检索结果-内蒙古大学图书馆

ieee symposium on computational intelligence and bioinformatics and computational biology (CIBCB)

作者： Chengwei Su Mark E. Borsuk Angeline Andrew Margaret Karagas Thayer School of Engineering Dartmouth College Hanover NH USA Dartmouth College Thayer School of Engineering Hanover NH USA Community and Family Medicine Geisel School of Medicine Lebanon NH USA

We consider the applicability of Bayesian networks (BNs) for discovering relations between genes, environment, and disease. Most state-of-the-art BN structure learning algorithms are not capable of learning structures from data containing missing values, which is a norm in genetic epidemiological data. In addition, there exists a wealth of existing prior knowledge which could be incorporated to improve computational efficiency in BN structure learning. To address these challenges, we applied a Markov chain Monte Carlo based BN structure learning algorithm to data from a population-based study of bladder cancer in New Hampshire, USA. A large improvement in computational efficiency is achieved under this approach.

关键词： Bayes methods Markov processes Genomics bioinformatics DNA Reservoirs Weight measurement

来源：评论

学校读者我要写书评

暂无评论

A Survey and Comparative Study of Statistical Tests for Identifying Differential Expression from Microarray Data

引用

ieee-ACM TRANSACTIONS ON computational biology AND bioinformatics 2014年第1期11卷 95-115页

作者： Bandyopadhyay, Sanghamitra Mallik, Saurav Mukhopadhyay, Anirban Indian Stat Inst Machine Intelligence Unit Kolkata 700108 W Bengal India Univ Kalyani Dept Comp Sci & Engn Kalyani 741235 W Bengal India

DNA microarray is a powerful technology that can simultaneously determine the levels of thousands of transcripts (generated, for example, from genes/miRNAs) across different experimental conditions or tissue samples. The motto of differential expression analysis is to identify the transcripts whose expressions change significantly across different types of samples or experimental conditions. A number of statistical testing methods are available for this purpose. In this paper, we provide a comprehensive survey on different parametric and non-parametric testing methodologies for identifying differential expression from microarray data sets. The performances of the different testing methods have been compared based on some real-life miRNA and mRNA expression data sets. For validating the resulting differentially expressed miRNAs, the outcomes of each test are checked with the information available for miRNA in the standard miRNA database PhenomiR 2.0. Subsequently, we have prepared different simulated data sets of different sample sizes (from 10 to 100 per group/population) and thereafter the power of each test have been calculated individually. The comparative simulated study might lead to formulate robust and comprehensive judgements about the performance of each test in the basis of assumption of data distribution. Finally, a list of advantages and limitations of the different statistical tests has been provided, along with indications of some areas where further studies are required.

关键词： Differentially expressed transcripts parametric and nonparametric tests multiple testing corrections power of test

来源：评论

学校读者我要写书评

暂无评论

Tuning receiver characteristics in bacterial quorum communication: An evolutionary approach using standard virtual biological parts

Tuning receiver characteristics in bacterial quorum communic...

引用

ieee symposium on computational intelligence and bioinformatics and computational biology (CIBCB)

作者： J. S. Hallinan O. Gilfellon G. Misirli A. Wipat School of Computing Science and the Centre for Synthetic Biology and Bioexploitation Newcastle University UK

Populations of bacteria acting in collaboration can produce complex behaviors which are not achievable by individual cells. There has, consequently, been considerable interest in the engineering of bacterial populations. Here we describe an approach for the engineering of aspects of bacterial quorum communication, using Standard Virtual Parts, a synthetic biology programming language, dubbed SVPWrite, and an evolutionary algorithm. We apply this system to engineering the output characteristics of the subtilin receiver system of Bacillus subtilis. Simple modifications, such as altering the strength of the output response to a subtilin input, are easily achieved. More complex adaptations, such as modifying the shape of the receiver response curve, necessitate alterations to the topology of the regulatory network. More generally, the use of Standard Virtual Parts and a programming language allow circuit design, simulation and evaluation to easily be automated, permitting exploration of a far larger proportion of design space than would be possible using standard manual design approaches.

