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Tomato Expression Database (TED) - An interactive management tool for tomato expression profiling data 2

Tomato Expression Database (TED) - An interactive management...

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2nd international computational systems bioinformatics conference

作者： Fei, ZJ Tang, XM Alba, R Payton, P Giovannoni, J Texas A&M Univ Dept Hort Sci College Stn TX 77843 USA

ISBN: (纸本)0769520006

Expression data for approximately 12000 ESTs over a time course of tomato fruit development was generated. In order to provide the research community access to our normalized microarray data as a tool to assess relative expression of genes of interest, we developed a publicly accessible online database Tomato Expression Database (TED: http://***). Through this database, we provide multiple approaches to pursue analysis of specific genes of interest and/or access the larger microarray data set to identify sets of genes that may behave in a pattern of interest to the user. A set of useful data mining and data visualization tools were developed and are under continuing expansion according to user's requirements. Developed initially as a data mining and analysis resource, TED also contains comprehensive annotation of each EST including homology derived from sequence similarity searches of GenBank and GO terms assigned manually according to putative functions.

关键词： Database systems

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SMASHing regulatory sites in DNA by human-mouse sequence comparisons 2

SMASHing regulatory sites in DNA by human-mouse sequence com...

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2nd international computational systems bioinformatics conference

作者： Zavolan, M Rajewsky, N Socci, nd Gaasterland, T Rockefeller Univ Lab Computat Genom New York NY 10021 USA

ISBN: (纸本)0769520006

Regulatory sequence elements provide important clues to understanding and predicting gene expression. Although the binding sites for hundreds of transcription factors are known, there has been no systematic attempt to incorporate this information in the annotation of the human genome. Cross species sequence comparisons are critical to a meaningful annotation of regulatory elements since they generally reside in conserved non-coding regions. To take advantage of the recently completed drafts of the mouse and human genomes for annotating transcription factor binding sites, we developed SMASH, a computational pipeline that identifies thousands of orthologous human/mouse proteins, maps them to genomic sequences, extracts and compares upstream regions and annotates putative regulatory elements in conserved, non-coding, upstream regions. Our current dataset consists of approximately 2500 human/mouse gene pairs. Transcription start sites were estimated by mapping quasi-full length cDNA sequences. SMASH uses a novel probabilistic method to identify putative conserved binding sites that takes into account the competition between transcription factors for binding DNA. SMASH presents the results via a genome browser web interface which displays the predicted regulatory information together with the current annotations for the human genome. Our results are validated by comparison to previously published experimental data. SMASH results compare favorably to other existing computational approaches.

关键词： Transcription factors

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Brain CT database for content-based image retrieval

Brain CT database for content-based image retrieval

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2nd international conference on bioinformatics and Biomedical Engineering, iCBBE 2008

作者： Yuan, Kehong Zou, Jiying Jia, Shaowei Xiao, Ping Chen, Wufan Graduate School at Shenzhen Tsinghua University China Shenzhen Hospical of Beijing University China School of Biomedical Engineering Southern Medical University China

ISBN: (纸本)9781424417483

Content-based image retrieval for medical image is a main way for computer-aided diagnosis. To storage medical image into the huge databases is its premise. In this paper, we provides efficient approach to develop the archives of large brain CT medical data, including quality control, ensuring consistency/integrity of information, expert verification of institutional findings, image correction, the validation for registration, and region of interest focusing on attention mechanism. The database is highly promising and shows the profit when it is used to implement brain CT image assistant diagnosis systems. © 2008 ieee.

关键词： Database systems

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Air quality evaluation of changchun by ArcGIS from 2003 to 2007

Air quality evaluation of changchun by ArcGIS from 2003 to 2...

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2nd international conference on bioinformatics and Biomedical Engineering, iCBBE 2008

作者： Jing, Nan Zhang, Zhen Jing, Tisong Department of Logistics Engineering School of Economics and Commerce South China University of Technology Guangzhou 510641 China Dept. of Computer Science South China University of Technology Guangzhou 510641 China Dept. of Computer Science Jinan University Guangzhou 510632 China College of Environment and Resource Jilin University Changchun 130026 China

ISBN: (纸本)9781424417483

The paper investigated the monitored data of NO2, O3 and SO3 in July 2003-2007 to gain a better understanding of the air quality in summer of Changchun, which is located in Northeast China. The dynamic information of air quality change between 2006 and 2007 was studied. By assessing the monitored data of the five years we found that O3 and NO2 played an important role in the air quality evaluation. By using ArcGIS, new relationships and correlations were established and spatial distribution of air pollution was more readily evaluated and quantified in this paper. © 2008 ieee.

关键词： Air quality

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Hyperspectral tongue imaging system used in tongue diagnosis

Hyperspectral tongue imaging system used in tongue diagnosis

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2nd international conference on bioinformatics and Biomedical Engineering, iCBBE 2008

作者： Li, Qingli Liu, Jingao Xiao, Gonghai Xue, Yongqi School of Information Science East China Normal University Shanghai China Shanghai Institute of Technical Physics Chinese Academy of Sciences Shanghai China

ISBN: (纸本)9781424417483

A hyperspectral tongue imaging system is developed and used in tongue diagnosis. The basic principles and instrumental systems as well as its applications in tongue diagnosis are introduced. A tongue segmentation algorithm which can simultaneously utilizes spectral and spatial information of the hyperspectral tongue images data is also presented. As the wavelength of the hyperspectral tongue images cover the whole visible light, spectrums were used to represent tongue colors and a new algorithm based on Gabor filters was proposed to analyze tongue textures. The experimental results show the hyperspectral tongue imaging system can make much benefit to the computer-aided tongue diagnosis system. © 2008 ieee.

