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Tiling array data is hard to interpret due to noise. The wavelet transformation is a widely used technique in signal processing for elucidating the true signal from noisy data. Consequently, we attempted to de...
As the canonical code is not universal, different theories about its origin and organization have appeared. The optimization or level of adaptation of the canonical genetic code was measured taking into accoun...
Alternative splicing (AS) is a process which generates several distinct mRNA isoforms from the same gene by splicing different portions out of the precursor transcript. Due to the (patho-)physiological importa...
Given n strings s1, …, s n each of length ℓ and a nonnegative integer d, the CLOSEST STRING problem asks to find a center string s such that none of the input strings has Ha...
This article is part of a Supplement: Volume 12 Supplement 1
Native structures of proteins are formed essentially due to the combining effects of local and distant (in the sense of sequence) interactions among residues. These interaction information are, explicitly or i...
This article is part of a Supplement: Volume 12 Supplement 1
DNA methylation has been shown to play an important role in the silencing of tumor suppressor genes in various tumor types. In order to have a system-wide understanding of the methylation changes that occur in...
Recent technology advances have enabled sequencing of individual genomes, promising to revolutionize biomedical research. However, deep sequencing remains more expensive than microarrays for performing whole-g...
This article is part of a Supplement: Volume 12 Supplement 1
Although many biological databases are applying semantic web technologies, meaningful biological hypothesis testing cannot be easily achieved. Database-driven high throughput genomic hypothesis testing require...
This article is part of a Supplement: Volume 12 Supplement 1
Predicting enzyme active-sites in proteins is an important issue not only for protein sciences but also for a variety of practical applications such as drug design. Because enzyme reaction mechanisms are based...
This article is part of a Supplement: Volume 12 Supplement 1
Clustering of unannotated transcripts is an important task to identify novel families of noncoding RNAs (ncRNAs). Several hierarchical clustering methods have been developed using similarity measures based on ...
This article is part of a Supplement: Volume 12 Supplement 1
Existing methods of predicting DNA-binding proteins used valuable features of physicochemical properties to design support vector machine (SVM) based classifiers. Generally, selection of physicochemical proper...
This article is part of a Supplement: Volume 12 Supplement 1
Gene clusters are genetically important, but their analysis poses significant computational challenges. One of the major reasons for these difficulties is gene conversion among the duplicated regions of the cl...
This article is part of a Supplement: Volume 12 Supplement 1
Graphs provide a natural framework for visualizing and analyzing networks of many types, including biological networks. Network clustering is a valuable approach for summarizing the structure in large networks...
This article is part of a Supplement: Volume 12 Supplement 1
HDX mass spectrometry is a powerful platform to probe protein structure dynamics during ligand binding, protein folding, enzyme catalysis, and such. HDX mass spectrometry analysis derives the protein structure...
This article is part of a Supplement: Volume 12 Supplement 1
In recent years, information about protein structure and function is described in a large amount of articles. However, a naive full-text search by specific keywords often fails to find desired articles, becaus...
This article is part of a Supplement: Volume 12 Supplement 1
MicroRNAs (miRNAs) are small RNA molecules that regulate gene expression at the post-transcriptional level. Recent studies have suggested that miRNAs and transcription factors are primary metazoan gene regulat...
This article is part of a Supplement: Volume 12 Supplement 1
The Gene Ontology (GO) provides a controlled vocabulary for describing genes and gene products. In spite of the undoubted importance of GO, several drawbacks associated with GO and GO-based annotations have be...
This article is part of a Supplement: Volume 12 Supplement 1
Recently, revealing the function of proteins with protein-protein interaction (PPI) networks is regarded as one of important issues in bioinformatics. With the development of experimental methods such as the y...
This article is part of a Supplement: Volume 12 Supplement 1
Accurate and efficient structural alignment of non-coding RNAs (ncRNAs) has grasped more and more attentions as recent studies unveiled the significance of ncRNAs in living organisms. While the Sankoff style s...
This article is part of a Supplement: Volume 12 Supplement 1
With the availability of large scale expression compendia it is now possible to view own findings in the light of what is already available and retrieve genes with an expression profile similar to a set of gen...
This article is part of a Supplement: Volume 12 Supplement 1
Metabolite profiles can be used for identifying molecular signatures and mechanisms underlying diseases since they reflect the outcome of complex upstream genomic, transcriptomic, proteomic and environmental e...
This article is part of a Supplement: Volume 12 Supplement 1
A new binding site comparison algorithm using optimal superposition of the continuous pharmacophoric property distributions is reported. The method demonstrates high sensitivity in discovering both, distantly ...
This article is part of a Supplement: Volume 12 Supplement 1
Hydrogen bonds (H-bonds) play a key role in both the formation and stabilization of protein structures. They form and break while a protein deforms, for instance during the transition from a non-functional to ...
This article is part of a Supplement: Volume 12 Supplement 1
Pharmacological interactions are useful for understanding ligand binding mechanisms of a therapeutic target. These interactions are often inferred from a set of active compounds that were acquired experimental...
This article is part of a Supplement: Volume 12 Supplement 1
A common assumption about enzyme active sites is that their structures are highly conserved to specifically distinguish between closely similar compounds. However, with the discovery of distinct enzymes with s...
This article is part of a Supplement: Volume 12 Supplement 1
In circulating influenza viruses, gradually accumulated mutations on the glycoprotein hemagglutinin (HA), which interacts with infectivity-neutralizing antibodies, lead to the escape of immune system (called a...
