Demystifying Biomedical Big Data: A User’s Guide

Payment
Обучение бесплатное
Certificate
Сертификация платная
Duration
2 часа курса
О курсе

With the continuous generation of massive amounts of biomedical data on a daily basis, whether from research laboratories or clinical labs, we need to improve our ability to understand and analyze the data in order to take full advantage of its power in scientific discoveries and patient care. For non-bioinformaticians, “handling” big data remains a daunting task. This course was designed to facilitate the understanding, analysis, and interpretation of biomedical big data to those in the biomedical field with limited or no significant experience in bioinformatics. The goal of this course is to “demystify” the process of analyzing biomedical big data through a series of lectures and online hands-on training sessions and demos. You will learn how to use publicly available online resources and tools for genomic, transcriptomic, and proteomic data analysis, as well as other analytic tools and online resources. This course is funded by a research grant from the US National Institutes of Health (NIH)-Big Data to Knowledge (BD2K) Initiative.

Программа
Demystifying Biomedical Big Data: A User’s Guide
Whether you are a student, basic scientist, researcher, clinician, or librarian, this course is designed to help you understand, analyze, and interpret biomedical big data.
Что Вы изучите?
  • Understand how biomedical data are being generated and processed
  • Learn about various biomedical big data resources (e.g. TCGA, G-DOC, UNIPROT, etc.)
  • Explore and analyze genomic, transcriptomic, and  proteomic data using various online analysis tools
  • Make sense of big data using systems biology resources and tools
  • Appreciate the value of big data in biomedical research and clinical practice (e.g. enabling precision medicine)
Лекторы
Bassem R. Haddad
Bassem R. Haddad
Course Director Georgetown University Medical Center
Bassem R. Haddad, MD, is a Professor of Oncology and Obstetrics and Gynecology, and a molecular cytogeneticist at Georgetown University Medical Center and the Co-Director of the Medical School Molecular and Human Genetics course. Dr. Haddad has an active molecular cytogenetics research laboratory working in the area of translational research and cancer biomarker discovery. His research focuses on understanding the genetic aberrations and instability that occur in genetic diseases, particularly cancer. Dr. Haddad received his MD and Residency training in Obstetrics and Gynecology from the American University of Beirut, and completed his fellowship training in Molecular Cytogenetics at Boston University School of Medicine, Baylor College of Medicine, and the NIH. He is a longtime member of the Georgetown University Medical School faculty and has been involved in genetic teaching for many years. Dr. Haddad is very interested in innovative approaches in medical education and has previously developed and directed another MOOC course released on edX in June 2014, Genomic Medicine Gets Personal.
Sheila Cohen Zimmet
Sheila Cohen Zimmet
Senior Associate Vice President for Regulatory Affairs, GU Medical Center Georgetown University
Sheila Cohen Zimmet, BSN, JD, is the Senior Associate Vice President for Regulatory Affairs at Georgetown University Medical Center, an Adjunct Associate Professor in the Department of Pharmacology and Physiology, a Faculty Associate in the Georgetown University Center for Clinical Bioethics, and a member of the National Advisory Child Health and Human Development Council of the National Institutes of Health. She holds a BS in nursing degree from Georgetown University School of Nursing and a juris doctor degree from Georgetown University Law Center.
Robert Clarke
Robert Clarke
Dean for Research and Professor of Oncology Georgetown University Medical Center
Robert Clarke, Ph.D., D.Sc., is the Dean for Research at Georgetown University Medical Center and co-Director of the Breast Cancer Program at the Georgetown-Lombardi Comprehensive Cancer Center. Dr. Clarke's research interests include the cellular and molecular mechanisms driving endocrine resistance in breast cancer as well as drug resistance, drug/hormone interactions, and the application of molecular profiling to predict breast cancer phenotypes and identify functionally relevant gene signaling networks. Dr. Clarke leads several multinational molecular medicine studies in breast cancer, in collaboration with colleagues at Lombardi Comprehensive Cancer Center, Virginia Tech and the University of Edinburgh. Dr. Clarke received a PhD and DSc in Biochemistry from The Queen’s University of Belfast, UK.
