Current Bioinformatics - Volume 4, Issue 3, 2009

Phenotype at crop level is the result of the interaction among many genes whose expression is often dependent on environmental conditions and developmental stage. Multilevel, computer-based, data integration thus plays a fundamental role in the understanding of many important agronomic traits such as yield and resource use efficiencies. Bioinformatics is the key for realizing the full potential of post-genomic revo Read More

Protein subcellular localization is one of the key characteristic to understand its biological function. Proteins are transported to specific organelles and suborganelles after they are synthesized. They take part in cell activity and function efficiently when correctly localized. Inaccurate subcellular localization will have great impact on cellular function. Prediction of protein subcellular localization is one of the important areas in prote Read More

Understanding the genetic machinery of plant growth and development is of fundamental importance in agriculture and biology. Recently, a novel statistical framework, coined functional mapping, has been developed to study the genetic architecture of the dynamic pattern of phenotypic development at different levels of organization. By integrating mathematical aspects of cellular and biological processes, functional map Read More

Traditional Chinese Medicine (TCM) is characterized by regulating the integrity of the human body and has accumulated thousand-year experience in the use of Herb Formula (“Fu-Fang“ in Chinese) for managing complicated TCM Syndrome (“ZHENG” in Chinese). In recent years, there has been increasing concern about the application of bioinformatics and systems biology approaches for deciphering the scientific basis and the s Read More

The identification of catalytic residues of an enzyme is one of the most important steps towards understanding its biological roles and exploring its applications. Thus far, a range of catalytic residue prediction methods have been developed, which play an increasingly important role in complementing the experimental characterization of enzymatic functions. The available approaches can be split into two broad categori Read More

Network biology is conceptualized as an interdisciplinary field, lying at the intersection among graph theory, statistical mechanics and biology. Great efforts have been made to promote the concept of network biology and its various applications in life science. In this review, we focus on the modules that are functional entities and building blocks of a complex network. We first introduce the basic concepts and hot spots of net Read More

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Protein inference is the final but very important step to identify proteins in biological complex from tandem mass spectrometry analysis. Assembling peptides identified from tandem mass spectra is one of the most widely used methods for protein inference in proteomics studies. The “bottom-up” approaches cut off the connection between peptides and proteins and thus significantly complicate the protein inference. Fi Read More

MicroRNAs (miRNAs) are small, non-coding RNAs that participate in the post-transcriptional regulation of messenger RNAs (mRNAs) by degrading or inhibiting translation. Some of the topical studies strongly suggest that the disorders in the normal activities of miRNAs might cause many diseases. Generally, such studies concern patient-specific expression profiles for the purposes like pruning, clustering or classification. This paper Read More

Molecular disease mechanisms typically constitute abnormalities in the regulation of genes producing many kinds of alterations in the expression levels. To identify disease-altered genes better, we have developed an approach that searches for the genes which present a significant rank alteration in the rank of their expression profiles, by comparing an altered rank with another gene. The approach provides groups of ge Read More