Related papers: Assessing Technical Performance in Differential Ge…
In precision medicine, Dynamic Treatment Regimes (DTRs) are treatment protocols that adapt over time in response to a patient's observed characteristics. A DTR is a set of decision functions that takes an individual patient's information as…
Experimental comparisons of performance represent an important aspect of research on optimization algorithms. In this work we present a methodology for defining the required sample sizes for designing experiments with desired statistical…
Motivated by differential co-expression analysis in genomics, we consider in this paper estimation and testing of high-dimensional differential correlation matrices. An adaptive thresholding procedure is introduced and theoretical…
Gene regulation involves a hierarchy of events that extend from specific protein-DNA interactions to the combinatorial assembly of nucleoprotein complexes. The effects of DNA sequence on these processes have typically been studied based…
The intrinsic stochasticity of gene expression can lead to large variability in protein levels for genetically identical cells. Such variability in protein levels can arise from infrequent synthesis of mRNAs which in turn give rise to…
To adapt kernel two-sample and independence testing to complex structured data, aggregation of multiple kernels is frequently employed to boost testing power compared to single-kernel tests. However, we observe a phenomenon that directly…
Addressing the reproducibility crisis in artificial intelligence through the validation of reported experimental results is a challenging task. It necessitates either the reimplementation of techniques or a meticulous assessment of papers…
RNA-Seq data characteristically exhibits large variances, which need to be appropriately accounted for in the model. We first explore the effects of this variability on the maximum likelihood estimator (MLE) of the overdispersion parameter…
In medical device comparison studies, equivalency test is commonly used to demonstrate two measurement methods agree up to a pre-specified performance goal based on the paired repeated measures. Such equivalency test often involves…
In the last years, tens of thousands gene expression profiles for cells of several organisms have been monitored. Gene expression is a complex transcriptional process where mRNA molecules are translated into proteins, which control most of…
Modern cell-perturbation experiments expose cells to panels of hundreds of stimuli, such as cytokines or CRISPR guides that perform gene knockouts. These experiments are designed to investigate whether a particular gene is upregulated or…
Identifying differentially expressed genes from RNA sequencing data remains a challenging task because of the considerable uncertainties in parameter estimation and the small sample sizes in typical applications. Here we introduce Bayesian…
Motivation: Alternative splicing is an important mechanism in which the regions of pre-mRNAs are differentially joined in order to form different transcript isoforms. Alternative splicing is involved in the regulation of normal…
Microarray is a technology to quantitatively monitor the expression of large number of genes in parallel. It has become one of the main tools for global gene expression analysis in molecular biology research in recent years. The large…
The present study investigates the performance of several statistical tests to detect publication bias in diagnostic meta-analysis by means of simulation. While bivariate models should be used to pool data from primary studies in diagnostic…
Transcription of genes is the focus of most forms of regulation of gene expression. Even though careful biochemical experimentation has revealed the molecular mechanisms of transcription initiation for a number of different promoters in…
Accurate diagnostic tests are essential for effective screening and treatment. However, individual biomarkers often fail to provide sufficient diagnostic accuracy, as they typically capture only one aspect of the complex disease process.…
In this review, we present an overview of the main aspects related to the statistical evaluation of medical tests for diagnosis and prognosis. Measures of diagnostic performance for binary tests, such as sensitivity, specificity, and…
The notion of experiment precision quantifies the variance of user ratings in a subjective experiment. Although there exist measures that assess subjective experiment precision, there are no systematic analyses of these measures available…
Biomedical studies that use electronic health records (EHR) data for inference are often subject to bias due to measurement error. The measurement error present in EHR data is typically complex, consisting of errors of unknown functional…