Bioinformatics & Computational Biology Program Courses

The courses listed below inlcude required courses of the core curriculum, research and milestone courses, as well as program specific advanced topics, seminars, journal clubs and tutorials for specialization in Bioinformatics & Computational Biology.

  • Professionalism and Research Conduct (PARC) | BBS 601

    Programs: Biochemistry & Molecular Pharmacology, Bioinformatics & Computational Biology, Cancer Biology, Cell Biology, Immunology & Microbiology, Interdisciplinary, MD/PhD, Neuroscience, Translational Science

    This is a required course for all 3rd year Basic Sciences students and all MD/PhD students entering doctoral study but who are not on the CPHR track. The PARC course helps to center our students in areas that are foundational to success in research - responsible data management, management of intellectual property, the ethical use of research subjects, recognizing and resolving conflicts of interest, professionalism in peer review and publishing, engaging mentors and career exploration and planning. The PARC course comprises faculty-led presentations and small group discussions with case studies and workshop material. An on line learning module (CITI training program comprising many case studies) is also included which must be completed before the end of the fall semester. Students required to take the fall PARC course will be block-registered.

    Coordinator: Anthony Carruthers

    Semester Offered: Fall 

    Last Taught: Fall 2015

  • Communicating Science | BBS 602

    Programs: Biochemistry & Molecular Pharmacology, Bioinformatics & Computational Biology, Cancer Biology, Cell Biology, Immunology & Microbiology, Interdisciplinary, Neuroscience, Translational Science

    This course seeks to help prospective scientists in the biological and medical sciences communicate their work effectively, in writing, graphics, and oral presentations. The course teaches how to prepare a research paper using words, statistics, and figures; how to present science to a lay audience; how to write a grant proposal; and how to present orally to scientific peers.

    Coordinator: Philip Zamore

    Semester Offered: Summer

    Last Taught: Taught every summer

  • Biomedical Sciences Block I - Lecture | BBS 611

    Programs: Biochemistry & Molecular Pharmacology, Bioinformatics & Computational Biology, Cancer Biology, Cell Biology, Immunology & Microbiology, Interdisciplinary, Neuroscience, Pathway to Graduate Study, Translational Science

    A series of lecturers presenting the principles of the sciences basic to medicine, emphasizing contemporary topics in biological chemistry.

    Coordinator: David Lambright

    Semester Offered: Fall

    Last Taught: Taught every fall

  • Biomedical Sciences Block I - RAPS | BBS 611R

    Programs: Biochemistry & Molecular Pharmacology, Bioinformatics & Computational Biology, Cancer Biology, Cell Biology, Immunology & Microbiology, Interdisciplinary, Neuroscience, Pathway to Graduate Study, Translational Science

    Problems sets and article reviews develop the deductive reasoning methods for interpretation of experimental data emphasizing comtempory topics in biological chemistry.

    Coordinator: David Lambright

    Semester Offered: Fall

    Last Taught: Taught every fall

  • Biomedical Sciences Block II - Lecture | BBS 612

    Programs: Biochemistry & Molecular Pharmacology, Bioinformatics & Computational Biology, Cancer Biology, Cell Biology, Immunology & Microbiology, Interdisciplinary, Neuroscience, Pathway to Graduate Study, Translational Science

    A series of lecturers presenting the principles of the sciences basic to medicine, emphasizing contemporary topics in transfer of genetic information.

    Coordinator: Paul Kaufman

    Semester Offered: Fall

    Last Taught: Taught every fall

  • Biomedical Sciences Block II - RAPS | BBS 612R

    Programs: Biochemistry & Molecular Pharmacology, Bioinformatics & Computational Biology, Cancer Biology, Cell Biology, Immunology & Microbiology, Interdisciplinary, Neuroscience, Pathway to Graduate Study, Translational Science

    Problems sets and article reviews develop the deductive reasoning methods for interpretation of experimental data emphasizing comtempory topics in the transfer of genetic information.

    Coordinator: Thomas Fazzio

    Semester Offered: Fall

    Last Taught: Taught every fall

  • Biomedical Sciences Block III - Lecture | BBS 613

    Programs: Biochemistry & Molecular Pharmacology, Bioinformatics & Computational Biology, Cancer Biology, Cell Biology, Immunology & Microbiology, Interdisciplinary, Neuroscience, Pathway to Graduate Study, Translational Science

    A series of lecturers presenting the principles of the sciences basic to medicine, emphasizing contemporary topics in cellular architecture and regulation.

