数据库

Bayesian methods are rapidly becoming popular tools for making statistical inference in various fields of science including biology, engineering, finance, and genetics. One of the key aspects of Bayesian inferential method is its logical foundation that provides a coherent framew ...

In 2003, the completion of the Human Genome Project (1) together with advances in computational resources (2) were expected to launch an era where the genetic and genomic contributions to many common diseases would be found. In the years following, however, researchers became increasingly f ...

In this chapter we will explore Bayesian alternatives to the t-test. We saw in Chapter 1 how t-test can be used to test whether the expected outcomes of the two groups are equal or not. In Chapter 3 we saw how to make inferences from a Bayesian perspective in principle. In this chapter we will put these together to dev ...

Ever-increasing size of the biomedical literature makes more precise information retrieval and tapping into implicit knowledge in scientific literature a necessity. In this chapter, first, three new variants of the expectation–maximization (EM) method for semisupervised do ...

In this chapter, we will focus on the role of bioinformatics to analyze a protein after its protein structure has been determined. First, we present how to validate protein structures for quality assurance. Then, we discuss how to analyze protein–protein interfaces and how to predict the biomol ...

The observation that similar protein sequences fold into similar three-dimensional structures provides a basis for the methods which predict structural features of a novel protein based on the similarity between its sequence and sequences of known protein structures. Similarity ...

Interest in simulation of large-scale metabolic networks, species development, and genesis of various diseases requires new simulation techniques to accommodate the high complexity of realistic biological networks. Information geometry and topological formalisms are p ...

Discovery of DNA sequence variants responsible for human phenotypic variation is key to advances in molecular diagnostics and medicines. Historically, variants that alter the protein-coding sequence of genes have been targeted when attempting to identify a trait’s etiology; this ...

A famous joke story that exhibits the traditionally awkward alliance between theory and experiment and showing the differences between experimental biologists and theoretical modelers is when a University sends a biologist, a mathematician, a physicist, and a computer scientist ...

This paper presents current progress in the development of semantic data integration environment which is a part of the Biomedical Informatics Research Network (BIRN; http://www.nbirn.net) project. BIRN is sponsored by the National Center for Research Resources (NCRR), a component of ...

To promote scientific discovery and education, the federated Biomedical Informatics Research Network (BIRN) Data Repository (BDR) supports data storage, sharing, querying, and downloading for the biomedical community, enabling the integration of multiple data resources f ...

Organizing and annotating biomedical data in structured ways has gained much interest and focus in the last 30 years. Driven by decreases in digital storage costs and advances in genetics sequencing, imaging, electronic data collection, and microarray technologies, data is being coll ...

Single Sign-On (SSO) is a practical requirement for software applications, which rely on distributed, networked services requiring authentication. SSO is as much a convenient feature for users as it is a security concern for application designers. The security requirement becomes cr ...

The field of high-performance computing (HPC) has provided a wide array of strategies for supplying additional computing power to the goal of reducing the total “clock time” required to complete various computational processes. These strategies range from the development of higher- ...

Imagination is the critical point in developing of realistic intelligence (AI) systems. One way to approach imagination would be simulation of its properties and operations. We developed two models “Brain Network Hierarchy of Languages,” and “Semantical Holographic Calculus” and s ...

There is a standard genetic code that is used by most organisms, but exceptions exist in which particular codons are translated with a different meaning, i.e., as a different amino acid. The characterization of the genetic code of an organism is hence a key step for properly analyzing and translating i ...

The analysis of DNA composition and codon usage reveals many factors that influence the evolution of genes and genomes. In this chapter, we show how to use CodonExplorer, a web tool and interactive database that contains millions of genes, to better understand the principles governing evolut ...

Reliable detection of cis-regulatory elements in promoter regions is a difficult and unsolved problem in computational biology. The intricacy of transcriptional regulation in higher eukaryotes, primarily in metazoans, could be a major driving force of organismal complexity. E ...

The sequence of many eukaryotic genomes is nowadays available from a personal computer to any researcher in the world-wide scientific community. However, the sequences are worthless without the adequate annotation of the biological meaningful elements. The annotation of the genes, ...

Genomic DNA is being sequenced and annotated at a rapid rate, with terabases of DNA currently deposited in GenBank and other repositories. Genome browsers provide an essential collection of resources to visualize and analyze chromosomal DNA. The University of California, Santa Cruz (UC ...