Fall 2022
Introductory Bioinformatics
Soohyun Lee PhD, Senior Bioinformatics Scientist, Exact Sciences
This course is designed to cover an introductory level overview of bioinformatics. It covers commonly used bioinformatics tools and algorithms as well as standard formats, with the focus on DNA/RNA sequence and sequencing data analysis. The topics include sequence alignment, motif detection, conservation analysis, Markov models, short-read sequencing data alignment, variant detection and visualization, peak calling, clustering methods, standard formats, random access tools, and performance analysis. Web-based tools and databases are also covered. Pipeline development frameworks and cloud-based approaches are discussed briefly. This course does not include artificial intelligence or machine learning techniques or theoretical analysis of algorithms. Programming is not the focus of the course, but students are welcome to apply their programming skills to the course material.
Prerequisites: Basic knowledge of molecular biology (DNA, RNA, and protein) required. Knowledge in genomics and epigenetics a plus but not required. Statistics and programming skills a plus but not required.
Spring 2023
Introductory Bioinformatics
Soohyun Lee PhD, Senior Bioinformatics Scientist, Exact Sciences
This course is designed to cover an introductory level overview of bioinformatics. It covers commonly used bioinformatics tools and algorithms as well as standard formats, with the focus on DNA/RNA sequence and sequencing data analysis. The topics include sequence alignment, motif detection, conservation analysis, Markov models, short-read sequencing data alignment, variant detection and visualization, peak calling, clustering methods, standard formats, random access tools, and performance analysis. Web-based tools and databases are also covered. Pipeline development frameworks and cloud-based approaches are discussed briefly. This course does not include artificial intelligence or machine learning techniques or theoretical analysis of algorithms. Programming is not the focus of the course, but students are welcome to apply their programming skills to the course material.
Prerequisites: Basic knowledge of molecular biology (DNA, RNA, and protein) required. Knowledge in genomics and epigenetics a plus but not required. Statistics and programming skills a plus but not required.
Fall 2022
Ethics and Trends in Biotechnology
Timothy J. Furlan PhD, Burnett Family Distinguished Chair in Ethics, University of St. Thomas, Director, Center for Ethical Leadership, and Senior Editor, Pediatric Ethicscope
Biotechnology offers exciting and promising prospects for healing the sick and relieving suffering. But exactly because of their impressive powers to alter the workings of body and mind, the dual uses of the same technologies also make them attractive to people who are not sick, but who would use them to look younger, perform better, or feel happier. These applications of biotechnology are already presenting us with some unfamiliar and very difficult challenges. In this course, we consider such possible beyond therapy uses and explore both their scientific basis and the ethical and social issues they are likely to raise. We consider how pursuing the goals of better children, superior performance, ageless bodies, or happy souls might be aided or hindered, elevated or degraded, by seeking them through a wide variety of technological means. Among the biotechnological techniques considered are techniques for screening genes and testing embryos, choosing sex of children, modifying the behavior of children, augmenting muscle size and strength, enhancing athletic performance, slowing senescence, blunting painful memories, brightening mood, and altering basic temperaments. Toward the end of the course, we begin to ask what kinds of human beings and what sort of society we might be creating in the coming age of biotechnology.
Prerequisites: BIOS E-1a, BIOS E-1b, BIOS E-12, or the equivalents.
Spring 2023
Ethics and Trends in Biotechnology
Masha Fridkis-Hareli PhD, President, ATR, LLC
Biotechnology offers exciting and promising prospects for healing the sick and relieving suffering. But exactly because of their impressive powers to alter the workings of body and mind, the dual uses of the same technologies also make them attractive to people who are not sick, but who would use them to look younger, perform better, or feel happier. These applications of biotechnology are already presenting us with some unfamiliar and very difficult challenges. In this course, we consider such possible beyond therapy uses and explore both their scientific basis and the ethical and social issues they are likely to raise. We consider how pursuing the goals of better children, superior performance, ageless bodies, or happy souls might be aided or hindered, elevated or degraded, by seeking them through a wide variety of technological means. Among the biotechnological techniques considered are techniques for screening genes and testing embryos, choosing sex of children, modifying the behavior of children, augmenting muscle size and strength, enhancing athletic performance, slowing senescence, blunting painful memories, brightening mood, and altering basic temperaments. Toward the end of the course, we begin to ask what kinds of human beings and what sort of society we might be creating in the coming age of biotechnology.
