生物信息学技术

Sequence-based comparisons have been the workhorse of bioinformatics for the past four decades, furthering our understanding of gene function and evolution. Over the last decade, a plethora of technologies have matured for measuring Protein–protein interactions (PPIs) at large s ...

Many important biological processes, such as the signaling pathways, require protein–protein interactions (PPIs) that are designed for fast response to stimuli. These interactions are usually transient, easily formed, and disrupted, yet specific. Many of these transient inter ...

Automatic discovery of functional complexes from protein interaction data is a rewarding but challenging problem. While previous approaches use approximations to extract dense modules, our approach exactly solves the problem of dense module enumeration. Furthermore, const ...

KEGG (http://www.genome.jp/kegg/) is an integrated database resource for linking genomes or molecular datasets to molecular networks (pathways, etc.) representing higher-level systemic functions of the cell, the organism, and the ecosystem. Major efforts have been undertaken f ...

One of the challenges of genetic data analysis is to combine information from sources that are distributed around the world and accessible through a wide array of different methods and interfaces. The HIV database and its footsteps, the hepatitis C virus (HCV) and hemorrhagic fever virus (HFV) d ...

A host of data on genetic variation from the Human Genome and International HapMap projects, and advances in high-throughput genotyping technologies, have made genome-wide association (GWA) studies technically feasible. GWA studies help in the discovery and quantification of the g ...

Networks of functional associations between genes have recently been successfully used for gene function and disease-related research. A typical approach for constructing such functional linkage gene networks (FLNs) is based on the integration of diverse high-throughput fun ...

Thanks for the dramatic reduction of the costs of high-throughput techniques in modern biotechnology, searching for differentially expressed genes is already a common procedure in identifying biomarkers or signatures of phenotypic states such as diseases or compound treatmen ...

Pathway databases collect the bioreactions and molecular interactions that define the processes of life. The MetaCyc family of pathway databases consists of thousands of databases that were derived through computational inference of metabolic pathways from the MetaCyc pathw ...

Protein interactions, as well as the networks they formed, play a key role in many cellular processes and the distortion of the protein interacting interfaces may lead to the development of many diseases. In this chapter, we will briefly introduce the background knowledge of the protein–prot ...

In this chapter, we first discuss protein localization in bacteria and evaluate some localization prediction tools on an independent dataset. Next, we focus on β-barrel outer membrane proteins (BOMPs), describing and evaluating new tools for BOMP detection and topology prediction. F ...

Nuclear Magnetic Resonance (NMR) techniques are widely used in the drug discovery process. The primary feature exploited in these investigations is the large difference in mass between drugs and receptors (usually proteins) and the effect this has on the rotational or translational co ...

The vast amounts of chemical and biological data available through robotic high-throughput assays and micro-array technologies require computational techniques for visualization, analysis, and predictive �modeling. Predictive cheminformatics and bioinformati ...

Databases that provide links between bioactive compounds and their protein targets are increasingly important in drug discovery and chemical biology. They join the expanding universes of cheminformatics via chemical structures on the one hand and bioinformatics via sequences ...

Virtual screening is an established technique that has successfully been deployed in the identification of novel biologically active molecules. Whether for ligand-based or for structure-based virtual screening, a chemical collection needs to be properly processed prior to in si ...

Drug discovery in the late twentieth and early twenty-first century has witnessed a myriad of changes that were adopted to predict whether a compound is likely to be successful, or conversely enable identification of molecules with liabilities as early as possible. These changes include i ...

Methylation of Cytosine together with other epigenetic traits plays an important role in the development and regulation of both healthy and diseased cells. Changes in the methylation patterns have been shown to be associated with the development of cancer, growth, neurodevelopment ...

With the advent of next-generation sequencing (NGS) technology, methods previously developed for microarrays have been adapted for use by NGS. Here we describe in detail a protocol for Barcode analysis by sequencing (Bar-seq) to assess pooled competitive growth of individually barco ...

Complex biological systems comprise a large number of interacting molecules. The identification and detailed characterization of the functions of the involved genes and proteins are crucial for modeling and understanding such systems. To interrogate the various cellular proc ...

Research into the molecular mechanism of Dupuytren’s disease (DD) illustrates all the problems common to drug discovery in orphan diseases, but also in more commonly investigated ailments. Current findings characterize DD as a disease with complex molecular pathology, with changes ...