关键词： Biological system modeling Integrated circuit modeling Genetics Microorganisms Standards computational modeling Receivers

来源：评论

学校读者我要写书评

暂无评论

A Many-Core Hardware Acceleration Platform for Short Read Mapping Problem Using Distributed Memory Interface with 3D-stacked Architecture 16

A Many-Core Hardware Acceleration Platform for Short Read Ma...

引用

16th International symposium on System-on-Chip (SoC)

作者： Liu, Pei Hemani, Ahmed Paul, Kolin Royal Inst Technol KTH Sch ICT Dept Elect Syst Stockholm Sweden Indian Inst Technol Dept Comp Sci & Engn New Delhi 110016 India

ISBN: (纸本)9781479968909

Next Generation Sequencing technologies produce huge amounts of short reads consisting randomly fragmented DNA base pair strings, while assembling poses a challenge on the mapping of short reads to a reference genome in terms of both sensitivity and execution time. In this paper, we propose a many-core hardware acceleration platform for short read mapping based on hash-index method, which benefit from a distributed memory interface with 3D-stacked architecture for local memory access. Our design provides an amazingly 45012 times speedup over software approach for single end short reads and 21102 times for paired end reads, while also beats similar single FPGA solution for 1466 times in case of single end reads.

关键词： 3D integration bioinformatics computational biology genetics short read mapping VLSI

来源：评论

学校读者我要写书评

暂无评论

Latent Dirichlet Allocation based on Gibbs Sampling for gene function prediction

Latent Dirichlet Allocation based on Gibbs Sampling for gene...

引用

ieee symposium on computational intelligence and bioinformatics and computational biology (CIBCB)

作者： Pietro Pinoli Davide Chicco Marco Masseroli Politecnico di Milano Milano Lombardia IT University High School Irvine CA US

Gene function annotations are key elements in biology and bioinformatics. A typical annotation is the association between a gene and a feature term that describes a functional feature of the gene by using a controlled vocabulary term (e.g. a Gene Ontology (GO) feature term). Unfortunately, available annotations contain errors and biologically validated ones are incomplete by definition, since new knowledge is continuously discovered. Thus, computational algorithms which are able to provide ranked lists of predicted new gene annotations are an excellent contribution to the bioinformatics research. Here, we propose two variants of the known Latent Dirichlet Allocation (LDA) algorithm applied to the prediction of gene annotations. LDA is a very efficient machine learning method built on a set of multinomial probability distributions over a set of topics, given a document (a gene, in our case), and on a set of multinomial probability distributions over a set of words (feature terms, in our case), given a topic. In topic modeling, a topic can be considered as a latent meta-category of words, and a document as a mixture of topics. Our two LDA variants use the collapsed Gibbs Sampling method during the training phase, with two distinct initialization approaches to adapt the LDA mathematical model to the biomolecular annotation scenario. Using six outdated datasets of GO annotations of human and brown rat genes, we compared the annotations predicted by our methods to the ones given by the truncated Singular Value Decomposition (tSVD) method previously developed; then, we validated them by using the annotations available in an updated version of the same datasets. Obtained results show the efficiency of our new proposed algorithms.

关键词： Probability distribution Prediction algorithms Vectors bioinformatics Semantics Resource management Ontologies

来源：评论

学校读者我要写书评

暂无评论

A Markov random field-based Bayesian model to identify genes with differential methylation

A Markov random field-based Bayesian model to identify genes...