Yuriy Gusev
Yuriy Gusev
Course Director Georgetown University Medical Center
Dr. Yuriy Gusev is an Associate Professor of Bioinformatics and a Bioinformatics Lead at the Georgetown Innovation Center for Biomedical Informatics (ICBI). He has over 20 years of experience in academic and industry research in the fields of bioinformatics, systems biology, biomarker discovery, and computational modeling of biological systems. Dr, Gusev is leading efforts of a bioinformatics analytical team in the development of pipelines for multi-omics and Next Generation Sequencing data analysis and integration. His team has been involved in many enterprise scale projects including the Georgetown Database of Cancer (G-DOC), the In silico Research Center of Excellence, and Georgetown Center for Systems Biology of Cancer as well as external collaborations with NCI, FDA and Argonne National Labs. Dr. Gusev has many years of experience in teaching and training in bioinformatics and computational biology at several academic centers in US including Johns Hopkins School of Medicine and Whiting School of Engineering. He has also developed several new curricula for graduate and undergraduate programs at Georgetown. Dr. Gusev has received his training in applied mathematics and computational biology at St. Petersburg University, Russia and completed his postdoctoral training in cancer genetics at the Waksman Institute of Rutgers University.
Peter McGarvey
Peter McGarvey
Course Director Georgetown University Medical Center
Dr. McGarvey, is Deputy Director of the Innovation Center for Biomedical Informatics and Associate Professor in the Department of Biochemistry and Molecular and Cellular Biology. Dr. McGarvey has academic and commercial experience in molecular biology, biotechnology, bioinformatics and software development, and his research interests include genomic and proteomic analysis, biological databases, and data visualization. Currently, Dr. McGarvey helps manage the CPTAC Data Center, The Protein Information Resource, the UniProt Knowledgebase and is involved in various other funded projects such as the Clinical Genome Resource and the GUMC CTSA . Dr. McGarvey has a PhD in Biological Sciences from the University of Michigan and MS in Technology Management from University of Maryland University College.
John. L. Marshall
John. L. Marshall
Chief, Hematology and Oncology, Lombardi Comprehensive Cancer Center Georgetown University Medical C...
Dr. John Marshall is a Professor of Medicine and Oncology, the Chief of Hematology and Oncology, and the Director of the Otto J Ruesch Center for the Cure of Gastrointestinal Cancers, at the Lombardi Comprehensive Cancer Center, Georgetown University Medical Center. Dr. Marshall received his training at Duke University, the University of Louisville, and Georgetown University. Dr. Marshall is an internationally recognized expert in new drug development for GI cancer, with expertise in phase I, II, and III trial design, and has served as Principal Investigator for more than one hundred clinical trials. While he has an interest in many areas of cancer research, his primary focus has been on the development of vaccines to treat cancer. Dr. Marshall has become an outspoken advocate for GI cancer patients and the importance of clinical research participation. Most recently, he has established the Otto J Ruesch Center for the Cure of GI Cancers, an organization solely focused on improving the lives of GI cancer patients through innovative research, personalized medicine, and focused advocacy.
Krithika Bhuvaneshwar
Krithika Bhuvaneshwar
Research Associate II (Bioinformatics) and Project Manager, Innovation Center for Biomedical Informa...
Ms. Krithika Bhuvaneshwar has over 8 years professional work experience and combines her interdisciplinary skills in bioinformatics and biostatistics for numerous projects within ICBI. Krithika has applied her bioinformatics expertise to develop novel algorithms and analysis pipelines for clinical, genomic and expression profiling data management, quality control and integrative downstream analysis. Her research responsibilities also include clinical data management; utilizing cloud computing for high throughput bioinformatic analysis of genome sequencing data and other omics data, statistical and bayesian analysis; systems biology and pathway analysis. Krithika has worked with collaborators to develop supporting evidence to confirm of their lab findings in publicly available studies. In this regard, she has performed computational analysis of gene expression and RNA-seq data from public datasets in G-DOC, The Cancer Genome Atlas (TCGA), NCBI dbGAP and other datasets from public repository Gene Expression Omnibus (GEO). She is also the project manager for the Georgetown Database of Cancer (G-DOC) project.
Ben Busby
Ben Busby
As the Genomic Outreach Coordinator at NCBI, Dr. Busby is responsible for genomics education, product management and normalization across large datasets. In these capacities, he frequently gives talks at major academic institutions, arranges online educational experiences and in-person hackathons, collects use cases and develop personas for users of NCBI genomics resources, manages user centered software design, and develop tools for normalization of RNAseq and other genomic data types. As the Chair of the Bioinformatics Department at FAES, Dr. Busby has worked with over 300 students, both in group settings and individually. He guides individual students to establish projects working on computational aspects of their individual research interests, spanning a diverse spectrum of topics, with an emphasis on high-throughput data analysis. Dr. Busby’s research at NCBI was primarily focused on algorithm development for answering large-scale biological questions. In addition to his own biological research, he collaborated with several other researchers, and develop new projects based on novel algorithmic methods.
