It still remains mostly unknown which of the variations or mutations occurring in the human genomes contribute to etiology of diseases. We employ versatile applications of next generation sequencing technologies, such as Whole Genome/Exome Seq, RNA Seq, ChIP Seq and Bisulfite Seq to understand the biological meaning of the identified genomic mutations. Advent of the next generation sequencing technologies has enabled us to analyze thousands of human genomes. Consequently, a rapidly increasing number of mutations have been identified and associated with various diseases, such as cancers. However, it still remains elusive how these mutations invoke changes in epigenome, transcriptome, or proteome functions. For the diseases as exemplified below, we are conducting an integrative analysis of multi-omics data, namely DNA methylation, histone modifications, biding patterns of transcriptional regulatory factors and gene expression patterns. Furthermore, to complement currently undetectable layers of transcriptome regulations, we are developing novel methods, based on the latest genomic technologies, such as next generation sequencing, single cell analysis and single molecule sequencing technologies. Also, as a one of the representative sequencing centers in Japan, we are distributing the next sequencing platforms and the related technologies widely to the research community.

Bioinformatics is a research, development, or application of computational tools and approaches for expanding the use of biological data, including those to acquire, store, organize, archive, analyze, or visualize such data. Its goal is to enable biological discovery based on existing information or in other words transform biological information into knowledge. In recent years bioinformatics became integral part of biology and it is present in almost all biomedical disciplines.

The institute's research spans wide range of topics related to broadly understood genomic evolution. We are interested in basic processes that shape our genomes such as gene families evolution (globins, mitochondrial outer membrane proteins), genome structure (Genomic ScrapYard, U12-type introns), and cancer genomics. We are also engaged in software development such as TEclass, TinT, or NanoPipe.

The department deals with parasitic diseases in the region of North Sulawesi, Indonesia. We receive clinical samples from referral hospitals and we identify the morphology of the parasites causing the diseases by microscopy examinations. Samples that we receive ranging from stools, blood, tissue, to sputum. We also perform polymerase chain reaction (PCR) of these samples to further identify the genotype of the parasites. Recently, we are involved in sequencing to unveil the host-parasites transciptomics interactions, drug-resistant mutations in malaria parasites, and DENV serotype identification. We are also in charge of parasitology to the medical students and we have introduced them to molecular techniques through practicums and thesis assignments.

Population genetic study of major vaccine candidate antigens of global malaria parasites is one of major research fields in our laboratory. We are also conducting molecular surveillance of drug-resistance malaria parasites in Myanmar. We have been doing these studies with collaborators in Korea, Myanmar, Malaysia, and Uganda. Understanding parasite-host interactions is another major topic in our laboratory. Biochemical and immunological approaches of parasite-derived molecules and their interactions with hosts or host cells will provide in-depth information for parasitic diseases and vaccine/therapeutic drug development.

Recent selected publications

• Lee J, Kim TI, Kang JM, Jun H, Le HG, Thai TL, Sohn WM, Myint MK, Lin K, Kim TS, Na BK (2018) Prevalence of glucose-6-phosphate dehydrogenase (G6PD) deficiency among malaria patients in Upper Myanmar - BMC Infect Dis. 18(1):131.
• Thai TL, Jun H, Lee J, Kang JM, Le HG, Lin K, Thant KZ, Sohn WM, Kim TS, Na BK (2018) Genetic diversity of merozoite surface protein-1 C-terminal 42 kDa of Plasmodium falciparum (PfMSP-142) may be greater than previously known in global isolates - Parasit Vectors. 11(1):455.
• Le HG, Kang JM, Moe M, Jun H, Thai TL, Lee J, Myint MK, Lin K, Sohn WM, Shin HJ, Kim TS, Na BK (2018) "Genetic polymorphism and natural selection of circumsporozoite surface protein in Plasmodium falciparum field isolates from Myanmar" - Malar J. 17(1):361.

The relationship between a parasite and its host is interesting yet complex, involving many events. A key towards a better understanding of parasite-host interactions lies in the knowledge of molecules that are part of the parasite-host interface and parasite molecules that interact with host cell components. In our research, we focus on the genomics and molecular biology of various organisms, including the protozoan parasite Eimeria and holoparasitic plant Rafflesia. We employ next generation sequencing technologies for production of data that will enable us to analyse genomes and transcriptomes, and to identify novel molecules in these model organisms. Further characterization of these molecules may unveil essential information underlying their biology, including that of parasite-host interaction.

Our research is focused on the study of human diseases and health related organisms from a genomics perspective. Our ultimate goal is to bring to bear novel technologies and molecular insights to help earlier diagnosis and improve outcomes for our patients.

The following projects are focus of the laboratory

• Genetic analysis of virulence factors and antimicrobial resistance genetic determinant found in foodborne infectious bacterial pathogens.
• Molecular diagnostics of zoonotic infectious pathogens based on target genome analysis
• Molecular epidemiology of vector-borne infectious pathogens in Kenya in relation to other sub-Sahara African countries

In the international cooperation and education division, we conduct research in a wide range of areas, including field work to study the biological behavior of zoonotic pathogens, study on immunity to infectious diseases and genome analysis. In particular, working in collaboration with research organizations and universities in Southeastern African countries, including Uganda and Zambia, we are conducting molecular biological research to study the molecular epidemiology of human and animal protozoan diseases (trypanosoma and theileria) and disease vectors (tsetse flies and Ixodid ticks), genomic functions and the molecular biology of hemorrhagic fever viruses. We are also conducting basic immunological research required for the development of vaccines against zoonoses-in particular, research on the roles of antigen presenting cells in immune responses.

The Ireland Vietnam Blood Borne Virus Initiative (IVVI) is a collaborative programme between UCD and the National Institute of Hygiene and Epidemiology (NIHE) in Hanoi. The programme aims to develop capacity in clinical and diagnostic virology and virus research in Vietnam through infrastructure development and specialized training programmes. The concept was developed by Professor William Hall, Director of CRID, in response to the significant morbidity and mortality associated with blood borne virus (BBV) infections in Vietnam. Initial studies which have been recently published have focused on the molecular epidemiology and analysis of HIV and Hepatitis B and C viruses (HBV, HCV) in Vietnam, which have highlighted the extraordinary diversity of viral species there. The initiative has also been involved in molecular analysis of Dengue and Chikungunya viruses in Vietnam and has demonstrated dynamic changes in circulating Dengue virus serotypes which have significant implications for clinical outcomes.

When outbreak of vector-borne diseases (e.g., dengue hemorrhagic fever, chikungunya fever, and malaria) are occurred. The best way to stop outbreak is vector control using insecticides. The continuous usage of insecticide lead mosquitoes to resist with insecticide which is the biggest obstacle of vector control program.

Our research is studying in the insecticide resistance of mosquitoes to pyrethroids which widely used in the vector control program. By molecular studies related mechanisms, such as mutation of sodium channel (kdr resistance gene), expression of detoxification enzymes and others, give important information that are benefit for development of new substances or management methods for the vector control program. Novel molecular techniques will help us to fulfill our study.