ATID: a web-oriented database for collection of publicly available alternative translational initiation events
Alternative translational initiation is an important cellular mechanism contributing to the diversity of protein products and functions. We develop a database that provides a comprehensive collection of alternative translational initiation events. The purpose of this alternative translational initiation database (ATID) is to facilitate the systematic study of alternative translational initiation of genes. The current version of database contains 300 genes from Homo sapiens, Mus musculus and other species. Each of the genes has two or more isoforms due to alternative translational initiation. Resources in ATID, including gene information, alternative products of genes and domain structures of isoforms, are provided through a user-friendly web interface.


AVAILABILITY
The ATID database is available for public use at http://bioinfo.au.tsinghua.edu.cn/atie/.

title: htSNPer1.0: software for haplotype block partition and htSNPs selection
abstract: BackgroundThere is recently great interest in haplotype block structure and haplotype tagging SNPs (htSNPs) in the human genome for its implication on htSNPs-based association mapping strategy for complex disease. Different definitions have been used to characterize the haplotype block structure in the human genome, and several different performance criteria and algorithms have been suggested on htSNPs selection. heuristic algorithm, generalized branch-and-bound algorithm, is applied to the searching of minimal set of haplotype tagging SNPs (htSNPs) according to different htSNPs performance criteria. We develop a software htSNPer1.0 to implement the algorithm, and integrate three htSNPs performance criteria and four haplotype block definitions for haplotype block partitioning. It is a software with powerful Graphical User Interface (GUI), which can be used to characterize the haplotype block structure and select htSNPs in the candidate gene or interested genomic regions. It can find the global optimization with only a fraction of the computing time consumed by exhaustive searching algorithm.ConclusionhtSNPer1.0 allows molecular geneticists to perform haplotype block analysis and htSNPs selection using different definitions and performance criteria. The software is a powerful tool for those focusing on association mapping based on strategy of haplotype block and htSNPs.

title: MicroRNA identification based on sequence and structure alignment
abstract: MicroRNAs (miRNA) are approximately 22 nt long non-coding RNAs that are derived from larger hairpin RNA precursors and play important regulatory roles in both animals and plants. The short length of the miRNA sequences and relatively low conservation of pre-miRNA sequences restrict the conventional sequence-alignment-based methods to finding only relatively close homologs. On the other hand, it has been reported that miRNA genes are more conserved in the secondary structure rather than in primary sequences. Therefore, secondary structural features should be more fully exploited in the homologue search for new miRNA genes.



In this paper, we present a novel genome-wide computational approach to detect miRNAs in animals based on both sequence and structure alignment. Experiments show this approach has higher sensitivity and comparable specificity than other reported homologue searching methods. We applied this method on Anopheles gambiae and detected 59 new miRNA genes.



This program is available at http://bioinfo.au.tsinghua.edu.cn/miralign.



Supplementary information is available at http://bioinfo.au.tsinghua.edu.cn/miralign/supplementary.htm.

title: Computing Exact p-Value for Structured Motif
abstract: Extracting motifs from a set of DNA sequences is important in computational biology. Occurrence probability is a common used statistics to evaluate the statistical significance of a motif. A main problem is how to calculate the occurrence probability of the motif on the random model of DNA sequence efficiently and accurately. In this paper, we are interested in a particular motif model which is useful in transcription process. This motif, which is called structured motif, is composed two motif words on single nucleotide alphabet and with fixed spacers between them. We present an efficient algorithm to calculate the exact occurrence probability of a structured motif on a given sequence. It is the first nontrivial algorithm to calculate the exact p-value for such kind of motifs.

title: ArnetMiner: An Expertise Oriented Search System for Web Community
abstract: Expertise Oriented Search aims at providing comprehensive analysis and mining for people from distributed sources. In this paper, we give an overview of the expertise oriented search system (ArnetMiner). The system addresses several key research issues in extraction and mining of a researcher social network. The system is in operation on the internet for more than one year and receives accesses from about 1,500 users per month. Feedbacks from users and system logs indicate that users consider the system can really help people to find and share information in the web community.