    Coordinator: Peter Pryciak

    Semester Offered: Spring

    Last Taught: Taught every spring

  • Biomedical Sciences Block III - RAPS | BBS 613R

    Programs: Biochemistry & Molecular Pharmacology, Bioinformatics & Computational Biology, Cancer Biology, Cell Biology, Immunology & Microbiology, Interdisciplinary, Neuroscience, Pathway to Graduate Study, Translational Science

    Problems sets and article reviews develop the deductive reasoning methods for interpretation of experimental data emphasizing comtempory topics in cellular architecture and regulation.

    Coordinator: Peter Pryciak

    Semester Offered: Spring

    Last Taught: Taught every spring

  • Using Animals in Biomedical Research | BBS 701

    Programs: Biochemistry & Molecular Pharmacology, Bioinformatics & Computational Biology, Cancer Biology, Cell Biology, Immunology & Microbiology, Interdisciplinary, Neuroscience, Translational Science

    It is to the benefit of both science and animals to have a formal understanding of animal needs and animal use in the research environment. The goal of this course is to provide a sufficient appreciation of laboratory animal biology, care, and use to engender better science and enhanced animal welfare. Topics include controversies surrounding animal use in research; choosing an animal model; the Institutional Animal Care and Use Committee; normative biology of rodent and non-rodent laboratory animals; diseases and other stressors and their effects on research; humane experimental endpoints and pain and its alleviation. There are also two laboratory sessions.

    Coordinator: Jerald Silverman

    Semester Offered: Fall

    Last Taught: Fall 2015

  • Molecular Evolution | BBS 705

    Programs: Bioinformatics & Computational Biology

    The course will focus on the quantitative study of molecular evolution using sequence and structural data, showing how both classical and novel methods in population genetics, bioinformatics and computational biology can be used to assess the variability in the genomic sequences and make inferences about the underlying processes of natural selection and evolution. The course is primariy aimed at the students interested in quantitative aspects of biology, and may be useful to practicing biologists desiring a deeper understanding of the computational and stastical techniques.

    Coordinator: Konstantin Zeldovich

    Semester Offered: Spring

    Last Taught: Spring 2014

  • Human Genetics | BBS 736

    Programs: Biochemistry & Molecular Pharmacology, Bioinformatics & Computational Biology, Cancer Biology, Cell Biology, Immunology & Microbiology, Interdisciplinary, Neuroscience, Translational Science

    This course focuses on the human genetic knowledge and concepts which underlies almost every aspect of human health, both in normal function and disease. We will cover chromosomal, single gene, and multifactorial disorders, including quantitative analysis of Mendelian and non-Mendelian inheritance, human cancer genetics, and recent developments in human genome research. Problem solving will involve clinical, molecular and statistical data. We hope to provide a framework for understanding a fast growing and highly technical field, and an appreciation of how current research impacts many aspects of medicine as well as biomedical research. This course follows the Medical School calendar - check with Course Coordinator regarding class schedule.

    Course Coordinator: John Landers

    Semester Offered: Fall

    Last Taught: Fall 2015

  • Advanced Topics in Bioinformatics | BBS 741

    Programs: Biochemistry & Molecular Pharmacology, Bioinformatics & Computational Biology

    The Adanced Topics in Bioinformatics course covers several important areas of modern bioinformatics and computational biology. The course is aimed not only at students specializing in bioinformatics, but also general biology students who would like to utilize bioinformatics tools in their daily research. The course will begin with an overview of modern sources of bioinformatics data, including high-throughput sequencing and microarrays, followed by a thorough presentation of sequence search and alignment algorithms, and the structure of the eukaryotic genome. Next, we will introduce population genetics - spanning from molecular phylogenetics to natural selection, with an emphasis on analyzing genomic datasets. The biophysical section of the course will include discussions of protein structure and folding, as well as the physical architecture of the genome in vivo, and the relations between sequences and structures for proteins and DNA. The course will include 10 lectures, followed by work on individual or group research projects, presented in lieu of the final exam.

    Course Coordinator: Zhiping Weng

    Semester Offered: Spring

    Last Taught: Spring 2015

  • Quantitative Informatics in Biology and Medicine | BBS 785

    Programs: Bioinformatics & Computational Biology, Translational Science

    The goal of this course is to introduce GSBS graduate students to the informatics approaches spanning bioinformatics to medical informatics and epidemiology. The course is structured in 5 week sections covering fundamentals of bioinformatics, applications of bioinformatics and genomics, and clinical research informatics.

    Course Coordinator: Jeffrey Bailey

    Semester Offered: Fall

    Last Taught: Has not been taught within 

  • Bioinformatics Basics: Sequence Analysis Bootcamp | BBS 809

    Programs: Bioinformatics & Computational Biology

    This is a six-week, one-credit course that will consist of a series of lectures on Unix , R language and bioinformatics tools for molecular biologists. The main goal is to introduce the audience to the basics of the bioinformatics of deep sequencing data analysis. No prior computer or programming skills are required to follow the lectures. This bootcamp starts with a quick introduction to the Unix environment. Then genomic databases and file formats will be discussed. Then usage of Galaxy, a graphical user interface for bioinformatics tools, will be demonstrated. This is followed by the basics of RNA-Seq data analysis and visualizing RNA-Seq data. The last part of this bootcamp is on statistical analysis. A brief introduction to R programming language is followed by statistical tools and methods for RNA-Seq data analysis. Performance on assignments (problem sets) will determine the course grade.

