cells (iPSC), the efficient correction of the sickle gene, and a safe and effective cure for sickle cell disease in a humanized mouse model. In recent studies, Dr. Townes’ group has used CRISPR/Cas enhanced gene replacement to correct mutations in iPSC derived from skin fibroblasts of UAB patients with Sickle Cell Disease (SCD) and Severe Combined Immune Disorder (SCID). Collaborations (past or current): Drs. Myers and Barsh. 

Andrew West, Ph.D.

Dr. West’s primary goal is to utilize emerging genetic and genomic approaches to help understand the molecular basis of neurological disorders and develop targeted therapeutic strategies. His laboratory has a major focus on the new and exciting molecule recently discovered as a major cause of familial Parkinson's disease, the LRRK2 protein kinase. They have developed innovative biochemical approaches over the last few years that demonstrate that this kinase may be overactive in Parkinson's disease, and therapeutic approaches to knockdown this activity may provide neuroprotective benefit to Parkinson's disease patients. They are interested in all aspects of pursuing this protein as a drug target, including biomarker assays, antibody and transgenic animal development, and discovery of specific compounds that modify LRRK2 activity together with our collaborators in the pharmaceutical industry. An emerging area of interest in his laboratory is to help contribute to the understanding of autism and identification of new genetic-based models and therapeutic strategies. Dr. West has also assembled together one of the largest collections of post-mortem brain material and is analyzing this material using state of the art genetic approaches including RNAseq and whole genome resequencing, together with collaborators. Collaborations (past or current): Drs. Standaert, Payami, Hartman, Absher, and Myers. 

Shih-Hsin Yang, M.D., Ph.D.

Dr. Yang is a physician-scientist radiation oncologist with interests in exploiting cancer pathways to uncover rational combinations of targeted therapies to enhance the therapeutic ratio.  His work also involves uncovering potential biomarkers to inform and guide therapy in a more personalized medicine approach. To this end, he currently serves on the UAB Personalized Medicine Integration Team and is the Medical Director for the UAB Molecular Tumor Board.  These efforts have provided expanded access to targeted therapies for patients whose tumor harbors an actionable mutation found via Next Generation Sequencing approaches.  In the laboratory, he recently acquired the nCounter platform by Nanostring Technologies, which allows for targeted analysis of molecular pathways at multiple levels, including DNA copy number variation, gene expression, microRNA, and protein analysis. Dr. Yang will serve on trainee mentoring committees and lead the monthly Molecular Tumor Board conferences as part of the Educational Program. 

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Mentors in Training

Sara Cooper, Ph.D.

Dr. Sara Cooper has been a Faculty Investigator at the HudsonAlpha Institute for Biotechnology since 2011.  Her laboratory focuses on metabolomics and is working on integrating high-throughput sequencing based data into this area. Her 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. Dr. Cooper’s interest and experience in assay development and analysis put me in a unique position to fully take advantage of the rich genomic and metabolomic datasets. Collaborations (past or current): Drs. G. Cooper, Myers, and Hartman.

Jeremy Day, Ph.D.

Dr. Day is an Assistant Professor in the Department of Neurobiology. His major research interest is the neurobiological regulation of reward-related memory systems in the brain and the role of these systems in drug addiction. Dr. Day’s laboratory approaches this broad topic at diverse levels of analysis that integrate molecular, genetic, and epigenetic tools with techniques that probe the function of single neurons and entire neuronal circuits. He is also interested in understanding mechanisms of epigenetic regulation in normal and disease states, and in using tools that manipulate the epigenome to treat pathological brain diseases. More specific to this application, his lab has broad experience with epigenetic analyses, whole-genome sequencing, and genome editing tools to understand the role of specific genes and epigenetic modifications at these genes in neuronal function and behavior. Collaborations (past or current): Drs. Olsen, Sweatt, and Lubin.

Mick Edmonds, Ph.D.

Dr. Edmonds obtained both his B.S. and M.S. in Molecular Biology from Washington State University in Pullman, WA and Ph.D in Molecular and Cellular Pathology from the University of Alabama at Birmingham (UAB). In 2016 he joined the faculty in the Genetics Department at the University of Alabama at Birmingham. Dr. Edmonds’ thesis work focused on elucidating the complex transcriptional and epigenetic events required for breast cancer metastasis. He received many awards and a Department of Defense pre-doctoral fellowship during his thesis studies. As a postdoc, his research and training focused on identifying novel initiators and drivers of human lung cancer, using patient lung tumors and genetically engineered mouse models. While training at Vanderbilt, he was awarded a National Research Service Award (NRSA) and an American Cancer Society and Kirby Foundation Postdoctoral fellowship. He also identified a novel driver of human lung cancer, miR-31, which was the first miRNA shown to drive epithelial cancer progression. His lab at UAB is currently examining the role of novel miRNA involved in cancer metastasis and identifying ncRNA necessary for lung cancer progression.

