Related papers: Estimating the proportion of differentially expres…
This paper presents a novel method to segment/decode DNA sequences based on n-grams statistical language model. Firstly, we find the length of most DNA 'words' is 12 to 15 bps by analyzing the genomes of 12 model species. Then we design an…
The extension of DNA confined to nanochannels has been studied intensively and in detail. Yet quantitative comparisons between experiments and model calculations are difficult because most theoretical predictions involve undetermined…
Gene Regulatory Network (GRN) plays an important role in knowing insight of cellular life cycle. It gives information about at which different environmental conditions genes of particular interest get over expressed or under expressed.…
Motivation: ``Molecular signatures'' or ``gene-expression signatures'' are used to predict patients' characteristics using data from coexpressed genes. Signatures can enhance understanding about biological mechanisms and have diagnostic…
Even though there is a plethora of research in Microarray gene expression data analysis, still, it poses challenges for researchers to effectively and efficiently analyze the large yet complex expression of genes. The feature (gene)…
This paper examines two methods for finding whether long-range correlations exist in DNA: a fractal measure and a mutual information technique. We evaluate the performance and implications of these methods in detail. In particular we…
Microarray techniques are widely used in Gene expression analysis. These techniques are based on discovering submatrices of genes that share similar expression patterns across a set of experimental conditions with coherence constraint.…
Detecting the interactions of genetic compounds like genes, SNPs, proteins, metabolites, etc. can potentially unravel the mechanisms behind complex traits and common genetic disorders. Several methods have been taken into consideration for…
In recent times whole-genome gene expression analysis has turned out to be a highly important tool to study the coordinated function of a very large number of genes within their corresponding cellular environment, especially in relation to…
One of the outstanding challenges in comparative genomics is to interpret the evolutionary importance of regulatory variation between species. Rigorous molecular evolution-based methods to infer evidence for natural selection from…
Measuring gene expression simultaneously in both hosts and symbionts offers a powerful approach to explore the biology underlying species interactions. Such dual or simultaneous RNAseq approaches have primarily been used to gain insight…
High-dimensional phenotypes hold promise for richer findings in association studies, but testing of several phenotype traits aggravates the grand challenge of association studies, that of multiple testing. Several methods have recently been…
BioDynaMo is a biological processes simulator developed by an international community of researchers and software engineers working closely with neuroscientists. The authors have been working on gene expression, i.e. the process by which…
A general method for obtaining highly efficient factorial designs of relatively small sizes is developed for cDNA microarray experiments. The method allows the main effects and interactions of successive orders to be of possibly unequal…
A prespecified set of genes may be enriched, to varying degrees, for genes that have altered expression levels relative to two or more states of a cell. Knowing the enrichment of gene sets defined by functional categories, such as gene…
Microarrays have been developed that tile the entire nonrepetitive genomes of many different organisms, allowing for the unbiased mapping of active transcription regions or protein binding sites across the entire genome. These tiling array…
In immunological studies, the characterization of small, functionally distinct cell subsets from blood and tissue is crucial to decipher system level biological changes. An increasing number of studies rely on assays that provide…
DNA microarray technology enables the simultaneous measurement of expression levels of thousands of genes, thereby facilitating the understanding of the molecular mechanisms underlying complex diseases such as brain tumors and the…
Motivation: The discovery of relationships between gene expression measurements and phenotypic responses is hampered by both computational and statistical impediments. Conventional statistical methods are less than ideal because they either…
MicroRNAs (miRNAs) are small non-coding RNAs that function as regulators of gene expression. In recent years, there has been a tremendous and growing interest among researchers to investigate the role of miRNAs in normal cellular as well as…