2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)最新文献_第5页

Annotation guided local similarity search in multiple sequences and its application to mitochondrial genomes 注释引导的多序列局部相似性搜索及其在线粒体基因组中的应用

2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE) Pub Date : 2012-11-11 DOI: 10.1109/BIBE.2012.6399666

Ruby L. V. Moritz, Matthias Bernt, M. Middendorf

引用次数: 1

A graph theoretic mathematical model for Alzheimer's disease: Using a systems biology approach 阿尔茨海默病的图论数学模型:使用系统生物学方法

2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE) Pub Date : 2012-11-11 DOI: 10.1109/BIBE.2012.6399723

C. R. Kyrtsos, J. Baras

引用次数: 6

Using protein-domain information for multiple sequence alignment 利用蛋白质结构域信息进行多序列比对

2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE) Pub Date : 2012-11-11 DOI: 10.1109/BIBE.2012.6399667

Layal Al Ait, Eduardo Corel, B. Morgenstern

引用次数: 4

Evolving very-compact fuzzy models for gene expression data analysis 进化非常紧凑的模糊模型用于基因表达数据分析

2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE) Pub Date : 2012-11-11 DOI: 10.1109/BIBE.2012.6399650

Miguel Arturo Barreto-Sanz, A. Bujard, C. Peña-Reyes

{"title":"Evolving very-compact fuzzy models for gene expression data analysis","authors":"Miguel Arturo Barreto-Sanz, A. Bujard, C. Peña-Reyes","doi":"10.1109/BIBE.2012.6399650","DOIUrl":"https://doi.org/10.1109/BIBE.2012.6399650","url":null,"abstract":"Selecting predicitve gene pools from thousands of gene expression values is one of the main tasks in microarray data analysis. For this purpose multivariate techniques have proven much better, in terms of predicitve value and biological relevance, than univariate techniques as they are able to capture relevant relationships and interactions between genes. An additional goal for gene-expression profiling is finding models that, besides being predictive, are also understandable so as they can provide some insight on the underlying mechanisms. Models based on fuzzy logic might, potentially, exhibit both characteristics. However, accuracy and interpretability are usually contradictory objectives, and one must accept a trade off between them. Indeed, literature shows that the approaches based on fuzzy logic may be divided in two groups: accurate but complex models (i.e, with many rules using many variables per rule) on one hand, and models with only few short rules (thus, interpretable) but exhibiting limited accuracy. We present in this paper the application of Fuzzy CoCo, our cooperative coevolutionary fuzzy modelling approach, in order to deal efficiently with the accuracy-interpretability tradeoff. Fuzzy CoCo is able to find very compact fuzzy models, in terms of number of rules and number of variables per rule, while still exhibiting high predictive power. To validate the performance of our approach, we tested Fuzzy CoCo on four known data sets addressing each one a form of cancer: Leukemia, colon, lung, and prostate. We compared our results-in terms of maximum number of rules, number of variables per rule, and accuracy-with those of other similar works (i.e., based on fuzzy logic). Our models reached similar or better accuracy while being considerably smaller.","PeriodicalId":330164,"journal":{"name":"2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122294885","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: 1

A collaborative Wiki-based tool for semantic management of medical interventions 一个基于维基的协作工具，用于医疗干预的语义管理

2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE) Pub Date : 2012-11-11 DOI: 10.1109/BIBE.2012.6399698

Dionysia Kontotasiou, D. Zarpalas, Charalampos Bratsas, P. Bamidis

引用次数: 0

sCoIn: A scoring algorithm based on complex interactions for reverse engineering regulatory networks sCoIn:一种基于复杂交互的评分算法，用于逆向工程监管网络

2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE) Pub Date : 2012-11-11 DOI: 10.1109/BIBE.2012.6399735

Vijender Chaitankar, P. Ghosh, M. Elasri, K. Gust, E. Perkins

{"title":"sCoIn: A scoring algorithm based on complex interactions for reverse engineering regulatory networks","authors":"Vijender Chaitankar, P. Ghosh, M. Elasri, K. Gust, E. Perkins","doi":"10.1109/BIBE.2012.6399735","DOIUrl":"https://doi.org/10.1109/BIBE.2012.6399735","url":null,"abstract":"Structural analysis over well studied transcriptional regulatory networks indicates that these complex networks are made up of small set of reoccurring patterns called motifs. While information theoretic approaches have been immensely popular, these approaches rely on inferring the regulatory networks by aggregating pair-wise interactions. In this paper, we propose novel structure based information theoretic approaches to infer transcriptional regulatory networks from the microarray expression data. The core idea is to go beyond pair-wise interactions and consider more complex structures as found in motifs. While this increases the network inference complexity over pair-wise interaction based approaches, it achieves much higher accuracy and yet is scalable to genome-level inference. Detailed performance analyses based on benchmark precision and recall metrics on the known Escherichia coli's transcriptional regulatory network indicates that the accuracy of the proposed algorithms is consistently higher in comparison to popular algorithms such as context likelihood of relatedness (CLR), relevance networks (RN) and GEneNetwork Inference with Ensemble of trees (GENIE3). In the proposed approaches the size of structures was limited to three node cases (any node and its two parents). Analysis on a smaller network showed that the performance of the algorithm improved when more complex structures were considered for inference, although such higher level structures may be computationally challenging to infer networks at the genome scale.","PeriodicalId":330164,"journal":{"name":"2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)","volume":"150 5 Suppl 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128885736","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: 3