Merry-Lynn McDonald, MSc, Ph.D. 

Dr. McDonald is an Assistant Professor of Medicine in the Division of Pulmonary, Allergy, and Critical Care Medicine at UAB. She is a genetic epidemiologist having completed her PhD with Dr. Suzanne Leal at Baylor College of Medicine and post-doctoral training with Dr. Edwin Silverman in the Channing Division of Network Medicine, Harvard School of Medicine, Brigham and Women's Medicine.  Her research program is focused on using network medicine approaches to deciphering the etiology of cachexia in chronic obstructive pulmonary disease (COPD). Other projects in her lab include performing genome-wide association study analysis of data from the Million Veterans Program and genomics analyses using data from TOPMed.  This work is expected to yield several high impact publications. Resources also exist for trainees to develop their own projects. Collaborations (past or current): Drs. Tiwari and S. Cooper. 

Lizhong Wang, Ph.D.

Dr. Wang’s current research focuses on using genetics, epigenome editing, and mouse models to identify cancer-causing genes, targets, pathways and new therapeutic approaches in human cancers. His research group has established the new concept of epithelial FOXP3 as the first X-linked tumor suppressor gene in breast cancer (Cell, 129: 1275-86, 2007) and in prostate cancer (Cancer Cell, 16: 336-46, 2009). Recently, he has taken a new research direction to pursue innovative projects in identifying FOXP3-mediated gene networks in breast cancer and developing genetically engineered animal models. In addition, Dr. Wang has also developed a novel epigenome-editing method to reactivate the endogenous FOXP3 at the X-inactivated allele for therapeutic purposes. Collaborations (past or current): Drs. Bridges, Liu, Singh, and Absher. 

Elizabeth Worthey, Ph.D.

Dr. Worthey is a new faculty Investigator and the Bioinformatics Program Director at the HudsonAlpha Institute for Biotechnology, She has extensive experience in the fields of human genetics, molecular genetics, bioinformatics, and translational and clinical genomics. Her main research focus is on applying cutting edge technologies to identify and study potential differentiators in disease induction, progression, outcome, and treatment including identification of novel therapeutics. She has also been involved in developing novel methods and tools to study how molecular alterations contribute to basic biology, host - human pathogen interaction, and human diseases; pediatric and adult cancer, ocular, vascular, neurologic, pulmonary, developmental, and immune disorders.

Dengui Zhi, Ph.D.

Dr. Zhi’s research work interfaces between computer science, bioinformatics, statistical genetics, systems biology, and biostatistics.  HIs own methodological research focuses on methods for modeling and analysis of complex modern Omics data for the study of complex human diseases. This is exemplified by my recently-awarded PI grant on “next-generation bioinformatics for next-generation sequencing” (R01HG008115). Besides methodological development, he works with different collaborators in research areas related to cardiovascular, brain cancer, lymphoma, lung, nutrition, and OB/GYN research on the experimental design and analyses of genome-scale Omics big data, including genomic, transcriptomic, epigenomic, and microbiomic data. Collaborations (past or current): Drs. Tiwari, Arnett, Ballinger, Allison, Limdi, Liu, and Absher.

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Content Mentors

Daniel Bullard, Ph.D.

Dr. Bullard has served as the Director for the Genetics, Genomics, and Bioinformatics (GGB) graduate program since 2009. His research work focuses on defining the cellular and genetic mechanisms by which adhesion molecules, such as the beta-2 integrins, ICAM-1, and the selectins regulate immune and inflammatory processes, especially during the development of diseases such as systemic lupus erythematosus, vasculitis disorders, rheumatoid arthritis, and multiple sclerosis. He has developed many of the current genetics/genomics-related courses that are offered through the GGB graduate program and is the head of the GGB Curriculum Committee. Several of these classes will be available for postdoctoral trainees to take to complete their core competences in Genomic Medicine. Thus, Dr. Bullard will play a key role in the Education Program for trainees and will also serve on the Executive Committee. 

