Bioinformatics

The listing of a course description here does not guarantee a course’s being offered in a particular term. Please refer to the published schedule of classes on the MyBU Student Portal for confirmation a class is actually being taught and for specific course meeting dates and times.

• CDS BF 501: Masters Project
  Participation in a research project under the direction of a faculty advisor.
• CDS BF 502: Masters Project
  Participation in a research project under the direction of a faculty advisor.
• CDS BF 510: INST RACISM SCI
  INST RACISM SCI
• CDS BF 527: Bioinformatics Foundations
  Graduate Prerequisites: MS program standing in Bioinformatics. - Bioinformatics is the science of managing and analyzing large-scale molecular biology data (such as the DNA sequence of the human genome). The goal of this work is to identify interesting patterns and complex behaviors within living systems that would be difficult or impossible to see without computer assistance. This course introduces graduate and upper-level undergraduate students to the core data (molecular sequences, structures, phenotypes, and networks) and problems in bioinformatics, along with the databases and tools that have been developed to study them. Computer labs emphasize the acquisition of practical bioinformatics skills, including programming. Familiarity with basic molecular biology and arithmetic are the only prerequisites; no prior knowledge of advanced mathematics or programming is assumed.
• CDS BF 528: Genomic Data Analysis
  Undergraduate Prerequisites: MS program standing in Bioinformatics. - The objective of this course is expose students to the topics and technologies used in modern bioinformatics studies. The course covers a mix of biological and computational topics, including: high throughput genomics techniques; high throughput sequencing assays; differential gene expression techniques; phylogenetic techniques; microbiome/metagenomics techniques; metabolomics & proteomics; systems, network, and integrative biology; basic linux cluster usage; python & R scripting; computational workflow & replication strategies; genomics data visualization techniques; & biological databases.
• CDS BF 541: Bioinformatics Internship
  Internships provide the bridge between classroom/laboratory study and real- world employment. Each student must complete an internship with a minimum of 400 hours of on-the-job experience (e.g., 10 weeks full-time work in the summer). The format is very flexible, and part-time internships running concurrently with classes or employment are acceptable. Students must consult with their academic advisor to assess the suitability of a proposed internship.
• CDS BF 550: Foundations of Programming, Data Analytics, and Machine Learning in Python
  Graduate Prerequisites: 1. Intro programming course in any language or Intro to CS & Programming Using Python from EdX. 2. Ability to install fully functional Anaconda Python 3.7 (or later). 3. Bring laptop with #2 to class. - This course is for students trained in life sciences with minimal exposure to programming, statistics, and data analysis. The goal of the course is to develop both practical skills and theoretical foundations in handling data sets and developing simple computational solutions to problems arising in biomedical research. The course builds expertise in four areas: Programming, Mathematical Methods, Data Analytics, and Machine Learning.
• CDS BF 571: Dynamics and Evolution of Biological Networks
  Graduate Prerequisites: (CASMA226 & CASMA242) EK102 can be used in lieu of the MA242 pre-req. Familiarity with differential equations and linear algebra at equivalent levels and the con sent of instructor can be used in lieu of both pre-reqs. - The course focuses on mathematical models for exploring the organization, dynamics, and evolution of biochemical and genetic networks. Topics include: introductions to metabolic and genetic networks, deterministic and stochastic kinetics of biochemical pathways; genome-scale models of metabolic reaction fluxes; models of regulatory networks; modular architecture of biological networks.
• CDS BF 591: Bioinformatics Special Topics
  Bioinformatics Special Topics
• CDS BF 690: Bioinformatics Challenge Project
  Graduate Prerequisites: MS program standing in Bioinformatics. - Project course for first year Bioinformatics graduate students. Open-ended problems will involve bioinformatics as a key element, typically requiring the use of large data sets and computational analysis to make predictions about molecular function, molecular interactions, regulation, etc. Projects will be proposed by the Bioinformatics program faculty and selected by student in teams of three. The end result will be a set of predictions, some of which can be validated retrospectively using data available through online sources and some of which will require experimental validation. During the last 2 months of the academic year, teams will design feasible validation experiments in consultation with the experimental faculty.
