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Bio-informatics
Bio-informatics
The yearly flu epidemics often occur as a tion integration systems for biologists. One of the
Principal Investigators: Wen-Lian Hsu, Jan-Ming Ho, Chun-Nan Hsu, Ming-Tat Ko, Chung-Yen
Lin, Der-Tsai Lee, Arthur Chun-Chieh Shih and Ting-Yi Sung result of the lack of immunity against these new agent-based systems is to support an SNP project of
Postdoctoral Fellows: Han-Shen Huang, Laurent Lin, Wen-Dar Lin, and Kun-Pin Wu strains. The World Health Organization (WHO) an- National Genotyping Center (NGC) at IBMS. Fast-

nually recommends three influenza strains currently SNP allows the researchers at NGC to efficiently
Our research can be divided into the follow- ence on human-mouse synteny mapping by UniMark- in worldwide circulation for vaccine manufacturers prioritize risk-causing SNPs to conduct genotyping
ing areas: 1. Genomics; 2. Proteomics; 3. Structural er-synteny method, we plan to develop an efficient to massively produce the vaccines. However, each and enables them to successfully identify a novel

bioinformatics; 4. Biological literature mining; and 5. synteny mapping and annotation system for vertebrate year Taiwan needs four million flu vaccines, import- promoter polymorphism that contributes to Adverse
Systems biology. Since 2003, at IIS we have started genomes. ed from USA or other countries. To avoid a lack of Drug Responses (ADRs). More identification will
recruiting Ph.D. students in Bioinformatics of the Tai- drugs and vaccines in case of a global fl u outbreak, be announced in the near future. One of the agent- Research Groups
Large-scale and large-number sequence analysis and
wan International Graduate Program (TIGP). There the Department of Health, Executive Yuan, has based systems won the best paper award in a local
its applications to phyloinformatics
are 15 students currently. The number of applicants planned to establish a domestic GMP plant to pro- bioinformatics conference in 2003. An article about
this year is more than the total number of applicants In the post-genomic era, the number of sequenc- duce local flu vaccines. Beginning in 2006 in col- FastSNP will appear in the 2006 Web Server Special
for the past three years. es available for reconstructing the evolutionary history laboration with IBMS we participate in a three-year Issue of Nucleid Acid Research.
of genes and species has increased 20-fold in the past CDC (Center for Disease Control, Taiwan) project
1. Genomics Development of Gene Ontology browsing/
Research Groups
decade. But most tools available to date are limited to for development of influenza vaccine. We plan to
maninpulating utility
EST annotation pipeline system processing only small data sets. Especially, the cost study the evolutionary mechanisms of influenza
for constructing the tree of a large group of organisms viruses from sequence data as well as to establish Due to the increasing requirements for func-
Large scale DNA sequencing has become a
is very high when using an optimal character-based a computational model that can predict potentially tionally annotating gene products with Gene Ontol-
worldwide-used methodology. EST sequencing is a
method such as maximum likelihood. Thus, to de- emerging strains in coming epidemic seasons. One ogy (GO), more and more pipelines are producing
feasible way for studying functional genomics under
velop new computational tools for building very large of our goals is to be able to provide a quantitative GO-related biological data. In order to facilitate bi-
limited resources, so there are a lot of EST sequencing
phylogenetic trees and for comparing and visualizing model for vaccine strain selection. ologists§ browsing and manipulation of their data,
projects all over the world. However, the essential step
huge data sets is urgent. In this project, we focus on we designed a Java-based software called GOBU.
of an EST sequencing project is the bioinformatics Agent-based information integration for
the study and processing of large-number sequence The underlying architecture of GOBU enables arbi-
analysis. A good annotation pipeline can provide biol- bioinformatics
alignments and their phylogenies. We plan to build a trary data description, data integration and extend-
ogists the most complete information about their EST
problem-solving environment, develop effi cient algo- More than 600 Web-based bioinformatics able user interface, and thus is feasible for browsing
data and help them with further studies. In the last few
rithms for constructing large-scale phylogenetic trees, resources, including databases, links, and analysis annotations for various pipelines. We have applied
years, we have in collaboration with biologists in the
such as supertrees, and develop effective visualization tools, are available for biological knowledge dis- this software to our EST annotation pipeline and
Institute of Biomedical Sciences (IBMS) of Academia
tools for visualizing supertrees. We have developed a covery. But to integrate them requires tremendous microarray experiments.
Sinica, provided the EST annotation service systems,
versatile alignment visualization system, SinicView efforts. We have been working on an intelligent
Bio101 and Bio301, for some functional genomics 2. Proteomics
(Sequence-aligning INnovative and Interactive Com- agent-based approach to information integration
projects and also developed a fast gene ontology an-
parison VIEWer), which enables users to efficiently and have built a tool for rapidly training intel- Quantitative proteomics based on high-throughput
notator for the EST annotation, called ESTFastAnno-
compare and evaluate assorted alignment results ob- ligent agents. This tool provides bioinformatics mass spectrometry data
tator.
tained by different tools. This work appeared in BMC researchers a scalable, flexible and extensible solu-

An efficient synteny mapping and annotation system Bioinformatics 2006. More information can be found tion to query these resources with a single uniform Most current quantitative experiments aim to
for vertebrate genomes at the Computational Genomics Lab. website at http:// interface. With this tool, users can train an agent determine relative protein expression levels in dif-
biocomp.iis.sinica.edu.tw/ in the Genomics Research to learn a specialized session of Web browsing ferent cell states or cells grown under different con-
Synteny mapping, or detecting regions that are ditions. Various stable isotope labeling techniques,
Center. and extraction without programming. Instead, they
orthologous between genomes, is a key step in stud- e.g., ICAT and iTRAQ, followed by liquid chroma-
can train intelligent agents by click-and-drag in a
ies of comparative genomics. Synteny mapping of all Influenza virus study and vaccine strain selection tography-tandem mass spectrometry (LC-MS/MS)
programming-by-example manner. As a result, a
model vertebrate genomes will make the global view are frequently used to quantify protein expressions.
In recent years, the study of molecular phylog- large number of agents can be created to integrate
of genome evolution clear, enhance the functional To expedite the analysis of vast amounts of spectral
enies of influenza viruses has become increasingly a large number of Web sites in a matter of days to
decoding of genomes in a comprehensive way beyond data generated, we have developed a fully automat-
important for epidemiologists and evolutionary biolo- answer biologists’ queries. We have successfully
genes so far, and serve as a foundation of comparative ed tool for multiplexed quantitation using iTRAQ
gists. built and deployed many agent-based informa-
vertebrate genomics. Based on our successful experi-

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