Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003最新文献_第3页

Fast and sensitive probe selection for DNA chips using jumps in matching statistics 利用匹配统计跳变快速灵敏地选择DNA芯片探针

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227304

S. Rahmann

引用次数: 31

Using natural language processing and the gene ontology to populate a structured pathway database 利用自然语言处理和基因本体构建结构化的路径数据库

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227433

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

{"title":"Using natural language processing and the gene ontology to populate a structured pathway database","authors":"David Dehoney, R. Harte, Yan Lu, Daniel Chin","doi":"10.1109/CSB.2003.1227433","DOIUrl":"https://doi.org/10.1109/CSB.2003.1227433","url":null,"abstract":"Reading literature is one of the most time consuming tasks a busy scientist has to contend with. As the volume of literature continues to grow there is a need to sort through this information in a more efficient manner. Mapping the pathways of genes and proteins of interest is one goal that requires frequent reference to the literature. Pathway databases can help here and scientists currently have a choice between buying access to externally curated pathway databases or building their own in house. However such databases are either expensive to license or slow to populate manually. Building upon easily available, open-source tools we have developed a pipeline to automate the collection, structuring and storage of gene and protein interaction data from the literature. As a team of both biologists and computer scientists we integrated our natural language processing (NLP) software with the gene ontology (GO) to collect and translate unstructured text data into structured interaction data. For NLP we used a machine learning approach with a rule induction program, RAPIER (http://www. cs. utexas. edu/users/mUrapier. html). RAPIER was modified to learn rules from tagged documents, and then it was trained on a corpus tagged by expert curators. The resulting rules were used to extract information from a test corpus automatically. Extracted genes and proteins were mapped onto Locuslink, and extracted interactions were mapped onto GO. Once information was structured in this way it was stored in a pathway database and this formal structure allowed us to perform advanced data mining and visualization.","PeriodicalId":147883,"journal":{"name":"Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003","volume":"21 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":"115065647","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

Efficient reconstruction of phylogenetic networks with constrained recombination 基于约束重组的系统发育网络的高效重构

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227337

D. Gusfield, Satish Eddhu, C. Langley

{"title":"Efficient reconstruction of phylogenetic networks with constrained recombination","authors":"D. Gusfield, Satish Eddhu, C. Langley","doi":"10.1109/CSB.2003.1227337","DOIUrl":"https://doi.org/10.1109/CSB.2003.1227337","url":null,"abstract":"A phylogenetic network is a generalization of a phylogenetic tree, allowing structural properties that are not treelike. With the growth of genomic data, much of which does not fit ideal tree models, there is greater need to understand the algorithmics and combinatorics of phylogenetic networks. We consider the problem of determining whether the sequences can be derived on a phylogenetic network where the recombination cycles are node disjoint. In this paper, we call such a phylogenetic network a \"galled-tree\". By more deeply analysing the combinatorial constraints on cycle-disjoint phylogenetic networks, we obtain an efficient algorithm that is guaranteed to be both a necessary and sufficient test for the existence of a galled-tree for the data. If there is a galled-tree, the algorithm constructs one and obtains an implicit representation of all the galled trees for the data, and can create these in linear time for each one. We also note two additional results related to galled trees: first, any set of sequences that can be derived on a galled tree can be derived on a true tree (without recombination cycles), where at most one back mutation is allowed per site; second, the site compatibility problem (which is NP-hard in general) can be solved in linear time for any set of sequences that can be derived on a galled tree. The combinatorial constraints we develop apply (for the most part) to node-disjoint cycles in any phylogenetic network (not just galled-trees), and can be used for example to prove that a given site cannot be on a node-disjoint cycle in any phylogenetic network. Perhaps more important than the specific results about galled-trees, we introduce an approach that can be used to study recombination in phylogenetic networks that go beyond galled-trees.","PeriodicalId":147883,"journal":{"name":"Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003","volume":"32 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":"122175422","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: 93

Bridging paradigm gaps between biology and engineering 弥合生物学和工程学之间的范例差距

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227290

Jehoshua Bruck

引用次数: 0

Automated protein NMR resonance assignments 自动蛋白质核磁共振分配

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227319

Xiang Wan, Dong Xu, C. Slupsky, Guohui Lin

{"title":"Automated protein NMR resonance assignments","authors":"Xiang Wan, Dong Xu, C. Slupsky, Guohui Lin","doi":"10.1109/CSB.2003.1227319","DOIUrl":"https://doi.org/10.1109/CSB.2003.1227319","url":null,"abstract":"NMR resonance peak assignment is one of the key steps in solving an NMR protein structure. The assignment process links resonance peaks to individual residues of the target protein sequence, providing the prerequisite for establishing intra- and inter-residue spatial relationships between atoms. The assignment process is tedious and time-consuming, which could take many weeks. Though there exist a number of computer programs to assist the assignment process, many NMR labs are still doing the assignments manually to ensure quality. This paper presents (1) a new scoring system for mapping spin systems to residues, (2) an automated adjacency information extraction procedure from NMR spectra, and (3) a very fast assignment algorithm based on our previous proposed greedy filtering method and a maximum matching algorithm to automate the assignment process. The computational tests on 70 instances of (pseudo) experimental NMR data of 14 proteins demonstrate that the new score scheme has much better discerning power with the aid of adjacency information between spin systems simulated across various NMR spectra. Typically, with automated extraction of adjacency information, our method achieves nearly complete assignments for most of the proteins. The experiment shows very promising perspective that the fast automated assignment algorithm together with the new score scheme and automated adjacency extraction may be ready for practical use.","PeriodicalId":147883,"journal":{"name":"Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003","volume":"8 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":"127229192","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: 10

Estimating recombination rate distribution by optimal quantization 最优量化估计重组率分布

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227346

Mingzhou Song, S. Boissinot, R. Haralick, I. T. Phillips

引用次数: 2

Analysis of phylogenetic profiles using Bayesian decomposition 基于贝叶斯分解的系统发育分析

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227380

Ghislain Bidaut, K. Suhre, J. Claverie, M. Ochs

引用次数: 1

A flexible pipeline for experimental design, processing, and analysis of microarray data 一个灵活的管道实验设计，处理和分析微阵列数据

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227349

Stephen Osborn, S. Kennedy, Daniel Chin

引用次数: 1

CoMRI: a compressed multiresolution index structure for sequence similarity queries CoMRI:用于序列相似性查询的压缩多分辨率索引结构

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227406

Hong Sun, Ozgur Ozturk, H. Ferhatosmanoğlu

引用次数: 7

A new approach for gene annotation using unambiguous sequence joining 基于无二义序列连接的基因注释新方法

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227336

A. Tchourbanov, Daniel J. Quest, H. Ali, M. Pauley, R. Norgren

引用次数: 6