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Despite experiments showing that the number of microRNA (miRNA) target sites is critical for miRNA targeting, most existing methods focus on identifying individual miRNA target sites and do not model contribut...
Scientists striving to unlock mysteries within complex biological systems face myriad barriers in effectively integrating available information to enhance their understanding. While experimental techniques and...
A significant problem in the study of mechanisms of an organism's development is the elucidation of interrelated factors which are making an impact on the different levels of the organism, such as genes, biolo...
The availability of multiple whole genome sequences has facilitated in silico identification of fixed and polymorphic transposable elements (TE). Whereas polymorphic loci serve as makers for phylogenetic and fore...
Digital atlases provide a common semantic and spatial coordinate system that can be leveraged to compare, contrast, and correlate data from disparate sources. As the quality and amount of biological data conti...
High complexity is considered a hallmark of living systems. Here we investigate the complexity of temporal gene expression patterns using the concept of Permutation Entropy (PE) first introduced in dynamical s...
Most genomic data have ultra-high dimensions with more than 10,000 genes (probes). Regularization methods with L1 and L p penalty have been extensively studied in survival a...
As protein interactions mediate most cellular mechanisms, protein-protein interaction networks are essential in the study of cellular processes. Consequently, several large-scale interactome mapping projects h...
DNA instability profiles have been used recently for predicting the transcriptional start site and the location of core promoters, and to gain insight into promoter action. It was also shown that the use of th...
With the expansion of public repositories such as the Gene Expression Omnibus (GEO), we are rapidly cataloging cellular transcriptional responses to diverse experimental conditions. Methods that query these re...
InterPro is a collection of protein signatures for the classification and automated annotation of proteins. Interproscan is a software tool that scans protein sequences against Interpro member databases using ...
This article is part of a Supplement: Volume 11 Supplement 12
There is a huge demand on bioinformaticians to provide their biologists with user friendly and scalable software infrastructures to capture, exchange, and exploit the unprecedented amounts of new *omics data. ...
This article is part of a Supplement: Volume 11 Supplement 12
Computer languages can be domain-related, and in the case of multidisciplinary projects, knowledge of several languages will be needed in order to quickly implements ideas. Moreover, each computer language has...
This article is part of a Supplement: Volume 11 Supplement 12
The HapMap project is a publicly available catalogue of common genetic variants that occur in humans, currently including several million SNPs across 1115 individuals spanning 11 different populations. This im...
This article is part of a Supplement: Volume 11 Supplement 12
With the rapid accumulation of phosphoproteomics data, phosphorylation-site prediction is becoming an increasingly active research area. More than a dozen phosphorylation-site prediction tools have been releas...
This article is part of a Supplement: Volume 11 Supplement 12
The biosciences increasingly face the challenge of integrating a wide variety of available data, information and knowledge in order to gain an understanding of biological systems. Data integration is supported...
This article is part of a Supplement: Volume 11 Supplement 12
The emergence and uptake of Semantic Web technologies by the Life Sciences provides exciting opportunities for exploring novel ways to conduct in silico science. Web Service Workflows are already becoming first-c...
This article is part of a Supplement: Volume 11 Supplement 12
An important focus of genomic science is the discovery and characterization of all functional elements within genomes. In silico methods are used in genome studies to discover putative regulatory genomic elements...
This article is part of a Supplement: Volume 11 Supplement 12
The Open Source movement and its technologies are popular in the bioinformatics community because they provide freely available tools and resources for research. In order to feed the steady demand for updates ...
This article is part of a Supplement: Volume 11 Supplement 12
Widespread adoption of high-throughput sequencing has greatly increased the scale and sophistication of computational infrastructure needed to perform genomic research. An alternative to building and maintaini...
This article is part of a Supplement: Volume 11 Supplement 12
Clouds and MapReduce have shown themselves to be a broadly useful approach to scientific computing especially for parallel data intensive applications. However they have limited applicability to some areas suc...
This article is part of a Supplement: Volume 11 Supplement 12
Since the introduction of next-generation DNA sequencers the rapid increase in sequencer throughput, and associated drop in costs, has resulted in more than a dozen human genomes being resequenced over the las...
This article is part of a Supplement: Volume 11 Supplement 12
Bioinformatics researchers are now confronted with analysis of ultra large-scale data sets, a problem that will only increase at an alarming rate in coming years. Recent developments in open source software, t...
This article is part of a Supplement: Volume 11 Supplement 12
Small RNAs are known to regulate diverse gene expression processes including translation, transcription, and splicing. Among small RNAs, the microRNAs (miRNAs) of 17 to 27 nucleotides (nts) undergo biogeneses ...
We propose a sequence clustering algorithm and compare the partition quality and execution time of the proposed algorithm with those of a popular existing algorithm. The proposed clustering algorithm uses a gr...
Expression levels for 47294 transcripts in lymphoblastoid cell lines from all 270 HapMap phase II individuals, and genotypes (both HapMap phase II and III) of 3.96 million single nucleotide polymorphisms (SNPs...
Traditional genome alignment methods consider sequence alignment as a variation of the string edit distance problem, and perform alignment by matching characters of the two sequences. They are often computatio...
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...
A ‘head-to-head’ (h2h) gene pair is defined as a genomic locus in which two adjacent genes are divergently transcribed from opposite strands of DNA. In our previous work, this gene organization was found to be...
This article is part of a Supplement: Volume 11 Supplement 11
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
Most mass spectrometry (MS) based proteomic studies depend on searching acquired tandem mass (MS/MS) spectra against databases of known protein sequences. In these experiments, however, a large number of high ...
This article is part of a Supplement: Volume 11 Supplement 11
As an obligate intracellular parasite, Apicomplexa interacts with the host in the special living environment, competing for energy and nutrients from the host cells by manipulating the host metabolism. Previou...
This article is part of a Supplement: Volume 11 Supplement 11
The characterization of structural variations (SV) such as insertions, deletions and copy number variations is a critical step in the process of understanding the full genetic architecture of organisms. Copy n...
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
The human leukocyte antigen system (HLA) contains many highly variable genes. HLA genes play an important role in the human immune system, and HLA gene matching is crucial for the success of human organ transp...
This article is part of a Supplement: Volume 11 Supplement 11
Clostridium beijerinckii is a valuable bacteria species which has the ability of ABE (acetone, butanol and ethanol) production. It has been shown that Phosphotransferase (PTS) is an important and common system fo...
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
The environment has been playing an instrumental role in shaping and maintaining the morphological, physiological and biochemical diversities of prokaryotes. It has been debatable whether the whole-genome Guan...
This article is part of a Supplement: Volume 11 Supplement 11
Traditional Chinese Medicine (TCM) is characterized by the wide use of herbal formulae, which are capable of systematically treating diseases determined by interactions among various herbs. However, the combin...
This article is part of a Supplement: Volume 11 Supplement 11
Inference of causal regulators responsible for gene expression changes under different conditions is of great importance but remains rather challenging. To date, most approaches use direct binding targets of t...
This article is part of a Supplement: Volume 11 Supplement 11
A bisection-type algorithm for the grammar-based compression of tree-structured data has been proposed recently. In this framework, an elementary ordered-tree grammar (EOTG) and an elementary unordered-tree gr...
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
Recent advancements of experimental techniques for determining protein tertiary structures raise significant challenges for protein bioinformatics. With the number of known structures of unknown function expan...
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...
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