582618 Proteomics & bioinformatics (2 cr)

"Proteomics & bioinformatics" course gives an introduction to the available proteomic technologies and the data mining tools. It covers the essential elements of the proteomic technology and its applications. With the usage of several examples the importance of the proteomics applications will be illustrated.

Results of the course are available in the CS intranet and on the 2nd floor noticeboard.

Note: Lecture slides updated on 16 May 2007!

Lecture Schedule

7.5.2007	Lecture slides: ppt Introduction into the -ome terms: Genome, Transcriptome, Proteome, Reactome The Proteome Overview of Analytical Proteomics Separation of the Protein Mixtures Two-Dimensional Gel Electrophoresis High Performance Liquid Chromatography (HPLC) Mass Spectrometers for Protein & Peptide Analysis Applications of Proteomics
8.5.2007	Lecture slides: ppt Gel Image Analysis Data Acquisition Gel Processing/ Visualization Spot Detection & Quantification Gel Matching, Gel Comparison Gel Annotation, Building a Database (Swiss-2DPage, World2DPage, Make2Ddb) Protein Identification by Peptide Mass Fingerprinting Data (PMF) Software Tools for PMF: Scoring the Results (MOWSE, Mascot, MS-Fit, PeptIdent, ProFound, Aldente)
9.5.2007	Lecture slides: ppt Peptide Sequence Analysis & Protein Identification with Tandem Mass Spectrometry Data De Novo versus Peptide Fragment Fingerprinting (PFF) Algorithms & Software Tools (Sequest, Mascot)
10.5.2007	Lecture slides: ppt Proteomics Databases and Protein Characterization Tools
11.5.2007	Lecture slides: ppt Mining Proteomes Protein Expression Profiling Comparative Proteomics with 2D Gels Comparative Proteomics with LC-MS & Isotope Tags Identifying Protein-Protein Interactions Proteomics Discovery of Biomarkers Diagnostic Proteomics Clinical Proteomics Intro to Biological Systems Protein-Protein Interactions Ontologies

Exercises

Exercises will be available at a later time.

Time and Place

Lectures and exercises will take place at Exactum, Kumpula

Lectures: 7.5-11.5.2007 Monday-Friday 10.15-12.00 in room C221
Exercises: 8.5 and 10.5.2007 Tuesday and Thursday 13.15-15.00 in room B121

Enrolling for the Course

You can enrol for the course at ilmo.cs.helsinki.fi.

A maximum of 15 students is allowed to officially register, however the lectures are open to everyone who wants to attend. Precedence will be given to the students of the MBI Programme.

Exam

There will be no course exam.

Grading

To successfully pass the course a project needs to be carried out. The projects will be graded in the scale from 0-5 with 5 being excellent and 1 the lowest passing grade.

Teaching language

Teaching language will be English.

Credits

2 credits will be given to students successfully passing the course.

Course Organizers

Sophia Kossida, Foundation for Biomedical Research of the Academy of Athens, Greece
Esa Pitkänen, Department of Computer Science, University of Helsinki
Juho Rousu, Department of Computer Science, University of Helsinki

Projects

A project list will be available at a later time.

Project Submission

Projects will have to be submitted electronically to: skossida@bioacademy.gr by the 25th of May 2007 at 20:00.

Give Feedback about the Course

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Course Book

Introduction to Proteomics, Tools for the New Biology - Daniel C. Liebler, Humana Press

Additional Material

Proteomics for Biological Discovery - Timothy D. Veenstra and John R. Yates, John Wiley & Sons, Inc.
Informatics in Proteomics- Sudhir Srivastava, Taylor & Francis Group
Some review papers will be added at a later time.

Contact

For any questions regarding the course, please contact: S Kossida at: skossida@bioacademy.gr

Previous update: 15.06.2007 16:43 - Esa Pitkänen

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