Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001)最新文献

Mining genome variation to associate disease with transcription factor binding site alteration 挖掘基因组变异将疾病与转录因子结合位点改变联系起来

Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001) Pub Date : 2001-03-04 DOI: 10.1109/BIBE.2001.974424

J. Ponomarenko, T. Merkulova, G. Orlova, E. Gorshkova, Oleg N. Fokin, M. Ponomarenko

引用次数: 0

Integrating co-regulated gene-groups and pair-wise genome comparisons to automate reconstruction of microbial pathways 整合共调控基因组和成对基因组比较，自动重建微生物途径

Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001) Pub Date : 2001-03-04 DOI: 10.1109/BIBE.2001.974431

A. Bansal

{"title":"Integrating co-regulated gene-groups and pair-wise genome comparisons to automate reconstruction of microbial pathways","authors":"A. Bansal","doi":"10.1109/BIBE.2001.974431","DOIUrl":"https://doi.org/10.1109/BIBE.2001.974431","url":null,"abstract":"This paper extends previously described automated techniques by automatically integrating the information about automatically derived co-transcribed gene-groups, functionally similar gene-groups derived using automated pair-wise genome comparisons and automatically derived orthologs (functionally equivalent genes) to derive microbial metabolic pathways. The method integrates automatically derived co-transcribed gene-groups with orthologous and homologous gene-groups (http://www.mcs.kent.edu//spl sim/arvind/orthos.html), the biochemical pathway template available at the KEGG database. (http://www.genome.ad.jp), the enzyme information derived from the SwissProt enzyme database (http://expasy.hcuge.ch/) and Ligand database (http://www.genome.ad.jp). The technique refines existing pathways (based upon network of reactions of enzymes) by associating corresponding non-enzymatic, regulatory, and cotranscribed proteins to enzymes. The technique has been illustrated by deriving a major pathway of M. tuberculosis by comparison with seven microbial genomes including E coli and B. subtilis - two microbes well explored in wet laboratories.","PeriodicalId":405124,"journal":{"name":"Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001)","volume":"80 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2001-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126202223","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: 8

Development of a robotic device for MRI-guided interventions in the breast 一种用于核磁共振引导乳腺干预的机器人装置的开发

Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001) Pub Date : 2001-03-04 DOI: 10.1109/BIBE.2001.974430

N. Tsekos, J. Shudy, E. Yacoub, Panagiotis V. Tsekos, I. Koutlas

引用次数: 41

TRUFFLER: programs to study microbial community composition and flux from fluorescent DNA fingerprinting data TRUFFLER:从荧光DNA指纹数据中研究微生物群落组成和通量的程序

Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001) Pub Date : 2001-03-04 DOI: 10.1109/BIBE.2001.974421

M. Wise, A. Osborn

{"title":"TRUFFLER: programs to study microbial community composition and flux from fluorescent DNA fingerprinting data","authors":"M. Wise, A. Osborn","doi":"10.1109/BIBE.2001.974421","DOIUrl":"https://doi.org/10.1109/BIBE.2001.974421","url":null,"abstract":"Terminal-restriction fragment length polymorphism (T-RFLP) and length heterogeneity-polymerase chain reaction (LH-PCR) are DNA fingerprinting technologies which use PCR amplification of a gene of interest e.g. small subunit rRNA gene, to study microbial community structure and dynamics. Either one or both of the forward and reverse strand primers used to amplify the gene are fluorescently labelled. The products of restriction endonuclease digestion are electrophoresed with an automated sequencer that detects only the terminal (labelled) restriction fragments (T-RFs). In LH-PCR, products are electrophoresed without digestion, with different fragment lengths being due to inherent variation in the amplified sequence. A novel software system, TRUFFLER, has been developed to mimic this process in silico allowing comparison of experimental data against databases of theoretically determined T-RFs. As a given combination of forward and reverse primers and restriction endonuclease can yield identical T-RFs across a number of species, combinations of different endonucleases (and/or primers) are typically used In addition to fragment length data, data on fluorescence levels is also available. Computationally, this can be viewed as a constraint satisfaction problem which can be solved to allow identification of the dominant members of the microbial community, often down to individual species or at least genus level, and their relative proportions.","PeriodicalId":405124,"journal":{"name":"Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001)","volume":"108 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2001-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132047272","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

Comparing algorithms for large-scale sequence analysis 大规模序列分析的算法比较

Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001) Pub Date : 2001-03-04 DOI: 10.1109/BIBE.2001.974416