GCVT — A Genome Comparison and Viewing Tool GCVT -一个基因组比较和观察工具

2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE) Pub Date : 2012-11-11 DOI: 10.1109/BIBE.2012.6399708

S. Baichoo, P. Ujoodha, Yovish Bissessur

引用次数: 0

Investigating survival prognosis of glioblastoma using evolutional properties of gene networks 利用基因网络的进化特性研究胶质母细胞瘤的生存预后

2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE) Pub Date : 2012-11-11 DOI: 10.1109/BIBE.2012.6399722

A. Upton, Theodoros N. Arvanitis

{"title":"Investigating survival prognosis of glioblastoma using evolutional properties of gene networks","authors":"A. Upton, Theodoros N. Arvanitis","doi":"10.1109/BIBE.2012.6399722","DOIUrl":"https://doi.org/10.1109/BIBE.2012.6399722","url":null,"abstract":"In recent years, there has been widespread interest and a large number of publications on the application of graph theory techniques into constructing and analyzing biologically-informed gene networks from cancer cell line data sets. Current research efforts have predominantly looked at an overall static, topological, representation of the network, and have not investigated the application of graph theoretical techniques to evolutionary investigations of cancer. A number of these studies have used graph theory metrics, such as degree, betweenness, and closeness centrality, to identify important hub genes in these networks. However, these have not fully investigated the importance of genes across the different stages of the disease. Previous human glioblastoma publications have identified four subtypes of glioblastoma in adults, based on signature genes. In one such publication, Verhaak et al. found that the subtypes correspond to a narrow median survival range, from 11.3 months for the most aggressive subtype, to 13.1 months for the least aggressive one. In this work, we present an evolutionary graph theory study of glioblastoma based on survival data categorization, confirming genes associated with different survival times identified using established graph theory metrics. The work is extending the application of graph theory approaches to evolutionary studies of cancer cell line data.","PeriodicalId":330164,"journal":{"name":"2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)","volume":"7 2 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133482693","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: 6

Point-of-care diagnosis of Urinary Tract Infection (UTI) using Surface enhanced Raman Spectroscopy (SERS) 表面增强拉曼光谱(SERS)在尿路感染(UTI)即时诊断中的应用

2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE) Pub Date : 2012-11-11 DOI: 10.1109/BIBE.2012.6399646

Katerina Hadjigeorgiou, E. Kastanos, A. Kyriakides, C. Pitris

{"title":"Point-of-care diagnosis of Urinary Tract Infection (UTI) using Surface enhanced Raman Spectroscopy (SERS)","authors":"Katerina Hadjigeorgiou, E. Kastanos, A. Kyriakides, C. Pitris","doi":"10.1109/BIBE.2012.6399646","DOIUrl":"https://doi.org/10.1109/BIBE.2012.6399646","url":null,"abstract":"There are three stages to a complete UTI diagnosis: (1) identification of a urine sample as positive/negative for an infection, (2) identification of the responsible bacterium, (3) antibiogram to determine the antibiotic to which the bacteria are most sensitive to. Using conventional methods, all three stages require bacterial cultures in order to provide results. This long delay in diagnosis causes a rise in ineffective treatments, chronic infections, health care costs and antibiotic resistance. In this work, SERS is used to identify a sample as positive/negative for a UTI as well as to obtain an antibiogram against different antibiotics. SERS spectra of serial dilutions of E. coli bacteria mixed with silver nanoparticles, showed a linear correlation between spectral intensity and concentration. For antibiotic sensitivity testing, SERS spectra of three species of gram negative bacteria were collected four hours after exposure to the antibiotics ciprofloxacin and amoxicillin. Spectral analysis revealed clear separation between bacterial samples exposed to antibiotics to which they were sensitive and samples exposed to antibiotics to which they were resistant. With the enhancement provided by SERS, the technique can be applied directly to urine samples leading to the development of a new, rapid method for UTI diagnosis and antibiogram.","PeriodicalId":330164,"journal":{"name":"2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)","volume":"9 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132385416","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: 2

Calibrated probabilistic predictions for biomedical applications 生物医学应用的校准概率预测

2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE) Pub Date : 2012-11-11 DOI: 10.1109/BIBE.2012.6399676

A. Lambrou, H. Papadopoulos, A. Gammerman

引用次数: 2