Bioinformatics is the information technology to deal with biological data. Recently emerging systems biology has drawn great interest inspired by world-wide efforts for modeling and analyzing biological processes with a systems perspective. Bioinformatics, which has analyzed multi-omics data such as genomics, transcriptomics, and proteomics, and explored novel biological patterns embedded within the data, now has a transition to its application to systems biology, called systems bioinformatics. Systems bioinformatics includes various research areas: system modeling, system structure and dynamics analysis, causality analysis, and multi-omics data fusion. In this review, we introduce bioinformatics for genomics, transcriptomics, proteomics, and systems biology according to the different aspects of biological processes.
Biological Processes ; Computational Biology ; Genomics ; Proteomics ; Systems Biology

Bioinformatics is a rapidly emerging field of biomedical research. A flood of large-scale genomic, proteomic and postgenomic data means that many of the challenges in biomedical research are now challenges in informatics. Clinical informatics has long developed technologies to improve biomedical research and clinical care by integrating experimental and clinical information systems. Biomedical informatics, powered by high throughput technologies, genomic-scale databases, and advanced clinical information system, is likely to transform our biomedical understanding forever much the same way that biochemistry did to biology a generation ago. The emergence of health and biomedical informatics revolutionizing both bioinformatics and clinical informatics will eventually change the current practice of medicine, including diagnostics, therapeutics, and prognostics.
Biochemistry ; Biology ; Computational Biology ; Gene Expression ; Genomics ; Human Genome Project ; Informatics* ; Information Systems ; Medical Informatics ; Oligonucleotide Array Sequence Analysis

Taxus is the source plant of anti-cancer drug paclitaxel and its biosynthetic precursor, analogs and derivatives, which has been studying for decades. There are many endemic Taxus species in China, which have been studied in the field of multiple disciplines. Based on the recent studies of the researchers, this review comments on the study of Taxus biology and chemistry. The bibliometric method is used to quantify the global scientific production of Taxus-related research, and identify patterns and tendencies of Taxus-related articles. Gaps are present in knowledge about the genomics, epigenomics, transcriptomics, proteomics, metabolomics and bioinformatics of Taxus and their endophytic fungi. Systems biology and various omics technologies will play an increasingly important role in the coming decades.
Computational Biology ; Endophytes ; chemistry ; isolation & purification ; Epigenomics ; methods ; Fungi ; chemistry ; isolation & purification ; Gene Expression Profiling ; Genomics ; methods ; Metabolomics ; Molecular Biology ; Paclitaxel ; biosynthesis ; chemistry ; isolation & purification ; Phylogeny ; Plants, Medicinal ; chemistry ; classification ; genetics ; microbiology ; Proteomics ; Systems Biology ; Taxus ; chemistry ; classification ; genetics ; microbiology

The National Agricultural Biotechnology Information Center (NABIC) constructed an agricultural biology-based infrastructure and developed a biological information-based database. The major functions of the NABIC are focused on biotechnological developments for agricultural bioinformatics and providing a web-based service to construct bioinformatics workflows easily, such as protein function prediction and genome systems biology programs. The NABIC has concentrated on the functional genomics of major crops, building an integrated biotechnology database for agro-biotech information that focuses on the proteomics of major agricultural resources, such as rice, Chinese cabbage, rice Ds-tagging lines, and microorganisms.
Asian Continental Ancestry Group ; Biotechnology ; Brassica ; Computational Biology ; Genome ; Genomics ; Humans ; Information Centers ; Proteomics ; Systems Biology

Translational medicine is an emerging idea in current medical research area. Typically, for the purpose of bridging the gap between basic and clinical research, it not only emphasizes the urgency and necessity to break the traditional working formats, including single subject centered research team and limited cooperation among different scientific groups, but also highlights a more close and frequent interaction between basic scientist and clinician. In order to reach this goal, the theory and method of systems biology should be employed. This paper mainly focused on a central issue that how to carry out an investigation on early clinical diagnosis of xenobiotic-induced intrauterine growth retardation (IUGR) by using research concept of translational medicine and method of systems biology. Briefly, a hypothesis of common mechanism of IUGR was first proposed and subsequent validation was performed via integrating--omics (e.g. genomics, proteomics, cytomics, metabonomics/metabolomics) and molecular biology techniques. Metabonomics was further utilized to explore IUGR biomarker and establish preliminary forecasting model by bioinformatics and computational biology, which is available for early diagnosis of IUGR and make a complement to current evaluation criteria.
Biomarkers ; analysis ; Computational Biology ; Early Diagnosis ; Female ; Fetal Growth Retardation ; chemically induced ; diagnosis ; metabolism ; Genomics ; Humans ; Metabolomics ; Pregnancy ; Proteomics ; Systems Biology ; Translational Medical Research ; Xenobiotics ; toxicity

