|
My research career until now can be
divided into three periods: 1994-2001,2002-2006, and from 2007 until now.
Before I was promoted as an assistant research fellow, my major research
focused on image and signal processing. At that period, I had published a
few of journal papers and several ones in IEEE Transactions on Image Processing which is the top journal in
that field. In the second period, I started to enter the field of
bioinformatics and had developed several tools for sequence alignment and
visualization. Although I am a computer scientist by training, I found that
to study biological issues are much more interesting than to develop tools.
So, I spent a lot of time to study biology and read many literatures during
this period. Moreover, I also believe that studying biological problems and
questions through collaboration with biologists can enhance my
understanding of what problems and questions are important and interesting
to the biology community. Thus, in the third period my major research topics focus on
studying biological issues collaborated with
biologists as well as developing bioinformatics tools. From 2008 to 2012, my research
result can be divided into three major parts: plant photosynthesis,
microRNA biology, and bioinformatic kernel and
tool development.
1. Plant
Photosynthesis: Genomics, Genetics, and Evolution
Photosynthesis is the process of
converting light energy to chemical energy and the requested energy is
supported by mitochondria where is the main power source of a cell to
generated ATPs. Photosynthesis is important not only for plants themselves but also for the survival of other living
organisms in the Earth. For studying the genomics, genetics, and evolution
of plant photosynthesis, we have completed three studies. First, we
sequenced and annotated a mitochondrial
genome (mtDNA) from Taitung
cycad which was the first completed gymnosperm mtDNA.
The mtDNA demonstrated atypical features in
contrast to other mtDNAs previously elucidated
for other land plants. In the
second study, we acquired the transcriptomic data of two separated
photosynthesis cells by deep sequencing and analyzed the functional
differences of the differentially expressed genes between these two cells. In the last study, we directly
used the paralog information and analyzed how
co-duplicated genes play a role in the evolution of C4 photosynthesis in
grasses.
2. MicroRNA Biology
MicroRNAs (miRNAs)
play an important role in posttranscriptional regulation of genes. However, whether some human miRNAs had not been found yet and what the origins of many miRNAs
were still unclear. For studying these two questions, we proposed different
methods to predict new miRNAs from their
regulatory relationship in the human genome and to find human miRNA homologs in the genomes of distant species. Moreover,
we also analyzed plant small RNA-seq data and
found important miRNAs involving in the
stress-response pathways of Pi deprivation and other nutrient deficiencies.
3. Bioinformatics Kernel and
Tool Development
In the third
part, we focused on developing tools for genome sequence assembly and a
kernel method for clustering. We have completed an alignment tool for
aligning sequences containing rearrangement events, a de novo short read assembler, and a novel spectral clustering
method.
|
