Addressing the shortcomings of three recent Bayesian methods for detecting interspecific recombination in DNA sequence alignments.

abstract：:Accurately measuring epigenetic marks such as 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) at the single-nucleotide level, requires combining data from DNA processing methods including traditional (BS), oxidative (oxBS) or Tet-Assisted (TAB) bisulfite conversion. We introduce the R package MLML2R, which...

journal_title：Statistical applications in genetics and molecular biology

authors： Kiihl SF,Martinez-Garrido MJ,Domingo-Relloso A,Bermudez J,Tellez-Plaza M

更新日期：2019-01-17 00:00:00

abstract：:Mass spectrometry is an important high-throughput technique for profiling small molecular compounds in biological samples and is widely used to identify potential diagnostic and prognostic compounds associated with disease. Commonly, this data generated by mass spectrometry has many missing values resulting when a com...

journal_title：Statistical applications in genetics and molecular biology

authors： Taylor SL,Leiserowitz GS,Kim K

更新日期：2013-12-01 00:00:00

abstract：:In recent years, alignment-free methods have been widely applied in comparing genome sequences, as these methods compute efficiently and provide desirable phylogenetic analysis results. These methods have been successfully combined with hierarchical clustering methods for finding phylogenetic trees. However, it may no...

journal_title：Statistical applications in genetics and molecular biology

authors： Huang HH,Girimurugan SB

更新日期：2019-02-15 00:00:00

abstract：:The objective of the present paper is to develop a truly functional Bayesian method specifically designed for time series microarray data. The method allows one to identify differentially expressed genes in a time-course microarray experiment, to rank them and to estimate their expression profiles. Each gene expressio...

journal_title：Statistical applications in genetics and molecular biology

authors： Angelini C,De Canditiis D,Mutarelli M,Pensky M

更新日期：2007-01-01 00:00:00

abstract：:In the exploding field of gene expression techniques such as DNA microarrays, there are still few general probabilistic methods for analysis of variance. Linear models and ANOVA are heavily used tools in many other disciplines of scientific research. The usual F-statistic is unsatisfactory for microarray data, which e...

journal_title：Statistical applications in genetics and molecular biology

authors： Lönnstedt I,Rimini R,Nilsson P

更新日期：2005-01-01 00:00:00

abstract：:An important application of gene expression microarray data is classification of biological samples or prediction of clinical and other outcomes. One necessary part of multivariate statistical analysis in such applications is dimension reduction. This paper provides a comparison study of three dimension reduction tech...

journal_title：Statistical applications in genetics and molecular biology

authors： Dai JJ,Lieu L,Rocke D

更新日期：2006-01-01 00:00:00

abstract：:Output from analysis of a high-throughput 'omics' experiment very often is a ranked list. One commonly encountered example is a ranked list of differentially expressed genes from a gene expression experiment, with a length of many hundreds of genes. There are numerous situations where interest is in the comparison of ...

journal_title：Statistical applications in genetics and molecular biology

authors： Donald MR,Wilson SR

更新日期：2017-03-01 00:00:00

abstract：:Recent analytic and technological breakthroughs have set the stage for genome-wide linkage disequilibrium studies to map disease-susceptibility variants. This paper discusses a probabilistic methodology for making disease-mapping inferences in large-scale case-control genetic studies. The semi-Bayesian approach promot...

journal_title：Statistical applications in genetics and molecular biology

authors： Schrodi SJ

更新日期：2005-01-01 00:00:00

abstract：:We present an approach to association studies involving a dozen or so ;response' variables and a few hundred ;explanatory' variables which emphasizes transparency, simplicity, and protection against spurious results. The methods proposed are largely non-parametric, and they are systematically rounded-off by the Benjam...

journal_title：Statistical applications in genetics and molecular biology

authors： Ferreira JA,Berkhof J,Souverein O,Zwinderman K

更新日期：2009-01-01 00:00:00

abstract：:We present a Bayesian hierarchical model for detecting differentially expressed genes using a mixture prior on the parameters representing differential effects. We formulate an easily interpretable 3-component mixture to classify genes as over-expressed, under-expressed and non-differentially expressed, and model gene...

