2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)最新文献_第10页

MODULA: A network module based local protein interaction network alignment method MODULA:一种基于网络模块的局部蛋白质相互作用网络比对方法

2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Pub Date : 2015-11-09 DOI: 10.1109/BIBM.2015.7359918

P. Guzzi, P. Veltri, Swarup Roy, J. Kalita

{"title":"MODULA: A network module based local protein interaction network alignment method","authors":"P. Guzzi, P. Veltri, Swarup Roy, J. Kalita","doi":"10.1109/BIBM.2015.7359918","DOIUrl":"https://doi.org/10.1109/BIBM.2015.7359918","url":null,"abstract":"Biological networks are usually used to model interactions among biological macromolecules in a cells. For instance protein-protein interaction networks (PIN) are used to model and analyse the set of interactions among proteins. The comparison of networks may result in the identification of conserved patterns of interactions corresponding to biological relevant entities such as protein complexes and pathways. Several algorithms, known as network alignment algorithms, have been proposed to unravel relations between different species at the interactome level. Algorithms may be categorized in two main classes: merge and mine and mine and merge. Algorithms belonging to the first class initially merge input network into a single integrated and then mine such networks. Conversely algorithms belonging to the second class initially analyze separately two input networks then integrate such results. In this paper we present MODULA (Network Module based PPI Aligner), a novel approach for local network alignment that belong to the second class. The algorithm at first identifies compact modules from input networks. Modules of both networks are then matched using functional knowledge. Then it uses high scoring pairs of modules as seeds to build a bigger alignment. In order to asses MODULA we compared it to the state of the art local alignment algorithms over a rather extensive and updated dataset.","PeriodicalId":186217,"journal":{"name":"2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","volume":"3 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129599393","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

Dealing with incompleteness in multidimensional analysis of health records: An experience on fetal growth 处理健康记录多维分析中的不完整性:胎儿生长的经验

2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Pub Date : 2015-11-09 DOI: 10.1109/BIBM.2015.7359825

Mario Alessandro Bochicchio, L. Vaira, E. Cicinelli, A. Vimercati

引用次数: 2

A novel approach to identify shared fragments in drugs and natural products 一种鉴定药物和天然产物共享片段的新方法

2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Pub Date : 2015-11-09 DOI: 10.1109/BIBM.2015.7359746

Akshay Balasubramanya, I. Thapa, D. Bastola, D. Ghersi

{"title":"A novel approach to identify shared fragments in drugs and natural products","authors":"Akshay Balasubramanya, I. Thapa, D. Bastola, D. Ghersi","doi":"10.1109/BIBM.2015.7359746","DOIUrl":"https://doi.org/10.1109/BIBM.2015.7359746","url":null,"abstract":"Fragment-based approaches have now become an important component of the drug discovery process. At the same time, pharmaceutical chemists are more often turning to the natural world and its extremely large and diverse collection of natural compounds to discover new leads that can potentially be turned into drugs. In this study we introduce and discuss a computational pipeline to automatically extract statistically overrepresented chemical fragments in therapeutic classes, and search for similar fragments in a large database of natural products. By systematically identifying enriched fragments in therapeutic groups, we are able to extract and focus on few fragments that are likely to be active or structurally important as scaffolds. We show that several therapeutic classes (including antibacterial, antineoplastic, and drugs active on the cardiovascular system, among others) have enriched fragments that are also found in many natural compounds. Further, our method is able to detect fragments shared by a drug and a natural product even when the global similarity between the two molecules is generally low. A further development of this computational pipeline is to help predict putative therapeutic activities of natural compounds, and to help identify novel leads for drug discovery.","PeriodicalId":186217,"journal":{"name":"2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130733104","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

Ancestral reconstruction under weighted maximum matching 加权最大匹配下的祖先重构

2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Pub Date : 2015-11-09 DOI: 10.1109/BIBM.2015.7359889

Lingxi Zhou, William Hoskins, Jieyi Zhao, Jijun Tang

引用次数: 6

Functional connectivity of Chinese characters processing: A meta-analysis 汉字加工的功能连通性:一个元分析

2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Pub Date : 2015-11-09 DOI: 10.1109/BIBM.2015.7359853

Yaoxin Nie, Jieyao Wei, Linlin Zhu, Qian Zhou, Zhendong Niu

引用次数: 1

A longitudinal support vector regression for prediction of ALS score 纵向支持向量回归预测ALS评分

2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Pub Date : 2015-11-09 DOI: 10.1109/BIBM.2015.7359912

Wei Du, Huey Cheung, Calvin A. Johnson, I. Goldberg, M. Thambisetty, Kevin Becker

