Accommodating uncertainty in a tree set for function estimation.

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：: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：: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：: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：: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：: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：: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：: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：: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：: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 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：: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：: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：:We present a weighted-LASSO method to infer the parameters of a first-order vector auto-regressive model that describes time course expression data generated by directed gene-to-gene regulation networks. These networks are assumed to own prior internal structures of connectivity which drive the inference method. This ...

journal_title：Statistical applications in genetics and molecular biology

authors： Charbonnier C,Chiquet J,Ambroise C

更新日期：2010-01-01 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：: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：: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：: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：: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：:Usually, a pedigree is sampled and included in the sample that is analyzed after following a predefined non-random sampling design comprising several specific procedures. To obtain a pedigree analysis result free from the bias caused by the sampling procedures, a correction is applied to the pedigree likelihood. The s...

journal_title：Statistical applications in genetics and molecular biology

authors： Ginsburg E,Malkin I,Elston RC

更新日期：2003-01-01 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：: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：: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 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：: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：: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：: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：: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：: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