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Foundation of Computational Biology

Course No. BIOL 601
Sections 101
Title Foundation of Computational Biology
Course Website
Prerequisite(s) a knowledge of basic ideas in genetics and molecular biology and an elementary knowledge of programming, data structures and algorithms is required, and some programming will be expected.
Instructor Qun Ma
  • Office Room No. : GITC 3801
  • Office Phone : 973-642-4497
  • Fax : 973-596-5777
  • Email : qun.ma@njit.edu
  • Website: http://web.njit.edu/~qma
  • Lab : The Applied Bioinformatics Laboratory
  • Instructor Office Hours

    Description This course assumes that someone coming from a background in computer science has a knowledge of basic ideas in genetics and molecular biology. We will discuss the biological and technological motivation of problems.

    For those with a background in biology, an elementary knowledge of programming, data structures and algorithms is required, and some programming will be expected.
    Topics Course Outline (15 week schedule)
    1 Sequence databases
    2 Mapping databases
    3 Information retrieval from biodatabases
    4 Genomic databases
    5, 6 DNA sequence analysis: predicting functional elements
    7 RNA secondary structure prediction
    8 Midterm
    9 Identifying microRNAs
    10 Sequence polymorphisms
    11 Haplotype mapping
    12, 13 Protein structure prediction
    14 Protein structure and function analysis
    15 Final

    The final will be take-home.

    Two classes will be devoted to presentations of projects.
    Text Book(s) Texts:
    1. Andreas D. Baxevanis and B.F. Francis Ouellette, Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Third Edition, 2005 (required)
    2. Arthur Lesk, Introduction to Bioinformatics, Oxford University Press (Recommended)
    Time & Place Tuesday 6:00 pm - 9:05 pm FAC 206
    Other Info Texts will be supplemented by scientific papers.

    Assignments:
    Some of the assignments will be hands on use of programming (using perl or python), use of databases and bioinformatics toolkits or tools on the web.

    Grades:
    Grades will be based on letters: a, b, c, d, f.

    Homework 25%
    Midterm 25%
    Project 25%
    Final 25%



    Academic Honor Code

    The NJIT academic honor code
    (http://www.njit.edu/academics/honorcode.php)applies in full to this
    class. Note in particular that copying programs, in full or in part, is
    forbidden. You may discuss ideas and concepts with your fellow
    students, but you may NOT copy any code.




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