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Gene Set/Pathway enrichment analysis

This is one of the most frequently used tools in bioinformantics, people used DAVID a lot, however few people realized DAVID stands on a soft ground as it soly relies on KEGG. KEGG has many limitations, including, incompatible data formats, inconsistent molecular representations, inconsistent molecular relationship representations, inconsistent referrals to pathway names, and incomprehensive data from different databases. Dr. Zhou overcome these issues through extraction, normalization and integration of pathway data from several major public databases (KEGG, WikiPathways, BioCyc, etc) and he build a database called IntPath to hosts the integrated pathway data for convenient public access. 

Please visit IntPath: http://compbio.ddns.comp.nus.edu.sg:8080/IntPath/ and you will be amazed by how comprehensive the enrichment analysis can be. 

Functional annotation for your gene list---pathway enrichment analysis

Pathway data are important for understanding the relationship between genes, proteins and many other molecules in living organisms. Many well-established databases are dedicated to collecting pathway data for public access. However, the effectiveness of these databases is seriously hindered by issues such as incompatible data formats, inconsistent molecular representations, inconsistent molecular relationship representations, inconsistent referrals to pathway names, and incomprehensive data from different databases. Dr. Zhou overcome these issues through extraction, normalization and integration of pathway data from several major public databases (KEGG, WikiPathways, BioCyc, etc). Dr. Zhou build a database called IntPath that not only hosts the integrated pathway gene relationship data for public access but also maintains the necessary updates in the long run.

Dr. Zhou have overcome in IntPath the issues of compatibility, consistency, and comprehensiveness that often hamper effective use of pathway databases. We have included four organisms in the current release of IntPath. Our methodology and programs described in this work can be easily applied to other organisms; and we will include more model organisms and important pathogens in future releases of IntPath. IntPath maintains regular updates and is freely available at http://compbio.ddns.comp.nus.edu.sg:8080/IntPath

The ground breaking technology in predicting protein-protiein interaction(PPI ) through Domain-domain interactions(DDI).

The ground breaking technology in predicting protein-protiein interaction(PPI ) through Domain-domain interactions(DDI).

http://www.biomedcentral.com/1752-0509/7/S6/S6

Stringent DDI-based Prediction of H. sapiens-M. tuberculosis H37Rv Protein-Protein Interactions

Hufeng Zhou¹²³⁴, Javad Rezaei², Willy Hugo², Shangzhi Gao⁵, Jingjing Jin², Mengyuan Fan¹², Chern-Han Yong¹², Michal Wozniak¹⁶ and Limsoon Wong^2*

In this paper, Dr. Zhou developed a novel ground breaking technology in predicting protein-protiein interaction(PPI ) through Domain-domain interactions(DDI).

How to using STRING database correctly?

So many people has done it in a wrong why, in this paper, Dr. Zhou describe all the hidden limitations of STRING database and he proposed the correct way of using STRING database and his correct way of using STRING database has been widely accepted and cited.
Refer to his work,
*Zhou, Hufeng, and Limsoon Wong. “Comparative analysis and assessment of M. tuberculosis H37Rv protein-protein interaction datasets.” BMC genomics 12, no. Suppl 3 (2011): S20.
http://www.biomedcentral.com/1471-2164/12/S3/S20

The unique advantage of IntPath

Pathway Enrichment Analysis has been so widely used, but few people realize the tools they use like DAVID, KEGG have many limitations. Especially the  "Incompleteness" limitation seriously affect the enrichment results. Here the IntPath database largely solves the incomplete problem by integrating and curating many available main stream Pathway data from different source. It is the most complete pathway database ever created. Try IntPath "Identify Pathways" function for pathway enrichment for your interested gene list, you will be amazed by the enrichment pathway results you see directly from the output.

http://compbio.ddns.comp.nus.edu.sg:8080/IntPath/

周胡峰博士的科研很酷

[1] 周胡峰博士大作Progress in computational studies of host-pathogen interactions.，融合100多篇文献，提取精华，写成的博士论文的导论。这篇发表在JBCB的综述刚刚支持免费阅读（之前收费的）。欢迎大家阅读，转载，引用，http://www.worldscientific.com/doi/abs/10.1142/S0219720012300018

[2] People has been using STRING database wrongly for a long time. In this paper Dr. Zhou described the drawback of STRING database and B2H data set, and he also talks about how to use STRING database correctly and it has be applaud  by the community.

[3]周胡峰博士第一篇发表的一作论文，Comparative analysis and assessment of M. tuberculosis H37Rv protein-protein interaction datasets 发表在BMC genomics上，这篇工作曾经在InCob conference 做大会发言。这篇工作成功的解决了M. tuberculosis H37Rv protein-protein interaction datasets的质量问题，为以后的工作作出了重要铺垫。欢迎大家阅读，转载，引用，http://www.biomedcentral.com/1471-2164/12/S3/S20

[4]How to using STRING database correctly?
so many people has done it in a wrong why, in this paper, Dr. Zhou describe all the hidden limitations of STRING database and he proposed the correct way of using STRING database and his correct way of using STRING database has been widely accepted and cited.
Refer to his work,
*Zhou, Hufeng, and Limsoon Wong. “Comparative analysis and assessment of M. tuberculosis H37Rv protein-protein interaction datasets.” BMC genomics 12, no. Suppl 3 (2011): S20.
http://www.biomedcentral.com/1471-2164/12/S3/S20


[5]The unique advantage of IntPath
Pathway Enrichment Analysis has been so widely used, but few people realize the tools they use like DAVID, KEGG have many limitations. Especially the  "Incompleteness" limitation seriously affect the enrichment results. Here the IntPath database largely solves the incomplete problem by integrating and curating many available main stream Pathway data from different source. It is the most complete pathway database ever created. Try IntPath "Identify Pathways" function for pathway enrichment for your interested gene list, you will be amazed by the enrichment pathway results you see directly from the output.
http://compbio.ddns.comp.nus.edu.sg:8080/IntPath/