Courses

5 Credits | Fall Semester
This course comprises SYSM 5930 Critical Readings in Systems Medicine and SYSM 5970 Clinical Bioinformatics. Part-time students may wish to take SYSM 5930 and 5970 in separate semesters.

This course integrates principles of physiology with genomics utilizing the concepts of Systems Biology. With the completion of several sequencing projects: the Human Genome, the HAPMAP, the ENCODE, and the Genome Wide Association Studies, the field of Physiological Genomics has emerged from the need to link function to thousands of mapped genes and better understand human physiology at all levels of biological organization. The course concepts and tools for student mastery represent advanced competencies of how we can utilize genomic knowledge to re-establish physiologic wellness if there has been some aberration of the genome leading to a pathologic outcome. This course will cover the function of human body systems and will provide a strong foundation to understand the relationship of genes to complex physiological functions. The course is designed as a combination of lectures, an interactive journal club, and hands-on sessions. Students will focus on both monogenic and more complex polygenic diseases to critically analyze and dissect the genetic effects on the physiological function of major organ systems. The hands-on session will cover the use of various clinical data. Each week will focus on an organ system and its diseases. Students will have a unique opportunity to analyze real patient exome sequencing data and learn to write a clinical report based on disease findings. The goal of this course is to provide students with a strong understanding of the function of major organ systems as a basis for understanding human health, learn how to analyze research papers, and think critically on the effects of genetics/genomics on human pathophysiology.

3 Credits | Spring Semester

Advances in genomics have led to a major paradigm shift in medical practice. While medicine has always been “personal,” the availability of genomic data has made it possible to individualize care for many patients. This online course will provide an introduction to genomic medicine and will cover five main themes:

1. Clinical genetics and genomics
2. Laboratory techniques
3. Consumer genomics
4. Ethical, legal, and social issues
5. Present and future opportunities and challenges.

3 Credits | Fall Semester

This course will introduce the idea of how to reason via statistical models to get and interpret information from big biological data. To introduce the idea of how formal models of data are used, examples will also be drawn from related sciences. Students will learn how to apply regression-type models to data and assess the consistency (or inconsistency) of the results they produce with theory. The course will encourage students to set biological or medical problems they are working on within the context of formal statistical models.

3 Credits | Fall Semester

This didactic course will provide an overview of the field of Biomedical Informatics from different perspectives. This course will provide an overview of biology and medicine relevant to healthcare from an informatics perspective. This course focuses on utilizing data to solve relevant health and informatics problems that the healthcare system is facing. Emphasis is given to understanding the basic building blocks, various information resources, and the application areas of Biomedical Informatics. Students will learn to explore the process of developing and applying computational techniques for determining the information needs of healthcare providers and patients. This class uses lectures, flipped classroom approaches where needed as well as student-led discussions. Relevant topics include Electronic Health Records, Patient Quality Assessment and Improvements, Evidence-Based Medicine, Natural Language Processing, Consumer and Public Health Informatics.

3 Credits | Spring Semester

Translational bioinformatics is a field that enables transformation of basic science discoveries into clinically applicable knowledge. This provides opportunities for the practice of precision medicine and the application of systems approaches. This course will expose students to the wide range of biomedical data, from publicly available next-generation sequencing data to genetic and genomic data as applicable to cancer research. The course will comprise of a combination of lectures, invited seminars, and hands-on computer-based exercises utilizing web-based bioinformatics tools and publicly available databases Using different cancer types as examples, students will learn how to analyze data generated by genomics, epigenomics, transcriptomics, proteomics, metabolomics and other high-throughput approaches. The main goal is to understand these diseases from a Systems Perspective and learn to translate this knowledge from bench to bedside. Students will learn to perform NGS, RNAseq data analysis and use of many cancer resources.

2 Credits | Spring Semester

This didactic course is designed to provide students an in-depth understanding of molecular phenotyping technologies for basic, clinical and translational research. The course will cover the basics of mass spectrometry-based metabolomics approach. We will discuss strategies for data generation as well as multivariate data mining tools and finally the clinical applications of this technology for studying disease onset and progression, drug metabolism and toxicity, discovery and validation of disease biomarkers and the effect of different treatments (drugs, radiation etc.) on the overall metabolism. The course will also include laboratory sessions that would provide practical insights into operations of a mass spectrometer and the use of interactive software for data analysis.

2 Credits | Fall Semester
*Note: Students can take this on its own or as part of SYSM 5720.

This is a new, interactive journal club formatted course guided by GUMC faculty, focusing on recent research published in any area of Systems Medicine. Students will take turns presenting selected papers, critically analyze them and lead discussions. Papers will be selected in consultation with GUMC faculty. The main goal of the course is to help students to think and analyze a research paper critically.

