Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003最新文献_第4页

Towards index-based similarity search for protein structure databases 基于索引的蛋白质结构数据库相似性搜索研究

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227314

Orhan Çamoglu, Tamer Kahveci, Ambuj K. Singh

引用次数: 38

The cybertory sequence file system for managing large DNA sequences 用于管理大型DNA序列的cybertory序列文件系统

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227403

Carl E. McMillin, R. Horton

引用次数: 0

Refining the extraction of relevant documents from biomedical literature to create a corpus for pathway text mining 对生物医学文献中相关文档的提取进行细化，建立路径文本挖掘的语料库

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227432

R. Harte, Yan Lu, Stephen Osborn, David Dehoney, Daniel Chin

{"title":"Refining the extraction of relevant documents from biomedical literature to create a corpus for pathway text mining","authors":"R. Harte, Yan Lu, Stephen Osborn, David Dehoney, Daniel Chin","doi":"10.1109/CSB.2003.1227432","DOIUrl":"https://doi.org/10.1109/CSB.2003.1227432","url":null,"abstract":"For biologists to keep up with developments in their field or related fields, automation is desirable to more efficiently read and interpret a rapidly growing literature. Identification of proteins or genes and their interactions can facilitate the mapping of canonical or evolving pathways from the literature. In order to mine such data, we developed procedures and tools to pre-qualify documents for further analysis. Initially, a corpus of documents for proteins of interest was built using alternate symbols from Locuslink and the Stanford SOURCE as MEDLINE search terms. The query was refined using the optimum keywords together with MeSH terms combined in a Boolean query to minimize false positives. The document space was examined using a strategy employing; latent semantic indexing (LSI), which uses Entrez's \"related papers\" utility for MEDLINE. Documents' relationships were visualized using an undirected graph and scored by their relatedness. Distinct document clusters, formed by the most highly connected related papers, are mostly composed of abstracts relating to one aspect of research. This feature was used to filter irrelevant abstracts, which resulted in a reduction in corpus size of 10% to 30% depending on the domain. The excluded documents were examined to confirm their lack of relevance. Corpora consisted of the most relevant documents thus reducing the number of false positives and irrelevant examples in the training set for pathway mapping. Documents were tagged, using a modified version of GATE2, with terms based on GO for rule induction using RAPIER.","PeriodicalId":147883,"journal":{"name":"Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2003-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131173933","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

Computational simulation of lipid bilayer reorientation at gaps 间隙处脂质双分子层重定向的计算模拟

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227374

P. Kasson, V. Pande

引用次数: 0

MedfoLink: bridging the gap between IT and the medical community MedfoLink:弥合IT和医学界之间的差距

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227436

J. Gerrein, A. Kherlopian, Vezen Wu, Mitchell Berman, A. Wald

引用次数: 1

Genome on demand: interactive substring searching 基因组按需:交互式子串搜索

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227405

Tamer Kahveci, Ambuj K. Singh

引用次数: 2

SMASHing regulatory sites in DNA by human-mouse sequence comparisons 通过人鼠序列比较粉碎DNA中的调控位点

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227328

M. Zavolan, N. Socci, N. Rajewsky, T. Gaasterland

{"title":"SMASHing regulatory sites in DNA by human-mouse sequence comparisons","authors":"M. Zavolan, N. Socci, N. Rajewsky, T. Gaasterland","doi":"10.1109/CSB.2003.1227328","DOIUrl":"https://doi.org/10.1109/CSB.2003.1227328","url":null,"abstract":"Regulatory sequence elements provide important clues to understanding and predicting gene expression. Although the binding sites for hundreds of transcription factors are known, there has been no systematic attempt to incorporate this information in the annotation of the human genome. Cross species sequence comparisons are critical to a meaningful annotation of regulatory elements since they generally reside in conserved noncoding regions. To take advantage of the recently completed drafts of the mouse and human genomes for annotating transcription factor binding sites, we developed SMASH, a computational pipeline that identifies thousands of orthologous human/mouse proteins, maps them to genomic sequences, extracts and compares upstream regions and annotates putative regulatory elements in conserved, noncoding, upstream regions. Our current dataset consists of approximately 2500 human/mouse gene pairs. Transcription start sites were estimated by mapping quasifull length cDNA sequences. SMASH uses a novel probabilistic method to identify putative conserved binding sites that takes into account the competition between transcription factors for binding DNA. SMASH presents the results via a genome browser web interface which displays the predicted regulatory information together with the current annotations for the human genome. Our results are validated by comparison to previously published experimental data. SMASH results compare favorably to other existing computational approaches.","PeriodicalId":147883,"journal":{"name":"Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003","volume":"5 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2003-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130258277","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: 19

