Proceedings. IEEE Computer Society Bioinformatics Conference最新文献_第5页

A pattern matching algorithm for codon optimization and CpG motif-engineering in DNA expression vectors. DNA表达载体中密码子优化和CpG基序工程的模式匹配算法。

Proceedings. IEEE Computer Society Bioinformatics Conference Pub Date : 2003-01-01

Ravi Vijaya Satya, Amar Mukherjee, Udaykumar Ranga

引用次数: 0

A block coding method that leads to significantly lower entropy values for the proteins and coding sections of Haemophilus influenzae. 一种块编码方法，可显著降低流感嗜血杆菌蛋白质和编码部分的熵值。

Proceedings. IEEE Computer Society Bioinformatics Conference Pub Date : 2003-01-01

G Sampath

引用次数: 0

Clustering time-varying gene expression profiles using scale-space signals. 利用尺度空间信号聚类时变基因表达谱。

Proceedings. IEEE Computer Society Bioinformatics Conference Pub Date : 2003-01-01

Tanveer Syeda-Mahmood

{"title":"Clustering time-varying gene expression profiles using scale-space signals.","authors":"Tanveer Syeda-Mahmood","doi":"","DOIUrl":"","url":null,"abstract":"The functional state of an organism is determined largely by the pattern of expression of its genes. The analysis of gene expression data from gene chips has primarily revolved around clustering and classification of the data using machine learning techniques based on the intensity of expression alone with the time-varying pattern mostly ignored. In this paper, we present a pattern recognition-based approach to capturing similarity by finding salient changes in the time-varying expression patterns of genes. Such changes can give clues about important events, such as gene regulation by cell-cycle phases, or even signal the onset of a disease. Specifically, we observe that dissimilarity between time series is revealed by the sharp twists and bends produced in a higher-dimensional curve formed from the constituent signals. Scale-space analysis is used to detect the sharp twists and turns and their relative strength with respect to the component signals is estimated to form a shape similarity measure between time profiles. A clustering algorithm is presented to cluster gene profiles using the scale-space distance as a similarity metric. Multi-dimensional curves formed from time series within clusters are used as cluster prototypes or indexes to the gene expression database, and are used to retrieve the functionally similar genes to a query gene profile. Extensive comparison of clustering using scale-space distance in comparison to traditional Euclidean distance is presented on the yeast genome database.","PeriodicalId":87204,"journal":{"name":"Proceedings. IEEE Computer Society Bioinformatics Conference","volume":"2 ","pages":"48-56"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25834432","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

Refactoring reusable business components 重构可重用的业务组件

Proceedings. IEEE Computer Society Bioinformatics Conference Pub Date : 2003-01-01 DOI: 10.1109/MITP.2003.1176488

C. Neill, Binny S. Gill

引用次数: 5

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

Proceedings. IEEE Computer Society Bioinformatics Conference Pub Date : 2003-01-01

Xiang Wan, Dong Xu, Carolyn M Slupsky, Guohui Lin

{"title":"Automated protein NMR resonance assignments.","authors":"Xiang Wan, Dong Xu, Carolyn M Slupsky, Guohui Lin","doi":"","DOIUrl":"","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":87204,"journal":{"name":"Proceedings. IEEE Computer Society Bioinformatics Conference","volume":"2 ","pages":"197-208"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25833755","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

Experimental studies of the Universal Chemical Key (UCK) algorithm on the NCI database of chemical compounds. 通用化学密钥(UCK)算法在NCI化合物数据库中的实验研究。

Proceedings. IEEE Computer Society Bioinformatics Conference Pub Date : 2003-01-01

Robert Grossman, Pavan Kasturi, Donald Hamelberg, Bing Liu

引用次数: 0

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。

Proceedings. IEEE Computer Society Bioinformatics Conference Pub Date : 2003-01-01

Alexandre Tchourbanov, Daniel Quest, Hesham Ali, Mark Pauley, Robert Norgren

引用次数: 0

Epitope prediction algorithms for peptide-based vaccine design. 基于肽的疫苗设计的表位预测算法。

Proceedings. IEEE Computer Society Bioinformatics Conference Pub Date : 2003-01-01

Liliana Florea, Bjarni Halldórsson, Oliver Kohlbacher, Russell Schwartz, Stephen Hoffman, Sorin Istrail

{"title":"Epitope prediction algorithms for peptide-based vaccine design.","authors":"Liliana Florea, Bjarni Halldórsson, Oliver Kohlbacher, Russell Schwartz, Stephen Hoffman, Sorin Istrail","doi":"","DOIUrl":"","url":null,"abstract":"Peptide-based vaccines, in which small peptides derived from target proteins (eptiopes) are used to provoke an immune reaction, have attracted considerable attention recently as a potential means both of treating infectious diseases and promoting the destruction of cancerous cells by a patient's own immune system. With the availability of large sequence databases and computers fast enough for rapid processing of large numbers of peptides, computer aided design of peptide-based vaccines has emerged as a promising approach to screening among billions of possible immune-active peptides to find those likely to provoke an immune response to a particular cell type. In this paper, we describe the development of three novel classes of methods for the prediction problem. We present a quadratic programming approach that can be trained on quantitative as well as qualitative data. The second method uses linear programming to counteract the fact that our training data contains mostly positive examples. The third class of methods uses sequence profiles obtained by clustering known epitopes to score candidate peptides. By integrating these methods, using a simple voting heuristic, we achieve improved accuracy over the state of the art.","PeriodicalId":87204,"journal":{"name":"Proceedings. IEEE Computer Society Bioinformatics Conference","volume":"2 ","pages":"17-26"},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26133913","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

GeneCards/spl trade/ 2002: an evolving human gene compendium GeneCards/spl trade/ 2002:一个进化的人类基因纲要

Proceedings. IEEE Computer Society Bioinformatics Conference Pub Date : 2002-12-10 DOI: 10.1109/CSB.2002.1039362

M. Safran, Irina Solomon, O. Shmueli, Michal Lapidot, S. Shen-Orr, A. Adato, Uri Ben-Dor, Nir Esterman, Naomi Rosen, Inga Peter, T. Olender, V. Chalifa-Caspi, D. Lancet

引用次数: 1

Parallel Monte Carlo methods for physical mapping of chromosomes 染色体物理映射的平行蒙特卡罗方法

Proceedings. IEEE Computer Society Bioinformatics Conference Pub Date : 2002-08-14 DOI: 10.1109/CSB.2002.1039330

S. Bhandarkar, J. Arnold

引用次数: 5