Shin-Han Shiu

From Shiu Lab
(Redirected from User:Shiu)
Jump to: navigation, search



  • Office location: 2265 Molecular Plant Science Building [direction]
  • Mailing address: Michigan State University, Plant Biology Laboratories, 612 Wilson Road, Room 166, East Lansing, MI 48824-1312
  • (O) 517-353-7196
  • email: shius (at) msu (dot) edu

Brief Bio

  • 2012, Visiting Associate Research Fellow, Biodiversity Center, Academia Sinica, Taiwan
  • 2011-present, Associate Professor, Dept of Plant Biology, Michigan State University
  • 2006-2011, 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.


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 in education is to foster the abilities of the students at all levels to think critically and lead intellectual pursues independently.

My approach for realizing my goal is to create a learning environment where the learners actively participate in dialogs, exchange opinions in groups, learn by doing, and solve authentic problems that we face as scientists. In this environment, the learners practice identifying the core questions and hypotheses, assessing the best approaches to solutions, designing experiments, analyzing the outcomes quantitatively, and making interpretations. In addition, the environment I strive to provide scaffolding to support the students and, by gradually removing them from their comfort zones, foster greater independence.