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The Split ends (Spen) family are large proteins characterised by N-terminal RNA recognition motifs (RRMs) and a conserved SPOC (Spen paralog and ortholog C-terminal) domain. The aim of this study is to charact...
Oligonucleotide frequencies were shown to be conserved signatures for bacterial genomes, however, the underlying constraints have yet not been resolved in detail. In this paper we analyzed oligonucleotide usag...
In population-based studies, it is generally recognized that single nucleotide polymorphism (SNP) markers are not independent. Rather, they are carried by haplotypes, groups of SNPs that tend to be coinherited...
The proliferation of structural and functional studies of RNA has revealed an increasing range of RNA's structural repertoire. Toward the objective of systematic cataloguing of RNA's structural repertoire, we ...
Research involving expressed sequence tags (ESTs) is intricately coupled to the existence of large, well-annotated sequence repositories. Comparatively complete and satisfactory annotated public sequence libra...
Multi-locus sequence typing (MLST) is a method of typing that facilitates the discrimination of microbial isolates by comparing the sequences of housekeeping gene fragments. The mlstdbNet software enables the ...
The behaviors of cells in metazoans are context dependent, thus large-scale multi-cellular modeling is often necessary, for which cellular automata are natural candidates. Two related issues are involved in ce...
The increasing complexity of genomic data presents several challenges for biologists. Limited computer monitor views of data complexity and the dynamic nature of data in the midst of discovery increase the cha...
Identification and characterization of novel Plasmodium gene families is necessary for developing new anti-malarial therapeutics. The products of the Plasmodium falciparum gene, MB2, were shown previously to have...
The original article was published in BMC Bioinformatics 2004 5:5
Due to the high cost and low reproducibility of many microarray experiments, it is not surprising to find a limited number of patient samples in each study, and very few common identified marker genes among di...
When processing microarray data sets, we recently noticed that some gene names were being changed inadvertently to non-gene names.
Post-translational phosphorylation is one of the most common protein modifications. Phosphoserine, threonine and tyrosine residues play critical roles in the regulation of many cellular processes. The fast gro...
Detailed knowledge of the subcellular location of each expressed protein is critical to a full understanding of its function. Fluorescence microscopy, in combination with methods for fluorescent tagging, is th...
When DNA microarray data are used for gene clustering, genotype/phenotype correlation studies, or tissue classification the signal intensities are usually transformed and normalized in several steps in order t...
The PathoLogic program constructs Pathway/Genome databases by using a genome's annotation to predict the set of metabolic pathways present in an organism. PathoLogic determines the set of reactions composing t...
The increasing number of protein sequences and 3D structure obtained from genomic initiatives is leading many of us to focus on proteomics, and to dedicate our experimental and computational efforts on the cre...
Microarray-based comparative genomic hybridisation (array CGH) is a technique by which variation in relative copy numbers between two genomes can be analysed by competitive hybridisation to DNA microarrays. Th...
The original article was published in BMC Bioinformatics 2004 5:6
Despite the passing of more than a year since the first outbreak of Severe Acute Respiratory Syndrome (SARS), efficient counter-measures are still few and many believe that reappearance of SARS, or a similar d...
RNA secondary structure prediction methods based on probabilistic modeling can be developed using stochastic context-free grammars (SCFGs). Such methods can readily combine different sources of information tha...
A routine goal in the analysis of microarray data is to identify genes with expression levels that correlate with known classes of experiments. In a growing number of array data sets, it has been shown that th...
Carbohydrates are involved in a variety of fundamental biological processes and pathological situations. They therefore have a large pharmaceutical and diagnostic potential. Knowledge of the 3D structure of gl...
Rhabdomyosarcoma is a relatively common tumour of the soft tissue, probably due to regulatory disruption of growth and differentiation of skeletal muscle stem cells. Identification of genes differentially expr...
A number of completely sequenced eukaryotic genome data are available in the public domain. Eukaryotic genes are either 'intron containing' or 'intronless'. Eukaryotic 'intronless' genes are interesting datase...
