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Discovery of new medicinal agents from natural sources has largely been an adventitious process based on screening of plant and microbial extracts combined with bioassay-guided identification and natural produ...
A fundamental activity in biomedical research is Knowledge Discovery which has the ability to search through large amounts of biomedical information such as documents and data. High performance computational i...
This article is part of a Supplement: Volume 10 Supplement 6
In the biological sciences, the need to analyse vast amounts of information has become commonplace. Such large-scale analyses often involve drawing together data from a variety of different databases, held rem...
This article is part of a Supplement: Volume 10 Supplement 6
As biological networks often show complex topological features, mathematical methods are required to extract meaningful information. Clustering methods are useful in this setting, as they allow the summary of ...
This article is part of a Supplement: Volume 10 Supplement 6
A standardized and cost-effective molecular identification system is now an urgent need for Fungi owing to their wide involvement in human life quality. In particular the potential use of mitochondrial DNA spe...
This article is part of a Supplement: Volume 10 Supplement 6
Chemogenomics is an emerging inter-disciplinary approach to drug discovery that combines traditional ligand-based approaches with biological information on drug targets and lies at the interface of chemistry, ...
This article is part of a Supplement: Volume 10 Supplement 6
The identification of protein coding elements in sets of mammalian conserved elements is one of the major challenges in the current molecular biology research. Many features have been proposed for automaticall...
This article is part of a Supplement: Volume 10 Supplement 6
Recent years have seen an increased amount of natural language processing (NLP) work on full text biomedical journal publications. Much of this work is done with Open Access journal articles. Such work assumes...
The structural analysis of protein ligand binding sites can provide information relevant for assigning functions to unknown proteins, to guide the drug discovery process and to infer relations among distant pr...
Interaction graphs (signed directed graphs) provide an important qualitative modeling approach for Systems Biology. They enable the analysis of causal relationships in cellular networks and can even be useful ...
In moderate-throughput SNP genotyping there was a gap in the workflow, between choosing a set of SNPs and submitting their sequences to proprietary assay design software, which was not met by existing software...
Proteomic protein identification results need to be compared across laboratories and platforms, and thus a reliable method is needed to estimate false discovery rates. The target-decoy strategy is a platform-i...
Noise filtering techniques are needed in electron tomography to allow proper interpretation of datasets. The standard linear filtering techniques are characterized by a tradeoff between the amount of reduced n...
The Enteropathogen Resource Integration Center (ERIC; http://​www.​ericbrc.​org) has a goal of providing bioinformatics support for the scientific communi...
Analysis of allelic variation for relevant genes and monitoring chromosome segment transmission during selection are important approaches in plant breeding and ecology. To minimize the number of required molec...
DNA sequence comparison is based on optimal local alignment of two sequences using a similarity score. However, some new DNA sequencing technologies do not directly measure the base sequence, but rather an enc...
Predicting the location of functionally important sites from protein sequence and/or structure is a long-standing problem in computational biology. Most current approaches make use of sequence conservation, as...
Microarray analysis of immunoprecipitated chromatin (ChIP-chip) has evolved from a novel technique to a standard approach for the systematic study of protein-DNA interactions. In ChIP-chip, sites of protein-DN...
Copy number variations (CNVs) may play an important role in disease risk by altering dosage of genes and other regulatory elements, which may have functional and, ultimately, phenotypic consequences. Therefore...
Despite increasing popularity and improvements in terminal restriction fragment length polymorphism (T-RFLP) and other microbial community fingerprinting techniques, there are still numerous obstacles that ham...
High-throughput molecular approaches for gene expression profiling, such as Serial Analysis of Gene Expression (SAGE), Massively Parallel Signature Sequencing (MPSS) or Sequencing-by-Synthesis (SBS) represent ...
How to detect protein complexes is an important and challenging task in post genomic era. As the increasing amount of protein-protein interaction (PPI) data are available, we are able to identify protein compl...
Virtual screening methods start to be well established as effective approaches to identify hits, candidates and leads for drug discovery research. Among those, structure based virtual screening (SBVS) approach...
In many bacteria, intragenomic diversity in synonymous codon usage among genes has been reported. However, no quantitative attempt has been made to compare the diversity levels among different genomes. Here, w...