Ashlea Carver
Ashlea Carver
Deputy Conflicts Officer and Regulatory Affairs Associate Georgetown University Medical Center
Ashlea Carver, JD, is the Deputy Conflicts Officer at Georgetown University Medical Center and Regulatory Associate at Georgetown University Medical Center and has experience with tobacco control and the regulation of food and drugs. She holds a juris doctor degree from the University of South Carolina School of Law.
Jerry SH Lee
Jerry SH Lee
Dr. Lee serves as a Health Sciences Director within the National Cancer Institute’s (NCI) Office of the Director where his chief responsibility is to help direct the NCI’s Center for Strategic Scientific Initiatives (CSSI). In this role, he provides leadership and input in planning, developing, and implementing rapid strategic scientific and technology initiatives that keep the Institute ahead of the scientific curve of potential new exciting areas and discoveries. This may involve direct development and application of advanced technologies, creation of new trans-disciplinary teams, and/or use of available federal funding mechanisms to forge novel partnerships that emphasize innovation and convergence of scientific disciplines. Since its inception in 2003, the Center has supported more than 2,000 trans-disciplinary projects through programs such as the Innovation Molecular Analysis Technologies (IMAT), NCI Alliance for Nanotechnology in Cancer, The Cancer Genome Atlas (TCGA), Clinical Proteomic Tumor Analysis Consortium (CPTAC), Physical Sciences-Oncology Centers (PS-OC), Provocative Questions (PQ), and Cancer Target Discovery and Development (CTD2) network. These exploratory initiatives that focus on the integration of advanced technologies, trans-disciplinary approaches, infrastructures, and standards, to accelerate the creation of publicly available, broadly accessible, multi-dimensional data, knowledge, and tools to empower the entire cancer research continuum for patient benefit. Prior to joining the NCI, his research involved elucidating mechanisms of age-related diseases and has co-authored over twenty papers, five book chapters, and one book. He continues research as an adjunct associate professor at Johns Hopkins University, where he also earned his bachelor`s degree in biomedical engineering and Ph.D. in chemical and biomolecular engineering. He also holds an appointment at the Washington D.C. Veterans Affairs Medical Center and collaborates with clinicians on next generation patient-centered outcomes research. Dr. Lee is a member of the Innovation Policy Forum of the National Academies Board on Science, Technology, and Economic Policy, the Foundation for the NIH’s Biomarkers’ Consortium Cancer Steering Committee, the Health and Environmental Sciences Institute’s Board of Trustees, and the editorial board of Convergence Science Physical Oncology journal. In 2016, Dr. Lee was assigned to Office of the Vice President to serve as the Deputy Director for Cancer Research and Technology for the White House Cancer Moonshot Task Force. A few key efforts he helped coordinate include the Applied Proteogenomics OrganizationaL Learning and Outcomes Network (APOLLO), international collaborations to share molecular characterization datasets, the Blood Profiling Atlas in Cancer pilot, as well as co-chairing an interagency group focused on cancer data and technology policy issues.
Subha Madhavan
Subha Madhavan
Director, Innovation Center for Biomedical Informatics (ICBI) Georgetown University
Dr. Madhavan is the Founding Director of the Innovation Center for Biomedical Informatics (ICBI) at the Georgetown University Medical Center and Associate Professor of Oncology. She is a world-class leader in data science, clinical informatics and health IT who is responsible for several biomedical informatics efforts including the Georgetown Database of Cancer (G-DOC) a resource for both researchers and clinicians to realize the goals of personalized medicine, the NCI In Silico Research Center for Excellence, and co-directs Lombardi Cancer Center’s Biostatistics and Bioinformatics shared resource. She leads the Biomedical Informatics program of the Georgetown-Howard Universities CTSA. Her group’s research focuses on extracting knowledge from big data to enrich evidence for use and effectiveness of precision therapies. She has contributed to novel information sciences findings in research articles published in journals such as Nature, Bioinformatics, Molecular and Cell Biology (MCB), AJPM, Frontiers in Oncology, Bioinformatics, Cancer Informatics, and Molecular Cancer Research (MCR). Dr. Madhavan has a Master of Science in Information Technology from University of Maryland and a Ph.D. in Molecular Biology and Biological Sciences from the Uniformed Services University for the Health Sciences through a highly ranked Indo-US Collaborative program. She conducted post-doctoral research at Johns Hopkins University.
Платформа
EdX
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