相关论文: Estimating the proportion of differentially expres…

We consider cDNA microarray experiments when the cell populations have a factorial structure, and investigate the problem of their optimal designing under a baseline parametrization where the objects of interest differ from those under the…

In this paper we describe a new technique for the comparison of populations of DNA strands. Comparison is vital to the study of ecological systems, at both the micro and macro scales. Existing methods make use of DNA sequencing and cloning,…

This commentary discusses a recently proposed measure of heterogeneity of DNA sequences and compares with the measures of complexity.

Gene regulation in eukaryotes is mainly effected through transcription factors binding to rather short recognition motifs generally located upstream of the coding region. We present a novel computational method to identify regulatory…

Motivation: Bulk RNA-Seq is a widely used method for studying gene expression across a variety of contexts. The significance of RNA-Seq studies has grown with the advent of high-throughput sequencing technologies. Computational methods have…

Many genomic experiments, notably microarray experiments seeking to detect differential gene expression, involve calculating a large number of p-values. This leads to the multiple testing problem: when the number of null hypotheses is…

This study proposes a data condensation method for multivariate kernel density estimation by genetic algorithm. First, our proposed algorithm generates multiple subsamples of a given size with replacement from the original sample. The…

The application of deep learning methods, particularly foundation models, in biological research has surged in recent years. These models can be text-based or trained on underlying biological data, especially omics data of various types.…

RNA-seq has become a de facto standard for measuring gene expression. Traditionally, RNA-seq experiments are mathematically averaged -- they sequence the mRNA of individuals from different treatment groups, hoping to correlate phenotype…

High-throughput RNA-sequencing (RNA-seq) technologies are powerful tools for understanding cellular state. Often it is of interest to quantify and summarize changes in cell state that occur between experimental or biological conditions.…

Genomic phenotypes, such as DNA methylation and chromatin accessibility, can be used to characterize the transcriptional and regulatory activity of DNA within a cell. Recent technological advances have made it possible to measure such…

This paper develops a theory for characterisation of DNA sequences based on their measure representation. The measures are shown to be random cascades generated by an infinitely divisible distribution. This probability distribution is…

Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for important functional elements, such as genes. They are also…

While multiple testing procedures have been the focus of much statistical research, an important facet of the problem is how to deal with possible confounding. Procedures have been developed by authors in genetics and statistics. In this…

Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as nuclear magnetic resonance, cryo-electron microscopy, small- and wide-angle X-ray scattering, chemical probing, single-molecule F\"orster resonance…

Recent advances in molecular biology allow the quantification of the transcriptome and scoring transcripts as differentially or equally expressed between two biological conditions. Although these two tasks are closely linked, the available…

Comparative transcriptomics has gained increasing popularity in genomic research thanks to the development of high-throughput technologies including microarray and next-generation RNA sequencing that have generated numerous transcriptomic…

Motivation: High-throughput sequencing enables expression analysis at the level of individual transcripts. The analysis of transcriptome expression levels and differential expression estimation requires a probabilistic approach to properly…

In large scale multiple testing problems, a two-class empirical Bayes approach can be used to control the false discovery rate (Fdr) for the entire array of hypotheses under study. A sample splitting step is incorporated to modify that…

Use of next-generation sequencing technologies to transcriptomics (RNA-seq) for gene expression profiling has found widespread application in studying different biological conditions including cancers. However, RNA-seq experiments are still…