发布求助
文献互助 智能选刊 最新文献

2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05)最新文献

筛选
英文 中文
Automated characterization of cellular migration phenomena 细胞迁移现象的自动表征
2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.26
C. Beaudry, M. Berens, T. E. Doker, A. Joy, Lina Karam, Z. Lacroix, Jad A. Lutfi, Sai Motoru
{"title":"Automated characterization of cellular migration phenomena","authors":"C. Beaudry, M. Berens, T. E. Doker, A. Joy, Lina Karam, Z. Lacroix, Jad A. Lutfi, Sai Motoru","doi":"10.1109/CSBW.2005.26","DOIUrl":"https://doi.org/10.1109/CSBW.2005.26","url":null,"abstract":"A new approach for cell migration analysis is presented from an automated image segmentation and ROI-compression. ROI-compression is accomplished through classical edge detection technique, followed by image opening to help identify the cell-occupied image region. That region is then compressed for better archival and analysis, to more efficiently identify migration rate and dispersion. Combining our approach with compression techniques such as offered by JPEG2000 will enhance the analysis of the images by providing the ability to vary parameters, work on compressed domain including proximity-based clustering of cells and cell count, etc.","PeriodicalId":123531,"journal":{"name":"2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05)","volume":"48 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2005-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115846775","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
BioNavigation: using ontologies to express meaningful navigational queries over biological resources 生物导航:使用本体来表达对生物资源有意义的导航查询
2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.32
Z. Lacroix, K. Parekh, Maria-Esther Vidal, M. Cardenas, Natalia Marquez, L. Raschid
{"title":"BioNavigation: using ontologies to express meaningful navigational queries over biological resources","authors":"Z. Lacroix, K. Parekh, Maria-Esther Vidal, M. Cardenas, Natalia Marquez, L. Raschid","doi":"10.1109/CSBW.2005.32","DOIUrl":"https://doi.org/10.1109/CSBW.2005.32","url":null,"abstract":"Exploiting the complex maze of publicly available biological resources to implement scientific data collection pipelines poses a multitude of challenges to biologists in accurately reflecting the scientific question at hand and in the selection of the best resources which satisfy their needs. We extended our BioNavigation system to address these challenges and aid the scientists visualize and navigate the resources, express their queries and determine the most suitable set of resources to evaluate them. For this purpose, we use an ontology that describes the higher logical level of scientific concepts and their relationships. A user can browse and visualize this ontology and then graphically select the relevant nodes and edges to build his query. We developed the ESearch algorithm that searches the physical level of resources to generate paths that express the ontological query. The algorithm also ranks the paths based on three semantic metrics; target object cardinality - to optimize the number of records in the output dataset, path cardinality - to optimize the number of links between the involved data sources, and evaluation cost - to minimize the cost that will be incurred to execute that evaluation path. These metrics allow the user to select the most optimum path that matches his requirements.","PeriodicalId":123531,"journal":{"name":"2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05)","volume":"4 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2005-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121080629","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: 7
Bacterial whole genome phylogeny using proteome comparison and optimal reversal distance 利用蛋白质组比较和最佳反转距离研究细菌全基因组系统发育
2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.29
N. Khiripet
{"title":"Bacterial whole genome phylogeny using proteome comparison and optimal reversal distance","authors":"N. Khiripet","doi":"10.1109/CSBW.2005.29","DOIUrl":"https://doi.org/10.1109/CSBW.2005.29","url":null,"abstract":"Traditional phylogenetic tree reconstruction is based on point mutations of a single gene. This approach is hardly suitable for genomes whose genes are almost identical and hardly captures evolutionary scenarios. To reconstruct a more conclusive phylogenetic tree of bacterial genome, all currently available complete bacterial genomic sequences were downloaded from the National Center for Biotechnology Information (NCBI). Each individual proteome was blasted against the collection and provided a number of homologous genes shared with others. Moreover, the syntenies of each two genomes can be considered as two signed permutations. One permutation can be rearranged into another in finite steps, called reversal distance. These two measures were combined and yield a phylogenetic tree that is highly consistent with the bacterial taxonomy.","PeriodicalId":123531,"journal":{"name":"2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05)","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2005-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125820435","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
ECOME: a simple model for an evolving consumption web ECOME:一个发展中的消费网络的简单模型
2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.56
C. Bystroff, S. DeLuca, C. McDaniel
