Oxford Index Search Results

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Bayes x Bioinformatics and Computational Biology x clear all

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Overview page. Subjects: Architecture.

[Ge]

Structural division in the length of a building or roof. The unit within a building between a pair of piers or buttresses; the division of a roof marked by its main trusses.

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MrBayes on a Graphics Processing Unit

Jianfu Zhou, Xiaoguang Liu, Douglas S. Stones, Qiang Xie and Gang Wang.

in Bioinformatics

May 2011; p ublished online March 2011 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 4488 words.

Motivation: Bayesian phylogenetic inference can be used to propose a ‘tree of life’ for a collection of species whose DNA sequences are known. While there are many packages...

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How Bayes tests of molecular phylogenies compare with frequentist approaches

Stéphane Aris-Brosou.

in Bioinformatics

March 2003; p ublished online March 2003 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 0 words.

Motivation: The desire to compare molecular phylogenies has stimulated the design of numerous tests. Most of these tests are formulated in a frequentist framework, and it is not known how...

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Corrected small-sample estimation of the Bayes error

Marcel Brun, David Sabbagh, Seungchan Kim and Edward R. Dougherty.

in Bioinformatics

May 2003; p ublished online May 2003 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 0 words.

Motivation: A major problem of pattern classification is estimation of the Bayes error when only small samples are available. One way to estimate the Bayes error is to design a classifier...

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MrBayes 3: Bayesian phylogenetic inference under mixed models

Fredrik Ronquist and John P. Huelsenbeck.

in Bioinformatics

August 2003; p ublished online August 2003 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 0 words.

Summary: MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This...

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Empirical Bayes conditional independence graphs for regulatory network recovery

Rami Mahdi, Abishek S. Madduri, Guoqing Wang, Yael Strulovici-Barel, Jacqueline Salit, Neil R. Hackett, Ronald G. Crystal and Jason G. Mezey.

in Bioinformatics

August 2012; p ublished online June 2012 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 6287 words.

Motivation: Computational inference methods that make use of graphical models to extract regulatory networks from gene expression data can have difficulty reconstructing dense...

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SlidingBayes: exploring recombination using a sliding window approach based on Bayesian phylogenetic inference

D. Paraskevis, K. Deforche, P. Lemey, G. Magiorkinis, A. Hatzakis and A.-M. Vandamme.

in Bioinformatics

April 2005; p ublished online November 2004 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 1620 words.

Summary: We developed a software tool (SlidingBayes) for recombination analysis based on Bayesian phylogenetic inference. Sliding-Bayes provides a powerful approach for...

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PurBayes: estimating tumor cellularity and subclonality in next-generation sequencing data

Nicholas B. Larson and Brooke L. Fridley.

in Bioinformatics

August 2013; p ublished online June 2013 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 1417 words.

Summary: We have developed a novel Bayesian method, PurBayes, to estimate tumor purity and detect intratumor heterogeneity based on next-generation sequencing data of paired...

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BayesPeak—an R package for analysing ChIP-seq data

Jonathan Cairns, Christiana Spyrou, Rory Stark, Mike L. Smith, Andy G. Lynch and Simon Tavaré.

in Bioinformatics

March 2011; p ublished online January 2011 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 1559 words.

Motivation: Identification of genomic regions of interest in ChIP-seq data, commonly referred to as peak-calling, aims to find the locations of transcription factor binding...

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BioBayes: A software package for Bayesian inference in systems biology

Vladislav Vyshemirsky and Mark Girolami.

in Bioinformatics

September 2008; p ublished online July 2008 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 1495 words.

Motivation: There are several levels of uncertainty involved in the mathematical modelling of biochemical systems. There often may be a degree of uncertainty about the values...

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PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

Nicolas Lartillot, Thomas Lepage and Samuel Blanquart.

in Bioinformatics

September 2009; p ublished online June 2009 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 1924 words.

Motivation: A variety of probabilistic models describing the evolution of DNA or protein sequences have been proposed for phylogenetic reconstruction or for molecular dating....

