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, Take-home quizzes and Questions, Midterm, Final.

Weights:

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

My Expectations: 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:

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

Additional reading materials will be placed to WebCT.
Other recommended books:

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

Bioinformatics and Functional Genomics
by Jonathan Pevsner

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. This Minor is approved, for information click here. An updated description and 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.

Assignment for Wednesday's class:

  • Read Chapter 1 in the textbook (introduction).
  • On WebCT go through the Computer Technology Competencies modules on Computer Operation Basics (we'll use iMACs with OSX in the computer lab) and on Internet Basics (you need to be done with this before Friday's class, it is advisable to at least try this before Wednesday, so you can ask for help) .
  • Formulate a question that you could ask on Wednesday (things you didn't understand, anything you want to hear more details about). A few of you will be selected at random to ask their question!
  • Read the excert from Thomas Mann's book on Dr. Faustus (Dr Faustus).
  • Think about the question "What is life?" 
       
       How could we detect it on Mars? 
      Could a robot or a computer ever be alive?
      What did you learn from the Dr. Faustus excerpt?

Don't be too sure that what you read in textbooks is actually useful.
For example, an often stated criterion is "being made from cells". While we can make this criterion true for life on Earth (there are some problems with organisms that are syncytia - but one can redefine what one means by cell :-)); life on a surface might be a prebiotic alternative. Or what about self-replicating nanorobots directed by an intelligent computer? [For entertaining introduction to nanotechnology, read the science fiction novel "Diamond Age" by Neal Stephenson

  • Some time in the (maybe) distant future a computer might pass the Turing test. Would we consider this entity "alive", or would this just be an example of A-life that still remains in an entirely different category? (If the latter, what is the justification for this category?)
  • Where in the evolution from prebiotic chemistry to today's biosphere is the line crossed to a living system? Is a self replicating template enough? If yes, why are viruses usually not considered to be alive?

Background Information:

Traditional criteria for Life:
  • Uptake and dissipation of Energy
  • Metabolism
  • Responsiveness
  • Gestalt (distinctive shape, separate from environment)
  • Growth
  • Reproduction with variation - Ability to evolve
Supplemental Reading