{"title":"ECOME: a simple model for an evolving consumption web","authors":"C. Bystroff, S. DeLuca, C. McDaniel","doi":"10.1109/CSBW.2005.56","DOIUrl":"https://doi.org/10.1109/CSBW.2005.56","url":null,"abstract":"ECOME is an interactive, graph-based model for simulating an evolving, closed consumption web. It demonstrates the fundamental behavior of a global ecosystem over evolutionary time using well-established ecological/evolutionary principles. Nodes in the graph send biomass along weighted, directed edges. New nodes evolve by speciation and disappear when biomass (i.e. population) shrinks to zero. Consumption rates, predator/prey relationships, and speciation rates are user-defined, following theoretic-distributions. The output shows the biomass and biodiversity over time for up to five trophic levels. Using this simple system, we demonstrate that closed ecosystems are inherently unstable in the absence of evolution or in the presence of a single, hyper-changing species, but are dynamically stable and robust to perturbations when the evolution rates for all species follow a normal distribution. Our new application provides provocative lessons for biology students during a time of mass extinction.","PeriodicalId":123531,"journal":{"name":"2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05)","volume":"23 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2005-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126149257","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
Creating a protein ontology resource 创建蛋白质本体资源
2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.46
A. Sidhu, T. Dillon, E. Chang
{"title":"Creating a protein ontology resource","authors":"A. Sidhu, T. Dillon, E. Chang","doi":"10.1109/CSBW.2005.46","DOIUrl":"https://doi.org/10.1109/CSBW.2005.46","url":null,"abstract":"Protein Data Integration approaches at the moment considers data sources as data repositories, but not as applications; which in turn may embody complex interactions with other data sources. Current approaches do not provide methods both for generic mapping protein data representation, depicting interactions in data it describes and for interfacing existing data. The proposed Protein Ontology shows the value of hierarchy and relationships present in proteomics data. The creation of a Protein Ontology provides understanding of diverse types of data like: (1) Protein Entry Details, (2) 3D Structural Representations of Proteins, (3) Structural Folds and domains conserved in proteins, (4) Functional Domains and Families created based on Physiological and Pathological Functions of Proteins, and (5) Various Constraints like Genetic Defects and Chemical Properties of Cell that affect Final Stable Molecular Structure of Protein. Protein Ontology describes the concepts of interest in protein complex mechanisms and proteomics process.","PeriodicalId":123531,"journal":{"name":"2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05)","volume":"128 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2005-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128483531","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
On discriminating a TATA-box from putative TATA boxes: a case study using plant genome 塔塔盒与假定塔塔盒的区分:以植物基因组为例
2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.99
R. Loganantharaj
{"title":"On discriminating a TATA-box from putative TATA boxes: a case study using plant genome","authors":"R. Loganantharaj","doi":"10.1109/CSBW.2005.99","DOIUrl":"https://doi.org/10.1109/CSBW.2005.99","url":null,"abstract":"Prediction of a promoter is one of the many active areas of bioinformatics. The outcome of a promoter detection algorithm is directly or indirectly influenced by the success of identifying the location of a TATA box in a promoter sequence. A profiling technique is very often used to find putative TATA boxes, but discriminating a TATA box from putative TATA boxes is still a challenging problem. In this work, we formulate the problem and provide solutions using both a linear and a non linear classifiers.","PeriodicalId":123531,"journal":{"name":"2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05)","volume":"37 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2005-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129169309","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
Digital pathological image analysis and cell segmentation 数字病理图像分析和细胞分割
2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.52
L. Hernández, Paula Gothreaux, George Collins, L. Shih, G. Campbell
{"title":"Digital pathological image analysis and cell segmentation","authors":"L. Hernández, Paula Gothreaux, George Collins, L. Shih, G. Campbell","doi":"10.1109/CSBW.2005.52","DOIUrl":"https://doi.org/10.1109/CSBW.2005.52","url":null,"abstract":"Summary form only given. This project proposes the use of Digital Signal Processing (DSP) for real-time capture and analysis of pathological slide images to improve accuracy and efficiency. Analyzing cell density statistics and average cell nuclei diameters of a slide image is useful to determine the abnormality of slide sample. Being tedious as it is in counting/measuring hundreds to thousands of cells in one sample slide under a microscope, the manual result, typically can be achieved by a pathologist, is often limited by human eye precision/efficiency. Millions of biopsy samples obtained daily around the world, from minor skin lesions to major tumors, are anxiously waiting to be screened/examined. As a high-level, interactive environment for data visualization/analysis/computation, MATLAB/spl reg/ is utilized currently to perform automatic image analysis and segmentation of brain cells on a computer. By comparing cell concentration and cell nuclei sizes between cancerous and normal image groups, MATLAB/spl reg/ can be programmed to distinguish normal brain cells from questionable ones. In general, pathological image analysis using a computer-based application could demonstrate great precision and efficiency for screening large quantities of cells on one or numerous sample slides. Currently, MATLAB/spl reg/ image analysis works on captured/digitized slide images and takes a minute per image to automatically pre-screen abnormalities that require further human expert analysis. With future real-time/parallel/machine-intelligent improvements, we hope that DSP can help physicians/pathologists/patients everywhere to get immediate diagnosis for effective/timely treatment, and can show accuracy within acceptable levels that are comparable to human pathologists in dealing with cell-overlapping and non-cell objects existing in slide images.","PeriodicalId":123531,"journal":{"name":"2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05)","volume":"2 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2005-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129774435","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