    Course Coordinator: Manuel Garber

    Semester Offered: Spring

    Last Taught: Fall 2015

  • Laboratory Rotation | BBS 850

    Programs: Biochemistry & Molecular Pharmacology, Bioinformatics & Computational Biology, Cancer Biology, Cell Biology, Immunology & Microbiology, Interdisciplinary, Neuroscience, Translational Science

    Laboratory rotations are defined periods of research experience under the direction of a faculty member. They are intended to familiarize the student with concepts and techniques in several areas of research and to assist the student in evaluating research laboratories and projects that might be developed into a dissertation project. The student will participate in an ongoing research project, gain familiarity with concepts underlying the research, acquire a working knowledge of techniques used in the research, and write a report and present an oral summary of the results of the research.

    Course Coordinator: Faculty member in whose lab student is working

    Semester Offered: Fall, Spring

    Last Taught: Taught every Fall and Spring semester

  • Laboratory Rotation | BBS 851

    Programs: Biochemistry & Molecular Pharmacology, Bioinformatics & Computational Biology, Cancer Biology, Cell Biology, Immunology & Microbiology, Interdisciplinary, Neuroscience, Translational Science

    Laboratory rotations are defined periods of research experience under the direction of a faculty member. They are intended to familiarize the student with concepts and techniques in several areas of research and to assist the student in evaluating research laboratories and projects that might be developed into a dissertation project. The student will participate in an ongoing research project, gain familiarity with concepts underlying the research, acquire a working knowledge of techniques used in the research, and write a report and present an oral summary of the results of the research.

    Course Coordinator: Faculty member in whose lab student is working

    Semester Offered: Summer

    Last Taught: Taught every Summer

  • BBS Qualifying Exam | BBS 860

    Programs: Biochemistry & Molecular Pharmacology, Bioinformatics & Computational Biology, Cancer Biology, Cell Biology, Immunology & Microbiology, Interdisciplinary, Neuroscience, Translational Science

    Students are required to register for this course in the fall semester of the academic year in which they are to pass their Qualifying Examination.

    Course Coordinator: Mary Ellen Lane

    Semester Offered: Fall

    Last Taught: Taught every year 

  • BBS TRAC Meeting | BBS 865

    Programs: Biochemistry & Molecular Pharmacology, Bioinformatics & Computational Biology, Cancer Biology, Cell Biology, Immunology & Microbiology, Interdisciplinary, Neuroscience, Translational Science

    All Graduate Students are required to have at least one TRAC meeting each academic year. After passing their Qualifying Examination and selection of their TRAC, students are required to register for this course each fall semester until their Dissertation Advisory Committee is formed.

    Course Coordinator: Mary Ellen Lane

    Semester Offered: Fall

    Last Taught: Taught every year

  • Pre-Qualifying Research | BBS 870

    Programs: Biochemistry & Molecular Pharmacology, Bioinformatics & Computational Biology, Cancer Biology, Cell Biology, Immunology & Microbiology, Interdisciplinary, Neuroscience, Translational Science

    This course is for students who have selected a Program and Thesis Advisor but who have not yet passed their Qualifying Examination.

    Course Coordinator: Student's Thesis Advisor

    Semester Offered: Fall, Spring, Summer

    Last Taught: Taught every semester

  • Thesis Research | BBS 900

    Programs: Biochemistry & Molecular Pharmacology, Bioinformatics & Computational Biology, Cancer Biology, Cell Biology, Immunology & Microbiology, Interdisciplinary, Neuroscience, Translational Science

    Students register for Thesis Research fall term of year three of the program, after passing the Qualifying Exam.

    Course Coordinator: Student's Thesis Advisor

    Semester Offered: Fall, Spring, Summer

    Last Taught: Taught every semester

  • Graduate Research | BBS 990

    Programs: Biochemistry & Molecular Pharmacology, Bioinformatics & Computational Biology, Cancer Biology, Cell Biology, Immunology & Microbiology, Interdisciplinary, Neuroscience, Translational Science

    Students register for Graduate Research fall term of year four in the PhD Program and will continue to register each semester until they complete all remaining requirements.

    Course Coordinator: Student's Thesis Advisor

    Semester Offered: Fall, Spring, Summer

    Last Taught: Taught every semester

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