Subcellular localization of a new protein sequence is very important and fruitful for understanding its function. As the number of new genomes has dramatically increased over recent years, a reliable and effic...
We have compared 38 isolates of the SARS-CoV complete genome. The main goal was twofold: first, to analyze and compare nucleotide sequences and to identify positions of single nucleotide polymorphism (SNP), in...
The identification of relevant biological features in large and complex datasets is an important step towards gaining insight in the processes underlying the data. Other advantages of feature selection include...
Microarray data must be normalized because they suffer from multiple biases. We have identified a source of spatial experimental variability that significantly affects data obtained with Cy3/Cy5 spotted glass ...
Existing sequence alignment algorithms assume that similarities between DNA or amino acid sequences are linearly ordered. That is, stretches of similar nucleotides or amino acids are in the same order in both ...
A new sequence independent bioinformatics approach allowing genome-wide search for proteins with similar three dimensional structures has been developed. By utilizing the numerical output of the sequence threa...
The usefulness of log2 transformation for cDNA microarray data has led to its widespread application to Affymetrix data. For Affymetrix data, where absolute intensities are indicative of number of transcripts, th...
Computational gene prediction continues to be an important problem, especially for genomes with little experimental data.
Because loops connect regular secondary structures, analysis of the former depends directly on the definition of the latter. The numerous assignment methods, however, can offer different definitions. In a prev...
Transcriptional regulation is a key mechanism in the functioning of the cell, and is mostly effected through transcription factors binding to specific recognition motifs located upstream of the coding region o...
It is well known that different species have different protein domain repertoires, and indeed that some protein domains are kingdom specific. This information has not yet been incorporated into statistical met...
The Distributed Annotation System (DAS) allows merging of DNA sequence annotations from multiple sources and provides a single annotation view. A straightforward way to establish a DAS annotation server is to ...
The detection of small yet statistically significant differences in gene expression in spotted DNA microarray studies is an ongoing challenge. Meeting this challenge requires careful examination of the perform...
Several aspects of microarray data analysis are dependent on identification of genes expressed at or near the limits of detection. For example, regression-based normalization methods rely on the premise that m...
An increasing number of whole viral and bacterial genomes are being sequenced and deposited in public databases. In parallel to the mounting interest in whole genomes, the number of whole genome analyses softw...
Accessible surface area (ASA) or solvent accessibility of amino acids in a protein has important implications. Knowledge of surface residues helps in locating potential candidates of active sites. Therefore, a...
A large number of PROSITE patterns select false positives and/or miss known true positives. It is possible that – at least in some cases – the weak specificity and/or sensitivity of a pattern is due to the fac...
To examine interactions among the angiotensin converting enzyme (ACE) insertion/deletion, plasminogen activator inhibitor-1 (PAI-1) 4G/5G, and tissue plasminogen activator (t-PA) insertion/deletion gene polymorph...
Common existing phylogenetic tree visualisation tools are not able to display readable trees with more than a few thousand nodes. These existing methodologies are based in two dimensional space.
Image analysis is the first crucial step to obtain reliable results from microarray experiments. First, areas in the image belonging to single spots have to be identified. Then, those target areas have to be p...
Once specific genes are identified through high throughput genomics technologies there is a need to sort the final gene list to a manageable size for validation studies. The triaging and sorting of genes often...
Grouping proteins into sequence-based clusters is a fundamental step in many bioinformatic analyses (e.g., homology-based prediction of structure or function). Standard clustering methods such as single-linkage c...
Computer programs for the generation of multiple sequence alignments such as "Clustal W" allow detection of regions that are most conserved among many sequence variants. However, even for regions that are equa...
The explosion in biological information creates the need for databases that are easy to develop, easy to maintain and can be easily manipulated by annotators who are most likely to be biologists. However, depl...
To identify differentially expressed genes across experimental conditions in oligonucleotide microarray experiments, existing statistical methods commonly use a summary of probe-level expression data for each ...
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