E2

Taiwan Bioinformatics Institute

Unit 4 : Applied medical genomics

The genomic research has moved from single cell to the systems. In the meanwhile, high throughput parallel genomic sequencing (i.e. NGS) shifts the bottleneck in sequencing processes from experimental data production to computationally intensive informatics-based data analysis. As these new technologies permit large-scale quantitative studies of many biological networks, we anticipate large data-bases of biological interactions will drive the systems biology research in the coming years. To look forward to the future needs, our perspectives for future bioinformatics services will be mostly on customized services for the following areas:

1. Genome annotation. Functional characterization of sequences is the fundamental goal of the majority of sequencing projects. Our service will provide prediction and annotation of genes and regions for various genomes. In addition, we will implement software platforms and databases for pathway analysis, epigenomics regulation, and gene regulatory network systems.
2.  Genome comparison. Study given genome from a comparative standpoint is also an important way to illustrate biology. Our service will provide a cross-genomic view for setting the stage for evolutionary analysis and regulatory pattern discovery.
3. Array data analysis. Microarray platform is still considered the most reliable technology to detect known sequence variants and quantify expression level changes. We will provide customized services in enrichment and functional analysis according to GO and KEGG terms, transcriptional factors and expression profiles, and gene clustering analysis. In addition, we also offer advice about statistics significance of the results obtained and consultancy in data interpretation
4. NGS sequence analysis. The assembly of sequence fragments obtained by NGS technologies requires both considerable computing power and technology-specific algorithms. In addition to the application of the sequencer standard software package, we offer to analyze sequencing data and improve the quality of the assembly. Further applications including variant identification, expression level quantification, and specific motif characterizations will also be performed using commercial and/or in-house developed software.
5. Functional analysis. Follow-up analysis from NGS or array outputs will be provided. For example, prediction of biological significance of each identified sequence variant or cluster genes into groups according to different pathway functions. Further, we will integrate various –omics databases for large-scale data-mining and development of computational methodologies to assist in functional interpretation.
6. Text mining based analysis. We also offer alternative analysis through the use of our own text mining based techniques. These platforms allow users to identify the targets of interested by key words and pattern search in the PubMed database.
7. Database design and development. We are experts and have been involved in the design and development of several biological databases. We will provide our expertise to assist customer to develop their databases.
8. Genetic analysis. We offer statistic software and package for genetic association study, GWAS, and linkage analysis.
9. Consultation. We offer specialized consultation in analysis and annotation of genome sequences, databases of genomics and proteomics data, pathway analysis, and etc.
10. Workflow design and implementation. Workflow involves series steps of actions that work systematically to get job done. Workflow design and implementation are important to transform research-based outcome to application. As many current studies aim to be applied to future clinical medicine, we anticipate the bioinformatics pipeline established for now will eventually be converted into workflow for daily routines. Our expertise definitely can help in such transition.
11. In addition to the new customized services, we will continue our general online services which have provided more than 10 analytic tools and databases for the internet user, further we will conduct training courses and/or workshops to promote the use of computational systems.