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DTU course # 27104: The Scientific Communication of Comparative Genomics

Course Schedule for 2011

Performance will be evaluated by a poster (25%), a journal club report (25%), and a final written manuscript (50%). See the course schedule for more information about grading and course aims and objectives.

The textbook is written specifically for this course:
COMPUTING FOR COMPARATIVE GENOMICS: Bioinformatics for Microbiologists
by David W. Ussery, Stefano Borini, and Trudy M. Wassenaar

Springer, 2009. Link to Amazon.com Note that the DTU bookstore has ordered copies of the text. Links to PDF files for relevant papers will be provided on this web page (see below).

This is the tenth year for this course, which was first taught in the autumn of 2001. Links to the course programme for 2010 , 2009 , 2008 , 2007 , 2006 , 2005 , 2004 , 2003 and 2002 . Also, one-week versions of the course have been taught at other locations:

AIMS

The aim of this course is twofold; first it is to give the students a solid knowledge of methods for communication of scientific discoveries, and the second aim is to teach about methods for the comparison of genomes from microorganisms of interest such as those used for bioenergy or biofuels, food biotechnology such as lactic acid bacteria, industrially important filamentus fungi and yeast, as well as organisms with relevance for medical microbiology, biofilms and infection such as Pseudomonas, and other microbial organisms. The idea is to apply this newly gained knowledge of comparative genomics to a specific set of genomes of interest, using various type of communication skills learned in the course. Students that have followed this course should be able to understand and clearly communicate the results of the investigation of their microorganisms of interest to others using three different formats: a journal club report critiquing a recently published paper, a poster, and finally by writing a scientific paper which is formatted and suitable for publication.

The project includes management, organization structure, and strategies for communication of scientific findings. This will be supported by lectures on scientific publications, poster design and presentation, and manuscript writing.

Different disciplines dealing with comparison of microbial genomes will be brought together to produce a manuscript. Specifically the lectures will deal with: introduction to genomics; computational analyses of sequenced microbial genomes; what defines a microbial species; how to choose a set of genomes to compare; and microbial communities and their interactions.

Students that fully have followed the course are able to:

Read, understand and critique a paper published in the scientific literature.
Give a brief description of a new discovery in the field.
Design and produce a poster suitable for showing at a scientific meeting.
Contribute a section to a written scientific paper.
Plan the management and organization of a paper that could be published in a scientific journal.
Obtain up-to-date lists of the most recently sequenced microbial genomes.
Compare two or three genomes to each other.
Compare hundreds of genomes and easily find trends and genomes which are significantly different.
Quickly obtain the core- and pan-genome sets of genes for a given bacterial species or taxonomic group.
Compare metagenomic results to hundreds of projects already available.

Learning objectives

A student who has met the objectives of the course will be able to:

Describe the general methods for comparison of microbial genomes.
Compare a new genome sequence to other genomes already published.
Critique a scientific paper.
Explain basic interactions between microbial organisms within an ecosystem.
Use genomic databases and resources quickly and effeciently to compare genomes.
Make a scientific poster and use it to communicate new findings to scientific peers.
Explain the basic format and important items to include in writing a scientific paper.
Plan a scientific paper.
Write part of a scientific paper.

Student evaluation reports

Over the course of the semester, this course will develop communication skills in several different areas. The students will be divided into small groups to work on various projects. At any time during the semester, students should feel free to ask the course leader (Dave Ussery) if they would like to be assigned to a different group. It is possible that if all in the group are happy with the same members, the same group can work together for most of the projects.

Journal Club (25% of grade)		Journal clubs will be done during class, as assigned to groups throughout the semester. During the first few weeks of the course, a set of possible papers to be used for journal club will be distributed over the CampusNet web pages for this course. Students are encouraged to form their own groups of 4 students, and hopefully the first set of journal clubs will begin by the middle of September. Since there are more than 50 students in the course, we will have at least one journal club every week throughout the semester. Students are also encouraged to sign up for dates of their preference.
Poster (25% of grade)		Posters will be done by groups, and are due on 7 November, when they will all be displayed and evaluated. The posters will be (of course) about comparison of bacterial genomes; each group is encouraged to find some genomes of their interest to compare, and use some of the standard tools discussed in the course, such as "BLAST Atlases" for comparison against a reference chromosome, and box and whisker plots for comparison of frequency distribution of genomic properties across large numbers of genomes. A good starting point is the article "Ten Simple Rules for Good Poster Presentation"
Paper (50% of grade)	Link to eJournal.	One of the main goals of this course is to learn to write a scientific manuscript, and in fact we will publish these manuscripts, as part of an "eJournal", in collaboration with a course at the University of Michigan. The papers from our course at DTU will be refereed by students in Michigan, and similarly, the students here at DTU will referee papers submitted by students in Michigan. This is intended to part of the learning process for how to referee (and accept referee's reports) for scientific publications.

Prerequisites: Introduction to Bioinformatics (course #27011 or similar) and General Biotechnology and Life Science (course #27000 or similar). Entry level college math and biology are essential.
For those who would like a review of basic Bioinformatics, see the lecture notes for the CBS Introduction to Bioinformatics course. For a background in basic molecular biology/genetics, there are several good texts on-line. For those who whish more microbiological information, Brock Biology of Microogranisms, by Michael Madigan, John Martinko, and Jack Parker, is available in the DTU bookstore and recommended.

For more information, please contact David Ussery

This file was last modified Thursday 1st of September 2011 10:54:26 GMT