Andrew Carroll, Ph.D.

Dr. Carroll directs the Clinical Cytogentics Laboratory in the Department of Genetics of the University of Alabama at Birmingham School of Medicine. This laboratory offers the full range of cytogenetic and molecular cytogenetic testing including chromosome analysis, FISH, and array CGH.  During his 35 years in this position, he has had the opportunity to train dozens of graduate students, interns, residents and fellows about the various methods available for chromosome analysis and when it is most appropriate to apply each technique to answer a clinical/research question. Dr. Carroll will serve on trainee mentoring committees and will also be involved in the Genomic Medicine Practicum training. 

James Cimino, M.D.

Dr. Cimino is the Director of the UAB Institute for Informatics. His primary research focuses on improving both clinical decision making and health data capture. Examples of his work include engaging clinicians to document their findings paying more attention to completeness and clarity to support automated processing and secondary use of data, engaging patients to make contributions to their own records, reinventing the electronic health record to be more than a diary and order clerk, but rather an active partner in addressing patient problems and improving patient conditions, and redesigning the process by which new research findings and their underlying data are made available for computer-supported use in evidence-based practice.  Dr. Cimino will serve on the Advisory Committee and trainee mentoring committees, as well as participate in the Educational Program.

David Crossman, Ph.D.

Dr. Crossman is the Bioinformatics Director for the Heflin Center for Genomic Science. He has a strong background in systems biology and assists investigators, postdoctoral fellows, and graduate students with genomic and proteomic data analyses. He is also the Coursemaster for the graduate level Bioinformatics course (GBS 722). Dr. Crossman will serve on trainee mentoring committees and also participate in the Educational Program. 

Michael Crowley, Ph.D.

Dr. Crowley is Director of the Heflin Genomics Core Facility that also serves as the Comprehensive Genomics Shared Facility (CGSF) within the Comprehensive Cancer Center structure. This facility provides DNA sequencing, genotyping, microarray analysis and Next-Generation Sequencing services.  He is also the Coursemaster for the graduate level Genomic Structure/Function class (GBS 720). Dr. Crowley will serve on trainee mentoring committees and also participate in the Educational Program. 

Maria Descartes, M.D.

Dr. Descartes has over 20 years of experience as a clinical geneticist, especially in the care of complex patients that require long term management and multidisciplinary approach care admitted to Children’s Hospital and University of Alabama Hospital.  She is board certified in Pediatrics, Clinical Genetics, and Medical Biochemical Genetics and her areas of interest and expertise are in dysmorphology and syndrome identification/delineations, skeletal dysplasias, disorder of metabolism, and lysosomal storage disorders. She is the clinical director of the Lysosomal Storage Disease Center and the Connective Tissue and Skeletal Dysplasia Clinic for Adults and Children at UAB and has taught medical students, medical residents, genetic counseling students, graduate PhD program students, and postdoctoral fellows. Dr. Descartes will serve on trainee mentoring committees and will also be involved in the Genomic Medicine Practicum training.

Mona Fouad, M.D., M.P.H.

Dr. Fouad is the Director of the UAB Division of Preventive Medicine, Director of the UAB Minority Health and Health Disparities Research Center, and a past member of the NIH National Advisory Council on Minority Health and Health Disparities.  She has played a prominent leadership role in training minority researchers and leaders in the national effort to eliminate health disparities. Through this work Dr. Fouad has developed a strong interest in mentoring minority investigators, fellows, and young faculty, helping to train the next generation of leaders in the fight against health disparities. As PI on numerous federally funded projects and co-PI on additional grants, she directs the training and research cores for multiple projects. Dr. Fouad is also responsible for training and career development of minority students and faculty on the NCI-funded Morehouse School of Medicine/Tuskegee University/UAB Partnership. In addition, she leads the Research Training Core and is the PI of the NIMHD-funded Comprehensive Minority and Health Disparities Research Center (MHDRC), which focuses on the interdisciplinary research efforts needed to understand and eliminate problems related to cancer screening and diabetes/obesity in the Deep South.

Neil Lamb, Ph.D.

Dr. Lamb is the Vice President for Educational Outreach at the HudsonAlpha Institute for Biotechnology. He oversees all educational programming developed at the institute, ranging from elementary school to graduate students and from hands on lab kits to digital media activities. He has extensive experience in education, combined with a strong working knowledge of the genetics and genomics fields. Dr. Lamb will direct the Education and Outreach program for trainees as part of the Genomic Medicine Practicum.

