HTSC Course Instructors

Short Course Instructors

 Andrew Allen, Ph.D., Professor of Biostatistics and Bioinformatics and Director of the new Duke Center of Statistical Genetics and Genomics, Duke University, has expertise in statistical genetics and genomics, missing data, and clinical trials. He has done fundamental work on robust methods for haplotype inference and on statistical methods for mapping disease genes in high-dimensional data contexts. Recently, this work has focused on next-generation sequencing studies, where he has developed methods for analyzing rare (or even de novo) variation. He has applied these approaches to several neuropsychiatric sequencing studies and has discovered new disease genes in epilepsy and amyotrophic lateral sclerosis. Dr. Allen will teach in the area of statistical genetics and genomics.

 

 

Cliburn Chan, PhD is Associate Professor of Biostatistics and Bioinformatics and Statistical Science at Duke University, and also serves as Director of Biostatistics and Computational Biology for the Duke Center for AIDS Research (CFAR). Dr. Chan has training in both biomedical and quantitative science, having both a medical degree and a PhD in Nonlinear Dynamics. His research focuses on the development of mathematical, statistical and computational models for applications in immunology and infectious disease. Dr. Chan served as course director for two core courses in the MS program that emphasize communication and collaboration with biomedical researchers and clinicians (BIOS 703 and 706), and also serves on the departmental Education Advisory and the PhD admission committees. More recently, Dr. Chan conceived, developed and taught the second level graduate course in Statistical Computing and Computation (STA 663) in the Department of Statistical Science at Duke. Apart from graduate teaching and mentoring, Dr. Chan has previously served as the course co-director for Evolution, Immunity, Microbes and Medicine offered to freshmen in the competitive Duke Focus Program. Dr. Chan is an instructor with Software Carpentry, a volunteer organization to teach researchers basic software skills, and has run multiple introductory workshops on R, Python and Data Analysis at Duke for biomedical researchers. Having done research and teaching across the spectrum of medicine, biology, statistics and computing, Dr. Chan is an enthusiastic advocate of interdisciplinary research and education. Dr. Chan will serve as co-leader of the Computing focus section with Dr. McCarthy. 

David Corcoran, Ph.D., Research Scientist in the Duke Center for Genomic and Computational Biology, Duke, where he serves as Director of the Genomic Analysis and Bioinformatics Shared Resource. Dr. Corcoran has over 10 years of experience in the field of computational biology working with high-throughput genomic data. He also teaches workshops on RNA-Seq and other high-throughput assays at Duke. He will teach lectures in bioinformatics including the use of the Galaxy system for analysis of RNA-Seq. 

Holly Dressman, Ph.D., Associate Research Professor in the Department of Molecular Genetics and Microbiology and Co-Director of the Sequencing and Genomic Technologies Shared Resource. Dr Dressman has extensive expertise in project management, teaching, assay characterization, development, optimization, validation and verification. She serves as Co-Director of the Sequencing and Genomic Technologies Shared Resource at Duke University. This resource was created as a strategic merger between the Genome Sequencing and Microarray Shared Resources. Dr. Dressman directed the latter for 15 years supporting over 250 investigators resulting in over 300 publications. Dr. Dressman was a co-founder of Expression Analysis, a company that provides genomic services that has been acquired by Quintiles. Dr. Dressman has presented lectures in meetings, workshops and in Duke undergraduate and graduate level courses in biology and genomics. Dr. Dressman will teach sessions in wet laboratory practices. 

Benjamin Goldstein, PhD Assistant Professor of Biostatistics & Bioinformatics at Duke University.

 

 

 

 

Raluca Gordan, Ph.D., Assistant Professor of Biostatistics and Bioinformatics, Computer Science, and Molecular Genetics and Microbiology, Duke University, has expertise in genomics, computational and molecular biology, machine learning, and computer science. Dr. Gordan's research focuses on developing and using computational and experimental techniques to gain a mechanistic understanding of transcriptional regulation of gene expression. Dr. Gordan is leading a highly interdisciplinary research group comprised of molecular and computational biologists, biochemists, and biostatisticians. Dr. Gordan has served as an instructor for undergraduate and graduate computational genomics courses, tutorials on introductory computer programming for biomedical researchers, and graduate course modules on computational approaches to study protein-DNA interactions (aimed at genetics/genomics graduate students without a quantitative background). Dr. Gordan was a co-instructor for the 2015 NGS summer course. In the proposed course, she will work with Dr. Granek to teach the biology and bioinformatics sections. 

