Location: EBW 240

Time: Tu & Thu, 9:30 - 10:45

Instructors: Drs. Jianlin Cheng, Gavin Conant, Dmitry Korkin, Dong Xu

Office hours: Thu. 10:45 - 11:45, EBW 109

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

Syllabus

Schedule and Assignments

Lectures

1. Introduction [PDF slides][PPT slides]

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

2. Genome sequencing and assembly [slides]

Assignment: review one paper listed in Slide 53.

3. Gene annotation of a genome [slides]

Assignment: read one of papers listed at the end of slides and write a one-page summary, due Sept. 8, 2011.

4. Protein structure prediction [slides]

Assignment: review the following paper and write a one-page summary (due Sept. 9, 2011). Y. Zhang. Protein structure prediction: when is it useful? Current Opinion in Structural Biology, vol. 19, 145-155, 2009.

5. Protein function prediction [slides]

Review the following paper (due 9/13):
Friedberg. Automated function prediction - the genomic challenge. Brief. in Bioinformatics, 2006.

6. Protein interaction prediction [slides]

Reading (select one to review): select one paper mentioned in the slides to review and write a one-page summary.

7. Biological pathways and networks [slides]

Assignment: review the network paper mentioned in the lectur. The assignment is due Sept. 21 (one day later than originally planned).

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

Tools

Genome Assembly Tools
  • A list genome assembly and mapping tools
  • Celera assembly tool
  • The Velvet assembly tool
    • Gene Prediction Tools
  • Glimmer
  • GeneMark
  • GeneScan
  • Jigsaw
  • FGENESH
  • RepeatMasker
    • Genome Browser
  • UCSC Genome Browser
  • Ensembl Genome Browser
  • NCBI MapView
  • CGView - Circular Genhome Viewer
    • Protein Structure and Function Databases
    Protein Data Bank(PDB), Gene Ontology, UniProt, Pfam

    Pathway and Protein Interaction Databases
     KEGG, Reactome, MIPS Protein Interaction Database, Database of Interacting Proteins (DIP), NIH Pathway Guide, BioCyc (including both EcoCyc and MetaCyc), BioModels, Metabolic network simulation, STRING - known and predicted protein interactions

     

     

     

    Related Courses taught by Prof. Jianlin Cheng

  • Supervised Machine Learning
  • Computational Modeling of Molecular Structures
  • Data Mining and Knowledge Discovery
  • Machine Learning for Bioinformatics
  • Problem Solving in Bioinformatics
  • Computational Optimization Mehtods