Prerequisites: BIOS E-1a, BIOS E-1b, BIOS E-12, or the equivalents.
Spring 2023
RNA Biology and Therapeutics
Kaveh Daneshvar PhD, Principal Scientist, Tome Biosciences
RNA molecules can store and transfer genetic information, as well as regulate cellular processes through enzymatic activity and their interaction with other biomolecules. In the past decade, advances in next-generation sequencing have revealed new classes of RNAs and the multiple layers of information and functions they carry. The newly discovered functions of different classes of RNA molecules and their roles in human development and disease have led to the emergence of RNA therapeutics. This course explores the intersection of modern basic and translational research on RNA biology along with the biotechnology industry's drug development efforts around RNA therapeutics. The course offers a unique opportunity for students, researchers, and biotechnology innovators to expand their knowledge about the growing science of RNA therapeutics and to develop a deep understanding of RNA-focused drug development in the biotech industry. This course opens with an introduction to the RNA world, including evolutionary theories about biomolecules, fundamental concepts related to the structure and functions of RNAs, current classifications of RNA molecules, and modern tools and techniques for studying RNAs. The course then covers current classes of RNA molecules and their roles in normal biology and in disease. This course focuses on two classes of RNA therapeutics: drugs that target normal or abnormal RNA transcripts (for example, small molecules, siRNAs, and anti-sense RNAs) and RNA-editing systems; and drugs and vaccines composed of RNAs.
Prerequisites: BIOS E-12.
Fall 2022
Proseminar: Introduction to Graduate Studies in Biotechnology
Margaret A. Lynch PhD, Director of Undergraduate-Faculty Research Partnerships, Brandeis University
In this proseminar, we focus on science writing, data interpretation, and collaborative and independent experimental design. Students who successfully complete the course are those who demonstrate an ability to assess information from the primary scientific literature, a command of oral and written communication skills, and the ability to generate a logical progression of experiments to help validate or nullify their hypothesis. Reading materials include publications on scientific writing, experimental design, and peer-reviewed journal articles. Because skills learned in this course are useful in subsequent courses, it is the first course that prospective Master of Liberal Arts (ALM) candidates should take toward the degree (or the second, if they are completing the expository writing prerequisite). While not designed to be a thesis or capstone proposal course, this course does serve as a foundation for eventual work on the thesis or capstone. This is the required admission course for the ALM in biotechnology. Students interested in the ALM in biology should enroll in BIOS E-200.
Prerequisites: Instructors assume that students already have undergraduate degrees in an area of life, physical, or computer science, as well as professional scientific training. Scientists coming from a physical or computer science background should successfully complete BIOS E-1a and BIOS E-1b as well as BIOS E-12 or their equivalents before attempting to take BIOT E-200. EXPO E-42c is strongly recommended. Students must earn a satisfactory score on the mandatory test of critical reading and writing skills or a B or higher grade in the alternate expository writing course.
Spring 2023
Proseminar: Introduction to Graduate Studies in Biotechnology
Elizabeth Wiltrout Leary PhD, Senior Program Manager, Clinical and Translational Science Institute, Tufts Medical Center
In this proseminar, we focus on science writing, data interpretation, and collaborative and independent experimental design. Students who successfully complete the course are those who demonstrate an ability to assess information from the primary scientific literature, a command of oral and written communication skills, and the ability to generate a logical progression of experiments to help validate or nullify their hypothesis. Reading materials include publications on scientific writing, experimental design, and peer-reviewed journal articles. Because skills learned in this course are useful in subsequent courses, it is the first course that prospective Master of Liberal Arts (ALM) candidates should take toward the degree (or the second, if they are completing the expository writing prerequisite). While not designed to be a thesis or capstone proposal course, this course does serve as a foundation for eventual work on the thesis or capstone. This is the required admission course for the ALM in biotechnology. Students interested in the ALM in biology should enroll in BIOS E-200.
Prerequisites: Instructors assume that students already have undergraduate degrees in an area of life, physical, or computer science, as well as professional scientific training. Scientists coming from a physical or computer science background should successfully complete BIOS E-1a and BIOS E-1b as well as BIOS E-12 or their equivalents before attempting to take BIOT E-200. EXPO E-42c is strongly recommended. Students must earn a satisfactory score on the mandatory test of critical reading and writing skills or a B or higher grade in the alternate expository writing course.
