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Bioinformatics is confronted with a new data explosion due to the availability of high throughput DNA sequencers. Data storage and analysis becomes a problem on local servers, and therefore it is needed to swi...
Microarray has been widely used to measure the gene expression level on the genome scale in the current decade. Many algorithms have been developed to reconstruct gene regulatory networks based on microarray d...
This article is part of a Supplement: Volume 11 Supplement 11
MicroRNAs (simply miRNAs) are derived from larger hairpin RNA precursors and play essential regular roles in both animals and plants. A number of computational methods for miRNA genes finding have been propose...
This article is part of a Supplement: Volume 11 Supplement 11
Weak motif discovery in DNA sequences is an important but unresolved problem in computational biology. Previous algorithms that aimed to solve the problem usually require a large amount of memory or execution ...
This article is part of a Supplement: Volume 11 Supplement 11
In the literature, there are fruitful algorithmic approaches for identification functional modules in protein-protein interactions (PPI) networks. Because of accumulation of large-scale interaction data on mul...
This article is part of a Supplement: Volume 11 Supplement 11
Embryogenesis is the process by which the embryo is formed, develops, and establishes developmental hierarchies of tissues. The recent advance in microarray technology made it possible to investigate the tissu...
This article is part of a Supplement: Volume 11 Supplement 11
Cellular processes and pathways, whose deregulation may contribute to the development of cancers, are often represented as cascades of proteins transmitting a signal from the cell surface to the nucleus. Howev...
Colon cancer is driven by mutations in a number of genes, the most notorious of which is Apc. Though much of Apc's signaling has been mechanistically identified over the years, it is not always clear which functi...
The opportunities for bacterial population genomics that are being realised by the application of parallel nucleotide sequencing require novel bioinformatics platforms. These must be capable of the storage, re...
The purpose of this manuscript is to provide, based on an extensive analysis of a proteomic data set, suggestions for proper statistical analysis for the discovery of sets of clinically relevant biomarkers. As...
The analysis of Inter-Alu PCR patterns obtained from human genomic DNA samples is a promising technique for a simultaneous analysis of many genomic loci flanked by Alu repetitive sequences in order to detect t...
Genomewide association studies have resulted in a great many genomic regions that are likely to harbor disease genes. Thorough interrogation of these specific regions is the logical next step, including region...
Mass spectrometry has become a standard method by which the proteomic profile of cell or tissue samples is characterized. To fully take advantage of tandem mass spectrometry (MS/MS) techniques in large scale p...
This article is part of a Supplement: Volume 11 Supplement 10
This article is part of a Supplement: Volume 11 Supplement 10
This article is part of a Supplement: Volume 11 Supplement 10
This article is part of a Supplement: Volume 11 Supplement 10
This article is part of a Supplement: Volume 11 Supplement 10
This article is part of a Supplement: Volume 11 Supplement 10
This article is part of a Supplement: Volume 11 Supplement 10
This article is part of a Supplement: Volume 11 Supplement 10
This article is part of a Supplement: Volume 11 Supplement 10
This article is part of a Supplement: Volume 11 Supplement 10
This article is part of a Supplement: Volume 11 Supplement 10
This meeting report gives an overview of the keynote lectures and a selection of the student oral and poster presentations at the 6th International Society for Computational Biology Student Council Symposium t...
This article is part of a Supplement: Volume 11 Supplement 10
This article is part of a Supplement: Volume 11 Supplement 10
This article is part of a Supplement: Volume 11 Supplement 10
One of the most commonly performed tasks when analysing high throughput gene expression data is to use clustering methods to classify the data into groups. There are a large number of methods available to perf...
Models for the simulation of metabolic networks require the accurate prediction of enzyme function. Based on a genomic sequence, enzymatic functions of gene products are today mainly predicted by sequence data...
The Gene Ontology (GO) is a well known controlled vocabulary describing the biological process, molecular function and cellular component aspects of gene annotation. It has become a widely used knowledge source i...
High-throughput profiling of DNA methylation status of CpG islands is crucial to understand the epigenetic regulation of genes. The microarray-based Infinium methylation assay by Illumina is one platform for l...
Recent studies have revealed the importance of considering the entire distribution of possible secondary structures in RNA secondary structure predictions; therefore, a new type of estimator is proposed includ...
External stimulations of cells by hormones, cytokines or growth factors activate signal transduction pathways that subsequently induce a re-arrangement of cellular gene expression. The analysis of such changes...
Physical maps are the substrate of genome sequencing and map-based cloning and their construction relies on the accurate assembly of BAC clones into large contigs that are then anchored to genetic maps with mo...
The preprocessing of gene expression data obtained from several platforms routinely includes the aggregation of multiple raw signal intensities to one expression value. Examples are the computation of a single...
The behaviour of biological systems can be deduced from their mathematical models. However, multiple sources of data in diverse forms are required in the construction of a model in order to define its componen...
Proton Magnetic Resonance (MR) Spectroscopy (MRS) is a widely available technique for those clinical centres equipped with MR scanners. Unlike the rest of MR-based techniques, MRS yields not images but spectra...
To exploit the flood of data from advances in high throughput imaging of optically sectioned nuclei, image analysis methods need to correctly detect thousands of nuclei, ideally in real time. Variability in nu...
Phylogeny-aware progressive alignment has been found to perform well in phylogenetic alignment benchmarks and to produce superior alignments for the inference of selection on codon sequences. Its implementatio...
Exon arrays provide a way to measure the expression of different isoforms of genes in an organism. Most of the procedures to deal with these arrays are focused on gene expression or on exon expression. Althoug...
Tandem mass spectrometry-based database searching has become an important technology for peptide and protein identification. One of the key challenges in database searching is the remarkable increase in comput...
The data from DNA microarrays are increasingly being used in order to understand effects of different conditions, exposures or diseases on the modulation of the expression of various genes in a biological syst...
The problem of determining the physical conformation of a protein dimer, given the structures of the two interacting proteins in their unbound state, is a difficult one. The location of the docking interface i...
The ever-increasing wealth of genomic sequence information provides an unprecedented opportunity for large-scale phylogenetic analysis. However, species phylogeny inference is obfuscated by incongruence among ...
Statistical bioinformatics is the study of biological data sets obtained by new micro-technologies by means of proper statistical methods. For a better understanding of environmental adaptations of proteins, o...
Massively parallel sequencing readouts of epigenomic assays are enabling integrative genome-wide analyses of genomic and epigenomic variation. Pash 3.0 performs sequence comparison and read mapping and can be ...
Data from metabolomic studies are typically complex and high-dimensional. Principal component analysis (PCA) is currently the most widely used statistical technique for analyzing metabolomic data. However, PCA...
In this paper, we introduce a progressive corner cutting method called Reticular Alignment for multiple sequence alignment. Unlike previous corner-cutting methods, our approach does not define a compact part o...
Word sense disambiguation (WSD) algorithms attempt to select the proper sense of ambiguous terms in text. Resources like the UMLS provide a reference thesaurus to be used to annotate the biomedical literature....
MHC class II binding predictions are widely used to identify epitope candidates in infectious agents, allergens, cancer and autoantigens. The vast majority of prediction algorithms for human MHC class II to da...
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