CCTS Informatics Expertise. Auburn University (AU) HudsonAlpha Institute for Biotechnology (HAIB)

Transcription

1 CCTS Informatics Expertise Name/Contact Information Expertise Experience Eric Peatman, PhD Associate Professor Auburn University School of Fisheries, Aquaculture and Aquatic Sciences 203 Swingle Hall Auburn University, AL Lab (334) Office (334) Auburn University (AU) HudsonAlpha Institute for Biotechnology (HAIB) Devin Absher, PhD Investigator HudsonAlpha Institute for Biotechnology 601 Genome Way NW Huntsville, AL (256) Multi-platform integration Statistical genetics Louisiana State University Health Sciences Center New Orleans (LSU) Judy Crabtree Assistant Professor of Genetics Co-Leader, LSU Genomics Core. Biomarker discovery

2 Christopher Taylor Associate Professor of Microbiology-Immunology Co-leader, LSU Genomics Core. Microbiome/microbial genomics Viral Sequencing Dr. Taylor s background is in computer science and computational biology. He has over a decade of experience with genomics technologies and currently leads the LSUHSC School of Medicine Bioinformatics Lab. His primary research focus is on 16S rrna sequencing of microbial communities and sequencing of microbial organisms. Lucio Miele, Professor of Medicine Stanley S. Scott Cancer Center lmiele@lsuhsc.edu Multi-platform integration GWAS/GEP correlation Biomarker discovery Jovanny Zabaleta, Assistant Professor, Stanley S. Scott Cancer Center. Leader, Stanley Scott Cancer Center Translational Genomics Core Methylome Zhide Fang Professor of Biostatistics Interim Director of Biostatistics Program, School of Public Health Statistical analysis and modeling of Highthroughput data (microarray and NGS). Survival Analysis, Longitudinal data analysis. Design of Experiments Dr. Fang has extensive experiences in analyzing data in genetics, molecular biology, genome biology, microbiology and systematic biology. His research interests lie in developing statistical methods for data analysis, including data pre-processing and down-stream analysis, of high throughput genomic data generated by microarrays and next-generation sequencing technologies, and development of statistical theory.

3 Pennington Sujoy Ghosh Associate Professor Adjunct Nutrient Sensing and Adipocyte Signaling Bioinformatics analysis of genome-wide association studies Disease and Biomarker Transcriptome analysis Identification of blood-based genomic and genetic biomarkers of whole genome expression profiling Integrative pathway analysis Dr. Ghosh is a Senior Research Investigator with more than 16 years of analytical bioinformatics experience in biopharmaceutical and biotechnology industries. His background in metabolic discovery medicine coupled with extensive international academic research collaborations provides a rich source of strategic insight for our initiatives in developing new innovative bioinformatics plans. Ron Horswell Associate Professor Health Care Quality Improvement Ronald.Horswell@pbrc.edu Cost effectiveness analysis Using and merging data from large clinical databases, including clinical data warehouses Propensity score-based comparisons of treatment effectiveness using observational data Instrumental variables-based comparisons of treatment effectiveness using observational data Design of clinical quality improvement and comparative effectiveness studies Dr. Horswell is Director of the Biomedical informatics Core for the LA CaTS translational science program and Director of Medical Informatics for the LSU Improving Clinical Outcomes (LSU ICON) program. He has extensive experience developing measures and measurement systems for health care quality assessment. He also has extensive experience using observational data for comparative effectiveness analyses. Design of clinical quality improvement projects and comparative William Johnson Professor of Biostatistics Director of Biostatistics Core Pennington Biomedical Research Ctr William.Johnson@pbrc.edu Design and analysis of clinical trials Mixed effects statistical models Design and analysis of data from hierarchical clusters of study units Models with repeated measures on multivariate data with patterned covariance structures Analytical methods for identifying latent clusters of multivariate outcomes Reduction of data dimensionality by principal component analysis Dr. Johnson is Senior Biostatistician and Director of Pennington s Biostatistics Core, Director of the Biostatistics and Epidemiology Core for the Louisiana Clinical and Translational Science (LA CaTS) Center, and Director of Biostatistics for the Botanical Research Center. He is a well-published expert on the theory and methods of statistical analysis for biomedical research with applications in the basic, clinical and population sciences. His expertise is broad based but grounded in a traditional statistics education and many years of research experience in a university-based multidisciplinary environment.

