Our missions

Using IT innovations to increase the quality of life (QoL).

In Focus:

(1) Network analysis of human protein interactions for Tumorigenesis and infectious diseases in the approach of systems biology

We have implemented a statistical model into our protein interaction database for validation of two-hybrid assays ofHelicobacter pylori, and prediction of putative protein interactions not yet discovered experimentally. By this approach, we can compare the interacting network of various strains with different virulence to decipher the secret between hosts and pathogens (http://dpi.nhri.org.tw/hp/, Bioinformatics  2005). Using the more sophisticated statistical method with expression profile, we integrated a database named as flydpi for the interactome of Drosophila Melanogaster(http://flydpi.nhri.org.tw, BMC Bioinfo, 2006). And we also constructed a topological analyzer for complex network named as Hubba (NAR, 2008, http://hubba.iis.sinica.edu.tw). Objectives of our work are to improve our understanding of the puzzle during development stage, carcinogenesis and infectious mechanism, and to furthermore introduce a new paradigm for the diagnosis and treatment of human disease to revolutionize current medical services delivered.

(2) Developing value-added databases and web applications for biomedical research communities

We have published several web applications and databases related with bioinformatics for biomedical research community. For example, the web application, Primer Design Assistant (PDA) (NAR, 2003, ,http://dbb.nhri.org.tw/primer/), can be helpful to large scale PCR for high throughput experiments like microarray experiments. From July 2003 to Mar 2008, the accumulated visits and processed sequences go beyond 100,000 and 620,000, respectively. PDA is not only served for research groups, but also was used to develop the rapid diagnostic kit for SARS for Central of Disease Control (CDC), Taiwan in 2004. Until now, there are several diagnostic kits developed by PDA.  Based on similar idea, we have implemented a platform for unique probe design for various uses in hybridization, like microarray and blots named as "Unique Probe Selector, UPS" (http://array.iis.sinica.edu.tw/ups , BMC Bioinfo 2008).

In 2005, we have implemented a phylogenetic platform for topology construction and visualization named as POWER (http://power.nhri.org.tw, NAR, 2005). We are working on the best model selection in automatic way and try to integrate two systems for biomedical research groups.

(3) Metagenomics

According to the advance in sequencing technology, time for sequencing large genome like human genome would not take several months/years but weeks/days. Several shotgun sequencing projects of various communities have been completed and started. Following the flood of massive sequence data, there are several interesting computational problems that arise from WGS sequencing of communities. Those issues related with how to compare communities, how to separate sequence from different organisms in silico, and how to model population structures using WGS assembly statistics, will be new challenges in the field of bioinformatics. Our approach here is to integrate various databases, gene expression analysis, proteomic results and phylogenetic reconstruction to achieve a comprehensive view of microbial communities.

More .......for Biomedical Research Community 

List of Publications 

我們的目標與責任

以創新資訊技術來增進人類的生命品質(Quality of Life)

 我們的研究重點

(1)   網路生物及系統生物學研究

利用大規模蛋白質交互實驗資料，以統計模型預測新的交互作用，並將兩者與相關生物註解資料庫加以整合，以web為基礎，建置多種模式生物的全蛋白質體交互網路如幽門桿菌(http://dpi.nhri.org.tw/hp, Bioinformatics 2005)，果蠅(http://flydpi.nhri.org.tw, BMC Bioinformatics 2006)，以及較為複雜的人類蛋白質交互關係推演法(BMC Bioinformatics, 2007, highly accessed)。研究團隊亦進行網路的拓樸分析，可將複雜生物網路中的關鍵蛋白與脆弱模組加以辨識，可做為網路醫學(Network medicine)研究重要工具(hubba, http://hub.iis.sinica.edu.tw, Nucleic Acids Research, 2008, spotlight, http://hub.iis.sinica.edu.tw/spotlight/, Gene 2014, cytohubba, http://hub.iis.sinica.edu.tw/cytohubba, BMC Genomics, 2014)。另外，目前本團隊正進行建置生物網路比對系統，以找出其中隱含的重要保守調控模組(http://hub.iis.sinica.edu.tw/Hunter, BMC Bioinformatics, 2009)，並以幹細胞分化機制與轉錄因子調節，及病原體感染宿主細胞交互調控機制為研究標的。

(2)   生物資訊加值資料庫與應用系統之建置

近幾年已發表多個生物資訊系統與分析工具於國際知名生物醫學期刊，譬如Primer Design Assistant (PDA) (http://dbb.nhri.org.tw/primer/, Nucleic Acids Research, 2003), 大規模PCR 核酸引子設計線上輔助系統，截自2014年九月，共有來自全球各地超過二十一萬人次上線使用，共已處理一百三十萬餘條序列，除了於2004年協助衛生署疾病管制局發展SARS快速診斷試劑之外，相關的研究也取得多項專利。

結合熱力學與實驗室經驗，研究團隊也發展出一套可作為基因晶片與雜合探針設計的自動化流程，Unique Probe Selector (UPS, http://array.iis.sinica.edu.tw/ups, BMC Bioinformatics 2008, BMC Genomics, 2010)，可提昇實驗精準度與減低雜訊，設計快速病原體偵測晶片與探針(Sensor, 2012)。

本研究室亦於2005年七月在Nucleic Acid Research，發表一個生物巨分子序列親源關係的分析架構自動化平台，POWER: PhylOgenetic WEb Repeater - An integrated and user-optimized framework for bio-molecular phylogenetic analysis (http://power.nhri.org.tw)，獲多個生物資訊網站推薦使用，如歐洲重要生物資訊網站Expasy將POWER列入Life Science Directory中。目前研究團隊已完成新一代系統的開發，解決親源樹建置過程裏重要的關鍵核心，也就是最佳親緣演化統計模型選取的問題，並協助多個國際研究團隊，以簡明的方式建構複雜的親緣分析關係(PALM, http://palm.iis.sinica.edu.tw/, PLoS ONE, 2009)，自2009年十二月發表以來，已有近4,100使用人次及22萬條處理序列。

(3) 實驗室電子記錄本（實驗室多人版與USB版本,相關資訊請參閱 http://eln.iis.sinica.edu.tw）

將實驗室中所產生的各種紀錄，以電子化方式儲存於網路伺服器/一般桌上型電腦/筆記型電腦/USB隨身碟，並經由瀏覽器方便管理、分享、搜尋、備份、列印，及與研究伙伴線上討論相關問題。

 
1. 大型實驗室群組版本: 相容於 Linux平台環境
2. 中小型實驗室與個人單機版本: 可相容於微軟視窗/麥金塔 作業環境。

聯絡人： 林仲彥 博士