Sparse inverse of covariance matrix of QTL effects with incomplete marker data.

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：: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：: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：: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：: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：:We evaluate variable selection by multiple tests controlling the false discovery rate (FDR) to build a linear score for prediction of clinical outcome in high-dimensional data. Quality of prediction is assessed by the receiver operating characteristic curve (ROC) for prediction in independent patients. Thus we try to ...

journal_title：Statistical applications in genetics and molecular biology

authors： Graf AC,Bauer P

更新日期：2009-01-01 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：: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：: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：: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：: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：: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 a hidden Markov model, one "estimates" the state of the hidden Markov chain at t by computing via the forwards-backwards algorithm the conditional distribution of the state vector given the observed data. The covariance matrix of this conditional distribution measures the information lost by failure to observe dire...

journal_title：Statistical applications in genetics and molecular biology

authors： Siegmund DO,Yakir B

更新日期：2007-01-01 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：: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：: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：: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：: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 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：: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

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：:The Dirichlet Process (DP) mixture model has become a popular choice for model-based clustering, largely because it allows the number of clusters to be inferred. The sequential updating and greedy search (SUGS) algorithm (Wang & Dunson, 2011) was proposed as a fast method for performing approximate Bayesian inference ...

journal_title：Statistical applications in genetics and molecular biology

authors： Crook OM,Gatto L,Kirk PDW

更新日期：2019-12-12 00:00:00

abstract：:We address a potential shortcoming of three probabilistic models for detecting interspecific recombination in DNA sequence alignments: the multiple change-point model (MCP) of Suchard et al. (2003), the dual multiple change-point model (DMCP) of Minin et al. (2005), and the phylogenetic factorial hidden Markov model (...

journal_title：Statistical applications in genetics and molecular biology

authors： Husmeier D,Mantzaris AV

更新日期：2008-01-01 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：: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：: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：: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：: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：: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：: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