Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003最新文献_第9页

Computing for the DOE genomes to life program 计算DOE基因组到生命计划

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227298

E. Uberbacher, David Thomassen, A. Patrinos, Gary Johnson, C. Oliver, M. Frazier

引用次数: 0

3D structural homology detection via unassigned residual dipolar couplings 通过未分配的剩余偶极耦合进行三维结构同源性检测

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227320

C. Langmead, B. Donald

{"title":"3D structural homology detection via unassigned residual dipolar couplings","authors":"C. Langmead, B. Donald","doi":"10.1109/CSB.2003.1227320","DOIUrl":"https://doi.org/10.1109/CSB.2003.1227320","url":null,"abstract":"Recognition of a protein's fold provides valuable information about its function. While many sequence-based homology prediction methods exist, an important challenge remains: two highly dissimilar sequences can have similar folds - how can we detect this rapidly, in the context of structural genomics? High-throughput NMR experiments, coupled with novel algorithms for data analysis, can address this challenge. We report an automated procedure for detecting 3D structural homologies from sparse, unassigned protein NMR data. Our method identifies the 3D structural models in a protein structural database whose geometries best fit the Unassigned experimental NMR data. It does not use sequence information and is thus not limited by sequence homology. The method can also be used to confirm or refute structural predictions made by other techniques such as protein threading or sequence homology. The algorithm runs in O(pnk/sup 3/) time, where p is the number of proteins in the database, n is the number of residues in the target protein, and k is the resolution of a rotation search. The method requires only uniform /sup 15/N-labelling of the protein and processes unassigned /sup H/N-/sup 15/N residual dipolar couplings, which can be acquired in a couple of hours. Our experiments on NMR data from 5 different proteins demonstrate that the method identifies closely related protein folds, despite low-sequence homology between the target protein and the computed model.","PeriodicalId":147883,"journal":{"name":"Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003","volume":"37 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":"114171162","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: 21

Minimum redundancy feature selection from microarray gene expression data 微阵列基因表达数据的最小冗余特征选择

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227396

C. Ding, Hanchuan Peng

引用次数: 2467

Substrate recognition by enzymes: a theoretical study 酶识别底物的理论研究

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227373

Kaori Ueno-Noto, K. Takano, M. Hara-Yokoyama

引用次数: 0

Preliminary wavelet analysis of genomic sequences 基因组序列的初步小波分析

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227391

Jianchang Ning, Charles N. Moore, J. Nelson

引用次数: 39

A query language to support scientific discovery 一种支持科学发现的查询语言

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227340

B. Eckman, K. Deutsch, M. Janer, Z. Lacroix, L. Raschid

引用次数: 8

Gene selection for cancer classification using bootstrapped genetic algorithms and support vector machines 基于自举遗传算法和支持向量机的癌症分类基因选择

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227389

Xue-wen Chen

引用次数: 52

Statistical issues in the analysis of the array CGH data 阵列CGH数据分析中的统计问题

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227347

J. Fridlyand, A. Snijders, D. Pinkel, D. Albertson, Ajay N. Jain

{"title":"Statistical issues in the analysis of the array CGH data","authors":"J. Fridlyand, A. Snijders, D. Pinkel, D. Albertson, Ajay N. Jain","doi":"10.1109/CSB.2003.1227347","DOIUrl":"https://doi.org/10.1109/CSB.2003.1227347","url":null,"abstract":"The development of solid tumors is associated with acquisition of complex genetic alterations, indicating that failures in the mechanisms that maintain the integrity of the genome contribute to tumor evolution. Thus, one expects that the particular types of genomic derangement seen in tumors reflect underlying failures in maintenance of genetic stability, as well as selection for changes that provide growth advantage. In order to investigate genomic alterations we are using microarray-based comparative genomic hybridization (array CGH). The computational task is to map and characterize the number and types of copy number alterations present in the tumors, and so define copy number phenotypes as well as to associate them with known biological markers. To utilize the spatial coherence between nearby clones, we use unsupervised Hidden Markov Models approach. The clones are partitioned into the states which represent underlying copy number of the group of clones. The method is demonstrated on the two cell line datasets with known copy number alterations for one of them. The biological conclusions drawn from the analyses are discussed.","PeriodicalId":147883,"journal":{"name":"Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003","volume":"101 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":"131327918","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

Identification of nonrandom patterns in structural and mutational data: the case of prion protein 鉴定结构和突变数据中的非随机模式:朊病毒蛋白的情况

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227420

I. B. Kuznetsov, S. Rackovsky

引用次数: 4

CTSS: a robust and efficient method for protein structure alignment based on local geometrical and biological features CTSS:一种基于局部几何和生物特征的蛋白质结构定位方法

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI: 10.1109/CSB.2003.1227316

Tolga Can, Yuan-fang Wang

{"title":"CTSS: a robust and efficient method for protein structure alignment based on local geometrical and biological features","authors":"Tolga Can, Yuan-fang Wang","doi":"10.1109/CSB.2003.1227316","DOIUrl":"https://doi.org/10.1109/CSB.2003.1227316","url":null,"abstract":"We present a new method for conducting protein structure similarity searches, which improves on the accuracy, robustness, and efficiency of some existing techniques. Our method is grounded in the theory of differential geometry on 3D space curve matching. We generate shape signatures for proteins that are invariant, localized, robust, compact, and biologically meaningful. To improve matching accuracy, we smooth the noisy raw atomic coordinate data with spline fitting. To improve matching efficiency, we adopt a hierarchical coarse-to-fine strategy. We use an efficient hashing-based technique to screen out unlikely candidates and perform detailed pairwise alignments only for a small number of candidates that survive the screening process. Contrary to other hashing based techniques, our technique employs domain specific information (not just geometric information) in constructing the hash key, and hence, is more tuned to the domain of biology. Furthermore, the invariancy, localization, and compactness of the shape signatures allow us to utilize a well-known local sequence alignment algorithm for aligning two protein structures. One measure of the efficacy of the proposed technique is that we were able to discover new, meaningful motifs that were not reported by other structure alignment methods.","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":"131242646","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: 78