Location: Lafferre Hall E3508

Time: Wed. & Friday, 11:00 - 12:15

Instructors: Drs. Jianlin Cheng, Toni Kazic, Dmitry Korkin, Chi-Ren Shyu, Dong Xu

Office hours: Fri. 10:00 - 11:00, EBW 109

Coordinator: Dr. Jianlin Cheng, chengji@missouri.edu

Syllabus

Schedule and Assignments

Lectures

1. Introduction [slides]

Reading (first 19 pages): Venter et al.. The Sequence of Human Genome. Science, 2001.

2. Genome sequencing and assembly [slides]

Assignment: review several genome assembly software tools listed in the slides (scope, strength, weakness, usability, language, platform).

3. Gene annotation of a genome [slides]

Reading: M. Brent. Genome annotation past, present, and future: how to define an ORF at each locus, Genome Research, 2005.

4. Protein structure prediction [slides]

Reading (select one to review):
(1) Rost and Sander. Prediction of protein secondary structure at better than 70% accuracy, 1993. (topic: secondary structure prediction);
(2) Simons et al. Assebmly of protein tertiary structures from fragments with similar local sequences using simulated annealing and bayesian scoring function, 1997 (topic: ab initio protein structure prediction);
(3) Xu and Xu. Protein threading using PROSPECT: design and evaluation, 2001 (topic: protein threading);
(4) Zhang and Skolnick. Automated structure prediction of weakly homologous proteins on a genomic scale, 2003 (topic: template-based protein structure prediction);
(5) Cheng and Baldi. Improved residue contact prediction using support vector machines and a large feature set, 2007 (topic: protein contact map prediction).

5. Protein function prediction [slides]

Reading (select one to review):
(1) Friedberg. Automated function prediction - the genomic challenge. Brief. in Bioinformatics, 2006.
(2) Sharan et al. Network-based prediction of protein function. Mol. Syst. Biol., 2007.
(3) Gherardini and Helmer-Citterich. Structure-based function prediction: approaches and applications. Brief. Funct. Genomic. Proteomic., 2008.

6. Protein interaction prediction [slides]

Reading (select one to review):
(1) Shrabanek et al. Computational Prediction of Protein-Protein Interactions. Mol. Biotechnol., 2008. (Review)
(2) Gray et al. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations., JMB, 2003.
(3) Davis et al. Protein complex compositions predicted by structural similarity. Nucleic Acids Res.,2006.
(4) Korkin et al. Structural modeling of protein interactions by analogy: application to PSD-95. Plos Comput Biol., 2006.

7. Biological pathways and networks [slides]

Project

Description

Develop a software pipeline to assemble and annotate a bacteria genome in six steps (assembly, gene prediction, protein structure prediction, protein function prediction, protein interaction predition, and reconstruction of biological pathways and networks).

Data

Sequence reads in initial sequencing phase (reads_prime.seq), quality scores, and its description (reads_prime.xml)
Sequence reads in finishing phase (reads_closure.seq), quality scores, and its description (reads_closure.xml)
Description of file formats