Elliot Lefkowitz, Ph.D.

Dr. Lefkowitz is currently the Director of Informatics for the UAB Center for Clinical and Translational Sciences (CCTS), an NIH/NCATS Clinical and Translational Science Award site; Director of the UAB AIDS Center (CFAR) Bioinformatics Facility; and Director of the Bioinformatics Core for the UAB Microbiome Facility. As Director of these Informatics facilities, he oversees a team of bioinformaticians and systems analysts who work and collaborate with UAB investigators to provide them with the broad range of tools and expertise necessary to support all of their informatics needs. These efforts have allowed him to establish informatics-related collaborations across many of the Schools at UAB. His own personal research interests are directed at contributing to the understanding of microbial genomics and evolution by developing and utilizing computational tools and bioinformatics techniques to mine sequence and other data for significant patterns characteristic of function and/or evolution. Dr. Lefkowitz will serve on trainee mentoring committees and also participate in the Educational Program. 

Fady Mikhail, Ph.D.

Dr. Mikhail is the Co-Director of the Clinical Cytogenetics lab in the Department of Genetics. The Cytogenetics lab provides diagnostic services by performing chromosome analysis, fluorescence in situ hybridization (FISH), and chromosomal microarray (CMA) from a wide variety of tissues. His research interests include identification of novel constitutional genomic disorders caused by microdeletions and microduplications using CMA technology with special interest in neurodevelopmental disorders, and characterization.  He has taught medical students, medical residents, genetic counseling students, graduate PhD program students, and postdoctoral fellows. Dr. Mikhail will serve on trainee mentoring committees and will also be involved in the Genomic Medicine Practicum training.

Mariko Nakano-Okuno, Ph.D.

Mariko Nakano-Okuno, Ph.D. is Assistant Professor of Bioethics at the Department of Medical Education, UAB School of Medicine, and Co-leader of the Bioethics Working Group for the Alabama Genomic Health Initiative.  She is engaged in the medical ethics curriculum at the UAB School of Medicine, teaches medical ethics courses, serves as a member of Hospital Ethics Committees, among her other missions at UAB. Her scholarly work includes both highly theoretical pieces such as Sidgwick and Contemporary Utilitarianism (monograph, Palgrave McMillan, 2011) and writings in applied bioethics such as "Ethics of iPSC-Based Clinical Research for Age-Related Macular Degeneration: Patient-Centered Risk-Benefit Analysis" (Stem Cell Reviews and Reports, 2014) 

Nathaniel Robin, M.D.

Dr. Robin’s two main activities are clinical service and education. He has been an active clinician since 1995 and has strong expertise in craniofacial disorders, hearing impairment, and inherited cardiac disease (eg, Long QT syndrome). As an educator, he has been active at both the post-graduate (residency) level and in undergraduate medical education. Dr. Robin has been a residency program director since 2000, first at Case Western then, since 2003, at UAB. At the national level he now serves as the co-chair for the APHMG Medical Genetics Residency Director Special Interest Group. As part of that group he developed and implemented a national in-service exam and also serves on the ACGME Residency Review Committee for Medical Genetics. In addition, he has been very active in medical education at the UAB School of Medicine, both as a leader in the effort to develop a new curriculum, and as a course master. Dr. Robin will serve on trainee mentoring committees and will also be involved in the Genomic Medicine Practicum training. 

Lisa Schwiebert, Ph.D.

In her role as Associate Dean, Dr. Schwiebert and her staff in the Office of Postdoctoral Education (OPE) work with postdoctoral fellows, faculty members, and administrators campus-wide to facilitate and enhance postdoctoral recruitment, oversight, and career development; approximately 250 postdoctoral fellows are in training at UAB currently. She has developed and also directs a year-round curriculum, including courses in lab management, grant writing, translational science, and job skills, and oversees award programs that emphasize career preparation for basic science and clinical postdoctoral fellows as well as graduate students. In addition, Dr. Schwiebert serves as the Program Director of the NIH-funded IRACDA Mentored Experiences in Research, Instruction, and Teaching (MERIT) Program at UAB. Her research focuses on investigating the effects of aerobic exercise on cellular and molecular responses in asthma, cystic fibrosis, and immunology.Dr. Schwiebert will serve on the T32 Advisory Committee and also participate in the Educational Program. 

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