MCB 3421 - Fall 2019

Introduction to Molecular Evolution and Bioinformatics

   Instructor: J. Peter Gogarten (OFFICE: BP room 404, gogarten@uconn.edu)

   Teaching Assistant: Sean Gosselin (sean.gosselin@uconn.edu)

   The class meets
        MW 11.15AM - 12.05PM    AND     Fridays 10.10.AM-11.40AM or 1.25PM-2.55PM
        Monday's and Wednesday's classes meet in TLS 301
        Friday's classes will meet in the computer lab located in the Whetton Graduate Center (Room 300A).

(for directions follow the above links to the UConn campus map)    

   Reading materials will be posted on huskyCT -- if you cannot get access, send your netID to gogarten@uconn.edu

   There also will be a discussion board on huskyCT. Contributions on the discussion board will count towards your participation grade.

   REFRESH THIS PAGE EVERY TIME YOU VISIT IT

Possibilities to boost your grade:

• Email questions (multiple choice preferred) that could be used for the exams! (counts towards participation).
• Optional Essay Assignment (can take the place of one take-home exam).

Exam Questions for Self Study:

Takehome Exams: #1, #2, #3, #4, additional questions to study for the midterm (with answers)
#5, #6, #7, #8, #9

List of Goals and Link to study materials
for each class - check them out - discuss if things are not clear.

IMPORTANT DATES:
      Midterm: Wednesday, October 16th, TLS 301 at 11.15am
        11/25-11/30 Thanksgiving break 
        12/6         Last Day of Classes
       Final: Monday, December 9th, TLS 301, 8am - 10am

  (Please let me know ahead of time, if you have a conflict for this time. See syllabus for exam policy.)

   Red: meets in the Computer Lab in the Whetten Graduate Center (300A)
   Blue: meets in TLS 301

• Class 01: Overview; topics; textbook; reading materials; How will grades be calculated?
• Class 02: Homology, basics of protein structure
• Computer-lab assignment 01: Intro to chimera - binding pocket substrate interactions
• Class 03: ATPase structure, function, and evolution; the RNA world concept; discussion of homology
• Computer-lab assignment 02: Comparing structures for ancient duplicated genes / following a structure through the catalytic cycle
• Class 04: ATP binding sites and convergent evolution,natural selection and definitions of life
• Class 05: Divergence of sequences, symbiotic relationships, inteins
• Computer-lab assignment 03: Exploring intein structures in chimera
• Class 06: The tangled tree of life.
• Class 07: Mutationism and the Modern Synthesis , Mutual Aid
• Computer-lab assignment 04: Literature Databanks and Entrez
• Class 08: Statistics of sequence comparison
• Class 09: Databanks, Blast, Unix
• Computer-lab assignment 05: Statistics of Sequence Comparison
• Class 10: Dayhoff and the history of bioinformatics
• Class 11: Strand-bias and recombination
• Computer-lab assignment 06: Blast searches using the command line
• Class 12: (A) cladistics (B) early humans
• Class 13: Ebola as an example for the usefulness of molecular evolution; review of endosymbiosis in eukaryotes
• Computer-lab assignment 07: Creating gene plots
• Class 14: Review Session
• Midterm
• Computer-lab assignment 08: Gene plots, strand bias, and mummer
• Class 15: Gene duplication and post mating hybridization barrriers, discussion lab 8, sequence alignment
• Class 16: Sequence alignment, multidimensional sequence space.
• Computerlab assinment 09: Dotlet and Jalview exercises on repetetive motifs, introns and sequence space.
• Class 17: Introns late versus introns early
• Class 18: Intro to trees and phylogenies
• Computerlab assigment 10: Phylogenies, bootstrap, model tests, LBA
• Class 19: Discussion of LBA, Why can gene trees be in conflict?
• Class 20: selection, determiinistic models, genetic drift
• Computerlab assignmnet #11: Simple scripts to handle genome sized data sets
• Class 21: Detecting positive and purifying selection
• Class 22: dN/dS continued
• Computerlab assignmnet #12: Bayesian analysis to determine evolutionary parameters in sequences.
• Class 23: Types of selection / GTAs and purifying selection
• Class 24: Intro to PSI blast.
• Computerlab assignmnet #13: PSI blast exercises

• Thanksgiving break

• Class 25: Discussion of PSIBlast lab, CNE, early Earth and bottlenecks
• Class 26: Review session
• Computerlab assignmnet #14: Phylogenetic analysis of an intein containing gene
  
  
• Final Monday, December 9th, TLS 301, 8am - 10am

Topics - If you have suggestion for additional topics, please let me know,

Syllabus <- (see for grade calculation, exam policy, and penalties for academic misconduct)

Academic misconduct includes, but is not limited to:
* Providing or receiving assistance on academic work (papers, projects, examinations) in a way that was not authorized by the instructor
* Any attempt to improperly influence (bribery, threats) any member of the faculty, staff, or administration of the University in any matter relating to academics or research
* Plagiarism
* Doing academic work for another student
* Presenting the same or substantially the same papers or projects in two or more courses without the explicit permission of the instructors
* Situations where one student knowingly assists another student in committing an act of academic misconduct, and any student doing so will be held equally accountable for the violation

For more information see the Community Standards at http://community.uconn.edu/

Send an Email to Peter Gogarten

Go the Gogarten-Lab homepage