International Journal of Bioinformatics Research and Applications最新文献_第4页

On using the wisdom of the crowd principles in classification, Application on breast cancer diagnosis and prognosis. 运用人群智慧原则进行分类，在乳腺癌诊断和预后中的应用。

International Journal of Bioinformatics Research and Applications Pub Date : 2017-01-01 DOI: 10.1504/IJBRA.2017.10013389

M. Amraoui, T. B. Stambouli, B. Alshaqaqi

引用次数: 1

Neural network and rough set hybrid scheme for prediction of missing associations 缺失关联预测的神经网络与粗糙集混合方案

International Journal of Bioinformatics Research and Applications Pub Date : 2015-11-01 DOI: 10.1504/IJBRA.2015.073237

A. Anitha, D. Acharjya

{"title":"Neural network and rough set hybrid scheme for prediction of missing associations","authors":"A. Anitha, D. Acharjya","doi":"10.1504/IJBRA.2015.073237","DOIUrl":"https://doi.org/10.1504/IJBRA.2015.073237","url":null,"abstract":"Currently, internet is the best tool for distributed computing, which involves spreading of data geographically. But, retrieving information from huge data is critical and has no relevance unless it provides certain information. Prediction of missing associations can be viewed as fundamental problems in machine learning where the main objective is to determine decisions for the missing associations. Mathematical models such as naive Bayes structure, human composed network structure, Bayesian network modelling, etc., were developed to this end. But, it has certain limitations and failed to include uncertainties. Therefore, effort has been made to process inconsistencies in the data with the introduction of rough set theory. This paper uses two processes, pre-process and post-process, to predict the decisions for the missing associations in the attribute values. In preprocess, rough set is used to reduce the dimensionality, whereas neural network is used in postprocess to explore the decision for the missing associations. A real-life example is provided to show the viability of the proposed research.","PeriodicalId":35444,"journal":{"name":"International Journal of Bioinformatics Research and Applications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJBRA.2015.073237","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"66702073","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: 20

Automatic segmentation of Potyviridae family polyproteins 波蒂病毒科多蛋白的自动分割

International Journal of Bioinformatics Research and Applications Pub Date : 2015-11-01 DOI: 10.1504/IJBRA.2015.073238

J. Vargas, J. A. Velasco, G. Alvarez, Diego Linares, E. Bravo

引用次数: 0

On the interconnection of stable protein complexes: inter-complex hubs and their conservation in Saccharomyces cerevisiae and Homo sapiens networks 关于稳定蛋白复合物的互连:在酿酒酵母和智人网络中的复合物中心及其保护

International Journal of Bioinformatics Research and Applications Pub Date : 2015-11-01 DOI: 10.1504/IJBRA.2015.073236

C. Guerra

{"title":"On the interconnection of stable protein complexes: inter-complex hubs and their conservation in Saccharomyces cerevisiae and Homo sapiens networks","authors":"C. Guerra","doi":"10.1504/IJBRA.2015.073236","DOIUrl":"https://doi.org/10.1504/IJBRA.2015.073236","url":null,"abstract":"Protein complexes are key molecular entities that perform a variety of essential cellular functions. The connectivity of proteins within a complex has been widely investigated with both experimental and computational techniques. We developed a computational approach to identify and characterise proteins that play a role in interconnecting complexes. We computed a measure of inter-complex centrality, the crossroad index, based on disjoint paths connecting proteins in distinct complexes and identified inter-complex hubs as proteins with a high value of the crossroad index. We applied the approach to a set of stable complexes in Saccharomyces cerevisiae and in Homo sapiens. Just as done for hubs, we evaluated the topological and biological properties of inter-complex hubs addressing the following questions. Do inter-complex hubs tend to be evolutionary conserved? What is the relation between crossroad index and essentiality? We found a good correlation between inter-complex hubs and both evolutionary conservation and essentiality.","PeriodicalId":35444,"journal":{"name":"International Journal of Bioinformatics Research and Applications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJBRA.2015.073236","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"66702063","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

Diversity and evolution of the envelope gene of dengue virus type 1 circulating in India in recent times 最近在印度流行的1型登革热病毒包膜基因的多样性和进化

International Journal of Bioinformatics Research and Applications Pub Date : 2015-11-01 DOI: 10.1504/IJBRA.2015.073235

S. Dey, A. Nandy, P. Nandy, Sukhen Das

引用次数: 3

In silico analysis, annotation and characterisation of putative ESTs from Sorghum bicolor associated with heat stress 与热胁迫相关的高粱双色基因est的硅分析、注释和表征

International Journal of Bioinformatics Research and Applications Pub Date : 2015-11-01 DOI: 10.1504/IJBRA.2015.073240