3 Credits | Fall Semester
*Note: Students can take this course on its own or as part of SYSM 5720.

This course will cover major concepts, methods and tools of bioinformatics as applied to translational science and Cancer. The course will provide a strong foundation for students with any background in the computational analysis and interpretation of biological data. The course is designed as a combination of lectures and self-learning hands-on sessions. The hands-on session will cover the use of Next-generation sequencing data and other publicly available clinical data.

2 Credits | Spring Semester

The aim of this course is to integrate the chemical and physical sciences to provide the molecular basis of protein function using structural biology approaches as tools. For an understanding of biological function, detailed knowledge of the three-dimensional structures of biological macromolecules and their interactions with ligands is required. This course will provide the basic knowledge needed to understand “structure-function” relationships and concepts of drug design. Students will understand the effect of mutations in disrupting the three-dimensional structure and ultimately leading to diseases. Students will also be exposed to basic concepts of pharmacogenomics. The course is suitable for scientists wishing to update their knowledge of molecular structural biology, or as part of the background studies of research students, particularly those whose undergraduate studies were in a different area.

2 Credits | Spring Semester

The approach most people bring to problem solving is based on the assumption that the challenge before them can be decomposed into a subset of simpler problems, and that any challenge can be met through a process of addressing these simpler questions and then following them up a “decision tree.” In fact, most of the challenges facing us today do not lend themselves to such a straightforward decomposition. They exist in a complex, interconnected ecosystem where context is everything, and we must view the whole as more than the sum of its parts in order to effect change.

This course will introduce you to the world of systems and systems thinking. You will learn to consider and shape the posture you take towards the complex challenges you face. You will understand the importance off embracing paradox and factoring in the inherent biases we all bring to how we see a problem before us. You will also be introduced to tools and methods to help understand, reason with, and make better decisions with problems in a system context.

2 Credits | Spring Semester

This course will cover the dynamic relationship between the microbiota and disease expression. It will consist of lectures, invited guest speakers, panels, and audiovisual material – all focusing on the epigenetic role of the microbiota in influencing the development of disease. Several clinical conditions, including inflammatory bowel disease (Crohn’s and ulcerative colitis), celiac disease, allergy and asthma, obesity, autoimmune diseases, neuropsychiatric conditions and cancer, will be examined through a microbial lens to learn more about the contribution of changes in the microbiota to disease states. A standard treatment will be compared to emerging microbial therapies. Students will learn about the role of next-generation microbial sequencing, including indications for, and how to interpret current testing modalities.

2 Credits | Spring Semester

This 2-credit seminar course explores the social and policy implications of cutting-edge issues and controversies related to genomics and precision medicine. No prerequisites are required as understandable scientific background will be provided. Classes will be interactive, with scholarly discussions and policy debates. Students will (1) prepare a policy brief, which will be peer reviewed; (2) write “blog type” reflections online; and (3) deliver several mini-presentations throughout the semester. The course will culminate with a take-home final exam.

2 Credits | Spring Semester

A hands-on introduction to methods and concepts used in technology companies to drive innovation and their application to systems medicine. This course will introduce students to key concepts in design thinking and lean startup as well as implications for healthcare and systems medicine. An ongoing project during the term will help students learn to apply these ideas and bring the concepts to life. 

We will be using the Google design sprint methodology and its application to health situations. The course will be structured according to the phases of the design sprint (understand, define, sketch, sketch, decide, prototype, and validate). Learn more about the design sprint approach.

3 Credits | Spring Semester

This course is designed for master-level students in the Department of Biochemistry and Molecular & Cellular Biology. Students will be expected to gain familiarity with gross anatomy and become conversant with any medical professional, including the allied health field. Body regions that will be covered include the thorax, abdomen, pelvis, upper and lower limbs. Majority of the lectures will be delivered online, but weekly quizzes, both formative and summative will be present synchronously to assess student understanding. Student assessment will be performed using multiple choice exams, principally using identification type question, but a certain number of higher order type questions will also form part of the examination. Students will be required to pass all portions of the course, not just obtain a cumulative grade. At the completion of the thorax, abdomen and pelvis sections, students will be introduced to the cadaver and have an opportunity to view prosected cadavers in the laboratory. This latter activity will be considered enrichment but will be mandatory for all students enrolled.

1 Credit | Spring Semester

This is an interactive journal club formatted course with a mixture of presentations and hands-on sessions. The course will focus on recent research published in selected areas of Personalized Medicine. Students will present selected papers developing critical analysis skills and lead discussions. Papers will be selected in consultation with GUMC faculty. The main goal of the course is to help students to think and analyze a research paper in the new field of Personalized Medicine critically. The course will include a wet-lab session which will give the students experience of performing Genotyping.