Initial large-scale exploration of protein-protein interactions in human brain 对人脑中蛋白质-蛋白质相互作用的初步大规模探索

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227322

J. Chen, A. Sivachenko, R. Bell, C. Kurschner, I. Ota, S. Sahasrabudhe

引用次数: 9

Local similarity in RNA secondary structures RNA二级结构的局部相似性

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227315

M. Höchsmann, Thomas Töller, R. Giegerich, S. Kurtz

{"title":"Local similarity in RNA secondary structures","authors":"M. Höchsmann, Thomas Töller, R. Giegerich, S. Kurtz","doi":"10.1109/CSB.2003.1227315","DOIUrl":"https://doi.org/10.1109/CSB.2003.1227315","url":null,"abstract":"We present a systematic treatment of alignment distance and local similarity algorithms on trees and forests. We build upon the tree alignment algorithm for ordered trees given by Jiang et. al (1995) and extend it to calculate local forest alignments, which is essential for finding local similar regions in RNA secondary structures. The time complexity of our algorithm is O(/F/sub 1///spl middot//F/sub 2//)/spl middot/deg(F/sub 1/)/spl middot/deg(F/sub 2/)/spl middot/(deg(F/sub 1/)+deg(F/sub 2/)) where /Fi/ is the number of nodes in forest Fi and deg(Fi) is the degree of Fi. We provide carefully engineered dynamic programming implementations using dense, two-dimensional tables which considerably reduces the space requirement. We suggest a new representation of RNA secondary structures as forests that allow reasonable scoring of edit operations on RNA secondary structures. The comparison of RNA secondary structures is facilitated by a new visualization technique for RNA secondary structure alignments. Finally, we show how potential regulatory motifs can be discovered solely by their structural preservation, and independent of their sequence conservation and position.","PeriodicalId":147883,"journal":{"name":"Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003","volume":"375 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2003-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129087835","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: 271

Representing and reasoning about signal networks: an illustration using NF/spl kappa/B dependent signaling pathways 信号网络的表示和推理:使用NF/spl kappa/B依赖的信号通路的说明

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227427

Chitta Baral, K. Chancellor, Tran Hoai Nam, Nhan Tran

{"title":"Representing and reasoning about signal networks: an illustration using NF/spl kappa/B dependent signaling pathways","authors":"Chitta Baral, K. Chancellor, Tran Hoai Nam, Nhan Tran","doi":"10.1109/CSB.2003.1227427","DOIUrl":"https://doi.org/10.1109/CSB.2003.1227427","url":null,"abstract":"We propose a formal language to represent and reason about signal transduction networks. The existing approaches such as ones based on Petri nets, and /spl pi/-calculus fall short in many ways and our work suggests that an artificial intelligence (AI) based approach may be well suited for many aspects. We apply a form of action language to represent and reason about NF/spl kappa/B dependent signaling pathways. Our language supports several essential features of reasoning with signal transduction knowledge, such as: reasoning with partial (or incomplete) knowledge, and reasoning about triggered evolutions of the world and elaboration tolerance. Because of its growing important role in cellular functions, we select NF/spl kappa/B dependent signaling to be our test bed. NF/spl kappa/B is a central mediator of the immune response, and it can regulate stress responses, as well as cell death/survival in several cell types. While many extracellular signals may lead to the activation of NF/spl kappa/B, few related pathways are elucidated. We study the tasks of representation of pathways, reasoning with pathways, explaining observations, and planning to alter the outcomes; and show that all of them can be well formulated in our framework. Thus our work shows that our AI based approach is a good candidate for feasible and practical representation of and reasoning about signal networks.","PeriodicalId":147883,"journal":{"name":"Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003","volume":"28 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2003-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130622260","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