Gobind Ram, A. Sharma

{"title":"In silico analysis, annotation and characterisation of putative ESTs from Sorghum bicolor associated with heat stress","authors":"Gobind Ram, A. Sharma","doi":"10.1504/IJBRA.2015.073240","DOIUrl":"https://doi.org/10.1504/IJBRA.2015.073240","url":null,"abstract":"Owing to their sessile nature, plants experience a variety of environmental stresses, but tolerance to these adverse conditions is a very complex phenomenon. Among all stresses, heat stress is the most important constraint that affects plant yield in rain-fed areas. To shed some light on candidate genes involved in heat stress, sequences potentially associated with heat shock resistance were retrieved and identified by in silico analysis using the public sequence database of various plants. A total of 30,000 EST sequences were mined and 24 putative ESTs associated with heat stress were picked up for further studies. In silico analysis revealed that all ESTs were linked with the HSP family. Gene Ontology (GO) analysis revealed that the deduced protein sequences of the heat-linked 24 ESTs were involved in various biological pathways regulating heat stress response. Hydropathy analysis revealed that all protein sequences were hydrophilic in nature. Based on the phylogenetic analysis, all HSP-related protein sequences were divided into seven groups. Analysis of cis-elements provides molecular evidence for the possible involvement of hydrophilic ESTs in the process of abiotic stress tolerance in sorghum. Based on these results, it was suggested that putative ESTs may play an important role in heat stress tolerance.","PeriodicalId":35444,"journal":{"name":"International Journal of Bioinformatics Research and Applications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJBRA.2015.073240","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"66702609","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

Docking analysis of gallic acid derivatives as HIV-1 protease inhibitors 没食子酸衍生物作为HIV-1蛋白酶抑制剂的对接分析

International Journal of Bioinformatics Research and Applications Pub Date : 2015-11-01 DOI: 10.1504/IJBRA.2015.073239

Anjali Singh, T. Pal

引用次数: 4

A combination of dual-tree discrete wavelet transform and minimum redundancy maximum relevance method for diagnosis of Alzheimer's disease 双树离散小波变换与最小冗余最大关联相结合的阿尔茨海默病诊断

International Journal of Bioinformatics Research and Applications Pub Date : 2015-09-01 DOI: 10.1504/IJBRA.2015.071944

N. Aggarwal, Bharti, R. Agrawal, S. Kumaran

{"title":"A combination of dual-tree discrete wavelet transform and minimum redundancy maximum relevance method for diagnosis of Alzheimer's disease","authors":"N. Aggarwal, Bharti, R. Agrawal, S. Kumaran","doi":"10.1504/IJBRA.2015.071944","DOIUrl":"https://doi.org/10.1504/IJBRA.2015.071944","url":null,"abstract":"In this paper, we propose a three-phased method for diagnosis of Alzheimer's disease using the structural magnetic resonance imaging (MRI). In first phase, gray matter tissue probability map is obtained from every brain MRI volume. Further, five regions of interest (ROIs) are extracted as per prior knowledge. In second phase, features are extracted from each ROI using 3D dual-tree discrete wavelet transform. In third phase, relevant features are selected using minimum redundancy maximum relevance features selection technique. The decision model is built with features so obtained, using a classifier. To evaluate the effectiveness of the proposed method, experiments are performed with four well-known classifiers on four data sets, built from a publicly available OASIS database. The performance is evaluated in terms of sensitivity, specificity and classification accuracy. It was observed that the proposed method outperforms existing methods in terms of all three performance measures. This is further validated with statistical tests.","PeriodicalId":35444,"journal":{"name":"International Journal of Bioinformatics Research and Applications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJBRA.2015.071944","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"66702006","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: 5

Bioinformatics: promises and progress 生物信息学:前景与进展

International Journal of Bioinformatics Research and Applications Pub Date : 2015-09-01 DOI: 10.1504/IJBRA.2015.071945

Shipra Gupta, G. Misra, S. Khurana

引用次数: 3

A permutation based simulated annealing algorithm to predict pseudoknotted RNA secondary structures 基于排列的模拟退火算法预测假结RNA二级结构

International Journal of Bioinformatics Research and Applications Pub Date : 2015-09-01 DOI: 10.1504/IJBRA.2015.071938

Herbert H. Tsang, K. Wiese

{"title":"A permutation based simulated annealing algorithm to predict pseudoknotted RNA secondary structures","authors":"Herbert H. Tsang, K. Wiese","doi":"10.1504/IJBRA.2015.071938","DOIUrl":"https://doi.org/10.1504/IJBRA.2015.071938","url":null,"abstract":"Pseudoknots are RNA tertiary structures which perform essential biological functions. This paper discusses SARNA-Predict-pk, a RNA pseudoknotted secondary structure prediction algorithm based on Simulated Annealing (SA). The research presented here extends previous work of SARNA-Predict and further examines the effect of the new algorithm to include prediction of RNA secondary structure with pseudoknots. An evaluation of the performance of SARNA-Predict-pk in terms of prediction accuracy is made via comparison with several state-of-the-art prediction algorithms using 20 individual known structures from seven RNA classes. We measured the sensitivity and specificity of nine prediction algorithms. Three of these are dynamic programming algorithms: Pseudoknot (pknotsRE), NUPACK, and pknotsRG-mfe. One is using the statistical clustering approach: Sfold and the other five are heuristic algorithms: SARNA-Predict-pk, ILM, STAR, IPknot and HotKnots algorithms. The results presented in this paper demonstrate that SARNA-Predict-pk can out-perform other state-of-the-art algorithms in terms of prediction accuracy. This supports the use of the proposed method on pseudoknotted RNA secondary structure prediction of other known structures.","PeriodicalId":35444,"journal":{"name":"International Journal of Bioinformatics Research and Applications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJBRA.2015.071938","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"66702443","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