CS3824 Introduction to Computational Biology and Bioinformatics - Spring 2008

Mon/Wed 2:30 - 3:45 pm PAM 2001

"Everything that the living things do ... can be described as the wiggling and jiggling of atoms" R. Feynman

"Nothing in Biology makes sense except in the light of evolution" Theodosius Dobzhansky.

Instructor:        Liqing Zhang
Office:              2160K Torgersen Hall
Phone:              (540)231-5040 (E-mail is strongly preferred)
Email:               lqzhang@vt.edu
Office Hours:   By appointment

Instructor:        Alexey Onufriev
Office:              2160C Torgersen Hall
Phone:              (540)231-4237 (E-mail is strongly preferred)
Email:               alexey@cs.vt.edu
Office Hours:    Just drop by any afternoon.

Text Books:

Date Tasks / Discussion Topics Presenter(s) Recommended Papers Recommended reading
Jan 14, 16 (1) Introduction
Zhang ... ...
Jan 23 (1) Intro into structural Bioinformatics

(2) The basics of protein structure
... SB pp. 15-41
Jan 28
The basics of nucleic acid structure

Onufriev ... SB pp. 41-75

"The Double Helix" by James D. Watson
Jan 30 Project Description Onufriev,Zhang (1) New York Times: Scientists Say They have Found a Code Beyond Genetics in DNA

(2) A Genomic Code for Nucleosome Positioning. E. Segal, Y. Fondufe-Mittendorf, L. Chen, A. Thastrom, Y. Field, I.K. Moore, J.Z. Wang, J. Widom. Nature , 2006
Feb 4 Algorithm in CBB Heath
  • Lecture notes
  • ...
    Feb 6 Algorithm in CBB Zhang ... ...
    Feb 11, 13 (1) Protein Folding

    Homology modeling

    Computational Prediction of Folding Rates
    Onufriev (1) The protein folding problem: when will it be solved? by: Ken A A Dill, S Banu B Ozkan, Thomas R R Weikl, John D D Chodera, Vincent A A Voelz Curr Opin Struct Biol (Volume 17, Issue 3, June 2007, Pages 342-346)

    (2) B. Kuhlman, G. Dantas, G. C. Ireton, G. Varani, B. L. Stoddard, D. Baker, Design of a Novel Globular Protein Fold with Atomic-Level Accuracy , Science, 302, 1364-1368, 2003. [No ned to go into every gory detail of every algorithm used, just focus on the general idea + key results ]

    (3) Plaxco et al. Contact order, transition state placement and the refolding rates of single domain proteins , J. Mol. Biol. 277, 985-994 (1998) [No need to read the whole thing, focus on the folding rate <-> contact order correlation]
    SB, pp 499-509, 547-558

    SB, pp 509-523

    SB, pp 443-476
    Feb 18, 20 Algorithm in CBB Heath (18th), Zhang (20th) ... ...
    Feb 25, 27 RNA Secondary Structure Prediction

    RNA Secondary Structure Prediction

    Drug Discovery

    (2) Kamb et al. (2007) Why is Cancer Drug Discovery so Difficult? Nature Rev. Drug Disc. 6: 115-120. ...
    Mar 10, 12 Genome rearrangement Zhang ... ...
    Mar 17, 19 Data mining in CBB Ramakrishnan ... ...
    Mar 24, 26 Problem solving environments, interdisciplinary teams in bioinformatics, the role of optimization, etc. Shaffer

  • Lecture 1 ppt file
  • Lecture 2 ppt file
  • Related Paper
  • Mar 31 Project progress. HW highlights. Onufriev

    ... ...
    April 2 Project progress. HW highlights. Zhang

    ... ...
    Apr 7, 9

    Understanding bacterial evolution
    Setubal ... ...
    Apr 14 Phylogenetic trees

    Zhang ... ...
    Apr 21, 23 Modeling and simulation Cao
  • Lecture and homework
  • Homework supplement
  • Apr 28,30 Epidemiology and population ecology Vullikanti and Madhav
  • Lecture
  • Homework

  • Class Project:

    Nucleosome positioning and the rate of gene evolution

    Homeworks (individual work required of each student):

  • HW on Structural Bioinformatics. Due by March 25th. Drop under Onufriev's office door.
  • Hw answers for Dr. heath's homework.
  • HW on Sequence analyses.