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RNA sequencing (RNA-seq) is the conventional genome-scale approach used to capture the expression levels of all detectable genes in a biological sample. This is now regularly used for population-based studies designed to identify genetic…
In this paper, we present a new approach for analyzing gene expression data that builds on topological characteristics of time series. Our goal is to identify cell cycle regulated genes in micro array dataset. We construct a point cloud out…
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.…
We have micromachined a silicon-chip device that transports DNA with a Brownian ratchet that rectifies the Brownian motion of microscopic particles. Transport properties for a DNA 50mer agree with theoretical predictions, and the DNA…
DNA labeling is a powerful tool in molecular biology and biotechnology that allows for the visualization, detection, and study of DNA at the molecular level. Under this paradigm, a DNA molecule is being labeled by specific k patterns and is…
With the continued improvement of sequencing technologies, the prospect of genome-based medicine is now at the forefront of scientific research. To realize this potential, however, we need a revolutionary sequencing method for the…
We consider a problem of data integration. Consider determining which genes affect a disease. The genes, which we call predictor objects, can be measured in different experiments on the same individual. We address the question of finding…
Recently, microRNAs (miRNAs) have emerged as central posttranscriptional regulators of gene expression. miRNAs regulate many key biological processes, including cell growth, death, development and differentiation. This discovery is…
Accurate information about protein content in the organism is instrumental for a better understanding of human biology and disease mechanisms. While the presence of certain types of proteins can be life-threatening, the abundance of others…
Transcriptomic analysis are characterized by being not directly quantitative and only providing relative measurements of expression levels up to an unknown individual scaling factor. This difficulty is enhanced for differential expression…
Microarray technology is a new and powerful tool for the concurrent monitoring of a large number of gene expressions. Each microarray experiment produces hundreds of images. Each digital image requires a large storage space. Hence,…
Cancer development is associated with aberrant DNA methylation, including increased stochastic variability. Statistical tests for discovering cancer methylation biomarkers have focused on changes in mean methylation. To improve the power of…
The human-associated microbiome is closely tied to human health and is of substantial clinical interest. Metagenomics-based tools are emerging for clinical diagnostics, tracking the spread of diseases, and surveillance of potential…
High throughput sequencing (HTS)-based technology enables identifying and quantifying non-culturable microbial organisms in all environments. Microbial sequences have enhanced our understanding of the human microbiome, the soil and plant…
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…
Gene expression and regulation rely on an apparently finely tuned set of reactions between some proteins and DNA. Such DNA-binding proteins have to find specific sequences on very long DNA molecules and they mostly do so in absence of any…
RNA interference (RNAi) is an endogenous cellular process in which small double-stranded RNAs lead to the destruction of mRNAs with complementary nucleoside sequence. With the production of RNAi libraries, large-scale RNAi screening in…
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…
One of the objectives of designing feature selection learning algorithms is to obtain classifiers that depend on a small number of attributes and have verifiable future performance guarantees. There are few, if any, approaches that…
DNA exhibits remarkable potential as a data storage solution due to its impressive storage density and long-term stability, stemming from its inherent biomolecular structure. However, developing this novel medium comes with its own set of…