Analysis of four different sets of predictive features for metalloproteins 金属蛋白四组不同预测特征的分析
2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.23
H. Seker, P. Haris
{"title":"Analysis of four different sets of predictive features for metalloproteins","authors":"H. Seker, P. Haris","doi":"10.1109/CSBW.2005.23","DOIUrl":"https://doi.org/10.1109/CSBW.2005.23","url":null,"abstract":"Metals bound to the protein are important for functional or structural roles. Despite their importance there is a distinct lack of research for identification of metalloproteins from sequence data and their predictive features that help distinguish them from non-metal binding proteins. In this study, four sets of features were analysed in order to see their ability to distinguish between metal and non-metal binding proteins. The analysis was carried out using a novel fuzzy logic method. The results show that the amino acid composition is more capable of distinguishing metal from non-metal binding proteins, than any of the other three features, yielding a predictive accuracy of 69.4%. Cofactors were the least useful feature for distinguishing metalloproteins. However, better results were obtained when physico-chemical and secondary structure features are used, yielding accuracies of 67.8% and 67.1%, respectively. Although the amino acid composition yields the highest predictive accuracy, considering the number of features, the latter two sets of features may be more appropriate for such analysis.","PeriodicalId":123531,"journal":{"name":"2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05)","volume":"22 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2005-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128251845","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
Operon prediction in cyanobacteria using comparative genomics 利用比较基因组学预测蓝藻的操纵子
2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.101
Natalia Khuri, N. S. Rao
{"title":"Operon prediction in cyanobacteria using comparative genomics","authors":"Natalia Khuri, N. S. Rao","doi":"10.1109/CSBW.2005.101","DOIUrl":"https://doi.org/10.1109/CSBW.2005.101","url":null,"abstract":"In this work, we performed a comprehensive analysis of the genome organization of eight publicly available cyanobacterial genomes and of the extensively studied Escherichia coli K12. Our comparison revealed striking similarities in organization of different microbial genomes. We examined the orientation of putative CDS, and distance distribution patterns between adjacent putative CDS in the whole genome as well as between genes within operons and across operon borders. Our results enabled us to calculate distance log-likeihoods for gene pairs to be part of the same operon and to apply this metric to predict operons in two newly sequenced cyanobacterial genomes, Synechococcus OS-A and OS-B'.","PeriodicalId":123531,"journal":{"name":"2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05)","volume":"44 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2005-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124518991","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
Classification method for prediction of multifactorial disease development using interaction between genetic and environmental factors 利用遗传和环境因素相互作用预测多因素疾病发展的分类方法
2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05) Pub Date : 2005-08-08 DOI: 10.1109/CSBW.2005.36
Yasuyuki Tomita, H. Honda, M. Yokota
{"title":"Classification method for prediction of multifactorial disease development using interaction between genetic and environmental factors","authors":"Yasuyuki Tomita, H. Honda, M. Yokota","doi":"10.1109/CSBW.2005.36","DOIUrl":"https://doi.org/10.1109/CSBW.2005.36","url":null,"abstract":"Multifactorial disease such as life style related diseases, for example, cancer, diabetes mellitus, myocardial infarction (Ml) and others, is thought to he caused by complex interactions between polygenic basis and various environmental factors. In this study, we used 22 polymorphisms on 16 candidate genes that have been characterized and potentially associated with MI in terms of biological function and 6 environmental factors. To predict development for MI and classify the subjects into personally optimum development patterns, we extracted risk factor candidates (RFCs) composed of state which is a derivative form of polymorphisms and environmental factors using statistical test and selected risk factors from RFCs using Criterion of Detecting Personal Group (CDPG) defined in this study. We could predict development of blinded data simulated as unknown their development more than 80% accuracy and identify their causal factors using CDPG.","PeriodicalId":123531,"journal":{"name":"2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05)","volume":"34 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2005-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132680704","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
首页 上一页 下一页 尾页
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整，为了账户安全，请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们：info@booksci.cn Book学术提供免费学术资源搜索服务，方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号：604180095
Book学术官方微信