INSTRUCTOR
Nevin Dale Young
320 Cargill Genomics Building
612-625-2225
Email: neviny@umn.edu
Home page:
http://umn.edu/home/neviny
Office hours by appointment
SYLLABUS
Overview
Plant genomics is a course for graduate and advanced undergraduate students who are interested in the application of genomics and bioinformatics to the study of plants. Students learn strategies for structural and functional genomic analysis by exploring the genomes of model plant systems, comparative genomics, genome expression and genome evolution. Students also learn the fundamentals of sequence analysis, database searching and data-mining through computer labs and independent projects. Class sessions consist of lectures, discussions, small group activities and hands-on computer labs.
Prerequisites
Introductory courses in genetics and either biochemistry or cell biology – or – consent of instructor.
In Plant Genomics
students learn:
Requirements
Everyone who attends class must enroll formally. This includes students who are taking Plant Genomics for credit, as well as students who plan to audit. Because class participation is a formal part of the final grade, students should plan to attend every class. If you do need to miss a class for a valid reason, please inform the instructor by email a day or two ahead of time. Active participation is expected every day, so assigned readings should be completed before coming to class.
Readings
Nearly all readings are found through the internet, with links listed below.
Exams
There will be two exams, one on October 15th and another on December 15th. There will not be make-ups, so plan on being in class these days. Each exam will consist of approximately five to ten "medium" answer questions.
Computer Homeworks
To provide practical experience with genome databases and the process of "data-mining", there will be a series of short computer-related homework assignments. The first three homeworks will be relatively short and focused. The final computer homework will be a multi-week assignment (starting approximately November 20th) consisting of an internet-based mini-project and student presentation. On the final project, students should plan to work in pairs or small groups. Students will be expected to turn in both group and individual reports electronically for this assignment.
Class Participation
There will be regular "break-out" sessions and other class-wide discussions throughout the semester. Students are expected to participate actively. Responsibilities will be distributed among everyone. Class participation will be noted and included in the final grade, especially in cases of "borderline" grades.
Grade Disputes
All grade disputes should be submitted in writing to the instructor within one week of receiving the graded assignment or exam. If the dispute can not be resolved satisfactorily, the assignment will be given to an expert outside of class to provide input. Please remember that re-graded exams and assignments can be lowered as well as raised.
Students with Disabilities
Students with any type of disability will be accommodated. For assistance, please contact University Disability Services (612-624-4037) or the instructor.
Scholastic Honesty Policy
Students in Plant
Genomics are expected to do their own work and submit their own
assignments (unless explicitly stated otherwise). Still, group
activities and discussion among students are strongly encouraged.
Details on the University of Minnesota's student honor code is found
at: http://www1.umn.edu/regents/policies/academic/StudentConduct.pdf.
NOTE: The
Pevsner Packet is available
for purchase at the St. Paul Campus Bookstore.
NOTE:
You
may need to log-in from a computer with a University of Minnesota URL
in order to access some of these readings.
September 8, 2009: Global
Views of
Biology
Lander ES (1996) The new genomics: Global views of biology. Science 274: 536.
September 10, 2009: DNA Sequencing and DNA
Chips
PCR technology
Sanger DNA sequencing
Cycle DNA sequencing
Solexa sequencing technology
DNA microarrays
Genechips
September 15, 2009: Aligning DNA Sequences
Pevsner J (2009)
Bioinformatics and Functional Genomics, Vol. 2. Wiley-Blackwell. Pages
47-76.
September 17, 2009: Searching Genome Databases
(LAB)
September 22, 2009: EST Libraries
September 24, 2009: Exploring Gene Indices (LAB)
Quakenbush
J et al (2001) The TIGR gene indices: Analysis of gene
transcript sequences in highly sampled eukaryotic species. Nucleic
Acids Research 29: 159-164.
September 29, 2009: Sequencing Plant Genomes
Pevsner J (2009)
Bioinformatics and Functional Genomics,
Vol. 2. Wiley-Blackwell. Pages 537-554.
October 1, 2009: Arabidopsis
Genome
Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
October 6, 2009: Comparative Genomics
October 20, 2009: Microarrays & DNA ChipsWortman JR, et al (2003) Annotating the Arabidopsis genome. Plant Physiology 132: 461-468.