• CDS BF 700: Advanced Topics in Bioinformatics
  Advanced Topics in Bioinformatics
• CDS BF 751: Omics Fundamentals
  Graduate Prerequisites: MSc. or PhD. program standing in Bioinformatics or consent of the instructor. - Modern research in the life sciences is an increasingly interdisciplinary endeavor where new fields of study have developed at the interfaces of biology, chemistry, physics, mathematics, and computer science. In many instances, the development of these new fields goes hand in hand with development of new experimental approaches to surveying the content of the cell. While traditional molecular cell biology and biochemistry courses often focus on the basic details of cell physiology and macromolecular (DNA, lipid, protein) structures, they too often neglect the quantitative aspects of number, scale, forces, etc. that are crucial to providing a larger context within living systems. This course aims at reframing the basic concepts of cell and molecular biology in a quantitative context and providing a basic overview of some of the key approaches used to develop a quantitative framework inside the cell. How this detailed information can then be applied to bioinformatics research problems will also be explored.
• CDS BF 752: Legal and Ethical Issues of Science and Technology
  This course is a broad introduction to law and ethics for biological scientists. Examining various theoretical approaches to bioethics and explore topics relevant to the biological sciences. Topics will include: authorship, research collaboration, research subject privacy, gene therapy, new reproductive techniques, ownership of data, direct to consumer genetic testing, funding, whistleblowing, and conflicts of interest. Additionally, when it comes to each of these topics we will also discuss the legal aspects and the role that government plays or can play.
• CDS BF 768: Biological Database Analysis
  Describes relational data models and database management systems. Teaches the theories and techniques of constructing relational databases with emphasis on those aspects needed for various biological data. Introduces the relational database query language SQL. Describes methods for ensuring data consistency and data retrieval efficiency. Object-oriented programming is introduced primarily as an implementation aid for constructing, loading, and accessing databases. Utilizes web-based programming tools to implement user access to databases. Emphasis will be on solving problems associated with large and complex data sets. Course includes a final project implementing a database using real data from a local biology/medical school lab.
• CDS BF 810: Laboratory Rotation System
  Three lab rotations are required during a PhD student's first year. One rotation must be experimental, one computational, and the third can be either option. Rotations typically last for a minimum of nine weeks and it is expected that the student will participate in the lab full time, except for time spent on classes and class work. Students report on each rotation by completing a Lab rotation Approval Form prior to the start of the rotation and a Lab Rotation Report Form at the end of the rotation.
• CDS BF 820: Bioinformatics Research Opportunities
  This course consists of a series of presentations by Bioinformatics faculty that focuses on research projects being investigated in their laboratories. Emphasis is placed on the description of collaborative projects involving experimental and computational approaches to Bioinformatics research problems.
• CDS BF 821: Bioinformatics Graduate Seminar
  During this class we will sample recent literature in areas of biology where quantitative analyses, computational models, and bioinformatics approaches have significant impact. Most papers in the list (available on the BU Blackboard site) were selected based on their innovative ideas and discoveries. Each week we will discuss two papers. Student presentations will be followed by open discussions focused both on the technical aspects and on the broader impacts.
• CDS BF 831: Translational Bioinformatics Seminar
  This course enrolls students who intend to pursue careers in medicine, dental medicine and/or medical research (either academic or industrial) as well as Bioinformatics graduate students. After commencing briefly with general introductory material (published reviews and other relevant background information), we proceed to examine, discuss and evaluate recent papers that directly illustrate the use of bioinformatics either in pre- clinical or clinical research settings. Papers will be drawn from high- impact journals such as Nature, Science, PNAS, Cell, and Science Translational Medicine. Students take turns presenting the papers to the class and provide brief critical reviews of each, both orally and in writing. They will also complete a term paper in the form of a research proposal directed to the goal of using bioinformatics to advance a medical intervention -- prognostic, diagnostic or therapeutic. Brief guest presentations by researchers working in BUSM (or BU Main Campus) laboratories will be arranged as appropriate. Previous guest facilitators have included faculty from the Department of Biostatistics, the Section of Computational Biomedicine, and the Department of Mathematics and Statistics as well as leading industrial research laboratories.
• CDS BF 900: PhD Research
  Graduate Prerequisites: restricted to pre-qualifying exam PhD students. - Participation in a research project under the direction of a faculty advisor leading to the preparation and defense of a PhD prospectus.
• CDS BF 901: Bioinformatics Thesis Research
  Graduate Prerequisites: restricted to post-qualifying exam PhD students. - Participation in a research project under the direction of a faculty advisor leading to the preparation and defense of a PhD prospectus. Variable cr.