引用

ieee symposium on computational intelligence and bioinformatics and computational biology (CIBCB)

作者： Xiao Wang Jinghua Gu Jianhua Xuan Robert Clarke Leena Hilakivi-Clarke Bradley Department of Electrical & Computer Engineering Virginia Tech Arlington VA USA Department of Oncology Georgetown University Medical Center Washington DC USA

The rapid development of biotechnology makes it possible to explore genome-wide DNA methylation mapping which has been demonstrated to be related to diseases including cancer. However, it also posts substantial challenges in identifying biologically meaningful methylation pattern changes. Several algorithms have been proposed to detect differential methylation events, such as differentially methylated CpG sites and differentially methylated regions. However, the intrinsic dependency of the CpG sites in a neighboring area has not yet been fully considered. In this paper, we propose a novel method for the identification of differentially methylated genes in a Markov random field-based Bayesian framework. Specifically, we use Markov random field to model the dependency of the neighboring CpG sites, and then estimate the differential methylation score of the CpG sites in a Bayesian framework through a sampling scheme. Finally, the differential methylation statuses of the genes are determined by the estimated scores of the involved CpG sites. In addition, significance test is conducted to assess the significance of the identified differentially methylated genes. Experimental results on both synthetic data and real data demonstrate the effectiveness of the proposed method in identifying genes with differential methylation patterns under different conditions.

关键词： Correlation DNA Manganese Data models Genomics bioinformatics Bayes methods

来源：评论

学校读者我要写书评

暂无评论

MetaPathways v2.0: A master-worker model for environmental Pathway/Genome Database construction on grids and clouds

MetaPathways v2.0: A master-worker model for environmental P...

引用

ieee symposium on computational intelligence and bioinformatics and computational biology (CIBCB)

作者： Niels W. Hanson Kishori M. Konwar Shang-Ju Wu Steven J. Hallam Graduate Program in Bioinformatics University of British Columbia Canada Department of Microbiology & Immunology University of British Columbia Canada

The development of high-throughput sequencing technologies over the past decade has generated a tidal wave of environmental sequence information from a variety of natural and human engineered ecosystems. The resulting flood of information into public databases and archived sequencing projects has exponentially expanded computational resource requirements rendering most local homology-based search methods inefficient. We recently introduced MetaPathways v1.0, a modular annotation and analysis pipeline for constructing environmental Pathway/Genome Databases (ePGDBs) from environmental sequence information capable of using the Sun Grid engine for external resource partitioning. However, a command-line interface and facile task management introduced user activation barriers with concomitant decrease in fault tolerance. Here we present MetaPathways v2.0 incorporating a graphical user interface (GUI) and refined task management methods. The MetaPathways GUI provides an intuitive display for setup and process monitoring and supports interactive data visualization and sub-setting via a custom Knowledge Engine data structure. A master-worker model is adopted for task management allowing users to scavenge computational results from a number of worker grids in an ad hoc, asynchronous, distributed network that dramatically increases fault tolerance. This model facilitates the use of EC2 instances extending ePGDB construction to the Amazon Elastic Cloud.

关键词： Engines Databases Data structures Graphical user interfaces Monitoring computational modeling Pipelines

来源：评论

学校读者我要写书评

暂无评论

SuperPhy A Pilot Resource for Integrated Phylogenetic and Epidemiological Analysis of Pathogens

SuperPhy <i>A Pilot Resource for Integrated Phylogenetic and...

引用

5th International Conference on bioinformatics Models, Methods and Algorithms (bioinformatics) is part of 7th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC)

作者： Whiteside, Matthew D. Laing, Chad R. Manji, Akiff Gannon, Victor P. J. Publ Hlth Agcy Canada Lab Foodborne Zoonoses Lethbridge AB Canada

ISBN: (纸本)9789897580123

Advances in DNA sequencing technology have created new opportunities in fields such as clinical medicine and epidemiology, where performing real-time, genome-based surveillance and identification of phenotypic characteristics of bacterial pathogens is now possible. New analytical tools and infrastructure are needed to analyze these genomic datasets, store the data, and provide the essential biological information to end-users. We have implemented an online whole-genome analyses platform called SuperPhy that uses Panseq as an engine to compare bacterial genomes, the Fisher's exact test to identify sub-group specific loci, and FastTree to create maximum-likelihood trees. SuperPhy facilitates the upload of genomes for both private and public use. Analyses include: 1) genomic comparisons of clinical isolates, and identification of virulence and antimicrobial resistance genes in silico, 2) associations between specific genotypes and phenotypic meta-data (e. g., geospatial distribution, host, source);3) identification of group-specific genome markers (presence/absence of specific genomic regions, and single-nucleotide polymorphisms) in bacterial populations;4) the ability to manipulate the display of phylogenetic trees;5) identify statistically significant clade-specific markers. The SuperPhy pilot database currently contains genome sequences for 1063 Escherichia coli strains. Future work will extend SuperPhy to include multiple pathogens.

