Model selection based on FDR-thresholding optimizing the area under the ROC-curve.

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：: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：:Germline mosaicism is a genetic condition in which some germ cells of an individual contain a mutation. This condition violates the assumptions underlying classic genetic analysis and may lead to failure of such analysis. In this work we extend the statistical model used for genetic linkage analysis in order to incorp...

journal_title：Statistical applications in genetics and molecular biology

authors： Weissbrod O,Geiger D

更新日期：2011-10-04 00:00:00

abstract：:Unraveling interactions among variables such as genetic, clinical, demographic and environmental factors is essential to understand the development of common and complex diseases. To increase the power to detect such variables interactions associated with clinical time-to-events outcomes, we borrowed established conce...

journal_title：Statistical applications in genetics and molecular biology

authors： Dazard JE,Ishwaran H,Mehlotra R,Weinberg A,Zimmerman P

更新日期：2018-02-17 00:00:00

abstract：:The genetic control of a complex trait can be studied by testing and mapping the genotypes of the underlying quantitative trait loci (QTLs) through their associations with observable marker genotypes. All existing statistical methods for QTL mapping assume an equilibrium population, allowing marker-QTL associations to...

journal_title：Statistical applications in genetics and molecular biology

authors： Wu S,Yang J,Wu R

更新日期：2010-01-01 00:00:00

abstract：:Multiple branching trees have been used to model the acquisition of HIV drug resistance mutations, and several different algorithms have been developed to construct the tree set that best describes the data. These algorithms have mainly focused on the structure of the tree set. The focal point of this paper is estimat...

journal_title：Statistical applications in genetics and molecular biology

authors： Healy BC,DeGruttola VG,Hu C

更新日期：2008-01-01 00:00:00

abstract：:Various discriminant methods have been applied for classification of tumors based on gene expression profiles, among which the nearest neighbor (NN) method has been reported to perform relatively well. Usually cross-validation (CV) is used to select the neighbor size as well as the number of variables for the NN metho...

journal_title：Statistical applications in genetics and molecular biology

authors： Paik M,Yang Y

更新日期：2004-01-01 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：:In this paper, we explore the use of M-quantile regression and M-quantile coefficients to detect statistical differences between temporal curves that belong to different experimental conditions. In particular, we consider the application of temporal gene expression data. Here, the aim is to detect genes whose temporal...

journal_title：Statistical applications in genetics and molecular biology

authors： Vinciotti V,Yu K

更新日期：2009-01-01 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：: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：: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：:Multi-color optical mapping is a new technique being developed to obtain detailed physical maps (indicating relative positions of various recognition sites) of DNA molecules. We consider a study design in which the data consist of noisy observations of multiple copies of a DNA molecule marked with colors at recognitio...

journal_title：Statistical applications in genetics and molecular biology

authors： Tong L,Mets L,McPeek MS

更新日期：2007-01-01 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：: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

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：: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：:Gene microarray technology is often used to compare the expression of thousand of genes in two different cell lines. Typically, one does not expect measurable changes in transcription amounts for a large number of genes; furthermore, the noise level of array experiments is rather high in relation to the available numb...

journal_title：Statistical applications in genetics and molecular biology

authors： Erickson S,Sabatti C

更新日期：2005-01-01 00:00:00

abstract：:In cellular biology, node-and-edge graph or "network" data collection often uses bait-prey technologies such as co-immunoprecipitation (CoIP). Bait-prey technologies assay relationships or "interactions" between protein pairs, with CoIP specifically measuring protein complex co-membership. Analyses of CoIP data freque...

journal_title：Statistical applications in genetics and molecular biology

authors： Scholtens DM,Spencer BD

更新日期：2015-08-01 00:00:00

abstract：:The ENCODE project has funded the generation of a diverse collection of methylation profiles using reduced representation bisulfite sequencing (RRBS) technology, enabling the analysis of epigenetic variation on a genomic scale at single-site resolution. A standard application of RRBS experiments is in the location of ...

journal_title：Statistical applications in genetics and molecular biology

authors： Lacey MR,Baribault C,Ehrlich M

更新日期：2013-12-01 00:00:00

abstract：:Longitudinal genomics data and survival outcome are common in biomedical studies, where the genomics data are often of high dimension. It is of great interest to select informative longitudinal biomarkers (e.g. genes) related to the survival outcome. In this paper, we develop a computationally efficient tool, LCox, fo...

journal_title：Statistical applications in genetics and molecular biology

authors： Sun J,Herazo-Maya JD,Wang JL,Kaminski N,Zhao H

更新日期：2019-02-13 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 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：:Polytomous phenotypes arise when a disease has multiple subtypes or when two dichotomous phenotypes are analyzed simultaneously. Few software programs offer the option to analyze such phenotypes in family studies, and none implements conditional polytomous logistic regression for within-family analysis robust to popul...

journal_title：Statistical applications in genetics and molecular biology

authors： Bureau A,Croteau J

更新日期：2017-03-01 00:00:00

abstract：:Likelihood-based cross-validation is a statistical tool for selecting a density estimate based on n i.i.d. observations from the true density among a collection of candidate density estimators. General examples are the selection of a model indexing a maximum likelihood estimator, and the selection of a bandwidth index...

journal_title：Statistical applications in genetics and molecular biology

authors： van der Laan MJ,Dudoit S,Keles S

更新日期：2004-01-01 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：: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：: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：:In this study, we propose a novel statistical framework for detecting progressive changes in molecular traits as response to a pathogenic stimulus. In particular, we propose to employ Bayesian hierarchical models to analyse changes in mean level, variance and correlation of metabolic traits in relation to covariates. ...

journal_title：Statistical applications in genetics and molecular biology

authors： Salamanca BV,Ebbels TM,Iorio MD

更新日期：2014-04-01 00:00:00