Spring 2023
Regulatory Aspects of Drug Development
Jonathon Parker PhD, Vice President, Head of Global Regulatory Sciences, Cerevel Therapeutics
The course provides an overview of the prescription drug development process and regulatory considerations for this process, including small molecules, biologics, and gene therapy. It focuses on the phases of pharmaceutical development, aspects influencing the pharmaceutical industry, and the regulatory themes and healthcare concepts that shape the decisions having an impact on the entire process.
Fall 2022
Biomedical Product Development
Sujata K. Bhatia PhD, MD, Professor of Microbiology and Immunology, Drexel University College of Medicine
This course examines the design and development of new therapeutic products. Students learn through case-based studies of product development for pharmaceuticals, biologics, medical devices, and combination therapies. The course describes the steps of biomedical product development, from conceptualization, to design, to manufacturing, to regulatory approval and commercialization. The course discusses both technical and business factors that contribute to the success or failure of new biomedical products. Appropriate design of preclinical and clinical trials is also included. Students gain an appreciation for emerging technologies in stem cells, gene therapy, tissue regeneration, personalized medicine, and targeted therapies. Additionally, students learn about the special challenges presented by emerging biomedical technologies. By the end of the course, each student completes a project to propose a new biomedical device and identify the regulatory strategy, technical milestones, and business milestones for the new device.
Prerequisites: Background in introductory biology and chemistry.
Fall 2022
Immunoassay Design and Development
Masha Fridkis-Hareli PhD, President, ATR, LLC
This introductory course explores assays commonly used in drug discovery and development. Immunoassays are key in characterization of drug candidates for efficacy and safety prior to market authorization. The overall goal of the course is to provide students with knowledge of different types of immunoassays including enzyme-linked immunosorbent assays (ELISA), flow cytometry, and cell-based assays. Topics include design and optimization process, reagent selection, assay validation, and implementation for various applications in drug profiling.
Fall 2022
Precapstone: Business Ideas and Entrepreneurial Innovation
Steven Denkin PhD, Director and Research Advisor, Biotechnology, Harvard Extension School - Nicolas Labovitis
This precapstone course prepares students to write and present their business plan in the capstone. It is mandatory for candidates in the Master of Liberal Arts, biotechnology, who wish to register for BIOT E-599 in the spring. Through idea discovery, market research, and prototype development, students identify an innovative biotechnology product or application. In addition to idea generation and development, students receive guidance and advising to work effectively in teams to develop and propose a viable idea, and write a draft business plan. During the semester, students meet with industry experts to discuss best practices.
Prerequisites: Registration is limited to officially admitted candidates in Master of Liberal Arts, biotechnology, who are in their penultimate semester. Prospective candidates and students with pending admission applications are not eligible. Candidates must be in good academic standing and in the process of successfully completing all degree requirements except the capstone, BIOT E-599, which they must enroll in the upcoming spring term as their final course. Candidates who do not meet these degree requirements are dropped from the course.
Spring 2023
Capstone: Business Ideas and Entrepreneurial Innovation
Steven Denkin PhD, Director and Research Advisor, Biotechnology, Harvard Extension School - Beth Zielinski-Habershaw PhD, Coordinator of Training, Pharmaceutical Development Institute, University of Rhode Island
This capstone course provides an opportunity for biotechnology professionals to create a business plan for a new biotechnology company, a ground-breaking drug, or an emerging technology such as a diagnostic or medical device. The biotech business plan includes background research on the idea and investigation of the following: market opportunity, market strategy, funding, intellectual property, patents, and management. In addition to the business plan report, each student writes his or her own executive summary. During the semester, students meet with industry experts to discuss best practices.
Prerequisites: Registration is limited to officially admitted candidates in the Master of Liberal Arts, biotechnology, capstone track. Candidates must be in good academic standing, ready to graduate in May with only the capstone left to complete (no other course registration is allowed simultaneously with the capstone). Prospective candidates and students with pending admission applications are not eligible. Candidates must have earned a B-minus or higher grade in BIOT E-597 in the prior fall term. Candidates who do not meet these requirements are dropped from the course.