Global
Views of Biology (September 8, 2009)
Homework
#1: Sequence Alignment and Genome Databases (September 17, 2009)
Homework
#2:
Exploring & Annotating Plant Genomes (Due October 15, 2009)
Homework
#3: Microarray Analysis of Gene Expression (Due November 10, 2009)
September 2, 2008: Global
Views of
Biology
Lander ES (1996) The new genomics: Global views of biology. Science 274: 536.
September 9, 2008: Genomic
Tools and Definitions
PCR technology
Sanger DNA sequencing
Brown TA (2006) Global studies of genome activity, In: Genomes, 2nd ed, Garland Science.
September 11,
2008: Bioinformatic
Tools and Definitions
Optional: Classic readings for students
who
want to know more about bioinformatic algorithms.
Ewing,
B. and Green, P. (1998) Base-calling of automated sequencer traces
using Phred. II. Error probabilities. Genome Research 8: 186-194.
Thompson,
J.D. et al (1994) CLUSTAL W: Improving the sensitivity of progressive
multiple sequence alignment through sequence weighting,
position-specifci gap penalties and weight matrix choice. Nucleic Acids
Research 22: 4673-4680.
Altschul,
S.F. et al (1997) Gapped BLAST and PSI-BLAST: A new generation of
protein database search programs. Nucleic Acids Research 25: 3390-4002.
September 16,
2008: Genbank
and Blast Searching
(LAB)
September 18, 2008: EST Libraries
September 23, 2008: Gene Indices (LAB)
Quakenbush
J et al (2001) The TIGR gene indices: analysis of gene
transcript sequences in highly sampled eukaryotic species. Nucleic
Acids Research 29: 159-164.
Dana Farber Gene Indices
(compbio.dfci.harvard.edu/tgi/faq2.html)
September 25, 2008: Genome
Sequencing
Green
ED (2001) Strategies for sequencing complex
genomes.
Nat Rev Genetics 2: 573-583.
September 30, 2008: Arabidopsis
Genome
Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
October 2, 2008: Other
Plant Genomes
October 7, 2008: Comparative
Genomics
October 21, 2008: Microarray TechnologyHaas BJ, et al (2005) Complete reannotation of the Arabidopsis genome: Methods, tools, protocols and the final release. BMC Biology 2005, 3:7.
Genomics Case Study
(September 2, 2008)
Genomics
Tools & Definitions (September 9, 2008)
Bioinformatics Tools &
Definition (September 11, 2008)
EST
Libraries (September 18, 2008)
Genome
Sequencing (September 25, 2008)
Arabidopsis
Genome (September 30, 2008)
Other
Plant Genomes (October 2, 2008)
Comparative
Genomics (October 7, 2008)
Exam Review Questions #1
(October 7, 2008)
Microarray
Technology (October 21, 2008)
Genome
Expression (October 23, 2008)
Genome
Expression Case Study (October 30, 2008)
QTLs
& eQTLs (November 4, 2008)
Genome
Diversity (November 6, 2008)
Genome Structure
(November 11, 2008)
Proteomics & Metabolomics (November 13, 2008)
Exam
Review Questions #2 (November 18, 2008)
Data-Mining Group Project (Due
December 2, 2008)
Bioinformatics
Tools Lab Activity-- Including homework #1 (September
16, 2008)
(Note: homework due September
16)
Bioinformatics Tools Powerpoint
(September 16, 2008)
Gene Index Lab Activity (September
23, 2008)
Gene Index Powerpoint (September
23, 2008)
Gene
Index Homework (due September 30, 2008)
Annotation
and Comparative Genomics Lab Activity (October 9, 2008)
Annotation
and Comparative Genomics Powerpoint (October 9, 2008)
Annotation
and Comparative Genomics Homework (due
October 16, 2008)
Gene
Expression Lab Activity (October 28, 2008)
Gene
Expression Powerpoint (October 28, 2008)
Gene Expression Links: Medicago Gene Atlas
Gene
Expression Homework (due November 4,
2008)
Last update: November 9, 2009
©
1998-2009 by Nevin Dale Young and the Regents of the University of
Minnesota
The University of Minnesota is an equal opportunity educator and
employer.