关键词： Imaging systems

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Rao-blackwellised particle filter for gene regulation networks

Rao-blackwellised particle filter for gene regulation networ...

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2nd international conference on bioinformatics and Biomedical Engineering, iCBBE 2008

作者： Sun, Xiaodian Zhou, Qinghua Theoretic Systems Lab. School of Life Science Fudan University Shanghai China College of Mathematics and Computer Hebei University Baoding China

ISBN: (纸本)9781424417483

we propose two stage state-space models for genetic networks and estimate the parameter using rao-blakwellised particle filter. This article offers three novel improvement strategies of RBPF. One is that considering multiple samples suits for time-course data (panel data), which seldom appear in engineer application but it was common in biology area. Another is proposing two-stage state space model for gene regulation network. The third is that we modified the RBPF, which requires single kalman filter iteration per input sample. A simple illustrative example and real world SOS data show that our method significantly reducing computational complexity and obtaining good convergence. All of those make the algorithm in this paper possible for real-time implementations. © 2008 ieee.

关键词： Kalman filters

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A novel segmentation method for CT head images using PSFCM-ES

A novel segmentation method for CT head images using PSFCM-E...

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2nd international conference on bioinformatics and Biomedical Engineering, iCBBE 2008

作者： Wei, Kaiping He, Bin Zhang, Tao Department of Computer Science Huazhong Normal University 430079 Wuhan China

ISBN: (纸本)9781424417483

With an expert system, a novel fuzzy c-means clustering method based on PSO and expert system (PSFCM-ES) is proposed in this paper. The algorithm is formulated by incorporating the spatial neighborhood information into the standard FCM clustering algorithm. The k-nearest neighbor (k-NN) algorithm is introduced for calculating the weight in the spatially weighted FCM algorithm so as to improve the performance of image clustering. To speed up the FCM algorithm, the iteration is carried out with the gray level histogram of image instead of the conventional whole data of image. PSO algorithm is included to select optimal cluster centers and expert system is also introduced to solve the labeling problems. Experimental results indicate the proposed approach is effective and efficient. © 2008 ieee.

关键词： Expert systems

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Grid approach to embarrassingly parallel CPU-intensive bioinformatics problems

Grid approach to embarrassingly parallel CPU-intensive bioin...

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e-Science 2006 - 2nd ieee international conference on e-Science and Grid Computing

作者： Stockinger, Heinz Pagni, Marco Cerutti, Lorenzo Falquet, Laurent Swiss Institute of Bioinformatics Vital-IT Quartier Sorge - Batiment Genopode CH-1015 Lausanne Switzerland

ISBN: (纸本)0769527345

bioinformatics algorithms such as sequence alignment methods based on profile-HMM (Hidden Markov Model) are popular but CPU-intensive. If large amounts of data are processed, a single computer often runs for many hours or even days. High performance infrastructures such as clusters or computational Grids provide the techniques to speed up the process by distributing the workload to remote nodes, running parts of the work load in parallel. Biologists often do not have access to such hardware systems. Therefore, we propose a new system using a modern Grid approach to optimise an embarrassingly parallel problem. We achieve speed ups by at least two orders of magnitude given that we can use a powerful, world-wide distributed Grid infrastructure. For large-scale problems our method can outperform algorithms designed for mid-size clusters even considering additional latencies imposed by Grid infrastructures. © 2006 ieee.

关键词： Grid computing

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miRSAT & miRCDB: An integrated microRNA sequence analysis tool and a cancer-associated microRNA Database

miRSAT & miRCDB: An integrated microRNA sequence analysis to...

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2nd international conference on bioinformatics and computational Biology 2010, BICoB 2010

作者： Xie, Boya Hochberg, Robert Ding, Qin Wu, Di Department of Computer Science East Carolina University Greenville NC 27858 United States Department of Physiology Brody School of Medicine East Carolina University Greenville NC 27834 United States

ISBN: (纸本)9781617381119

We developed a tool called miRSAT with a database called miRCDB for microRNA (miRNA) sequence analysis and cancer-related research. The miRSAT, or miRNA Sequence Analysis Tool, aims to provide computational sequence analysis for miRNAs of both animals and plants to help researchers discover possible relationships, functionalities, and evolutionary histories of miRNAs. On the other hand, miRCDB, or miRNA-Cancer DataBase, is the first database that stores detailed miRNA experimental expression profiles in human cancers. We also introduce a new coding system, EICD-O, to annotate miRNA expressions in cancers. Analyses may be performed on all miRNA sequences in the database, or on a subset of the sequences selected by species, family, order, class, phylum, sequence length and/or known cancer association. Moreover, the sequence analysis tool shows connections between similar/different miRNA sequences and similar/different expressions in cancers.

关键词： Database systems

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Crossing the language barrier using fuzzy logic

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2nd international conference on Fuzzy systems and Knowledge Discovery, FSKD 2005

作者： Chau, Rowena Yeh, Chung-Hsing School of Business Systems Faculty of Information Technology Monash University Clayton Vic. 3800 Australia

ISBN: (纸本)9783540283317

Cross-lingual text retrieval (CLTR) concerns the retrieval of documents across languages. To allow multilingual term matching, a multilingual thesaurus is needed. However, a multilingual thesaurus encoding exact translation equivalent is insufficient for effective CLTR since relevant documents are often indexed by cross-lingual related terms. In this paper, a novel approach for automatically constructing a multilingual thesaurus based on fuzzy set theory is proposed. By introducing a degree of relatedness between multilingual terms using the concept of membership degree, partial match of cross-lingual related terms is facilitated. Development of a fuzzy multilingual news retrieval system using the proposed approach is presented. © Springer-Verlag Berlin Heidelberg 2005.

关键词： computational linguistics

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