2011 IEEE 11th International Conference on Bioinformatics and Bioengineering最新文献_第4页

GERC: Tree Based Clustering for Gene Expression Data 基于树的基因表达数据聚类

2011 IEEE 11th International Conference on Bioinformatics and Bioengineering Pub Date : 2011-10-24 DOI: 10.1109/BIBE.2011.54

H. A. Ahmed, P. Mahanta, D. Bhattacharyya, J. Kalita

引用次数: 16

Constructing Suffix Tree of Endogenous Feature on FPGA for High-Performance Identification of DNA Signatures 基于FPGA的内源特征后缀树构建及DNA特征的高性能识别

2011 IEEE 11th International Conference on Bioinformatics and Bioengineering Pub Date : 2011-10-24 DOI: 10.1109/BIBE.2011.48

Lin Feng, Angela Jean, C. Leng, Lai Danbo

{"title":"Constructing Suffix Tree of Endogenous Feature on FPGA for High-Performance Identification of DNA Signatures","authors":"Lin Feng, Angela Jean, C. Leng, Lai Danbo","doi":"10.1109/BIBE.2011.48","DOIUrl":"https://doi.org/10.1109/BIBE.2011.48","url":null,"abstract":"Identification of DNA signatures is an important application which has been empowered by the increasing availability of thousands of bacterial and viral genomes through the next-generation sequencing (NGS) technologies. It is computationally challenging. In exploration for the solution, the suffix tree has been proposed as a data structure well suited to analyzing genomic sequences because it enables the storage of long strings in a logical, indexed manner for fast retrieval. We propose a new algorithm for identification of DNA signatures, based on exploitation of the endogenous features of a genomic sequence. These features are revealed in a construction of suffix array (an implementation of the generalized suffix tree). Furthermore, to greatly speed up the time-consuming process, the core algorithm is mapped and routed on to a Field-Programable Gate Array (FPGA) for parallel implementation. In this paper, we will focus primarily on the relationship of the data structure and the features associated. We will then describe the deployment of the hybrid computing system on a Hyper Transport compliant architecture. Illustrations are always given to clarify the technical details.","PeriodicalId":391184,"journal":{"name":"2011 IEEE 11th International Conference on Bioinformatics and Bioengineering","volume":"33 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126405575","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Development of Foot Orthotics Using Shape Memory Alloy for Preventing Falls 形状记忆合金预防跌倒足部矫形器的研制

2011 IEEE 11th International Conference on Bioinformatics and Bioengineering Pub Date : 2011-10-24 DOI: 10.1109/BIBE.2011.25

Yuki Shimizu, M. Kobayashi

引用次数: 2

Virtual Reality System Specifications for Pain Management Therapy 疼痛管理治疗的虚拟现实系统规范

2011 IEEE 11th International Conference on Bioinformatics and Bioengineering Pub Date : 2011-10-24 DOI: 10.1109/BIBE.2011.69

Hatim Aboalsamh, Hind Al Hashim, Faten Alrashed, Nada Alkhamis

引用次数: 4

A Heuristic Algorithm for Detecting Intercellular Interactions 一种检测细胞间相互作用的启发式算法

2011 IEEE 11th International Conference on Bioinformatics and Bioengineering Pub Date : 2011-10-24 DOI: 10.1109/BIBE.2011.9

Fahim Mohammad, R. Flight, Benjamin J. Harrison, J. Petruska, E. Rouchka

{"title":"A Heuristic Algorithm for Detecting Intercellular Interactions","authors":"Fahim Mohammad, R. Flight, Benjamin J. Harrison, J. Petruska, E. Rouchka","doi":"10.1109/BIBE.2011.9","DOIUrl":"https://doi.org/10.1109/BIBE.2011.9","url":null,"abstract":"Existing analytical tools enable broad-scale experimentation (\"-omics\") to provide a great deal of information about intracellular processes. However, extraction of information regarding intercellular interactions, particularly from separate datasets, is generally more limited, principally for lack of specialized analytical tools. In turn, few experiments are designed to examine intercellular interactions. Using the large number of previously identified interactions available in databases may provide a useful platform for analyzing these interactions. However, finding all possible interactions is a computationally intensive task and quickly becomes intractable using a naive approach on networks with hundreds of thousands of nodes and edges. A heuristic algorithm similar to the \"Backtracking algorithm\" is proposed to find all possible protein interactions across any two gene sets. The algorithm starts with an initial set of genes and incrementally adds a candidate to the interaction network and abandons each candidate x as soon as it is determined that x does not lead to a valid solution. An exclusion vector (EV) is used to accomplish this task and is populated at each step, maintaining a list of those nodes that need to be excluded from interactions in the future and thus restricting the size of the network. The EV also allows location awareness by using Gene Ontology (GO) cell component classifications to discard nodes that are not relevant for the network. This algorithm can be readily applied to pathway analysis and the determination of elements underlying intercellular interactions.","PeriodicalId":391184,"journal":{"name":"2011 IEEE 11th International Conference on Bioinformatics and Bioengineering","volume":"11 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121307063","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A Novel Recursive Feature Subset Selection Algorithm 一种新的递归特征子集选择算法