引用次数: 10

Direct higher order fuzzy rule-based classification system: Application in mortality prediction 直接高阶模糊规则分类系统在死亡率预测中的应用

2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Pub Date : 2015-11-09 DOI: 10.1109/BIBM.2015.7359795

A. D. Torshizi, L. Petzold, M. Cohen

引用次数: 3

Segmentation of Multicolor Fluorescence In-Situ Hybridization (M-FISH) image using an improved Fuzzy C-means clustering algorithm while incorporating both spatial and spectral information 利用改进的模糊c均值聚类算法对多色荧光原位杂交(M-FISH)图像进行分割，同时结合了空间和光谱信息

2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Pub Date : 2015-11-09 DOI: 10.1109/BIBM.2015.7359717

Jingyao Li, D. Lin, Yu-ping Wang

{"title":"Segmentation of Multicolor Fluorescence In-Situ Hybridization (M-FISH) image using an improved Fuzzy C-means clustering algorithm while incorporating both spatial and spectral information","authors":"Jingyao Li, D. Lin, Yu-ping Wang","doi":"10.1109/BIBM.2015.7359717","DOIUrl":"https://doi.org/10.1109/BIBM.2015.7359717","url":null,"abstract":"Multicolor Fluorescence In-Situ Hybridization (M-FISH) is an imaging technique for rapid detection of chromosomal abnormalities, where the segmentation of chromosomes has been a challenge. Multi-channel information of M-FISH images can be used in a segmentation algorithm to exploit the correlated information across channels for better image segmentation. In addition, the neighboring pixels share similar characteristics, so this spatial information can be further utilized to improve the robustness of the algorithm to the noise. Motivated by this fact, in this paper we proposed an improved Fuzzy C-means (FCM) clustering algorithm to overcome the problems of conventional FCM such as the sensitivity to noise by incorporating both spatial and spectral information. The experimental results on both simulated and real M-FISH images have shown that our proposed method can result in higher segmentation accuracy and lower false ratio than both conventional FCM and the improved adaptive FCM (IAFCM) we recently proposed.","PeriodicalId":186217,"journal":{"name":"2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","volume":"73 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128229950","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

A case-control genome-wide association study of metabolic syndrome in Korean 韩国人代谢综合征病例对照全基因组关联研究

2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Pub Date : 2015-11-09 DOI: 10.1109/BIBM.2015.7359952

Myungguen Chung, Seok Won Jeong, S. Park, S. Cho

{"title":"A case-control genome-wide association study of metabolic syndrome in Korean","authors":"Myungguen Chung, Seok Won Jeong, S. Park, S. Cho","doi":"10.1109/BIBM.2015.7359952","DOIUrl":"https://doi.org/10.1109/BIBM.2015.7359952","url":null,"abstract":"Metabolic syndrome (METS) constitutes several metabolic disorders including central obesity, dyslipidemia, glucose intolerances, and elevated blood pressure. METS is known to increase the risk of developing cardiovascular disease and diabetes. Genome-wide association study (GWAS) for 2,657 cases and 5,917 controls in Korean populations was performed to discover the genetic risk factors of METS. As a result, we identified 2 SNPs with genome-wide significance level p-values(<;5×10-8), 8SNPs with genome-wide suggestive p-values (5×10-8≤p-values<;1×10-5), and 2SNPs of more functional variants with borderline p-values (5×10-5≤p-values<;1×10-4). On the other hand, the multiple correction criteria of conventional GWASs exclude false-positive loci, but simultaneously, they discard many true-positive loci. To reconsider the discarded true-positive loci, we attempted to include the functional variants [nonsynonymous SNPs (nsSNPs) and expression quantitative trait loci (eQTL)] among the top 5000 SNPs based on the proportion of phenotypic variance explained by genotypic variance. In total, 159 eQTLs and 18 nsSNPs were presented in the top 5000 SNPs. Although they should be replicated in other independent populations, 6eQTLs and 2nsSNP loci were located in the molecular pathways of LPL, APOA5, and CHRM2, which were the significant or suggestive loci in the METS GWAS. Conclusively, our approach using the conventional GWAS, reconsidering functional variants and pathway-based interpretation, suggests a useful method to understand the GWAS results of complex traits and can be expanded in other genome-wide association studies.","PeriodicalId":186217,"journal":{"name":"2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","volume":"52 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134493096","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

Towards an efficient data assimilation in physically-based medical simulations 在基于物理的医学模拟中实现有效的数据同化

2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Pub Date : 2015-11-09 DOI: 10.1109/BIBM.2015.7359884

I. Peterlík, Antonin Klima

引用次数: 1