The 2010 ACM International Conference on Bioinformatics and Computational Biology : ACM-BCB 2010 : Niagara Falls, New York, U.S.A., August 2-4, 2010. ACM International Conference on Bioinformatics and Computational Biology (1st : 2010 :...最新文献

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Genome-wide compatible SNP intervals and their properties. 全基因组兼容SNP间隔及其性质。

The 2010 ACM International Conference on Bioinformatics and Computational Biology : ACM-BCB 2010 : Niagara Falls, New York, U.S.A., August 2-4, 2010. ACM International Conference on Bioinformatics and Computational Biology (1st : 2010 :... Pub Date : 2010-08-01 DOI: 10.1145/1854776.1854788

Jeremy Wang, Fernando Pardo-Manual de Villena, Kyle J Moore, Wei Wang, Qi Zhang, Leonard McMillan

{"title":"Genome-wide compatible SNP intervals and their properties.","authors":"Jeremy Wang, Fernando Pardo-Manual de Villena, Kyle J Moore, Wei Wang, Qi Zhang, Leonard McMillan","doi":"10.1145/1854776.1854788","DOIUrl":"https://doi.org/10.1145/1854776.1854788","url":null,"abstract":"Intraspecific genomes can be subdivided into blocks with limited diversity. Understanding the distribution and structure of these blocks will help to unravel many biological problems including the identification of genes associated with complex diseases, finding the ancestral origins of a given population, and localizing regions of historical recombination, gene conversion, and homoplasy. We present methods for partitioning a genome into blocks for which there are no apparent recombinations, thus providing parsimonious sets of compatible genome intervals based on the four-gamete test. Our contribution is a thorough analysis of the problem of dividing a genome into compatible intervals, in terms of its computational complexity, and by providing an achievable lower-bound on the minimal number of intervals required to cover an entire data set. In general, such minimal interval partitions are not unique. However, we identify properties that are common to every possible solution. We also define the notion of an interval set that achieves the interval lower-bound, yet maximizes interval overlap. We demonstrate algorithms for partitioning both haplotype data from inbred mice as well as outbred heterozygous genotype data using extensions of the standard four-gamete test. These methods allow our algorithms to be applied to a wide range of genomic data sets.","PeriodicalId":90977,"journal":{"name":"The 2010 ACM International Conference on Bioinformatics and Computational Biology : ACM-BCB 2010 : Niagara Falls, New York, U.S.A., August 2-4, 2010. ACM International Conference on Bioinformatics and Computational Biology (1st : 2010 :...","volume":"2010 ","pages":"43-52"},"PeriodicalIF":0.0,"publicationDate":"2010-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1145/1854776.1854788","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35619386","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 19

A Novel Network Model for Molecular Prognosis. 一种新的分子预后网络模型。

Ying-Wooi Wan, Swetha Bose, James Denvir, Nancy Lan Guo

{"title":"A Novel Network Model for Molecular Prognosis.","authors":"Ying-Wooi Wan, Swetha Bose, James Denvir, Nancy Lan Guo","doi":"10.1145/1854776.1854825","DOIUrl":"https://doi.org/10.1145/1854776.1854825","url":null,"abstract":"Network-based genome-wide association studies (NWAS) utilize the molecular interactions between genes and functional pathways in biomarker identification. This study presents a novel network-based methodology for identifying prognostic gene signatures to predict cancer recurrence. The methodology contains the following steps: 1) Constructing genome-wide coexpression networks for different disease states (metastatic vs. non-metastatic). Prediction logic is used to induct valid implication relations between each pair of gene expression profiles in terms of formal logic rules. 2) Identifying differential components associated with specific disease states from the genome-wide coexpression networks. 3) Dissecting network modules that are tightly connected with major disease signal hallmarks from the disease specific differential components. 4) Identifying most significant genes/probes associated with clinical outcome from the pathway connected network modules. Using this methodology, a 14-gene prognostic signature was identified for accurate patient stratification in early stage lung cancer.","PeriodicalId":90977,"journal":{"name":"The 2010 ACM International Conference on Bioinformatics and Computational Biology : ACM-BCB 2010 : Niagara Falls, New York, U.S.A., August 2-4, 2010. ACM International Conference on Bioinformatics and Computational Biology (1st : 2010 :...","volume":"2010 ","pages":"342-345"},"PeriodicalIF":0.0,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1145/1854776.1854825","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33205637","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5