By Luonan Chen;Rui-Sheng Wang;Xiang-Sun Zhang
Substitute strategies and instruments for examining biomolecular networksWith the new quick advances in molecular biology, high-throughput experimental equipment have led to huge, immense quantities of information that may be used to review biomolecular networks in residing organisms. With this improvement has come attractiveness of the truth that a sophisticated residing organism can't be totally understood via only interpreting person parts. really, it's the interactions of elements or biomolecular networks which are finally accountable for an organism's shape and serve as. This booklet addresses the real desire for a brand new set of computational instruments to bare crucial organic mechanisms from a structures biology approach.Readers gets accomplished assurance of interpreting biomolecular networks in mobile structures in response to to be had experimental information with an emphasis at the points of community, method, integration, and engineering. every one subject is handled extensive with particular organic difficulties and novel computational methods:GENE NETWORKS—Transcriptional legislation; reconstruction of gene regulatory networks; and inference of transcriptional regulatory networksPROTEIN interplay NETWORKS—Prediction of protein-protein interactions; topological constitution of biomolecular networks; alignment of biomolecular networks; and network-based prediction of protein functionMETABOLIC NETWORKS AND SIGNALING NETWORKS—Analysis, reconstruction, and purposes of metabolic networks; modeling and inference of signaling networks; and different issues and new trendsIn addition to theoretical effects and techniques, many computational software program instruments are referenced and to be had from the authors' websites. Biomolecular Networks is an necessary reference for researchers and graduate scholars in bioinformatics, computational biology, platforms biology, desktop technology, and utilized arithmetic.
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Extra resources for Biomolecular Networks: Methods and Applications in Systems Biology (Wiley Series in Bioinformatics)
Determining the four-letter order for a given DNA molecule is known as DNA sequencing. Since the ﬁrst full genome for a bacterium was sequenced in 1995, genomes of many organisms have been sequenced. The well-known Human Genome Project was completed in 2001, and a draft human genome was obtained. As mentioned earlier, information encoded in static DNA is passed to functional protein molecules through transcription and translation processes. However, not all portions of DNA are used for encoding proteins.
Coli K-12 that provides rich curated knowledge of the regulatory interactions and operon organization. Its current version also includes the information of noncoding RNAs. Except for ChIP-chip techniques, other experimental methods such as yeast one-hybrid (Y1H) assay [Dep06, VeV07] have also been used to map protein – DNA interactions. To play a fundamental role in transcription regulation, TFs are generally composed of at least two types of domains: a DNA-binding domain, which serves to interact with its cognate DNA target sequence; and a transcription regulation domain, which serves to activate or repress transcription.
For example, the huge deposit of gene expression proﬁles and protein– DNA interactions makes it possible to quantitatively study the regulatory relationships between genes. Reverse engineering of regulatory networks is one of main computational problems in this ﬁeld. Protein interaction data from high-throughput techniques are highly “noisy” and incomplete with unknown portion of false positives. We are required to systematically integrate these data and further estimate their conﬁdence by statistical techniques.
Biomolecular Networks: Methods and Applications in Systems Biology (Wiley Series in Bioinformatics) by Luonan Chen;Rui-Sheng Wang;Xiang-Sun Zhang