通讯机构：
[Xu, Ying] U;Univ Georgia, Dept Biochem & Mol Biol, Computat Syst Biol Lab, Athens, GA 30602 USA.
关键词：
genome;operon;rna
摘要：
We have recently developed a new version of the DOOR operon database, DOOR 2.0, which is available online at http://csbl.bmb.uga.edu/DOOR/ and will be updated on a regular basis. DOOR 2.0 contains genome-scale operons for 2072 prokaryotes with complete genomes, three times the number of genomes covered in the previous version published in 2009. DOOR 2.0 has a number of new features, compared with its previous version, including (i) more than 250 000 transcription units, experimentally validated or computationally predicted based on RNA-seq data, providing a dynamic functional view of the underlying operons; (ii) an integrated operon-centric data resource that provides not only operons for each covered genome but also their functional and regulatory information such as their cis-regulatory binding sites for transcription initiation and termination, gene expression levels estimated based on RNA-seq data and conservation information across multiple genomes; (iii) a high-performance web service for online operon prediction on user-provided genomic sequences; (iv) an intuitive genome browser to support visualization of user-selected data; and (v) a keyword-based Google-like search engine for finding the needed information intuitively and rapidly in this database.
作者机构：
[Yang, Jincai; Shen, Xianjun; Djigal, Hamza] Cent China Normal Univ, Sch Comp Sci, Wuhan 430079, Hubei, Peoples R China.
会议名称：
International Conference on Mechanical Engineering and Automation (ICMEA)
会议时间：
JAN 03-05, 2014
会议地点：
Beijing, PEOPLES R CHINA
会议主办单位：
[Djigal, Hamza;Yang, Jincai;Shen, Xianjun] Cent China Normal Univ, Sch Comp Sci, Wuhan 430079, Hubei, Peoples R China.
关键词：
Location Based Services;Continuous-Nearest-Neighbor Query;Voronoi Diagram;Semantic Caching;Mobile Database
摘要：
Location Based Services (LBS) have received increasing attention in recent years. In a mobile environment, the client, server and object may change their location. Given the limitations in mobile database, it is strongly recommended to minimize the number of connections and volume of data transmission from the servers. Data caching technique will be a profitable solution for this problem. In this paper we propose a new caching strategy called Path Semantic Caching (PSC) for Continuous Nearest-Neighbor Query (CNNQ), in which the mobile user issues a query to retrieve the Nearest-Neighbor (NN) of every point on a path. A Voronoi-based index is used in the server to support a CNNQ, while PSC is proposed to reduce the need for connecting and transmitting data from server which is costly. A simulation is conducted to examine the performance of our proposed caching technique in comparison with the case where no cache is used. The result shows that the PSC provides a considerable improvement in response time, number of connections to the server, and cache hit ratio.
期刊：
2013 IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE (BIBM),2013年:57-60 ISSN：2156-1125
通讯作者：
Shen, Xianjun
作者机构：
[Yang, Jincai; He, Tingting; Shen, Xianjun; Hu, Xiaohua; Zhao, Yanli; Li, Yanan] Cent China Normal Univ, Sch Comp, Wuhan, Peoples R China.;[Hu, Xiaohua] Drexel Univ, Coll Comp & Informat, Philadelphia, PA 19104 USA.
通讯机构：
[Shen, Xianjun] C;Cent China Normal Univ, Sch Comp, Wuhan, Peoples R China.
会议名称：
IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM)
会议时间：
DEC 18-21, 2013
会议地点：
Shanghai, PEOPLES R CHINA
会议主办单位：
[Shen, Xianjun;Zhao, Yanli;Li, Yanan;Yang, Jincai;He, Tingting;Hu, Xiaohua] Cent China Normal Univ, Sch Comp, Wuhan, Peoples R China.^[Hu, Xiaohua] Drexel Univ, Coll Comp & Informat, Philadelphia, PA 19104 USA.
会议论文集名称：
IEEE International Conference on Bioinformatics and Biomedicine-BIBM
关键词：
protein complexes;best neighbor node;modularity increment;Protein-Protein Interaction network
摘要：
In order to overcome the limitations of global modularity and the deficiency of local modularity, we introduce a hybrid modularity measure LGQ (Local-Global Quantification) which adopts a suitable modularity adjustable parameter to control the balance of global detecting capability and local search capability in Protein-Protein Interaction (PPI) network. On the other hand, a new protein complex mining algorithm called BN-LGQ has been proposed, which integrates the definitions of best neighbor node and the modularity increment. And by comparison with other known algorithms, the experimental results show BN-LGQ performs a better accuracy on predicting protein complexes and has a higher match with the reference protein complexes. Moreover, it can identify protein complexes with better biological significance in PPI network.
期刊：
International Journal of Computer Applications in Technology,2012年44(2):137-144 ISSN：0952-8091
通讯作者：
Zhang, D.(zdbff@yahoo.com.cn)
作者机构：
[Jincai Yang; Caixia Chen; Yanan Li; Xianjun Shen] Department of Computer Science, Central China Normal University, Wuhan, China;[Dabin Zhang] Department of Information Management, Central China Normal University, Wuhan, China
通讯机构：
Department of Information Management, Central China Normal University, China
摘要：
Knapsack problem is a classical combinatorial optimisation problem. This paper presents greedy continuous particle swarm optimisation (GCPSO) algorithm to solve the knapsack problem. First, the greedy strategy is introduced into the process of particles' initialisation based on standard particle swarm optimisation (SPSO). This strategy guarantees the particle swarm has a better beginning in a degree. Second, based on the analysis of the characteristics of the knapsack problem's solution space, and in terms of the binary code in evolutionary computation, the paper presents multi-state coding. To some extent, the multi-state coding reduces the data redundancy when encoding the solution of the knapsack problem. In experiments, the authors used discrete particle swarm algorithm as well as continuous particle swarm algorithm to find solutions for the knapsack problem. The experimental results show that the GCPSO algorithm provides better solution for the knapsack problems.
作者机构：
[Jincai Yang; Qi Chen; Zhonghua Wang; Jinzhu Hu] School of Computer Science,Huazhong Normal University
会议名称：
2012 3rd International Conference on Information Technology for Manufacturing Systems(ITMS 2012)
会议时间：
2012-09-08
会议地点：
Qingdao,China
关键词：
Mobile Computing;Moving Patterns;Data Allocation;Mobile Database
摘要：
Mobile users tend to submit transactions to servers nearby for execution so as to minimize the communication overhead incurred. Data replication is helpful because it can improve execution performance
