The measurement of the simultaneous expression values of thousands of genes or proteins from high throughput Omics platforms creates a large amount of data whose interpretation by inspection can be a daunting task. A major challenge of using such data is to translate these lists of genes/prot ...
The Omics revolution has provided the researcher with tools and methodologies for qualitative and quantitative assessment of a wide spectrum of molecular players spanning from the genome to the meta�bolome level. As a consequence, explorative analysis (in contrast to purely hypoth ...
Owing to the growing knowledge about the cellular molecular network and its alterations in diseases, most of the diseases become considered as “systems distortion of the cellular molecular network”. This view of diseases, which we call “systems pathology”, has brought about a new usage of the d ...
The advent of Omics technologies as genomics and proteomics has brought the hope of discovering novel biomarkers that can be used to diagnose, predict, and monitor the progress of disease. The importance of data mining to identify biological markers for the diagnostic classification and p ...
The exponential growth of high-throughput Omics data has provided an unprecedented opportunity for new target identification to fuel the dried-up drug discovery pipeline. However, the bioinformatics analysis of large amount and heterogeneous Omics data has posed a great deal of tec ...
Genomic, proteomic, and other omic-based approaches are now broadly used in biomedical research to facilitate the understanding of disease mechanisms and identification of molecular targets and biomarkers for therapeutic and diagnostic development. While the Omics technol ...
The increased use of antibodies as therapeutics, as well as the growing demand for large numbers of antibodies for high-throughput protein analyses, has been accompanied by a need for more specific antibodies. An array containing every protein for the relevant organism represents the ide ...
A suspension array hybridization assay is described for the detection of 31 mutations and polymorphisms in the cystic fibrosis transmembrane conductance regulator (CFTR) gene using Luminex� xMAP™ technology. The Luminex xMAP system allows simultaneous detection of up to 100 diffe ...
Microarray hybridization experiments are mostly based on quite small sample volumes being confined between the microarray itself and a cover slip or lifter slip on top of the narrow fluid layer. Under such conditions, the system is governed by the rules of microfluidics, i.e., by the regime of small ...
Physicians in the United States and Europe began testing patients who had idiopathic thrombotic events for inherited risk factors in 1990s. The College of American Pathologists (CAP) offered proficiency testing for molecular genetic screening for thrombophilia in 1997. Today, a hyp ...
The present chapter describes a microarray technology developed by Nanogen Inc., for the identification of DNA variations based on the use of microelectronics. The NMW 1000 NanoChip™ Molecular Biology Workstation allows the active deposition and concentration of charged biotiny ...
The need for large-scale and high-throughput methods for SNP genotyping has rapidly increased during the last decade. Our system, presented here, combines the highly specific genotyping principle of minisequencing with the advantages of a microarray format that allows highly mult ...
We have developed a sensitive method for the detection of specific genes simultaneously. First, DNA was amplified by a novel asymmetric multiplex PCR with universal primer(s). Second, the 6-carboxytetramethylrhodamine (TAMRA)-labeled PCR products were hybridized specifica ...
Integration of molecular medicine into standard clinical practice will require the availability of diagnostics that are sensitive, rapid, and robust. The backbone technology underlying the diagnostic will likely serve double duty during clinical trials in order to first valida ...
The understanding of the molecular mechanisms of cellular metabolism and proliferation necessitates accurate identification, isolation, and finally characterization of a specific cell or a population of cells and subsequently their subsets of biomolecules. For the simult ...
Deep sequencing has many possible applications; one of them is the identification and quantification of RNA editing sites. The most common type of RNA editing is adenosine to inosine (A-to-I) editing. A prerequisite for this editing process is a double-stranded RNA (dsRNA) structure. Such ds ...
Whole exome sequencing presents a powerful tool to study rare genetic disorders. The most challenging part of using exome sequencing for the purpose of disease-causing variant detection is analyzing, interpreting, and filtering the large number of detected variants. In this chapter we ...
Short tandem repeats (STRs), also known as microsatellites, have a wide range of applications, including medical genetics, forensics, and population genetics. High-throughput sequencing has the potential to profile large numbers of STRs, but cumbersome gapped alignment and STR-s ...
Mapping short reads to the reference genome is very often the prerequisite for applications utilizing the next-generation sequencing technologies. A dozen of software tools developed for this purpose have been widely used. But many practical issues remained when utilizing them to bu ...
Our ability to sequence the genomic data at our disposal is limited. At each experiment we can sequence reliably only a short fraction of even the smallest genome. We are then faced with the challenge of assembly—combining the short patches we have into a correct reconstruction of as large as possible a ...
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