Bioinformatics has become indispensable for biomedical researches. To facilitate knowledge discovery in the post-genomic era, our bioinformatic team has developed widely used analysis methods and databases for large-scale data, and provided computational services to both the domestic and international community. We have also performed meta-analyses to discover genetic principles, potential causes of complex diseases, and molecular targets for future diagnostic/therapeutic developments.

We have developed analytical tools for microbial genomics, metagenomics, and functional genomics.

• Lin HH, Liao YC. Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes. Scientific Reports 2016; 6: 24175.
• Liao YC, Lin HH, Sabharwal A, Haase EM, Scannapieco FA. MyPro: A seamless pipeline for automated prokaryotic genome assembly and annotation. Journal of Microbiological Methods 2015; 113: 72-4
• Lin SH, Liao YC. CISA: contig integrator for sequence assembly of bacterial genomes. PloS one 2013; 8(3): e60843.
• Weng MP, Liao BY. DroPhEA: Drosophila phenotype enrichment analysis for insect functional genomics. Bioinformatics (Oxford, England) 2011; 27(22): 3218-9.

We have sequenced, assembled and annotated the genomes of important pathogenic bacteria.

• Sabharwal A, Liao YC, Lin HH, Haase EM, Scannapieco FA. Draft genome sequences of 18 oral streptococcus strains that encode amylase-binding proteins. Genome Announcements 2015; 3(3).
• Liao YC, Liu TT, Chang JR, et al. Draft Genome Sequence of Mycobacterium tuberculosis Clinical Strain W06, a Prevalent Beijing Genotype Isolated in Taiwan. Genome Announcements 2015; 3(6).
• Remenyi R, Qi H, Su SY,…, Lin CY, et al. A comprehensive functional map of the hepatitis C virus genome provides a resource for probing viral proteins. mBio 2014; 5(5): e01469-14.

We have explored the molecular and phenotypic evolution of pathogenic microbes.

• Lin CH, Wang YB, Chen SH, Hsiung CA, Lin CY. Precise genotyping and recombination detection of Enterovirus. BMC Genomics 2015; 16 Suppl 12: S8.
• Liao YC, Lin HH, Lin CH, Chung WB. Identification of cytotoxic T lymphocyte epitopes on swine viruses: multi-epitope design for universal T cell vaccine. PloS one 2013; 8(12): e84443.
• Liao YC, Chen FC, Hsiung CA. Contrasting substitution patterns between HA proteins of avian and human influenza viruses: Implication for monitoring human influenza epidemics. Vaccine 2010; 28(50): 7890-6.

We have discovered genetic principles underlying mammalian gene and genome evolution.

• Liao BY, Weng MP. Unraveling the association between mRNA expressions and mutant phenotypes in a genome-wide assessment of mice. Proceedings of the National Academy of Sciences of the United States of America 2015; 112(15): 4707-12..
• Chen FC, Liao BY, Pan CL, Lin HY, Chang AY. Assessing determinants of exonic evolutionary rates in mammals. Molecular Biology and Evolution 2012; 29(10): 3121-9.
• Chuang TJ, Chen FC, Chen YZ. Position-dependent correlations between DNA methylation and the evolutionary rates of mammalian coding exons. Proceedings of the National Academy of Sciences of the United States of America 2012; 109(39): 15841-6.

We have revealed the genetic and epigenetic principles of human gene regulation.

• Liao BY, Weng MP. Unraveling the association between mRNA expressions and mutant phenotypes in a genome-wide assessment of mice. Proceedings of the National Academy of Sciences of the United States of America 2015; 112(15): 4707-12.
• Chen FC, Liao BY, Pan CL, Lin HY, Chang AY. Assessing determinants of exonic evolutionary rates in mammals. Molecular Biology and Evolution 2012; 29(10): 3121-9.
• Chang AY, Liao BY. DNA methylation rebalances gene dosage after mammalian gene duplications. Molecular Biology and Evolution 2012; 29(1): 133-44.

We have identified genetic markers and pathways involved in complex diseases (e.g. metabolic diseases and cancers).

• Wang Z, Seow WJ, Shiraishi K,…, Hsiao CF,…, et al. Meta-analysis of genome-wide association studies identifies multiple lung cancer susceptibility loci in never-smoking Asian women. Human Molecular genetics 2016; 25(3): 620-9.
• Hsu MK, Wu IC, Cheng CC,…,Chen FC. Triple-layer dissection of the lung adenocarcinoma transcriptome: regulation at the gene, transcript, and exon levels. Oncotarget 2015; 6(30): 28755-73.
• Chen P, Takeuchi F, Lee JY,…, Hsiung CA,…,et al. Multiple nonglycemic genomic loci are newly associated with blood level of glycated hemoglobin in East Asians. Diabetes 2014; 63(7): 2551-62.

We have served as a core member of Taiwan Bioinformatics Institute to develop most needed bioinformatics tools, and to provide state-of-the-art customized bioinformatics services to academic and industrial researchers.

• Lee CC, Liao YC, Lai YH, Lee CC, Chuang MC. Recognition of dual targets by a molecular beacon-based sensor: subtyping of influenza A virus. Analytical Chemistry 2015; 87(10): 5410-6.
• Leu JH, Liu KF, Chen KY,…, Lin CY, et al. The novel white spot syndrome virus-induced gene, PmERP15, encodes an ER stress-responsive protein in black tiger shrimp, Penaeus monodon. Developmental and Comparative Immunology 2015; 49(2): 239-48.
• Lin KH, Liao BY, Chang HW, et al. Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics. BMC Genomics 2015; 16.

We have developed simulation tools for modeling mechanisms causing complex diseases

• Yao PJ, Chung RH. SeqSIMLA2_exact: simulate multiple disease sites in large pedigrees with given disease status for diseases with low prevalence. Bioinformatics (Oxford, England) 2016; 32(4): 557-62.
• Chung RH, Tsai WY, Hsieh CH, Hung KY, Hsiung CA, Hauser ER. SeqSIMLA2: simulating correlated quantitative traits accounting for shared environmental effects in user-specified pedigree structure. Genetic Epidemiology 2015; 39(1): 20-4.
• Chung RH, Shih CC. SeqSIMLA: a sequence and phenotype simulation tool for complex disease studies. BMC Bioinformatics 2013; 14: 199.