BIMM 140 Lecture Course Information

 

Outline:

  1. Objectives
  2. Grading
  3. Textbooks and Readings
  4. Other Relevant Books

 

BIMM 140 Course Objectives

In this course, you will learn about publicly available data resources and a variety of approaches to the analysis of nucleic acid and protein sequences. These approaches comprise the core bioinformatics techniques used in genomic and post-genomic projects.

In the lectures we will present the concepts and algorithms behind the methods. The Quizzes and Final Exam will cover these lectures and the assigned readings; it will not cover the details of how to run specific software.

BIMM 140 will examine a broad range of topics in a short period. Our attention will focus on the available public data resources and how to find relevant information, the detection of homologous sequences and how they are used to create an "information map" allowing us to make inferences about the structure and function of novel molecules based on previously known molecules, nucleic acid and protein structure prediction methods, phylogenetic relationships, and brief looks at homology based structural modeling and human haplotype analysis.

 

Grading:

BIMM 140 Grading

Course Requirements

Content

% of
Grade
Quiz 1: Friday 11 April;
20 min, in Disc Session		 31 Mar - 9 Apr Lecs 10%
Quiz 2: Friday 25 April;
20 min, in Disc Session		 11 Apr - 23 Apr Lecs 10%
Quiz 3: Friday 9 May;
20 min, in Disc Session		 25 Apr - 7 May Lecs 10%
Quiz 4: Friday 23 May;
20 min, in Disc Session		 9 May - 21 May Lecs 10%
Final Exam: Thurs 12 June
11:30 - 2:30; WLH 2207		 Entire class 60%

 

Textbooks and Readings:

 

  1. Required Textbook: "Bioinformatics: Sequence and Genome Analysis. " David W. Mount.

    This new book covers almost all of the material covered in this course in sufficient detail that, although expensive, it should be worth keeping as a reference. Two copies of the text are on reserve in the Biomed library. Chapter readings are associated with given lectures as shown in the Syllabus.

    Questions on the Quizzes and Final Exam will, in part, be based on material in the required text.


Other Relevant Books:

In addition to the textbook and course reader used for this course, the following books cover some or all of the topics of this course, with varying degrees of mathematical rigor. Several other books are also available (search on 'bioinformatics' or 'computational biology' at amazon.com !!). Some of these books are, or will be, on reserve in the Biomedical Library:

  1. "Bioinformatics: Sequence and Genome Analysis." David Mount. Cold Spring Harbor Laboratory Press. 2001.
  2. "Developing Bioinformatics Computer Skills." Cynthia Cibas and Per Jambeck. O'Reilly and Associates. 2001.
  3. "Statistical Methods in Bioinformatics: An Introduction." Warren Ewens and Gregory Grant. Springer Verlag. June, 2001.
  4. "Bioinformatics: Sequence, Structure, and Databanks - A Practical Approach." Ed., Des Higgins and Willie Taylor. Oxford University Press. 2000.
  5. "Computational Molecular Biology: An Algorithmic Approach." Pavel Pevzner. MIT Press. 2000.
  6. "Data Analysis and Classification for Bioinformatics." Arun Jagota. AKJ Academics. 2000.
  7. "Post-Genome Informatics." Minoru Kanehisa. Oxford University Press. 2000.
  8. "Bioinformatics: Methods and Protocols." Eds., Stephen Misener and Stephen Krawetz. Human Press. 2000.
  9. "Computational Molecular Biology: An Introduction." Peter Clote and Rolf Backofen. John Wiley and Sons. 2000.
  10. "Bioinformatics Basics: Applications in Biological Science and Medicine." Hooman Rashidi and Lukas Buehler. CRC Press. 1999.
  11. "Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids." Richard Durbin, S. Eddy, A. Krogh, and G. Mitchison. Cambridge University Press. 1999.
  12. "Bioinformatics: The Machine Learning Approach." Pierre Baldi and Soren Brunak. MIT Press. 1998.
  13. "Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology." Dan Gusfield. Cambridge University Press. 1997.
  14. "Bioinformatics: The Machine Learning Approach." Pierre Baldi and Soren Brunak. MIT Press, 1998.
  15. "Introduction to Computational Molecular Biology." Joao Meidanis and Joao Carlos Setubal. PWS Publishing, Boston, 1997.
  16. "Computational Methods in Molecular Biology." Eds, S. Salzberg, D. Searls, and S. Kasif. Elsevier Science, 1997.
  17. "The Secrets of Life: A Mathematician's Introduction to Molecular Biology." Eds., Eric S. Lander and Michael S. Waterman. National Academy of Sciences Press, 1997.
  18. "DNA Sequencing : From Experimental Methods to Bioinformatics." Luke Alphey. Springer Verlag, 1997

Somewhat older and out-of-date but still very useful books:

  1. "Sequence Analysis Primer." Ed., Michael Gribskov and John Devereux. Oxford University Press, 1992.
  2. "Of URFs and ORFs: A Primer on How to Analyze Derived Amino Acid Sequences." Russell F. Doolittle. University Science Books. 1986.
  3. "Molecular Evolution: Computer Analysis of Protein and Nucleic Acid Sequences." Ed., Russell F. Doolittle. Methods of Enzymology, Vol 183. 1990.
  4. "Computer Methods for Macromolecular Sequence Analysis." Ed., Russell F. Doolittle. Methods of Enzymology, Vol 266. 1996.
  5. "Introduction to Computational Biology Maps, Sequences, and Genomes." Michael S. Waterman. CRC Press. 1995.
  6. "Computer Analysis of Sequence Data", parts I and II, Ed, Annette M. Griffin and Hugh G. Griffin, Humana Press, 1994.
  7. "Biocomputing: Informatics and Genome Projects." Ed, Douglas W. Smith. Academic Press. 1993.