4 Michael Salbaum Associate Professor Regulation of Gene Expression Director of Pennington Biomedical Genomics Core Gene expression Microarray Next-generation sequencing ChIPSeq Systems Biology Dr. Salbaum is a Developmental Biologist with expertise in the bioinformatics of gene expression patterns, and serves as Director of the Genomics Core at Pennington Biomedical. The Core provides technologies to analyze transcriptome, epigenome, or microbiome parameters, including statistical considerations concerning experimental design, wet bench techniques, bioinformatics analysis, and systems biology evaluation. Tulane Michelle Lacey, Associate Professor of Mathematics Adjunct Associate Professor of Biostatistics Director, Tulane Cancer Center Genomics Analysis Core mlacey1@tulane.edu Genomic and Epigenetic Analysis Statistical Modeling Phylogenetics Michelle Lacey is an interdisciplinary statistician with 10 years of experience in collaborating with biomedical researchers. Dr. Lacey directs the Tulane Cancer Center Genomics Analysis Core to provide statistical support to researchers conducting high-throughput experiments, and she maintains an independent research program in the areas of phylogenetic methods and epigenetic modeling and analysis. Erik Flemington, Ph.D. Professor of Pathology Zimmerman Professor of Cancer Research Program Director, Cancer Genetics Director, Cancer Crusaders Bioinformatics Core eflemin@tulane.edu Genome Alignment De novo assembly Differential gene and/or isoform expression analysis Fusion gene discovery Nucleotide sequence variation identification Microbiome analysis The Cancer Crusaders Next Generation Sequence Analysis Core provides standard analysis of genome and transcriptome data. In addition, the Core provides training and computational resources to enable researchers to explore and implement new algorithms and pipelines. Melody Baddoo Senior Research Scientist Cancer Crusaders Next Generation Sequence Analysis Core mbaddoo@tulane.edu microrna seed identification Circular RNA identification

5 Yao-Zhong Liu, Ph.D. Associate Professor Dept. of Biostatistics & Bioinformatics Director, Section of Functional Genomics Center for Bioinformatics and Genomics RNA-seq data analysis Genome-wide gene expression Metagenomics Sudesh Srivastava Professor Dept of Biostatistics & Bioinformatics Experimental design Statistical genetics Allison B. McCoy Assistant Professor Dept of Biostatistics & Bioinformatics Health informatics Dr. McCoy received her PhD in biomedical informatics from Vanderbilt University in 2010, and her primary area of expertise is in health informatics. Specifically, her research interests include applied clinical informatics and patient safety, and her current work is focused on the development of automated methods to generate, evaluate, and improve point-of-care clinical decision support within electronic health records. Jian Li, PhD, Assistant Professor, Department of Biostatistics & Bioinformatics Statistical genetics Multi-omics Dr. Li s research is focused on methodology development and application for multi-omics (such as genomic, transcriptomic, epigenomic and proteomic) data analyses. Example topics include using network and integrative methods in analyzing NGS DNA, sequence-based RNA/miRNA/protein expression data for finding genetic variants underlying human complex diseases such as cardiovascular diseases, cancer and obesity; and studying and characterizing genetic variants at different omic levels.

6 University of Alabama at Birmingham (UAB) Elliot J. Lefkowitz, PhD Director Microbial genomics and evolution Phylogenetic analysis Basic bioinformatics analysis Dr. Lefkowitz is a Professor in the Department of Microbiology. His research focuses on the genomics and evolution of microorganisms, especially viruses; the development and use of bioinformatics tools and techniques to support genomics research; and the provision of informatics support across the full spectrum of biomedical research. In addition to serving as Director of Informatics for the CCTS, he is also Director of Bioinformatics for the UAB Center for AIDS Research, and Director of Bioinformatics for the UAB Microbiome Facility. Eta S. Berner, EdD Co-Director eberner@uab.edu Health informatics evaluation Informatics education Dr. Berner is a former member of the Board of Directors of the American Medical Informatics Association, the External Scientific Panel for NHGRI s Emerge Network and the Technical Expert Panel for the AHRQ Clinical Decision Support Initiative. She is responsible for the development and oversight of CCTS Informatics educational activities and works with others at UAB to oversee and develop policies concerning consent and governance issues surrounding the use of clinical data for research. Geoff Gordon, MSEE Co-Director gdgordon@uab.edu Electronic health record Clinical data warehouse Mr. Gordon is an IT Director for the Health System Information Services division of UAB Health System, responsible for Web Development and the Enterprise Data Warehousing Initiative. He has been working in clinical analytics for the past 3 years and has over 20 years of software development experience, 15 in healthcare. James H. Willig, MD, MSPH Co-Director jwillig@uab.edu Clinical informatics Data quality Medical education Dr. Willig is the Medical Informatics Director of the UAB 1917 AIDS Clinic, Co-Director of the UAB HIV-Research and Informatics Service Center, and Director of Clinical Informatics for the UAB Health System Information Services. He also serves as the physician lead for the Clinical Data Warehouse Research Working Group. His own research involves the development and use of informatics tools and methods to support patient care, especially for patients living with HIV.