Joshua Granek, Ph.D., Assistant Professor of Biostatistics and Bioinformatics, Duke University, and member of the Duke Center for the Genomics of Microbial Systems is an expert in microbiology and microbial bioinformatics. His background is in both wet lab and computational biology, providing him unique insight into the distinct requirements of experimental and data analysis aspects of biology research. His areas of research have included transcriptional regulation, microbial biofilms, antimicrobial resistance, microbial pathogenesis, and pathogen evolution. This research has involved analysis of diverse classes of genome-scale data including de novo genome sequencing, QTL mapping, microarray and RNA-Seq transcriptional analysis, sRNA-seq, and high-throughput phenotyping. Dr. Granek offers regular workshops on Next-Generation Sequence analysis and has served as a Software Carpentry co-instructor with Dr. Chan. Dr. Granek will lecture and lead hands-on sessions in the biology, bioinformatics, and case-study sections of the course. 

 

Yi-Ju Li, Ph.D., Associate Professor at the Department of Biostatistics and Bioinformatics, Duke University, faculty member in the Computational Biology Section of Duke Molecular Physiology Institute (DMPI). Dr. Li is a statistical geneticist and has over 15 years of research experience in human genetic research. She has contributed to family-based association method development for quantitative traits and methods targeting X-linked genes. In addition, she has extended experience in genetic and genomic study design and all aspects of statistical approaches and interpretation of the results through many collaborative projects in neurodegenerative diseases (Alzheimer and Parkinson diseases), eye diseases (myopia and Fuchs endothelial corneal dystrophy), and postoperative outcomes of patients underwent cardiothoracic bypass graft surgery. She has mentored a number of graduate students (Master and Ph.D.), postdoctoral fellows, and staff Biostatisticians throughout her career. In this proposed course, Dr. Li will work with Dr. Owzar to teach statistical modules. Specifically, she will lecture experimental design class.

Anna Maria Masci, Ph.D., Research Scientist in Biostatistics and Bioinformatics, Duke, has expertise in molecular biology and biomedical ontology development. She has wet lab experience in which she has done extensive work in immunoglobulin cloning and sequencing as well as in molecular T cell repertoire. Dr. Masci in addition to the laboratory has expertise the informatics field. She has done fundamental work in biomedical ontology development in particular in Cell Ontology, Protein Ontology, Gene Ontology and Signaling Pathway Ontology. Dr. Masci has been involved in the organization and teaching of the “Practice of Biostatistics’ course during the first year of our master. Recently she has lecturing on ontologies in a summer course for STEM seeking training statistics, biology and informatics. She will lecture the informatics module “Data standards and biomedical ontologies for next generation sequencing data analysis”.

 

 

Janice McCarthy, Ph.D. Medical Instructor of of Biostatistics and Bioinformatics, Duke, has formal training in both pure mathematics and biochemistry, and has extensive computing experience with various programing languages (e.g., C, C++, CUDA and R) and the UNIX operating system. Dr. McCarthy teaches a core theory course in the MS program (BIOS 701) and co-teaches a course Statistical Computing and Computation STA-663 with Dr. Chan. She will teach the computing modules with Dr. Chan, and will administer the virtual environments provided by Duke's Office of Information and Technology. 

 

 

 

Kouros Owzar, PhD is Professor of Biostatistics and Bioinformatics at Duke University. He serves at the Director of Bioinformatics of the Duke Cancer Institute (DCI) and serves on its Executive Committee. Dr. Owzar’s research focuses on the development and application of statistical methodology and computational tools for cancer pharmacogenomics. Dr. Owzar was intimately involved in the design of both the departmental MS and PhD training programs and continues to be involved in almost every administrative and educational aspect of the program. He serves as course director for two core theory courses in the MS program (BIOS 704 and 707). He serves on the departmental Education Advisory Committee and its PhD admission committee, and chairs the Qualifying Examination Committee for the theory for both the MS and PhD program. Dr. Owzar has previously served as course director for Statistical Analysis of Gene Expression Data (CRP 256) in the Duke Clinical Research Training Program (CRTP). Dr. Owzar designed the course to teach statistical thought and computing techniques accessible to medical fellows and medical students. The course has served as an inspiration to Dr. Owzar to extend statistical and computational training to student bodies outside the statistical sciences. Dr. Owzar will also serve as co-leader for the Statistics focus section.

Jessica Tenenbaum, Ph.D., Assistant Professor of Biostatistics and Bioinformatics, Duke, Associate Director for Bioinformatics, DTRI, and Chair, AMIA Working Group for Genomics and Translational Bioinformatics, has expertise in data standards and research data warehousing. She has worked with data standards both as a producer and consumer and has participated in a number of NIH BD2K workshops on data standards. She oversees integrated data warehousing, combining omics and clinical data, for the MURDOCK Study (www.murdock-study.org). Dr. Tenenbaum will lecture on data standards and the use of publicly available tools and terminologies for phenotyping research participants in order to facilitate genomic analysis. 

 

Jichun XiePhd, Assistant Professor of Biostatistics & Bioinformatics at Duke University