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DivBayes and SubT: exploring species diversification using Bayesian statistics

Martin Ryberg, R. Henrik Nilsson and P. Brandon Matheny.

in Bioinformatics

September 2011; p ublished online July 2011 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 1256 words.

Summary: DivBayes is a program to estimate diversification rates from species richness and ages of a set of clades. SubT estimates diversification rates from node heights...

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BayesPI-BAR: a new biophysical model for characterization of regulatory sequence variations

Junbai Wang and Kirill Batmanov.

in Nucleic Acids Research

December 2015; p ublished online July 2015 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 9066 words.

Sequence variations in regulatory DNA regions are known to cause functionally important consequences for gene expression. DNA sequence variations may have an essential role in determining...

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An empirical bayes adjustment to increase the sensitivity of detecting differentially expressed genes in microarray experiments

Susmita Datta, Glen A. Satten, Dale J. Benos, Jiazeng Xia, Martin J. Heslin and Somnath Datta.

in Bioinformatics

January 2004; p ublished online January 2004 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 0 words.

Motivation: Detection of differentially expressed genes is one of the major goals of microarray experiments. Pairwise comparison for each gene is not appropriate without...

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Combining multi-species genomic data for microRNA identification using a Naïve Bayes classifier

Malik Yousef, Michael Nebozhyn, Hagit Shatkay, Stathis Kanterakis, Louise C. Showe and Michael K. Showe.

in Bioinformatics

June 2006; p ublished online March 2006 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 6336 words.

Motivation: Most computational methodologies for microRNA gene prediction utilize techniques based on sequence conservation and/or structural similarity. In this study we...

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GO-Bayes: Gene Ontology-based overrepresentation analysis using a Bayesian approach

Song Zhang, Jing Cao, Y. Megan Kong and Richard H. Scheuermann.

in Bioinformatics

April 2010; p ublished online February 2010 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 5826 words.

Motivation: A typical approach for the interpretation of high-throughput experiments, such as gene expression microarrays, is to produce groups of genes based on certain...

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NBC: the Naïve Bayes Classification tool webserver for taxonomic classification of metagenomic reads

Gail L. Rosen, Erin R. Reichenberger and Aaron M. Rosenfeld.

in Bioinformatics

January 2011; p ublished online November 2010 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 1549 words.

Motivation: Datasets from high-throughput sequencing technologies have yielded a vast amount of data about organisms in environmental samples. Yet, it is still a challenge to...

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Empirical Bayes screening of many p-values with applications to microarray studies

Susmita Datta and Somnath Datta.

in Bioinformatics

May 2005; p ublished online February 2005 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 7086 words.

Motivation: Statistical tests for the detection of differentially expressed genes lead to a large collection of p-values one for each gene comparison. Without any further...

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Site-heterogeneous mutation-selection models within the PhyloBayes-MPI package

Nicolas Rodrigue and Nicolas Lartillot.

in Bioinformatics

April 2014; p ublished online December 2013 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 1225 words.

Motivation: In recent years, there has been an increasing interest in the potential of codon substitution models for a variety of applications. However, the computational...

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Accurate identification of polyadenylation sites from 3′ end deep sequencing using a naïve Bayes classifier

Sarah Sheppard, Nathan D. Lawson and Lihua Julie Zhu.

in Bioinformatics

October 2013; p ublished online August 2013 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 6315 words.

Motivation: 3′ end processing is important for transcription termination, mRNA stability and regulation of gene expression. To identify 3′ ends, most techniques use an oligo-dT...

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Naïve Bayes for microRNA target predictions—machine learning for microRNA targets

Malik Yousef, Segun Jung, Andrew V. Kossenkov, Louise C. Showe and Michael K. Showe.

in Bioinformatics

November 2007; p ublished online October 2007 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 4762 words.

Motivation: Most computational methodologies for miRNA:mRNA target gene prediction use the seed segment of the miRNA and require cross-species sequence conservation in this...

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