> MIT 10.555 : bioinformatics
   methods | principles | applications

> spring 2004
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02.03.2004:
Welcome to 10.555! Syllabus and first lecture notes have been posted.

02.09.2004:
Lecture 2 notes have been posted.

MIT

> lecturers

Gregory Stephanopoulos Isidore Rigoutsos

> teaching assistant

Adrian Fay
  • afi@mit.edu

>the course

This course provides an introduction to Bioinformatics. We define this field by the principles and computational methods aiming at the upgrade of the information content of the large volume of biological data generated by genome sequencing, as well as cell-wide measurements of gene expression (DNA microarrays), protein profiles (proteomics), metabolites and metabolic fluxes. Additionally, bioinformatics is concerned with whole organism data, especially physiological variable measurements including organ function assessments, hormone levels, blood flow, neuronal activity etc., that characterize normal and pathophysiology. The overall goal of this data upgrade process is to elucidate cell function and physiology from a comprehensive set of measurements as opposed to using single markers of cellular function. Fundamentals from systems theory will be presented to define modeling philosophies and simulation methodologies for the integration of genomic and physiological data in the analysis of complex biological processes, e.g. genetic regulatory networks and metabolic pathways. Various computational methods will address a broad spectrum of problems in functional genomics and cell physiology, including; analysis of sequences, (alignment, homology discovery, gene annotation), gene clustering, pattern recognition/discovery in large-scale expression data, elucidation of genetic regulatory circuits, analysis of metabolic networks and signal transduction pathways. Applications of bioinformatics to metabolic engineering, drug design, and biotechnology will be also discussed.

> special features

  • Software tools
    The fundamentals of various methods will be presented in class (see syllabus). Software tools for the implementation of these methods will be provided in web sites or CDs.
  • Hands on sessions and demonstrations
    Approximately one third of each class will be devoted to demonstrations and hands on applications of methods. For students who can provide their own laptops executable files of software will be provided to facilitate the application of programs in class.
  • Real world problems
    Students can choose problems from their research as class project. Other problems from the instructor's research portfolio will also be presented.
  • Emphasis on functional genomics
    This class will address sequence driven problems (40%) and data driven problems (60%). The latter constitute the core of bioinformatics applications to cell physiology and functional genomics. As the volume of such data rapidly expands so will the need of bioinformatics methods to make physiological sense of them. This aspect of the course will be further enhanced by contributions from Dr. Joanne Kelleher, Professor of Physiology, George Washington University Medical School.

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