Bioinformatics is a rapidly emerging field of biomedical research. A flood of large-scale genomic and postgenomic data means that many of the challenges in biomedical research are now challenges in computational sciences. Clinical informatics has long developed methodologies to improve biomedical research and clinical care by integrating experimental and clinical information systems. The informatics revolutions both in bioinformatics and clinical informatics will eventually change the current practice of medicine, including diagnostics, therapeutics, and prognostics.Postgenome informatics, powered by high throughput technologies and genomic-scale databases, is likely to transform our biomedical understanding forever much the same way that biochemistry did a generation ago. The paper describes how these technologies will impact biomedical research and clinical care, emphasizing recent advances in biochip-based functional genomics and proteomics. Basic data preprocessing with normalization, primary pattern analysis, and machine learning algorithms will be presented. Use of integrated biochip informatics technologies, text mining of factual and literature databases, and integrated management of biomolecular databases will be discussed. Each step will be given with real examples in the context of clinical relevance. Issues of linking molecular genotype and clinical phenotype information will be discussed.
Machine Learning ; Biochemistry ; Computational Biology* ; Data Mining ; Genomics ; Genotype ; Informatics ; Information Systems ; Medical Informatics ; Phenotype ; Proteomics

This article is a mini-review that provides a general overview for next-generation sequencing (NGS) and introduces one of the most popular NGS applications, whole genome sequencing (WGS), developed from the expansion of human genomics. NGS technology has brought massively high throughput sequencing data to bear on research questions, enabling a new era of genomic research. Development of bioinformatic software for NGS has provided more opportunities for researchers to use various applications in genomic fields. De novo genome assembly and large scale DNA resequencing to understand genomic variations are popular genomic research tools for processing a tremendous amount of data at low cost. Studies on transcriptomes are now available, from previous-hybridization based microarray methods. Epigenetic studies are also available with NGS applications such as whole genome methylation sequencing and chromatin immunoprecipitation followed by sequencing. Human genetics has faced a new paradigm of research and medical genomics by sequencing technologies since the Human Genome Project. The trend of NGS technologies in human genomics has brought a new era of WGS by enabling the building of human genomes databases and providing appropriate human reference genomes, which is a necessary component of personalized medicine and precision medicine.
Chromatin Immunoprecipitation ; Computational Biology ; DNA ; Epigenomics ; Genetics, Medical ; Genome* ; Genome, Human ; Genomics ; High-Throughput Nucleotide Sequencing ; Human Genome Project ; Humans ; Methylation ; Precision Medicine ; Sequence Analysis, RNA ; Transcriptome

The basic graph layout technique, one of many visualization techniques, deals with the problem of positioning vertices in a way to maximize some measure of desirability in a graph. The technique is becoming critically important for further development of the field of systems biology. However, applying the appropriate automatic graph layout techniques to the genomic scale flow of metabolism requires an understanding of the characteristics and patterns of duplicate and shared vertices, which is crucial for bioinformatics software developers. In this paper, we provide the results of parsing KEGG XML files from a graph-theoretical perspective, for future research in the area of automatic layout techniques in biological pathway domains.
Computational Biology ; Metabolic Networks and Pathways ; Systems Biology

Integrating various pathway data collections to create new biological knowledge is a challenge, for which novel computational tools play a key role. For this purpose, we developed the Java-based conversion modules KGML2SBML and KGML2BioPAX to translate KGML (KEGG Markup Language) into a couple of common data exchange formats: SBML (Systems Biology Markup Language) and BioPAX (Biological Pathway Exchange). We hope that our work will be beneficial for other Java developers when they extend their bioinformatics system into SBML- or BioPAX-aware analysis tools. This is part of our ongoing effort to develop an ultimate KEGG-based pathway enrichment analysis system.
2,5-Dimethoxy-4-Methylamphetamine ; Biology ; Computational Biology ; Indonesia ; Systems Biology

Whereas genomics describes the study of genome, mainly represented by its gene expression on the DNA or RNA level, the term proteomics denotes the study of the proteome, which is the protein complement encoded by the genome. In recent years, the number of proteomic experiments increased tremendously. While all fields of proteomics have made major technological advances, the biggest step was seen in bioinformatics. Biological information management relies on sequence and structure databases and powerful software tools to translate experimental results into meaningful biological hypotheses and answers. In this resource article, I provide a collection of databases and software available on the Internet that are useful to interpret genomic and proteomic data. The article is a toolbox for researchers who have genomic or proteomic datasets and need to put their findings into a biological context.
Computational Biology ; Databases, Protein ; Genomics ; Internet ; Proteomics ; Software