RESEARCH
The long-term research goal of our laboratory is to utilize bioinformatic tools/databases in elucidating molecular and cellular aspects of functional transcription elements in human genome and their significance in oncogenesis and tumor progression. These functional transcription elements include traditional protein-coding genes and non-coding ones. Our research efforts are intended to elucidate functions and regulations of these transcription elements using bioinformatics data-mining and molecular experimental approaches. Previously, we have used the dbEST database for the discovery of novel human genes, identification of functional nucleotide polymorphisms (SNPs and InDels). Subsequently, we further discover and interrogate a new wobble-splicing mechanism at exon junctions that results in the generation of InDel variants in protein coding transcripts. In order to interrogate the functional aspects of these elements, we have developed gene oriented ortholog assignment and protein domain ortholog classification algorithms and databases. We have also emphasized on the discovery of non-coding regulatory microRNAs. Informatic pipelines are employed to discover and interrogate miRNAs from genomic sequences of viruses, parasites and animals. We have also engaged in the regulation features of human miRNAs in oncogenesis and their cancer biomarker potential in liquid biopsy. There are several bioinformatic databases established in our laboratory:
Virus miRNAs & target prediction service
Vir-Mir: http://alk.ibms.sinica.edu.tw
miRNA clusters
MetaMirClust: http://fgfr.ibms.sinica.edu.tw/MetaMirClust/
Conserved miRNAs in animal genomes
Zoo-Mir: http://insr.ibms.sinica.edu.tw
Protein ortholog discovery by comparative gene identification
Protein ortholog interrogation by domain features
Protein ortholog annotation by genomic loci
Duplicated gene loci variants
Transcript isoforms in human protein-coding genes
Representative Tissue Transcripts of Protein-coding Genes
microRNA Target Visualization Tool for TCGA cancers
Tissue Expression Profiles of MANE-select Transcripts
TEx-MST: https://texmst.ibms.sinica.edu.tw/
研究介紹
本研究室著重於開發生物資訊工具及資料庫，並將研究應用於改善癌症治療策略。對於蛋白質基因，我們建立數個人類同源基因研究之生物資訊資料庫應用於功能基因體，利用大規模基因表現資料庫，建立生物資訊工具來發現跨物種保留之同源蛋白質基因，並研究由單一核苷酸變異之功能性影響。此外，我們亦針對非編碼RNA基因進行生物資訊與分子生物學研究。其中，microRNA是極小片段的ncRNA，可以調控基因表現。 我們已建立數個microRNA發掘之生物資訊平台，並對於microRNA基因的轉錄調控進行深入研究。利用序列演化保留的特性，在五十餘個動物基因體中發現超過15000個以上高可信度的新microRNA基因。我們發現microRNA與人類癌症之關連性及血清與尿液中microRNA作為偵測癌症檢測(liquid biopsy)之應用。至今，一些已建立之線上生物資訊資料庫有：
Vir-Mir ; MetaMirClust ; Zoo-Mir ; CGI ; DODO ; GOOD ; dbDNV ; TREGT ; RTTPG ; miRTV ; TEx-MST