关键词： bioinformatics computational biology Population Genomics Epidemiology Phylogeny Bacterial Pathogenesis

来源：评论

学校读者我要写书评

暂无评论

computational identification of De-centric genetic regulatory relationships from functional genomic data

Computational identification of De-centric genetic regulator...

引用

10th International symposium on bioinformatics Research and Applications, ISBRA 2014

作者： Yue, Zongliang Wan, Ping Xie, Zhan Chen, Jake Y. Institute of Biopharmaceutical Informatics and Technology Wenzhou Medical University Wenzhou Zhejiang Province China School of Informatics and Computing Indiana University Indianapolis IN 46202 United States Indiana Center for Systems Biology and Personalized Medicine Indiana University Indianapolis IN 46202 United States Bioinformatics Lab Capital Normal University Beijing China

ISBN: (纸本)9783319081700

We developed a new computational technique to identify de-centric genetic regulatory relationship candidates. Our technique takes advantages of functional genomics data for the same species under different perturbation conditions, therefore making it complementary to current computational techniques including database search, clustering of gene expression profiles, motif matching, structural modeling, and network effect simulation methods. It is fast and addressed the need of biologists to determine activation/inhibition relationship details often missing in synthetic lethality or chip-seq experiments. We used GEO microarray data set GSE25644 with 158 different mutant genes in S. cerevisiae. We screened out 83 targets with 610 activation pairs and 93 targets with 494 inhibition pairs. In the Yeast Fitness database, 33 targets (40%) with 126 activation pairs and 31 targets (33%) with 97 inhibition pairs were identified. To be identified further are 50 targets with 484 activation pairs and 62 targets with 397 inhibition pairs. The aggregation test confirmed that all discovered de-centric regulatory relationships are significant from random discovery at a p-value=0.002;therefore, this method is highly complementary to others that tend to discover hub-related regulatory relationships. We also developed criteria for rejecting genetic regulator candidates x as a candidate regulator and assessing the ranking of the regulator-target relationship identified. The top 10 high suspected regulators determined by our criteria were found to be significant, pending future experimental verifications. © 2014 Springer International Publishing Switzerland.

关键词： Yeast

来源：评论

学校读者我要写书评

暂无评论

Randomized communication complexity of approximating kolmogorov complexity

Randomized communication complexity of approximating kolmogo...

引用

9th International Computer Science symposium in Russia, CSR 2014

作者： Vereshchagin, Nikolay Higher School of Economics Moscow State University Yandex Russia

ISBN: (纸本)9783319066851

The paper [Harry Buhrman, Michal Koucký, Nikolay Vereshchagin. Randomized Individual Communication Complexity. ieee Conference on computational Complexity 2008: 321-331] considered communication complexity of the following problem. Alice has a binary string x and Bob a binary string y, both of length n, and they want to compute or approximate Kolmogorov complexity C(x|y) of x conditional to y. It is easy to show that deterministic communication complexity of approximating C(x|y) with additive error α is at least n∈-∈2α∈-∈O(1). The above referenced paper asks what is randomized communication complexity of this problem and shows that for r-round randomized protocols its communication complexity is at least Ω((n/α)1/r ). In this paper, for some positive Ε, we show the lower bound 0.99n for (worst case) communication length of any randomized protocol that with probability at least 0.01 approximates C(x|y) with additive error Εn for all input pairs. © 2014 Springer International Publishing Switzerland.

关键词： computational complexity

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：