This article is part of a Supplement: Volume 12 Supplement 1
HSPs (Heat shock proteins) are highly conserved ubiquitous proteins among species which are involved in maintaining appropriate folding and conformation of other proteins and are thus referred to as molecular ...
This article is part of a Supplement: Volume 12 Supplement 1
The differentiation process from stem cells to fully differentiated cell types is controlled by the interplay of chromatin modifications and transcription factor activity. Histone modifications or transcriptio...
This article is part of a Supplement: Volume 12 Supplement 1
Beta-site amyloid precursor protein cleaving enzyme (BACE-1) is a single-membrane protein belongs to the aspartyl protease class of catabolic enzymes. This enzyme involved in the processing of the amyloid prec...
This article is part of a Supplement: Volume 12 Supplement 1
Many approaches utilize metabolic pathway information to reconstruct the phyletic tree of fully sequenced organisms, but how metabolic networks can add information to original genomic annotations has remained ...
This article is part of a Supplement: Volume 12 Supplement 1
In genome-wide association studies (GWAS), the number of single-nucleotide polymorphisms (SNPs) typically ranges between 500,000 and 1,000,000. Accordingly, detecting gene-gene interactions in GWAS is computat...
This article is part of a Supplement: Volume 12 Supplement 1
Gene set analysis is a powerful method of deducing biological meaning for an a priori defined set of genes. Numerous tools have been developed to test statistical enrichment or depletion in specific pathways o...
This article is part of a Supplement: Volume 12 Supplement 1
Humans are diploid, carrying two copies of each chromosome, one from each parent. Separating the paternal and maternal chromosomes is an important component of genetic analyses such as determining genetic asso...
This article is part of a Supplement: Volume 12 Supplement 1
Allosteric communication in proteins can be induced by the binding of effective ligands, mutations or covalent modifications that regulate a site distant from the perturbed region. To understand allosteric reg...
This article is part of a Supplement: Volume 12 Supplement 1
Phosphorylation motifs represent common patterns around the phosphorylation site. The discovery of such kinds of motifs reveals the underlying regulation mechanism and facilitates the prediction of unknown pho...
This article is part of a Supplement: Volume 12 Supplement 1
Metagenomics is the study of microbial organisms using sequencing applied directly to environmental samples. Technological advances in next-generation sequencing methods are fueling a rapid increase in the num...
This article is part of a Supplement: Volume 12 Supplement 1
The structure conservation in various α-helix subclasses reveals the sequence and context dependent factors causing distortions in the α-helix. The sequence-structure relationship in these subclasses can be used ...
This article is part of a Supplement: Volume 12 Supplement 1
For treating a complex disease such as cancer, we need effective means to control the biological network that underlies the disease. However, biological networks are typically robust to external perturbations,...
This article is part of a Supplement: Volume 12 Supplement 1
Signal transduction is the major mechanism through which cells transmit external stimuli to evoke intracellular biochemical responses. Understanding relationship between external stimuli and corresponding cell...
This article is part of a Supplement: Volume 12 Supplement 1
Discrimination of transcription factor binding sites (TFBS) from background sequences plays a key role in computational motif discovery. Current clustering based algorithms employ homogeneous model for problem...
This article is part of a Supplement: Volume 12 Supplement 1
The gene duplication (GD) problem seeks a species tree that implies the fewest gene duplication events across a given collection of gene trees. Solving this problem makes it possible to use large gene families...
This article is part of a Supplement: Volume 12 Supplement 1
Measuring similarities between tree structured data is important for analysis of RNA secondary structures, phylogenetic trees, glycan structures, and vascular trees. The edit distance is one of the most widely...
This article is part of a Supplement: Volume 12 Supplement 1
Determining the disulfide (S-S) bond pattern in a protein is often crucial for understanding its structure and function. In recent research, mass spectrometry (MS) based analysis has been applied to this probl...
This article is part of a Supplement: Volume 12 Supplement 1
Complex diseases are commonly caused by multiple genes and their interactions with each other. Genome-wide association (GWA) studies provide us the opportunity to capture those disease associated genes and gen...
This article is part of a Supplement: Volume 12 Supplement 1
Un-MAppable Reads Solution (UMARS) is a user-friendly web service focusing on retrieving valuable information from sequence reads that cannot be mapped back to reference genomes. Recently, next-generation sequ...
This article is part of a Supplement: Volume 12 Supplement 1
Modeling in systems biology is vital for understanding the complexity of biological systems across scales and predicting system-level behaviors. To obtain high-quality pathway databases, it is essential to imp...
This article is part of a Supplement: Volume 12 Supplement 1
Although high-throughput microarray based molecular diagnostic technologies show a great promise in cancer diagnosis, it is still far from a clinical application due to its low and instable sensitivities and s...
This article is part of a Supplement: Volume 12 Supplement 1
Ancestral Recombinations Graph (ARG) is a phylogenetic structure that encodes both duplication events, such as mutations, as well as genetic exchange events, such as recombinations: this captures the (genetic)...
This article is part of a Supplement: Volume 12 Supplement 1
We present a data structure enabling rapid heuristic solution to the ancestral genome reconstruction problem for given phylogenies under genomic rearrangement metrics. The efficiency of the greedy algorithm is...
This article is part of a Supplement: Volume 12 Supplement 1
Peptide identification from tandem mass spectrometry (MS/MS) data is one of the most important problems in computational proteomics. This technique relies heavily on the accurate assessment of the quality of p...
This article is part of a Supplement: Volume 12 Supplement 1
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