title: ArnetMiner: extraction and mining of academic social networks
abstract: This paper addresses several key issues in the ArnetMiner system, which aims at extracting and mining academic social networks. Specifically, the system focuses on: 1) Extracting researcher profiles automatically from the Web; 2) Integrating the publication data into the network from existing digital libraries; 3) Modeling the entire academic network; and 4) Providing search services for the academic network. So far, 448,470 researcher profiles have been extracted using a unified tagging approach. We integrate publications from online Web databases and propose a probabilistic framework to deal with the name ambiguity problem. Furthermore, we propose a unified modeling approach to simultaneously model topical aspects of papers, authors, and publication venues. Search services such as expertise search and people association search have been provided based on the modeling results. In this paper, we describe the architecture and main features of the system. We also present the empirical evaluation of the proposed methods.

title: Applying PageRank Algorithm in Requirement Concern Impact Analysis
abstract: As an important part of requirement management, managing requirement change plays a key role in controlling project schedule and costs at early stage. Effective requirement impact analysis would give proper assessment on the effect of certain requirement changes on the whole system, and provide useful information for making trade-off decisions on future system design and implementation. In this paper a quantitative approach to concern impact analysis at requirement level has been proposed with the application of PageRank algorithm, which is a successful link based web page sorting algorithm. At first, separation of concerns is applied during deriving formal requirement specification from textual requirement statements. Next, concerns are specified and concern relationship graph is established. Finally, PageRank algorithm is utilized on concern relationship graph for assessing the impact of concern changes. Our approach has been applied to hallway section in Light Control System and validation of analysis result has been stated.

title: Exploring digital government initiatives to expand Full Information Product Pricing (FIPP) networks in NAFTA
abstract: This poster describes research in progress made by the Research Group on Comparative and Transnational Digital government in North America. The main purpose of this project is to explore the impact of product labeling, information architectures and government-sponsored information policies on the expansion of the market share of organic, fair trade, and eco-friendly products in the NAFTA region. In these alternative markets, price is often complemented with information conveying the conditions under which a product is produced and distributed, which is transmitted through trusting networks or certifiable labels such as "Organic" or "Fair Trade." We call such networks Full Information Product Pricing (FIPP) Networks. The transparency of FIPP networks, enabled by the information technology and associated policy and standards, may have the potential to supplement a compliance-enforcement approach with a more market-based voluntary approach that relies on shifts in producer and consumer behavior to significantly expand the share of worker and environmentally friendly products traded. In this paper, we discuss our research focus, research plan, and results from preliminary studies.

title: Do You Know Where Your Data's Been? - Tamper-Evident Database Provenance
abstract: Database provenance chronicles the history of updates and modifications to data, and has received much attention due to its central role in scientific data management. However, the use of provenance information still requires a leap of faith. Without additional protections, provenance records are vulnerable to accidental corruption, and even malicious forgery, a problem that is most pronounced in the loosely-coupled multi-user environments often found in scientific research. 
 
This paper investigates the problem of providing integrity and tamper-detection for database provenance. We propose a checksum-based approach, which is well-suited to the unique characteristics of database provenance, including non-linear provenance objects and provenance associated with multiple fine granularities of data. We demonstrate that the proposed solution satisfies a set of desirable security properties, and that the additional time and space overhead incurred by the checksum approach is manageable, making the solution feasible in practice.

title: X-warehouse: building query pattern-driven data
abstract: In this paper, we propose an approach to materialize XML data warehouses based on the frequent query patterns discovered from historical queries issued by users. The schemas of integrated XML documents in the warehouse are built using these frequent query patterns represented as Frequent Query Pattern Trees (FreqQPTs). Using hierarchical clustering technique, FreqQPTs are clustered and merged to produce a specified number of integrated XML documents for actual data feeding. Maintenance issue of the data warehouse is also treated in this paper.

title: A Computational Framework and Browser for Supporting Automatic Genome Annotation
abstract: We present here a flexible computational framework to complete the large-scale computing tasks involved in automatic annotation of whole-genomes. The characteristics of this framework include a two-level job load system and NFS-based distributed store of replicated data. In addition, the storage structure of annotation results in a relational database system and a Web interface for graphical interactive browsing and searching on the data are also described. The framework has been used to identify a core set of human protein coding genes that are consistently annotated and of high quality, which can be accessed by the browser provided at http://bioinfo.hust.edu.cn/en/database/ben