Related papers: Estimating the proportion of differentially expres…
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…
Affymetrix Genechip microarrays are used widely to determine the simultaneous expression of genes in a given biological paradigm. Probes on the Genechip array are atomic entities which by definition are randomly distributed across the array…
Two-component mixture models are particularly useful for identifying differentially expressed genes, but their performance can deteriorate markedly when the alternative distribution departs from parametric assumptions or symmetry. We…
Motivation: Human genomic datasets often contain sensitive information that limits use and sharing of the data. In particular, simple anonymisation strategies fail to provide sufficient level of protection for genomic data, because the data…
A number of bioinformatic or biostatistical methods are available for analyzing DNA copy number profiles measured from microarray or sequencing technologies. In the absence of rich enough gold standard data sets, the performance of these…
Multi-sample microarray experiments have become a standard experimental method for studying biological systems. A frequent goal in such studies is to unravel the regulatory relationships between genes. During the last few years, regression…
One of the most popular tools for large scale gene expression studies are high-density oligonucleotide (GeneChip(R)) arrays. These currently have 16-20 small probe cells (``features'') for evaluating the transcript abundance of each gene.…
It is tempting to believe that we now own the genome. The ability to read and re-write it at will has ushered in a stunning period in the history of science. Nonetheless, there is an Achilles heel exposed by all of the genomic data that has…
As high-throughput sequencing has become common practice, the cost of sequencing large amounts of genetic data has been drastically reduced, leading to much larger data sets for analysis. One important task is to identify biological…
DNA microarray gene-expression data has been widely used to identify cancerous gene signatures. Microarray can increase the accuracy of cancer diagnosis and prognosis. However, analyzing the large amount of gene expression data from…
Hierarchical models are a powerful tool for high-throughput data with a small to moderate number of replicates, as they allow sharing information across units of information, for example, genes. We propose two such models and show its…
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…
miRNA and gene expression profiles have been proved useful for classifying cancer samples. Efficient classifiers have been recently sought and developed. A number of attempts to classify cancer samples using miRNA/gene expression profiles…
2D display is a fast and economical way of visualizing polymorphism and comparing genomes, which is based on the separation of DNA fragments in two steps, according first to their size and then to their sequence composition. In this paper,…
We propose generative neural network methods to generate DNA sequences and tune them to have desired properties. We present three approaches: creating synthetic DNA sequences using a generative adversarial network; a DNA-based variant of…
The accurate quantification of gene expression levels is crucial for transcriptome study. Microarray platforms are commonly used for simultaneously interrogating thousands of genes in the past decade, and recently RNA-Seq has emerged as a…
In the postgenome era many efforts have been dedicated to systematically elucidate the complex web of interacting genes and proteins. These efforts include experimental and computational methods. Microarray technology offers an opportunity…
Microarrays are made it possible to simultaneously monitor the expression profiles of thousands of genes under various experimental conditions. Identification of co-expressed genes and coherent patterns is the central goal in microarray or…
From the response to external stimuli to cell division and death, the dynamics of living cells is based on the expression of specific genes at specific times. The decision when to express a gene is implemented by the binding and unbinding…
Differential abundance analysis is a key component of microbiome studies. Although dozens of methods exist there is currently no consensus on the preferred methods. While the correctness of results in differential abundance analysis is an…