Shin-Han Shiu

From Shiu Lab

Contact

• S-306 Plant Biology Bldg., Department of Plant Biology, Michigan State University, East Lansing, MI 48824
• (O) 517-353-7196
• (L) 517-353-7244
• email: shius (at) msu (dot) edu

Brief Bio

• 2006-present, assistant professor, Dept of Plant Biology, Michigan State University
• 2002-2005, NIH Fellow, Dept of Ecology and Evolution, University of Chicago
• 2002-2002, Staff, MIPS-Institute for Bioinformatics, Forschungszentrum für Umwelt und Gesundheit, Germany.
• 1994-2001, Ph.D., Department of Botany, University of Wisconsin-Madison.
• 1992-1994, Second lieutenant, Army, Taiwan.
• 1988-1992, B.S., Department of Plant Pathology, National Taiwan University, Taiwan.
• Love basketball, hiking, and Simpsons.

Affilations

• The Plant Biology Department
• The Ecology, Evolutionary Biology, and Behavior Program
• The Quantitative Biology & Modeling Initiative
• The Genetics Program
• The Cellular and Molecular Biology Program

Research Interests

The long term goal in our research program is to understand the molecular basis of adaptations via studying the molecular evolutionary patterns of plant genes. In the near term, we are particularly interested in understanding the evolutionary history and functional differentiation between duplicate genes. Currently we have three major projects:

• Gene content evolution in plant genomes - Plants have significantly high rate of gene duplication due to frequent polyploidization events. As a result, plant genomes tend to have much higher proportion of recent duplicates than other organisms. In this area, we are interested in understanding how long duplicate genes persist and what factors affect their retention. We are conducting global gene family analysis with computational approaches. In addition, we are interested in sequencing recent polyploids to directly assess their gene contents.
• Functional divergence between duplicate genes - Once a gene is duplicated, as long as one copy retains the original function, the other copy is free to accumulate changes. The core questions are how fast such functional divergence occur, what types of genes diverge in function faster than the others and why, and what the nature of selection pressure is in driving functional divergence. To address these questions, we use functional genomic approaches to monitor the expression divergence between genes within and between plant species under various stress conditions. We also focus on a few plant transcription factor genes to examine their functional divergence in expression, phenotypic contribution, and binding sites.
• Genomic "dark matters" - Despite the availability of genome sequences and computational tools for identifying functional elements within genomes, substantial parts of the genomes bear signatures of functions but are not identified properly. We are particularly interested in small protein coding genes that tend to be missed by gene finders. Many small protein coding genes are found to serve as extracellular protein ligands mediating cell-cell communication and intracellular signaling molecules. Specifically we are using ultra-high throughput sequencing approach to first identify transcripts that are destine to be translated in the model plant Arabidopsis thaliana. Then we focus on the expression and knockout phenotypes of novel transcripts to establish the functions of these genome "dark matter".

Teaching philosophy

My goal as a teacher is to foster the learning skills of students so they can acquire knowledge efficiently when they leave schools. That is, I would like to be a teacher who teaches students how to learn. My training background is a mixture of molecular science, evolutionary genetics, and computational biology. Because of my expertise in the interface of these three disciplines, my teaching responsibility is mainly in quantitative biology courses where the major challenge is in introducing quantitative concepts to students with little or no quantitative background. To meet this challenge and to achieve my goal of teaching students how to learn, I believe in the use the active learning model in the classroom by:

• Having the students observe in lectures - so the students gain basic understanding on the core concepts,
• Asking the students to reflects on concepts individually - so they have a chance to think about what they just learned,
• Discussing their reflection in small groups - so the students can exchange opinions, learn collaboratively, and generate consensus,
• Conveying their consensus to the whole class - so the students gain a deeper sense of understanding on the concepts by teaching others,
• Experimenting with examples - so the students have a better understanding by learning from carefully chosen examples that are relevant to their experiences.

The active learning approach in itself is an evaluation of the learning goal. By reflection, discussion, and experimentation, the students have opportunities to compare their own understanding with others and verify the knowledge gained through examples. Therefore students are able to gradually identify their own learning styles and uncover what they do or do not understand through this process.

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