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 switch gain 1-0 1-1 -1-0 -1-(-1)

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

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 Ph.D. Committees Served On 6 Ph.D.-level Advisees Undergraduate Research Projects Advised Undergraduate Advisees

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'