Hadon Nash, Douglas Blair, J. Grefenstette

{"title":"Comparing algorithms for large-scale sequence analysis","authors":"Hadon Nash, Douglas Blair, J. Grefenstette","doi":"10.1109/BIBE.2001.974416","DOIUrl":"https://doi.org/10.1109/BIBE.2001.974416","url":null,"abstract":"The first step in homology analysis is usually the comparison of sequences by similarity search. The explosive growth of genomic databases makes it increasingly important to develop more rapid approaches to the comparison of large sequence databases while using the most sensitive methods available. This paper explores the consequences of this trade-off, comparing the results produced by BLAST and Smith-Waterman on genoinic- scale sequence searches. Stich comparisons are now possible thanks to the development of novel distributed computing platforms. This study uses the Parabon Frontier/sup TM/ Internet computing platform, which enables the effective use of the vast supply of idle computer cycles on the Internet for high-performance computing. We have ported both Smith-Waterman and BLAST to the Frontier platform, enabling the efficient use of these algorithms on large sequence databases. In addition, we present a novel visualization tool along with quantitative metrics for comparing the results of alternative sequence alignment algorithms. Our results compare the sensitivity of Smith-Waterman and BLAST for identifying homologies on proteome databases.","PeriodicalId":405124,"journal":{"name":"Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001)","volume":"10 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2001-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114273367","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: 13

Searching online journals for fluorescence microscope images depicting protein subcellular location patterns 搜索在线期刊荧光显微镜图像描绘蛋白质亚细胞定位模式

Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001) Pub Date : 2001-03-04 DOI: 10.1109/BIBE.2001.974420

R. Murphy, M. Velliste, Jie Yao, G. Porreca

引用次数: 76

A fast pruning algorithm for optimal sequence alignment 最优序列比对的快速剪枝算法

Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001) Pub Date : 2001-03-04 DOI: 10.1109/BIBE.2001.974411

Aaron Davidson

引用次数: 26

GIMS-a data warehouse for storage and analysis of genome sequence and functional data gims -用于存储和分析基因组序列和功能数据的数据仓库

Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001) Pub Date : 2001-03-04 DOI: 10.1109/BIBE.2001.974407

M. Cornell, N. Paton, Shengli Wu, C. Goble, Crispin J. Miller, Paul Kirby, K. Eilbeck, A. Brass, A. Hayes, S. Oliver

{"title":"GIMS-a data warehouse for storage and analysis of genome sequence and functional data","authors":"M. Cornell, N. Paton, Shengli Wu, C. Goble, Crispin J. Miller, Paul Kirby, K. Eilbeck, A. Brass, A. Hayes, S. Oliver","doi":"10.1109/BIBE.2001.974407","DOIUrl":"https://doi.org/10.1109/BIBE.2001.974407","url":null,"abstract":"Effective analysis of genome sequences and associated functional data requires access to many different kinds of biological information. For example, when analysing gene expression data, it may be useful to have access to the sequences upstream of the genes, or to the cellular location of their protein products. Such information is currently stored in different formats at different sites in a way that does not readily allow integrated analyses. The Genome Information Management System (GIMS) is an object database that integrates genome sequence data with functional data on the transcriptome and on protein-protein interactions in a single data warehouse. We have used GIMS to store the Saccharomyces cerevisiae (yeast) genome and to demonstrate how the integrated storage of diverse kinds of genomic data can be beneficial for analysing data using context-rich queries and analyses. GIMS allows data to be stored in a way that reflects the underlying mechanisms in the organism, and permits complex questions to be asked of the data. This paper provides an overview of the GIMS system and describes some analyses that illustrate its use for analysing functional data sets for S. cerevisiae.","PeriodicalId":405124,"journal":{"name":"Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001)","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2001-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129807557","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: 36

Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001) Pub Date : 2001-03-04 DOI: 10.1109/BIBE.2001.974410

Chun Tang, Li Zhang, A. Zhang, M. Ramanathan

引用次数: 189

An algebra for semantic interoperability of information sources 信息源的语义互操作性代数

Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001) Pub Date : 2001-03-04 DOI: 10.1109/BIBE.2001.974427

P. Mitra, G. Wiederhold

{"title":"An algebra for semantic interoperability of information sources","authors":"P. Mitra, G. Wiederhold","doi":"10.1109/BIBE.2001.974427","DOIUrl":"https://doi.org/10.1109/BIBE.2001.974427","url":null,"abstract":"Resolving heterogeneity among the various biological information systems is a crucial problem if we wish to gain value from the many distributed resources available to us. For example, information from multiple protein databases (e.g., Swiss-Prot and PDB) might need to be composed to answer queries posed by end-users. Problems of heterogeneity in hardware, operating systems, interfaces and data structures have been widely addressed, but issues of diverse semantics have been handled mainly in an ad-hoc fashion. This paper highlights the ONION (ONtology compositION) system that enables semantic interoperation among various information sources by articulating the ontologies associated with them. An articulation focuses on the semantically relevant intersection of information resources. Although the generation of articulations (semantic correspondences between the ontologies) cannot be fully automated, we take a semi-automatic approach. ONION uses heuristic algorithms for the automatic generation of suggested articulations. This paper outlines an algebra for ontology composition based on their articulations. We show the properties of the algebraic operators and how they depend upon the articulation functions that generate the articulations. Query optimization is enabled based on the properties of the algebraic operators.","PeriodicalId":405124,"journal":{"name":"Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001)","volume":"98 1-2 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2001-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133054682","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: 51