7 Matthew Wyatt, MSHI Assistant Director Clinical data access Clinical data warehouse Mr. Wyatt provides operational management for all aspects of Informatics day-to-day activities. He is responsible for oversight of institutional collaborative projects including those related to clinical data warehousing, clinical data capture at the point of care, and clinical data extraction. Keith Bobitt Senior System Analyst Software development Clinical data access Mr. Bobitt is a Senior System Analyst and Java developer. He is developing systems to extract data from i2b2 and VDW based Clinical Data Warehouses for cohort discovery and Java based software for direct database access of VDW systems and RESTful web interface access of i2b2 systems. David K. Crossman, PhD Instructor dkcrossm@uab.edu Exome sequence analysis RNA-seq analysis Dr. Crossman is an Instructor in the Department of Genetics. He directs the Bioinformatics Facility at the Heflin Center for Human Genetics and is responsible for the initial processing and analysis of Next-Gen Sequencing data obtained for Genomics Illumina sequencers. He provides CCTS investigators with expertise in microarray analysis, Next-Gen Sequencing analysis, mass spectrometry proteomics analysis, and Systems Biology pathway analysis. Don Dempsey, MS Programmer ddempsey@uab.edu Software development Medical education software development Mr. Dempsey is a web and Java developer who is responsible for the development of many of our web-based applications and databases. This includes working with clinical and translational researchers to create data capture forms and clinical, outcomes, and bioinformatics databases; assisting researchers with analysis and extraction of data from the Clinical Data Warehouse; developing new clinical and bioinformatics tools; and specific programming needed to develop the tools and systems supporting the needs of individual investigators.

8 Curtis Hendrickson Research Associate Human genome sequence analysis RNA-seq analysis Variant detection Virus sequence assembly and analysis Mr. Hendrickson provides expertise in data collection, integration, and reporting. This includes scientific database design, implementation, and support, as well as in web site design, web application development, and project management. He also supports a variety of bioinformaticsrelated services including Next-Gen Sequencing analysis, detection of sequence variants, and detection of gene regulatory motifs. Ranjit Kumar, PhD Research Associate rkumar@uab.edu Microbiome data analysis Metagenomic analysis Bacterial sequence assembly and analysis Basic bioinformatics analysis Dr. Kumar s research has focused on whole genome transcriptome analysis of bacterial pathogens, which led to identification of numerous novel non-coding RNAs and proteins. He has also worked on host-pathogen proteinprotein interactions by developing a non-redundant web based relational database that has advanced capabilities for host-pathogen interaction storage, retrieval, and data mining. He provides bioinformatics support and application development to investigators, especially focusing on the analysis of Next-Gen Sequencing data including microbiome and metagenomic analysis. He is responsible for the installation, maintenance, and support of all associated tools and data sources supporting microbiome analysis, and he has developed and is currently supporting the analytical pipeline used by the CCTS to support the analysis of data derived from human microbiome studies. John Osborne, MS Research Associate ozborn@uab.edu Human genome sequence analysis Bacterial sequence assembly and analysis Mr. Osborne works with clinical and translational researchers to create data capture forms and clinical, outcomes, and bioinformatics databases; assists researchers with analysis and extraction of data from the data warehouses; and works extensively with UAB investigators on the analysis of Next-Gen Sequencing data derived from patients enrolled in clinical research studies. He also develops new approaches and applications to support the extraction of clinical information from free-text records in order to store that information in structured database fields.

9 Travis Ptacek, PhD Postdoctoral Fellow Analysis of immune-related genes Microbiome data analysis Metagenomic analysis Bacterial sequence assembly and analysis Dr. Ptacek received his PhD in Genetics from UAB in His past research involved studies of genetic variants, single nucleotide and structural, within large case-control disease cohorts in a mixed wet and dry lab setting. He currently offers expertise in next generation sequence analysis, and in the managing, assembly and curation of large genetic/patient/animal databases. His current work as part of the CCTS involves genomic assembly, comparative genomics, genomic variant (SNP and structural) discovery, evaluation, and curation, RNAseq analysis including transcript discovery, ChIP seq analysis, and analysis of microbiome data for several projects in connection with the UAB Microbiome/Bioinformatic/Gnotobioitic Animal core. Liam Van Der Pol, MS Bioinformatician II liamvdp@uab.edu Application support and development Microbiome analysis Basic bioinformatics analysis Mr. Van Der Pol received his Masters degree in Bioinformatics in 2013 from Indiana University, Bloomington, IN. For his Master s thesis he worked on a project building a transcriptome for Wolbachia. This project sought to examine the genes being expressed by the bacterial parasite Wolbachia post-infection in the model organism host D. melanogaster, by purifying prokaryotic RNA from host tissue and sequencing with Illumina RNAseq then assembling transcripts with the Trinity assembler. Chindo Hicks, Associate Professor of Medicine Director, Institutional Bioinformatics Core Dan Roach, MD Acting Director of the Center for Strategic Health Innovation University of South Alabama droach@southalabama.edu University of Mississippi Medical Center (UMMC) Multi-platform integration Statistical genetics University of South Alabama (USA)

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