Computational systems bioinformatics. Computational Systems Bioinformatics Conference最新文献_第7页

Method for effective virtual screening and scaffold-hopping in chemical compounds. 化合物的有效虚拟筛选和跳架方法。

Computational systems bioinformatics. Computational Systems Bioinformatics Conference Pub Date : 2007-01-01

Nikil Wale, George Karypis, Ian A Watson

引用次数: 0

Modeling species-genes data for efficient phylogenetic inference. 为有效的系统发育推断建立物种-基因数据模型。

Computational systems bioinformatics. Computational Systems Bioinformatics Conference Pub Date : 2007-01-01

Wenyuan Li, Ying Liu

{"title":"Modeling species-genes data for efficient phylogenetic inference.","authors":"Wenyuan Li, Ying Liu","doi":"","DOIUrl":"","url":null,"abstract":"In recent years, biclique methods have been proposed to construct phylogenetic trees. One of the key steps of these methods is to find complete sub-matrices (without missing entries) from a species-genes data matrix. To enumerate all complete sub-matrices, (17) described an exact algorithm, whose running time is exponential. Furthermore, it generates a large number of complete sub-matrices, many of which may not be used for tree reconstruction. Further investigating and understanding the characteristics of species-genes data may be helpful for discovering complete sub-matrices. Therefore, in this paper, we focus on quantitatively studying and understanding the characteristics of species-genes data, which can be used to guide new algorithm design for efficient phylogenetic inference. In this paper, a mathematical model is constructed to simulate the real species-genes data. The results indicate that sequence-availability probability distributions follow power law, which leads to the skewness and sparseness of the real species-genes data. Moreover, a special structure, called \"ladder structure\", is discovered in the real species-genes data. This ladder structure is used to identify complete sub-matrices, and more importantly, to reveal overlapping relationships among complete sub-matrices. To discover the distinct ladder structure in real species-genes data, we propose an efficient evolutionary dynamical system, called \"generalized replicator dynamics\". Two species-genes data sets from green plants are used to illustrate the effectiveness of our model. Empirical study has shown that our model is effective and efficient in understanding species-genes data for phylogenetic inference.","PeriodicalId":72665,"journal":{"name":"Computational systems bioinformatics. Computational Systems Bioinformatics Conference","volume":" ","pages":"429-40"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27060938","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

Rule-based human gene normalization in biomedical text with confidence estimation. 基于规则的生物医学文本人类基因归一化与置信度估计。

Computational systems bioinformatics. Computational Systems Bioinformatics Conference Pub Date : 2007-01-01

William W Lau, Calvin A Johnson, Kevin G Becker

引用次数: 0

Prediction of transcription start sites based on feature selection using AMOSA. 基于AMOSA特征选择的转录起始位点预测。

Computational systems bioinformatics. Computational Systems Bioinformatics Conference Pub Date : 2007-01-01

Xi Wang, Sanghamitra Bandyopadhyay, Zhenyu Xuan, Xiaoyue Zhao, Michael Q Zhang, Xuegong Zhang

引用次数: 0

Mining molecular contexts of cancer via in-silico conditioning. 通过计算机调节挖掘癌症的分子背景。

Computational systems bioinformatics. Computational Systems Bioinformatics Conference Pub Date : 2007-01-01 DOI: 10.1142/9781860948732_0020

Seungchan Kim, Ina Sen, M. Bittner

引用次数: 14

Efficient algorithms for genome-wide tagSNP selection across populations via the linkage disequilibrium criterion. 基于连锁不平衡准则的全基因组标记snp选择算法。

Computational systems bioinformatics. Computational Systems Bioinformatics Conference Pub Date : 2007-01-01 DOI: 10.1142/9781860948732_0011

Lan Liu, Yonghui Wu, S. Lonardi, Tao Jiang

{"title":"Efficient algorithms for genome-wide tagSNP selection across populations via the linkage disequilibrium criterion.","authors":"Lan Liu, Yonghui Wu, S. Lonardi, Tao Jiang","doi":"10.1142/9781860948732_0011","DOIUrl":"https://doi.org/10.1142/9781860948732_0011","url":null,"abstract":"In this paper, we study the tagSNP selection problem on multiple populations using the pairwise r(2) linkage disequilibrium criterion. We propose a novel combinatorial optimization model for the tagSNP selection problem, called the minimum common tagSNP selection (MCTS) problem, and present efficient solutions for MCTS. Our approach consists of three main steps including (i) partitioning the SNP markers into small disjoint components, (ii) applying some data reduction rules to simplify the problem, and (iii) applying either a fast greedy algorithm or a Lagrangian relaxation algorithm to solve the remaining (general) MCTS. These algorithms also provide lower bounds on tagging (i.e. the minimum number of tagSNPs needed). The lower bounds allow us to evaluate how far our solution is from the optimum. To the best of our knowledge, it is the first time tagging lower bounds are discussed in the literature. We assess the performance of our algorithms on real HapMap data for genome-wide tagging. The experiments demonstrate that our algorithms run 3 to 4 orders of magnitude faster than the existing single-population tagging programs like FESTA, LD-Select and the multiple-population tagging method MultiPop-TagSelect. Our method also greatly reduces the required tagSNPs compared to LD-Select on a single population and MultiPop-TagSelect on multiple populations. Moreover, the numbers of tagSNPs selected by our algorithms are almost optimal since they are very close to the corresponding lower bounds obtained by our method.","PeriodicalId":72665,"journal":{"name":"Computational systems bioinformatics. Computational Systems Bioinformatics Conference","volume":"6 1","pages":"67-78"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64007343","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: 7