3 Credits | Fall Semester

The sequencing of the human genome was the beginning of the acceleration of the “big data” era in biology. We have seen technological advances and the availability of mobile sequencers that can generate DNA sequencing data in a matter of a few hours. The advent of these mobile sequencers has made it possible to generate sequencing data in a classroom. The objective of this course is to provide hands-on experience in using one such hand-held sequencer, the MinION to sequence a piece of DNA. and carry out Next-Generation Sequence analysis. Students will have a hands-on experience in the extraction, purification, loading of the DNA to the sequencer and the analysis of the Next Generation data collected from the sequencer. The course will be a combination of lectures and hands-on providing students in the “know-how” of DNA sequencing and analysis.

2 Credits | Fall Semester

Biochemistry is fundamental to understanding the underlying cause of diseases and their treatments. This didactic course will be an intensive course, covering many aspects of biochemistry including biomolecules and metabolism. This course will be approached from a medical perspective. The course is designed as a combination of lectures and practical computer-based exercises utilizing functionalities of web-based resources. The students will experience the effect of mutations and polymorphisms on the genes that are causative of the underlying disease in each metabolic pathway. The lectures will be presented as a series of case studies. Most encountered clinical cases will form the core of the course. Aspects of Complementary and Integrative Medicine (CIM) approaches to health and disease states will be discussed. At the end of the course, students will be able to understand these diseases from a biochemical, informatics, and integrative medicine perspective.

3 Credits | Fall Semester

This course will cover conceptual aspects of machine learning in application to high-throughput biomedical data. Throughout the course, students will get an understanding of opportunities and limitations of machine learning in the context of pre-clinical and clinical research. The course is designed as a combination of online resources, practical assignments and workshops that will be conducted on-location and online. Throughout the course, we will review several examples that demonstrate successes and limitations of conventional machine learning tools and associated studies. This course will be run by experts from Pine Biotech.

1 Credit | Spring Semester

While breakthroughs abound in cancer research, there is a profound disconnection in translating these discoveries into clinical medicine. This new didactic course will be based on the application of computational biology and high throughput technologies to cancer research. The course is designed as a combination of lectures and practical computer-based exercises utilizing functionalities of web-based cancer resources. The course will also cover some aspects of pharmacogenomics. The students will experience the use and applications of informatics resources and tools to different types of cancer. The main goal is to understand these diseases from a Systems Perspective.

3 Credits | Fall Semester

This 3-credit seminar course explores how applying ethical frameworks can promote best practices and policies in systems medicine. We will analyze key components of systems medicine, including genomics, personalized/precision medicine, public health, drug development, big data, and artificial intelligence, including machine learning and natural language processing. We will also assess implementation considerations for various stakeholders, including patients, consumers, industry, research participants, underserved populations, and healthcare systems. Finally, we will consider how systems medicine approaches can be effectively leveraged to reduce health disparities and improve health equity. Students will participate in scholarly discussions, prepare brief presentations, and provide short written commentaries on several topics.

3 Credits | Fall Semester

This comprehensive 3-credit course delves into the interdisciplinary field of Systems Medicine and explores its integration with Artificial Intelligence (AI) in the context of healthcare. Students will learn how AI techniques, including machine learning, deep learning, and data analytics, can be leveraged to analyze complex biological systems, decipher disease mechanisms, and personalize medical treatments. The course covers foundational concepts in systems medicine, including omics technologies, network biology, and personalized medicine, while examining how AI methodologies can enhance our understanding of health and disease.

Throughout the course, students will explore the interdisciplinary intersection of Systems Medicine and AI within healthcare. Through engaging lectures, interactive discussions, illuminating case studies, and hands-on projects, they will delve into AI techniques such as machine learning, deep learning, and data analytics. These techniques will be applied to analyze complex biological systems and personalize medical treatments, with a particular focus on integrating real-world data extracted from Electronic Health Record (EHR) systems. By the end of the course, students will have gained practical skills in AI-enabled systems medicine and developed the ability to apply these techniques to real-world biomedical problems, leveraging EHR data to enhance their understanding and impact in healthcare.

3 Credits | Spring Semester

This course will cover key concepts in structural biology to provide students with a comprehensive understanding of the molecular basis of protein structure and function. Methodologies of structural determination such as X-ray crystallography, Nuclear Magnetic Resonance Spectroscopy, and Electron Microscopy will be covered. In addition, the course delves into the intersection of artificial intelligence (AI), drug design, and structural biology, exploring how advanced computational methods are revolutionizing the process of drug discovery. Through a blend of theoretical lectures and hands-on practical sessions, students will learn how AI techniques such as machine learning and molecular modeling are leveraged to analyze molecular structures, predict ligand-receptor interactions, and accelerate the identification of novel therapeutic compounds.

