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Fabrication of microfluidic channels in common commercially available thermoplastic materials can be easily accomplished using hot embossing or ultraviolet (UV) laser ablation. Hot embossing involves replication of a microfluidic network in a polymer substrate from a stamp ( ...

In the present chapter, some basic definitions about the photolithography process are explained and then the standard preparation of the silicon wafer, the fabrication of the mold, and the preparation and assembly of poly(dimethylsiloxane) (PDMS)-based microchips are discussed. T ...

In this chapter, a detailed outline delineating the processing steps for microfabricating capillary electrophoresis (CE) with integrated electrochemical detection (ECD) platforms for performing analyte separation and detection is presented to enable persons familiar ...

Microchip capillary electrophoresis emerged in the early 1990s as an intresting and novel approach to the high-speed separation of biological compounds, including DNA and proteins. Since the early development in this area, growth in the research field has exploded and now includes chem ...

Reliable identification and assignment of cis-regulatory elements in promoter regions is a challenging problem in biology. The sophistication of transcriptional regulation in higher eukaryotes, particularly in metazoans, could be an important factor contributing to their ...

We present an all-atom molecular modeling method that can predict the binding specificity of a transcription factor based on its 3D structure, with no further information required. We use molecular dynamics and free energy calculations to compute the relative binding free energies for a t ...

The ever accumulating wealth of knowledge about protein interactions and the domain architecture of involved proteins in different organisms offers ways to understand the intricate interplay between interactome and proteome. Ultimately, the combination of these sources of in ...

The concept of molecular co-evolution drew attention in recent years as the basis for several algorithms for the prediction of protein–protein interactions. While being successful on specific data, the concept has never been tested on a large set of proteins. In this chapter we analyze the fea ...

Accurate mapping of protein–protein interaction networks in model organisms is a crucial first step toward subsequent quantitative study of the organization and evolution of biological systems. Data quality of experimental interactome maps can be assessed and improved by integ ...

Knowledge of transcriptional regulatory interactions (TRIs) is essential for exploring functional genomics and systems biology in any organism. While several results from genome-wide analysis of transcriptional regulatory networks are available, they are limited to model ...

There are several Quantitative Structure-Activity Relationship (QSAR) methods to assist in the design of compounds for medicinal use. Owing to the different QSAR methodologies, deciding which QSAR method to use depends on the composition of system of interest and the desired results. T ...

Three sets of molecular descriptors that can be computed from a molecular connection table are defined. The descriptors are based on the subdivision and classification of the molecular surface area according to atomic properties (such as contribution to logP, molar refractivity, and p ...

Partitioning techniques are widely used to classify compound sets or databases according to specific chemical or biological criteria. Partitioning is conceptually related to, yet algorithmically distinct from, conventional clustering methods and is particularly suita ...

Developments in the field of statistics often parallel or follow technological developments in the sciences to which statistical methods may be fruitfully applied. Because practitioners of the statistical arts often address particular applied problems, methods development ...

Microarray experiments try to measure simultaneously the quantity of many specific messenger RNA (mRNA) sequences contained in a sample. These quantities are called gene expression. The sample mRNA can be extracted from human tissue, plant material, or even yeast. Because thousands of t ...

Until recently, image-based experimentation in molecular biology has been primarily concerned with qualitative results produced as a result of such experiments as Northern blots, immunoblotting, and gel electrophoresis. These experiments result in a relatively small number ...

What is Proteomics? The term proteome denotes the PROTEin complement expressed by a genOME or tissue. While the genome is an invariant feature of an organism, the proteome depends on its developmental stage, the tissue considered, and environmental/experimental conditions. There are m ...

According to the Dictionary of Epidemiology, a biomarker is “a cellular or molecular indicator of exposure, health effects, or susceptibility” (1, p. 17). In this chapter, the primary focus is on markers of exposure, although the techniques described here can be applied to any type of biomarker. The ...

Sample size is an important interest of researchers in laboratory and clinical settings. The number of cases to be investigated profoundly affects the cost and duration of a study. Sample size is estimated to achieve a certain statistical power and a careful power and sample size analysis can pre ...

In this chapter, we focus on the study of associations between disease and inheritance of particular genetic variants, a field described as genetic epidemiology. Genetic variation based on polymorphism is common in human populations and appears to be a critical factor in determining sus ...