2011 IEEE 11th International Conference on Bioinformatics and Bioengineering Pub Date : 2011-10-24 DOI: 10.1109/BIBE.2011.19

A. Jafarian, A. Ngom, L. Rueda

引用次数: 4

Interval Trees for Detection of Overlapping Genetic Entities 用于重叠遗传实体检测的区间树

2011 IEEE 11th International Conference on Bioinformatics and Bioengineering Pub Date : 2011-10-24 DOI: 10.1109/BIBE.2011.49

Fahim Mohammad, R. Flight, Benjamin J. Harrison, J. Petruska, E. Rouchka

引用次数: 3

Photoelectric DNA-Detection Platform with Assembled Magnetic Beads 装配磁珠的光电dna检测平台

2011 IEEE 11th International Conference on Bioinformatics and Bioengineering Pub Date : 2011-10-24 DOI: 10.1109/BIBE.2011.44

Fei Li, Jin Xu

{"title":"Photoelectric DNA-Detection Platform with Assembled Magnetic Beads","authors":"Fei Li, Jin Xu","doi":"10.1109/BIBE.2011.44","DOIUrl":"https://doi.org/10.1109/BIBE.2011.44","url":null,"abstract":"In this work, we propose a DNA hybridization detection platform with assembled magnetic beads and integrated photodiodes on a silicon chip. DNA targets labeled magnetic beads generate an opaque area after hybridization, and the fabricated photodiode is utilized to turn ordinary light into electricity. Compared with the detected photocurrent before hybridization, the signal of DNA hybridization can be distinctly diagnosed by the light intensity changing. As far as we know, it is the first time to assemble magnetic beads with integrated photodiode on a silicon chip to detect DNA hybridization. The advantages of this detection platform are lower cost, higher precision and less time consuming. With this technique, we could successfully discriminate single base mismatched DNA from perfectly matched DNA sequence, which saves the time of amplifying hybridization signal. This detection platform also fits for DNA computing because magnetic property could easily eliminate unfeasible solutions of problem. The experimental result of a minimum vertex cover problem, which is solved by DNA computing on this platform, reveals the obvious benefits of this detection platform and its potential to be used to construct a fully automatic DNA computer with photoelectric readout.","PeriodicalId":391184,"journal":{"name":"2011 IEEE 11th International Conference on Bioinformatics and Bioengineering","volume":"25 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125805678","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Reconstruction of Histone Modification Network from Next-generation Sequencing Data 利用新一代测序数据重建组蛋白修饰网络

2011 IEEE 11th International Conference on Bioinformatics and Bioengineering Pub Date : 2011-10-24 DOI: 10.1109/BIBE.2011.35

Ngoc Tu Le, T. Ho

{"title":"Reconstruction of Histone Modification Network from Next-generation Sequencing Data","authors":"Ngoc Tu Le, T. Ho","doi":"10.1109/BIBE.2011.35","DOIUrl":"https://doi.org/10.1109/BIBE.2011.35","url":null,"abstract":"Post-translational modifications (PTMs) of his tone proteins play critical roles in establishing functionally separated domains on chromatin and regulating important biological processes, such as transcription. These modifications often act in cooperative manner, forming complicated \"histone codes\". Elucidation of functional relationships among them will, therefore, significantly increase our understanding of cell differentiation, development, and cancer pathogenesis. Biological evidence has shown that nucleosome positioning can provide invaluable information about interactive effects of PTMs. However, to our knowledge, none of previous works has exploited this information in the reconstruction of his tone modification networks. We propose a computational approach based on Bayesian network to reconstruct a network representing functional relationships of his tone modifications. Our approach employed the search-and-score method to infer the network structure using interactive information of his tone modifications, which is measured by the correlation between each modification with nucleosome positioning. When applied on human CD4+ T cell ChIP-Seq dataset, containing 38 different his tone modifications and binding information of three other proteins, H2A.Z, PolII and CTCF, our method not only outperformed previous approaches in recovering known relationships but also suggested many new ones, confirming its validity and efficiency. Our unbiased method for inferring the network structure can also be applied to reconstruct interaction networks of other epigenetic factors.","PeriodicalId":391184,"journal":{"name":"2011 IEEE 11th International Conference on Bioinformatics and Bioengineering","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131257401","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

Ergonomic Designs Based on Musculoskeletal Models 基于肌肉骨骼模型的人体工程学设计

2011 IEEE 11th International Conference on Bioinformatics and Bioengineering Pub Date : 2011-10-24 DOI: 10.1109/BIBE.2011.24

Chun-Ming Chang, J. Tsai

引用次数: 2