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Randomly shuffled sequences are routinely used in sequence analysis to evaluate the statistical significance of a biological sequence. In many cases, biologists need sophisticated shuffling tools that preserve...
Depending on their specific structures, noncoding RNAs (ncRNAs) play important roles in many biological processes. Interest in developing new topological indices based on RNA graphs has been revived in recent ...
Availability of information about transcription factors (TFs) is crucial for genome biology, as TFs play a central role in the regulation of gene expression. While manual literature curation is expensive and l...
This article is part of a Supplement: Volume 9 Supplement 3
One of the difficulties in mapping biomedical named entities, e.g. genes, proteins, chemicals and diseases, to their concept identifiers stems from the potential variability of the terms. Soft string matching ...
This article is part of a Supplement: Volume 9 Supplement 3
Although fold change is a commonly used criterion in quantitative proteomics for differentiating regulated proteins, it does not provide an estimation of false positive and false negative rates that is often d...
Several biological techniques result in the acquisition of functional sets of cDNAs that must be sequenced and analyzed. The emergence of redundant databases such as UniGene and centralized annotation engines ...
We present a methodology for high-throughput design of oligonucleotide fingerprints for microarray-based pathogen diagnostic assays. The oligonucleotide fingerprints, or DNA microarray probes, are designed for...
The number of protein targets with a known or predicted tri-dimensional structure and of drug-like chemical compounds is growing rapidly and so is the need for new therapeutic compounds or chemical probes. Per...
The systematic capture of appropriately annotated experimental data is a prerequisite for most bioinformatics analyses. Data capture is required not only for submission of data to public repositories, but also...
The identification and study of proteins from metagenomic datasets can shed light on the roles and interactions of the source organisms in their communities. However, metagenomic datasets are characterized by ...
A major obstacle in treatment of HIV is the ability of the virus to mutate rapidly into drug-resistant variants. A method for predicting the susceptibility of mutated HIV strains to antiviral agents would prov...
The expressed sequence tag (EST) methodology is an attractive option for the generation of sequence data for species for which no completely sequenced genome is available. The annotation and comparative analys...
Multi-dimensional scaling (MDS) is aimed to represent high dimensional data in a low dimensional space with preservation of the similarities between data points. This reduction in dimensionality is crucial for...
Ornithine decarboxylase antizymes are proteins which negatively regulate cellular polyamine levels via their affects on polyamine synthesis and cellular uptake. In virtually all organisms from yeast to mammals...
Current sequencing technologies give access to sequence information for genomes and metagenomes at a tremendous speed. Subsequent data processing is mainly performed by automatic pipelines provided by the sequ...
With the rapid emergence of RNA databases and newly identified non-coding RNAs, an efficient compression algorithm for RNA sequence and structural information is needed for the storage and analysis of such dat...
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of evolutionary events acting at the population level, like recombination between genes, hybridization between...
There has been considerable effort focused on developing efficient programs for tagging single-nucleotide polymorphisms (SNPs). Many of these programs do not account for potential reduced genomic coverage resu...
In the past decades, various protein subcellular-location (SCL) predictors have been developed. Most of these predictors, like TMHMM 2.0, SignalP 3.0, PrediSi and Phobius, aim at the identification of one or a...
Systematic approaches for identifying proteins involved in different types of cancer are needed. Experimental techniques such as microarrays are being used to characterize cancer, but validating their results ...
The identification and characterization of interacting domain pairs is an important step towards understanding protein interactions. In the last few years, several methods to predict domain interactions have b...
The conservation of gene order among prokaryotic genomes can provide valuable insight into gene function, protein interactions, or events by which genomes have evolved. Although some tools are available for vi...
Large-scale, comprehensive and standardized high-throughput mouse phenotyping has been established as a tool of functional genome research by the German Mouse Clinic and others. In all these projects, vast amo...
Comparative genomics has become a significant research area in recent years, following the availability of a number of sequenced genomes. The comparison of genomes is of great importance in the analysis of fun...
Analysis of sequence composition is a routine task in genome research. Organisms are characterized by their base composition, dinucleotide relative abundance, codon usage, and so on. Unique subsequences are ma...
Distance-based phylogeny inference methods first estimate evolutionary distances between every pair of taxa, then build a tree from the so-obtained distance matrix. These methods are fast and fairly accurate. ...
Mixture models of mutagenetic trees are evolutionary models that capture several pathways of ordered accumulation of genetic events observed in different subsets of patients. They were used to model HIV progre...
