生物信息学技术

We have developed and tested a genetic algorithm (GA) for pattern recognition, which identifies molecular descriptors that optimize the separation of the activity classes of olfactory stimulants in a plot of the two or three largest principal components of the data. Because principal co ...

Several different approaches have been proposed in the last decade to assess the binding affinity of a virtual small molecule ligand to a target protein, particularly with respect to screening large compound databases. Here we review the methods that have been proposed, and discuss techni ...

Given atomic coordinates for a particular conformation of a molecule and some property value assigned to each atom, one can easily calculate a chirality function that distinguishes enantiomers, is zero for an achiral molecule, and is a continuous function of the coordinates and properti ...

Preventing drug-drug interactions and reducing drug-related mortalities dictate cleaner and costlier medicines. The cost to bring a new drug to market has increased dramatically over the last 10 years, with post-discovery activities (preclinical and clinical) costs represent ...

This chapter reviews the techniques available for quantifying the effectiveness of methods for molecular similarity and molecular diversity, focusing in particular on similarity searching and on compound selection procedures. The evaluation criteria considered are based ...

One of the key questions that must be addressed when implementing a chemoinformatics system is whether the tools will be designed for use by the expert user or by the “bench scientist.” This decision can impact not only the style of tools that are rolled out, but is also a factor in terms of how these tools are deli ...

The objective of this chapter is to summarize and evaluate some of the most common chemoinformatic methods that are applied to the analysis of high-throughput-screening data. The chapter will briefly describe current high-throughput-screening practices and will stress how the maj ...

Integration of large and diverse biological data sets is a daunting problem facing systems biology researchers. Exploring the complex issues of data validation, integration, and representation, we present a systematic approach for the management and analysis of large biological d ...

Attaining a detailed understanding of the various biological networks in an organism lies at the core of the emerging discipline of systems biology. A precise description of the relationships formed between genes, mRNA molecules, and proteins is a necessary step toward a complete descri ...

The microarray has emerged as an important format for simultaneous analysis of tens of thousands of substances present in a sample. Successful adaptation of microarray assays to clinical diagnostics will require particular attention to issues of quality control and quality assura ...

Flow cytometric, microsphere-based immunoassays have been developed for the simultaneous detection of soluble analytes in a variety of sample types. The ability to discriminate between individual microspheres on the basis of size, fluorescent intensity, and/or wavelength has a ...

Transcriptomics has played an essential role as proof of concept in the development of experimental and bioinformatics approaches for the generation and analysis of Omics data. We are giving an introduction on how large-scale technologies for gene expression profiling, especially ...

Rapid improvements in high-throughput experimental technologies make it nowadays possible to study the expression, as well as changes in expression, of whole transcriptomes under different environmental conditions in a detailed view. We describe current approaches to identi ...

Mass spectrometry is today a key analytical technique to elucidate the amount and content of proteins expressed in a certain cellular context. The degree of automation in proteomics has yet to reach that of genomic techniques, but even current technologies make a manual inspection of the data i ...

The broad view of the state of biological systems cannot be complete without the added value of integrating proteomic and genomic data with metabolite measurement. By definition, metabolomics aims at quantifying not less than the totality of small molecules present in a biofluid, tissue, o ...

The advent of High Throughput Sequencing (HTS) methods opens new opportunities for the analysis of genomes and transcriptomes. While the sequencing of a whole mammalian genome took several years at the turn of this century, today it is only a matter of weeks. The race towards the thousand-dollar g ...

Progress in experimental procedures has led to rapid availability of Omics profiles. Various open-access as well as commercial tools have been developed for storage, analysis, and interpretation of transcriptomics, proteomics, and metabolomics data. Generally, major analysis ...

“-Omics” is a current suffix for numerous types of large-scale biological data generation procedures, which naturally demand the development of novel algorithms for data storage and analysis. With next generation genome sequencing burgeoning, it is pivotal to decipher a coding site on t ...

Omics data and computational approaches are today providing a key to disentangle the complex architecture of living systems. The integration and analysis of data of different nature allows to extract meaningful representations of signaling pathways and protein interactions ne ...

We provide a commented overview of the available databases for the systematic collection of pathway information and biological models essential for the interpretation of Omics data. Then, we present both the state of the art and the future challenges of network inference, a research area de ...