The pattern of single nucleotide polymorphisms, or SNPs, contains a tremendous amount of information with respect to the mechanisms of the micro-evolutionary process of a species. The inference of the roles of...
Cluster analysis has become a standard computational method for gene function discovery as well as for more general explanatory data analysis. A number of different approaches have been proposed for that purpo...
One of the main objectives of microarray analysis is to identify differentially expressed genes for different types of cells or treatments. Many statistical methods have been proposed to assess the treatment e...
Current microRNA (miRNA) research in progress has engendered rapid accumulation of expression data evolving from microarray experiments. Such experiments are generally performed over different tissues belongin...
Hydrogen/deuterium exchange mass spectrometry (H/DX-MS) experiments implemented to characterize protein interaction and protein folding generate large quantities of data. Organizing, processing and visualizing...
Gene set analysis (GSA) is a widely used strategy for gene expression data analysis based on pathway knowledge. GSA focuses on sets of related genes and has established major advantages over individual gene an...
Internal ribosomal entry sites (IRESs) provide alternative, cap-independent translation initiation sites in eukaryotic cells. IRES elements are important factors in viral genomes and are also useful tools for ...
Alpha-helical transmembrane (TM) proteins are involved in a wide range of important biological processes such as cell signaling, transport of membrane-impermeable molecules, cell-cell communication, cell recog...
Integration and exploration of data obtained from genome wide monitoring technologies has become a major challenge for many bioinformaticists and biologists due to its heterogeneity and high dimensionality. A ...
Many molecules of interest are flexible and undergo significant shape deformation as part of their function, but most existing methods of molecular shape comparison (MSC) treat them as rigid bodies, which may ...
The latest generation of Affymetrix microarrays are designed to interrogate expression over the entire length of every locus, thus giving the opportunity to study alternative splicing genome-wide. The Exon 1.0...
Transcriptional responses often consist of regulatory modules – sets of genes with a shared expression pattern that are controlled by the same regulatory mechanisms. Previous methods allow dissecting regulator...
The introduction of next generation sequencing approaches has caused a rapid increase in the number of completely sequenced genomes. As one result of this development, it is now feasible to analyze large group...
Searching for proteins that contain similar substructures is an important task in structural biology. The exact solution of most formulations of this problem, including a recently published method based on tab...
Multilocus Sequence Typing (MLST) is a frequently used typing method for the analysis of the clonal relationships among strains of several clinically relevant microbial species. MLST is based on the sequence o...
DNA sequence integrity, mRNA concentrations and protein-DNA interactions have been subject to genome-wide analyses based on microarrays with ever increasing efficiency and reliability over the past fifteen yea...
Protein-protein interaction (PPI) is essential to most biological processes. Abnormal interactions may have implications in a number of neurological syndromes. Given that the association and dissociation of pr...
Proteases of human pathogens are becoming increasingly important drug targets, hence it is necessary to understand their substrate specificity and to interpret this knowledge in practically useful ways. New me...
Advances in high-throughput technologies available to modern biology have created an increasing flood of experimentally determined facts. Ordering, managing and describing these raw results is the first step w...
Few overlap between independently developed gene signatures and poor inter-study applicability of gene signatures are two of major concerns raised in the development of microarray-based prognostic gene signatu...
Time-course microarray experiments produce vector gene expression profiles across a series of time points. Clustering genes based on these profiles is important in discovering functional related and co-regulat...
As a high-throughput technology that offers rapid quantification of multidimensional characteristics for millions of cells, flow cytometry (FCM) is widely used in health research, medical diagnosis and treatme...
Mass spectrometry-based biomarker discovery has long been hampered by the difficulty in reconciling lists of discriminatory peaks identified by different laboratories for the same diseases studied. We describe...
Next generation sequencing technologies hold great potential for many biological questions. While mainly used for genomic sequencing, they are also very promising for gene expression profiling. Sequencing of c...
Functional classification schemes (e.g. the Gene Ontology) that serve as the basis for annotation efforts in several organisms are often the source of gold standard information for computational efforts at sup...
High-throughput genotyping and phenotyping projects of large epidemiological study populations require sophisticated laboratory information management systems. Most epidemiological studies include subject-rela...
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