journal_title：Statistical applications in genetics and molecular biology

authors： Lewin A,Bochkina N,Richardson S

更新日期：2007-01-01 00:00:00

abstract：:Consider the standard multiple testing problem where many hypotheses are to be tested, each hypothesis is associated with a test statistic, and large test statistics provide evidence against the null hypotheses. One proposal to provide probabilistic control of Type-I errors is the use of procedures ensuring that the e...

journal_title：Statistical applications in genetics and molecular biology

authors： Rubin D,Dudoit S,van der Laan M

更新日期：2006-01-01 00:00:00

abstract：:Multiple testing procedures are commonly used in gene expression studies for the detection of differential expression, where typically thousands of genes are measured over at least two experimental conditions. Given the need for powerful testing procedures, and the attendant danger of false positives in multiple testi...

journal_title：Statistical applications in genetics and molecular biology

authors： Green GH,Diggle PJ

更新日期：2007-01-01 00:00:00

abstract：:In this paper, we address the problem of detecting outlier samples with highly different expression patterns in microarray data. Although outliers are not common, they appear even in widely used benchmark data sets and can negatively affect microarray data analysis. It is important to identify outliers in order to exp...

journal_title：Statistical applications in genetics and molecular biology

authors： Shieh AD,Hung YS

更新日期：2009-01-01 00:00:00

abstract：:Several important syndromes are caused by deleterious germline mutations of individual genes. In both clinical and research applications it is useful to evaluate the probability that an individual carries an inherited genetic variant of these genes, and to predict the risk of disease for that individual, using informa...

journal_title：Statistical applications in genetics and molecular biology

authors： Chen S,Wang W,Broman KW,Katki HA,Parmigiani G

更新日期：2004-01-01 00:00:00

abstract：:Approaches based upon sequence weights, to construct a position weight matrix of nucleotides from aligned inputs, are popular but little effort has been expended to measure their quality. We derive optimal sequence weights that minimize the sum of the variances of the estimators of base frequency parameters for sequen...

journal_title：Statistical applications in genetics and molecular biology

authors： Newberg LA,McCue LA,Lawrence CE

更新日期：2005-01-01 00:00:00

abstract：:Certain residues have no known function yet are co-conserved across distantly related protein families and diverse organisms, suggesting that they perform critical roles associated with as-yet-unidentified molecular properties and mechanisms. This raises the question of how to obtain additional clues regarding these m...

journal_title：Statistical applications in genetics and molecular biology

authors： Neuwald AF

更新日期：2011-01-01 00:00:00

abstract：:Combining correlated p-values from multiple hypothesis testing is a most frequently used method for integrating information in genetic and genomic data analysis. However, most existing methods for combining independent p-values from individual component problems into a single unified p-value are unsuitable for the cor...

journal_title：Statistical applications in genetics and molecular biology

authors： Chien LC

更新日期：2020-11-06 00:00:00

abstract：:Reproducibility of disease signatures and clinical biomarkers in multi-omics disease analysis has been a key challenge due to a multitude of factors. The heterogeneity of the limited sample, various biological factors such as environmental confounders, and the inherent experimental and technical noises, compounded wit...

journal_title：Statistical applications in genetics and molecular biology

authors： Liang Y,Kelemen A,Kelemen A

更新日期：2019-05-11 00:00:00

abstract：:The problem of finding periodically expressed genes from time course microarray experiments is at the center of numerous efforts to identify the molecular components of biological clocks. We present a new approach to this problem based on the cyclohedron test, which is a rank test inspired by recent advances in algebr...

journal_title：Statistical applications in genetics and molecular biology

authors： Morton J,Pachter L,Shiu A,Sturmfels B

更新日期：2007-01-01 00:00:00

abstract：:We develop an approach for microarray differential expression analysis, i.e. identifying genes whose expression levels differ between two or more groups. Current approaches to inference rely either on full parametric assumptions or on permutation-based techniques for sampling under the null distribution. In some situa...

