Instructor:

J.Peter Gogarten
Dept. Molecular and Cell Biology
University of Connecticut
Storrs, CT 06269-3125

Phone: 486-4061
Email: gogarten@uconn.edu

Office hours

 MW noon-1pm, or after arrangement. For fast response send an email!
For questions of general interest, use the bulletin board on WebCT.

Basis for grading:

Participation (webct discussion board, in class discussions),
Assignments from the computer labs,
Take-home quizzes and Questions,
Midterm,
Final.

Weights:

Final: 25%,
Midterm: 20%,
Take Home Exams, essay, presentations: 40%
(You can drop the worst 4 grades (3 for grad students) from the Take Home exams ).
Participation, bulletin board postings, and in-class assignments: 15%

Expectation: More than 3h reading/studying per week (most will do fine with about 3-6h/week).

For Honors student conversion - Students please send an email to gogarten@uconn.edu

C-credit can be arranged

Textbook:

 

Recommended books:

	Introduction to Bioinformatics (Paperback) by Arthur M Lesk, 3rd edition at Amazon
	Essential Bioinformatics (Paperback) by Jin Xiong Excellent book, it provides a very readable and concise overview of the most important tools and concepts in Bioinformatics Link to Amazon.com
	Bioinformatics for Dummies by Jean-Michel Claverie Excellent introductory bioinformatics book. Link to Amazon.com
	Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Third Edition Edited by Andreas D. Baxevanis and B. F. Francis Ouellette The book covers many aspect of bioinformatics that we do not cover in class, but it is an excellent reference. The section on phylogenetics is rather weak, but you have your instructors to provide you with much more detail. Don't buy the 2nd edition by mistake! link to Amazon.com link to publisher Excellent book to look up things and to consult if faced with a real world problem. Covers many more techniques and approaches than we will in this course.
	Bioinformatics And Molecular Evolution (Paperback) by Paul G. Higgs, Teresa K. Attwood The authors discuss in detail many applications in molecular evolution and bioinformatics. This book should be very useful to those who want to study some aspects of things covered in this course in more detail. Link to amazon.com
	Inferring Phylogenies by Joe Felsenstein ISBN: 0-87893-177-5;   $61.95 paper Excellent book on phylogenetics and many aspects of population genetics (e.g., gene coalescence in populations, a topic that is rather relevant to species phylogenies in microorganisms :)). For most MCBler this is not exactly bedtime reading, but if you need a well founded thorough explanation, this is a good book to consult. Link to publisher, link to amazon.com
	Molecular Evolution : A Phylogenetic Approach by Roderic D. M. Page, Edward C. Holmes Price: $63.95 Paperback - 352 pages (October 1998) Blackwell Science Inc; ISBN: 0865428891 This book gives an excellent introduction to terms, methods, and problems in molecular evolution.  It does not contain too many details on individual algorithm, but it provides a very readable overview.  Rather expensive!

 

Other recommended books: From Gaia to Selfish Genes, Selected Writings in the Life Sciences Edited by Connie Barlow MIT Press, isbn 0 262-52178-4 and Graur and Li: Fundamentals of Molecular Evolution, Second Edition

Topics (incomplete: open to student input)

    

Bioinformatics (general definition): 
   Area between Computer Sciences (Informatics) and Biology (genomics)
    (or application of the tools of informatics to biology)

Bioinformatics took off only with the availability of large amounts of genome information, thus a more narrow delineation might be:
 
     Area between Informatics and Genomics

Related areas: Computational biology, Cybernetics

 Typically bioinformatics is considered to include: 

management of biological databanks,

access to biological data, and

extracting useful information from biological data.
For more detailed discussion see Mark Gerstein's introduction

 

Bioinformatics at UConn:

Courses relevant for students of bioinformatics are offered through a variety of different departments, colleges and schools at UConn. There is at present no Major in BIOINFORMATICS; however, UConn offers a Minor in Bioinformatics that is suitable for students in MCB, EEB, PNB and CSE. For information click here. An updated audit sheet is here. You should be aware that Bioinformatics is a field in its infancy. Many schools have rushed to attach the name Bioinformatics to a program, but upon closer inspection one realizes that this is not what one would hope for in a Bioinformatics program. E.g., often a single databank course attached to a normal biochemistry curriculum. Everything considered, the offering at UConn could be more streamlined for CSE and Biology students, respectively, but regarding the content UConn's offering isn't bad either.