1. Progress Report for Year 2007
Shin-Han Shiu
P & T meeting, 4/2, 2008

2. Research output Funding Proposal Submitted (external)
NSF Genes & Genome System
Declined in Jan cycle, resubmitted in July, funded in 2008, $500,000
NSF Plant Genome Research Program
Declined, resubmitted in Jan, 2008
Active Funding (external)
NSF Plant Genome Comparative Sequencing Program
Research grant, 2nd and final year in 2008
Publication
Refereed: 7 papers, 1 as corresponding author
Non-refereed publication: 0
Professional meetings
2 posters
2 invited talks

3. Research accomplishment
Novel genes in the genome:
Developed computational methods that reveal the presence of thousands of potentially novel genes in the Arabidopsis thaliana genome.

4. Research accomplishment
Evolution of gene expression:
Determined cross-species expression divergence in plants in collaboration with Mike Thomashow
Applied computational methods to elucidate the regulatory evolution patterns of stress responsive genes in Arabidopsis thaliana
switch
gain
1-0
1-1
-1-0
-1-(-1)

5. Research accomplishment
Evolution of gene families:
Elucidate the evolutionary histories of multiple plant and fungal gene families.
e.g. Receptor-Like Kinase
O: over-representation
U: under-representation
T: tandem
N: non-tandem

6. Research goal Novel genes in the genome:
Global verification of novel gene expression
Classifying ESTs into putative coding vs. non-coding genes
Evolution of gene expression:
Cross-species expression divergence in plants
Evolution of cis-regulatory logic in plants and yeasts
Genetic basis of adaptation
Floral trait evolution in radish
Jeff Conner, Ian Dworkin (Zoo)
Computational integration of plant omics data
Functional annotation of chloroplast genes by considering bacterial gene clustering and co-expression
The Chloroplast 2010 Project

7. Teaching: Courses taught
Undergraduate:
None
Graduate
PLB802, Introduction to bioinformatics, 3 credit hrs
Non-PLB courses
Senior seminar, PLB499, 8 students, 1 credit, 1 lecture
Statistical Genetics, STT890, 22 students, 3 credits, 1 lecture
Student advising (* Including students of other Dept)
Students*
Indicate Number
M.S. Committees Served On 1
Masters-level Advisees
Ph.D. Committees Served On 6
Ph.D.-level Advisees
Undergraduate Research Projects Advised
Undergraduate Advisees

8. Teaching: Evaluation Summary on PLB 802
General statement
A good, useful course, positive feedback on the instructor but noted several issues.
Course content
Divergent opinion on the difficulty: a highly heterogeneous student population.
Insufficient background: instructor assumed knowledge on basic statistics and biology.
Confusing exercise/exam questions: too many double negatives
Workload:
Too much work: instructor demanded too much time to work on problem sets and projects
Course format:
More hands-on experience: should incorporate a laboratory component

9. Teaching: Improvement
Readings
Subscriber and reader to the "Tomorrow's Professor" mailing list
How Students Learn: Science in the Classroom
Seminar
Participation in the Center for Research on College Science Teaching and Learning seminar series.
Consultation with peers
Discussion with Diane Ebert-May, Gail Richmond (Teacher Education), Maria Zavodszky (BMB) on improving teaching in a interdisciplinary setting. Discussion with Yair Sachar-Hill, Kathy Osteryoung, and Rob Last on effective graduate education.
Workshop
Plan to apply for the Lilly Teaching Fellow program for Accepted.

10. Service Administrative activities PLB Systems Biology search
PLB graduate committee
PLB web committee
QBI public relation committee
GEDD symposium organization committee
Professional activies
Referee 17 manuscripts
Academic Editor for PLoS ONE
Outreach
2 presentations
Workshop on the Human Genome, East Lansing Public Library, 8 adult audience, 03/16, 07'
Genome and Biology, East Lansing Public High School, 29 AP Biology students 11/20, 07'