1 Credit | Fall Semester

The sequencing of the human genome that was completed in 2001 and the explosion of ”omic data” has accelerated our understanding of basic genetics and how we think of biology. We are now in the “omic” era of molecular biology that has given birth to the new field of Bioinformatics. All this data can be used meaningfully for biological and clinical research only if we can extract the relevant functional information from them and convert biological data into knowledge of biological systems. Fortunately, by using bioinformatics we can make headway in understanding and extracting relevant biological information from these sequences. The aim of this course is to introduce the various tools and resources that are available as applicable to biomedical research. This course is highly experiential with both lectures and “hands-on” sessions.

1 Credit | Spring Semester

This course is designed to provide students with a comprehensive background in the history of pharmacology and therapeutics leading to the current theory and practice of drug design and basic pharmacology, biochemistry, molecular biology and bioinformatics concepts that drive it. An understanding of fundamental biological and biotechnological concepts required to assess current and future approaches to drug discovery along the “critical path” from basic biomedical research to identification of cellular and molecular mechanisms of disease, drug targets, and rational design and high throughput screening of drug candidates will be gained.

3 Credits | Spring Semester

An introduction to bioinformatics in systems biology, covering microarray data analysis, proteomic/metabolomic informatics, and regulatory network and pathway analysis.

2 Credits | Fall & Spring Semesters

This course will cover NIH bioterrorism agents (categories A-C), which can be utilized as biological weapons. The microbiology of these agents will focus on structure, pathology, and virulence factors. The immune response to these agents will be presented. Viral agents will include Variola and hemorrhagic fevers (Ebola and Lassa). Bacterial agents will include B. anthracis, Yersinia pestis (plague), and Francisella tularensis (tularemia). Emerging infectious disease threats such as Nipah, Hantavirus, and SARS will also be covered. This course will cover NIH bioterrorism a

1 Credit | Fall Semester

This seminar will present a variety of nationally and globally recognized experts in the broad field of biohazardous threat agents and emerging infectious diseases. Individual topics will vary depending on the expertise of each speaker. Previous lectures have included:
D.A. Henderson: “From global smallpox eradication to biodefense”
David Kaplan: “Aum Shinrikyo”
Jeffrey Taubenberger: “Recovering the 1918 flu virus”
Don Burke: “Tracking new retroviruses in Central Africa”
Chad Roy: “Threat of aerosolized agents”

3 Credits | Spring & Summer Semesters

This course is an in-depth look at the central dogma of molecular biology. Emphasis will be placed on analysis of whole genomes and the impact of genome sequencing projects on biologists. Mechanisms of DNA replication, repair, and division and of gene expression in both prokaryotes and eukaryotes will also be discussed. Experimental approaches to issues in molecular biology will be emphasized using analysis of primary literature in addition to textbook readings.

2 Credits | Fall & Spring Semesters

This course provides students with an overview of the entire Drug Development process, from the inception of discovery to the final marketed product and review of the principles underlying the preclinical and clinical development of new therapeutic drugs and procedures. Presentations will describe and evaluate specific examples, and discussions to include regulatory, financial and ethical regulations that apply to Drug Development.

3 Credits | Fall Semester

The objective of the course is to explain in practical terms the basic principles of clinical trials, with particular emphasis on their scientific rationale, organization and planning, and methodology. Issues discussed include a design of randomized and non-randomized trials, size of a clinical trial, monitoring of trial progress, and some basic principles of statistical analysis. The intent is to present the methodology of clinical trials with emphasis on the practical aspects.

3 Credits | Fall Semester

Epidemiology overview and history; distributions of disease by time, place and person; association and causality; ecological studies; cross-sectional studies and surveys; case-control studies; analysis of case-control studies; types of bias in case-control studies; cohort studies; analysis of cohort studies; bias in cohort studies; population attributable risk; confounding factors; effect modification (interaction); analysis for confounding and interaction; multivariate analysis; sensitivity, specificity and screening; public health practice and prevention; special issues in cancer epidemiology, infectious disease epidemiology and genetic epidemiology. This course includes a discussion session.

3 Credits | Fall Semester

The Cancer Epigenetics course covers epigenetic mechanisms in human diseases, focusing on cancers. This is a combined lecture/literature review/discussion course designed for graduate students in Molecular/Cell Biology, Biochemistry, Physiology, Tumor Biology, Pharmacology, and Neuroscience. The course has five primary objectives:

Moreover, a broad range of topics will be covered by discussing landmark papers and emerging concepts in the field of epigenetic research. In the class, students will discuss background materials, including papers related to individual topics.

1. understanding the epigenetic regulation in normal & cancer cells
2. deciphering epigenetic pathways and molecular targets in malignant transformation
3. learning the impact of epigenetic alterations associated with cancers
4. reviewing recent advances in epigenetic issues/phenomena by highlighting the growing importance of epigenetic therapeutics in cancers
5. learning the scientific approaches/methods employed to define epigenetic-mediated cancer drivers and their therapeutic potential