Download RISE AND FALL OF GENE FAMILIES Dynamics of Their

Progress Report for Year 2007
Shin-Han Shiu
P & T meeting, 4/2, 2008
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
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.
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
Research accomplishment

Evolution of gene families:
 Elucidate the evolutionary histories of multiple plant and fungal gene
families.
 e.g. Receptor-Like Kinase
Response
Statistical test
Up regulation
RLK
Abiotic stress conditions
UV-B
O
Wounding
O
Drought
U
Cold4C
Heat
U
Salt
Osmotic
O
Biotic stess conditions
Flg22
GST-NPP1
HrcCP.infestans
Psph
HrpZ
AvrRpm1
DC3000
Down regulation
T/N
RLK
T/N
T
O
O
O
N
N
na
N
O
N
O
O
O
O
O
T
T
T
T
T
O
T
O
O: over-representation
U: under-representation
T: tandem
N: non-tandem
N
O
O
O
N
N
O
O
N
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
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
0
Ph.D. Committees Served On
6
Ph.D.-level Advisees
0
Undergraduate Research Projects Advised
1
Undergraduate Advisees
1
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
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 2008-9. Accepted.
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'