journal_title：Statistical applications in genetics and molecular biology

authors： Rossell D,Guerra R,Scott C

更新日期：2008-01-01 00:00:00

abstract：:In candidate gene association studies, usually several elementary hypotheses are tested simultaneously using one particular set of data. The data normally consist of partly correlated SNP information. Every SNP can be tested for association with the disease, e.g., using the Cochran-Armitage test for trend. To account ...

journal_title：Statistical applications in genetics and molecular biology

authors： Elsäβer A,Victor A,Hommel G

更新日期：2011-01-01 00:00:00

abstract：:With the increasing availability of experimental data on gene interactions, modeling of gene regulatory pathways has gained special attention. Gradient descent algorithms have been widely used for regression and classification applications. Unfortunately, results obtained after training a model by gradient descent are...

journal_title：Statistical applications in genetics and molecular biology

authors： Das M,Murthy CA,De RK

更新日期：2014-02-01 00:00:00

abstract：:Locus heterogeneity is one of the most important issues in gene mapping and can cause significant reductions in statistical power for gene mapping, yet no research to date has provided power and sample size calculations for family-based association methods in the presence of locus heterogeneity. The purpose of this re...

journal_title：Statistical applications in genetics and molecular biology

authors： Chen C,Yang G,Buyske S,Matise T,Finch SJ,Gordon D

更新日期：2009-01-01 00:00:00

abstract：:The approach adopted involved two-stages. First the 11205 measurements in the mass spectrometry data were reduced to 14 scores by a principal component analysis of the centered but otherwise untreated and unscaled data matrix. Then a linear classifier was derived by linear discriminant analysis using these 14 scores a...

journal_title：Statistical applications in genetics and molecular biology

authors： Fearn T

更新日期：2008-01-01 00:00:00

abstract：:Integrative analysis of copy number and gene expression data can help in understanding the cis and trans effect of copy number aberrations on transcription levels of genes involved in a pathway. To analyse how these copy number mediated gene-gene interactions differ between groups of samples we propose a new method, n...

journal_title：Statistical applications in genetics and molecular biology

authors： Chaturvedi N,Menezes RX,Goeman JJ,Wieringen WV

更新日期：2018-07-31 00:00:00

abstract：:High-throughput sequencing techniques are increasingly affordable and produce massive amounts of data. Together with other high-throughput technologies, such as microarrays, there are an enormous amount of resources in databases. The collection of these valuable data has been routine for more than a decade. Despite di...

journal_title：Statistical applications in genetics and molecular biology

authors： Schimek MG,Budinská E,Kugler KG,Švendová V,Ding J,Lin S

更新日期：2015-06-01 00:00:00

abstract：:In many population genetic problems, parameter estimation is obstructed by an intractable likelihood function. Therefore, approximate estimation methods have been developed, and with growing computational power, sampling-based methods became popular. However, these methods such as Approximate Bayesian Computation (ABC...

journal_title：Statistical applications in genetics and molecular biology

authors： Bertl J,Ewing G,Kosiol C,Futschik A

更新日期：2017-11-27 00:00:00

abstract：:Making sound proteomic inferences using ELISA microarray assay requires both an accurate prediction of protein concentration and a credible estimate of its error. We present a method using monotonic spline statistical models (MS), penalized constrained least squares fitting (PCLS) and Monte Carlo simulation (MC) to pr...

journal_title：Statistical applications in genetics and molecular biology

authors： Daly DS,Anderson KK,White AM,Gonzalez RM,Varnum SM,Zangar RC

更新日期：2008-01-01 00:00:00

abstract：:There has been increasing interest in predicting patients' survival after therapy by investigating gene expression microarray data. In the regression and classification models with high-dimensional genomic data, boosting has been successfully applied to build accurate predictive models and conduct variable selection s...

journal_title：Statistical applications in genetics and molecular biology

authors： Wang Z,Wang CY

更新日期：2010-01-01 00:00:00

abstract：:Many gene- and pathway-based association tests have been proposed in the literature. Among them, the SKAT is widely used, especially for rare variants association studies. In this paper, we investigate the connection between SKAT and a principal component analysis. This investigation leads to a procedure that encompas...

journal_title：Statistical applications in genetics and molecular biology

authors： Chen Z,Han S,Wang K

更新日期：2017-07-26 00:00:00