Algorithm for peptide sequencing by tandem mass spectrometry based on better preprocessing and anti-symmetric computational model. 基于改进预处理和反对称计算模型的串联质谱多肽测序算法。

Computational systems bioinformatics. Computational Systems Bioinformatics Conference Pub Date : 2007-01-01 DOI: 10.1142/9781860948732_0007

K. Ning, H. Leong

{"title":"Algorithm for peptide sequencing by tandem mass spectrometry based on better preprocessing and anti-symmetric computational model.","authors":"K. Ning, H. Leong","doi":"10.1142/9781860948732_0007","DOIUrl":"https://doi.org/10.1142/9781860948732_0007","url":null,"abstract":"Peptide sequencing by tandem mass spectrometry is a very important, interesting, yet challenging problem in proteomics. This problem is extensively investigated by researchers recently, and the peptide sequencing results are becoming more and more accurate. However, many of these algorithms are using computational models based on some unverified assumptions. We believe that the investigation of the validity of these assumptions and related problems will lead to improvements in current algorithms. In this paper, we have first investigated peptide sequencing without preprocessing the spectrum, and we have shown that by introducing preprocessing on spectrum, peptide sequencing can be faster, easier and more accurate. We have then investigated one very important problem, the anti-symmetric problem in the peptide sequencing problem, and we have proved by experiments that model that simply ignore anti-symmetric of model that remove all anti-symmetric instances are too simple for peptide sequencing problem. We have proposed a new model for anti-symmetric problem in more realistic way. We have also proposed a novel algorithm which incorporate preprocessing and new model for anti-symmetric issue, and experiments show that this algorithm has better performance on datasets examined.","PeriodicalId":72665,"journal":{"name":"Computational systems bioinformatics. Computational Systems Bioinformatics Conference","volume":"6 1","pages":"19-30"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64007490","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

Effective labeling of molecular surface points for cavity detection and location of putative binding sites. 有效标记分子表面点，用于空腔检测和推定结合位点的定位。

Computational systems bioinformatics. Computational Systems Bioinformatics Conference Pub Date : 2007-01-01 DOI: 10.1142/9781860948732_0028

M. Bock, C. Garutti, C. Guerra

引用次数: 18

Enhanced partial order curve comparison over multiple protein folding trajectories. 在多个蛋白质折叠轨迹上增强的偏序曲线比较。

Computational systems bioinformatics. Computational Systems Bioinformatics Conference Pub Date : 2007-01-01 DOI: 10.1142/9781860948732_0031

Hong Sun, H. Ferhatosmanoğlu, M. Ota, Yusu Wang

引用次数: 3

Reconciliation with non-binary species trees. 与非二种树的和解。

Computational systems bioinformatics. Computational Systems Bioinformatics Conference Pub Date : 2007-01-01 DOI: 10.1142/9781860948732_0044

B Vernot, M Stolzer, A Goldman, D Durand

{"title":"Reconciliation with non-binary species trees.","authors":"B Vernot, M Stolzer, A Goldman, D Durand","doi":"10.1142/9781860948732_0044","DOIUrl":"https://doi.org/10.1142/9781860948732_0044","url":null,"abstract":"Reconciliation is the process of resolving disagreement between gene and species trees, by invoking gene duplications and losses to explain topological incongruence. The resulting inferred duplication histories are a valuable source of information for a broad range of biological applications, including ortholog identification, estimating gene duplication times, and rooting and correcting gene trees. Reconciliation for binary trees is a tractable and well studied problem. However, a striking proportion of species trees are non-binary. For example, 64% of branch points in the NCBI taxonomy have three or more children. When applied to non-binary species trees, current algorithms overestimate the number of duplications because they cannot distinguish between duplication and deep coalescence. We present the first formal algorithm for reconciling binary gene trees with non-binary species trees under a duplication-loss parsimony model. Using a space efficient mapping from gene to species tree, our algorithm infers the minimum number of duplications and losses in O(|V(G)| . (k(S) + h(S))) time, where V(G) is the number of nodes in the gene tree, h(S) is the height of the species tree and k(S) is the width of its largest multifurcation. We also present a dynamic programming algorithm for a combined loss model, in which losses in sibling species may be represented as a single loss in the common ancestor. Our algorithms have been implemented in NOTUNG, a robust, production quality tree-fitting program, which provides a graphical user interface for exploratory analysis and also supports automated, high-throughput analysis of large data sets.","PeriodicalId":72665,"journal":{"name":"Computational systems bioinformatics. Computational Systems Bioinformatics Conference","volume":" ","pages":"441-52"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27060939","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: 73