The Golden Spike data set has been used to validate a number of methods for summarizing Affymetrix data sets, sometimes with seemingly contradictory results. Much less use has been made of this data set to eva...
Mass spectrometry is an essential analytical technique for high-throughput analysis in proteomics and metabolomics. The development of new separation techniques, precise mass analyzers and experimental protoco...
Web Services and Workflow Management Systems can support creation and deployment of network systems, able to automate data analysis and retrieval processes in biomedical research. Web Services have been implem...
This article is part of a Supplement: Volume 9 Supplement 2
In plant mitochondria, the post-transcriptional RNA editing process converts C to U at a number of specific sites of the mRNA sequence and usually restores phylogenetically conserved codons and the encoded ami...
This article is part of a Supplement: Volume 9 Supplement 2
Recent progresses in genotyping technologies allow the generation high-density genetic maps using hundreds of thousands of genetic markers for each DNA sample. The availability of this large amount of genotypi...
This article is part of a Supplement: Volume 9 Supplement 2
Microarray experiments enable simultaneous measurement of the expression levels of virtually all transcripts present in cells, thereby providing a ‘molecular picture’ of the cell state. On the other hand, the ...
This article is part of a Supplement: Volume 9 Supplement 2
Protein-protein interactions are at the basis of most cellular processes and crucial for many bio-technological applications. During the last few years the development of high-throughput technologies has produ...
This article is part of a Supplement: Volume 9 Supplement 2
Searching for similarities in protein and DNA databases has become a routine procedure in Molecular Biology. The Smith-Waterman algorithm has been available for more than 25 years. It is based on a dynamic pro...
This article is part of a Supplement: Volume 9 Supplement 2
The ESTree database (db) is a collection of Prunus persica and Prunus dulcis EST sequences that in its current version encompasses 75,404 sequences from 3 almond and 19 peach libraries. Nine peach genotypes and f...
This article is part of a Supplement: Volume 9 Supplement 2
Urokinase, its receptor and the integrins are functionally associated and involved in regulation of cell signaling, migration, adhesion and proliferation. No structural information is available on this potenti...
This article is part of a Supplement: Volume 9 Supplement 2
Present-day ‘-omics’ technologies produce overwhelming amounts of data which include genome sequences, information on gene expression (transcripts and proteins) and on cell metabolic status. These data represent ...
This article is part of a Supplement: Volume 9 Supplement 2
A basic question of protein structural studies is to which extent mutations affect the stability. This question may be addressed starting from sequence and/or from structure. In proteomics and genomics studies...
This article is part of a Supplement: Volume 9 Supplement 2
Baculovirus-expressed HIV-1 Pr55gag Virus-Like Particles (HIV-VLPs) induce maturation and activation of monocyte-derived dendritic cells (MDDCs) with a production of Th1- and Th2-specific cytokines.
This article is part of a Supplement: Volume 9 Supplement 2
The unsupervised discovery of structures (i.e. clusterings) underlying data is a central issue in several branches of bioinformatics. Methods based on the concept of stability have been recently proposed to as...
This article is part of a Supplement: Volume 9 Supplement 2
Brain, heart and skeletal muscle share similar properties of excitable tissue, featuring both discrete behavior (all-or-nothing response to electrical activation) and continuous behavior (recovery to rest foll...
This article is part of a Supplement: Volume 9 Supplement 2
The occurrence of very similar structural motifs brought about by different parts of non homologous proteins is often indicative of a common function. Indeed, relatively small local structures can mediate bind...
This article is part of a Supplement: Volume 9 Supplement 2
This article is part of a Supplement: Volume 9 Supplement 2
Machine-learning tools have gained considerable attention during the last few years for analyzing biological networks for protein function prediction. Kernel methods are suitable for learning from graph-based ...
Protein structure comparison is a key problem in bioinformatics. There exist several methods for doing protein comparison, being the solution of the Maximum Contact Map Overlap problem (MAX-CMO) one of the alt...
Accurate annotation of translation initiation sites (TISs) is essential for understanding the translation initiation mechanism. However, the reliability of TIS annotation in widely used databases such as RefSe...
Although there are a large number of thesauri for the biomedical domain many of them lack coverage in terms and their variant forms. Automatic thesaurus construction based on patterns was first suggested by He...
Visualization of sequence annotation is a common feature in many bioinformatics tools. For many applications it is desirable to restrict the display of such annotation according to a score cutoff, as biologica...
When analyzing microarray data a primary objective is often to find differentially expressed genes. With empirical Bayes and penalized t-tests the sample variances are adjusted towards a global estimate, produ...
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