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Clustering of gene expression patterns is a well-studied technique for elucidating trends across large numbers of transcripts and for identifying likely co-regulated genes. Even the best clustering methods, ho...
Methods for predicting protein function directly from amino acid sequences are useful tools in the study of uncharacterised protein families and in comparative genomics. Until now, this problem has been approa...
A large number of genes usually show differential expressions in a microarray experiment with two types of tissues, and the p-values of a proper statistical test are often used to quantify the significance of the...
In recent years protein structure prediction methods using local structure information have shown promising improvements. The quality of new fold predictions has risen significantly and in fold recognition inc...
Many proteomics initiatives require integration of all information with uniformcriteria from collection of samples and data display to publication of experimental results. The integration and exchanging of the...
The choice of probe set algorithms for expression summary in a GeneChip study has a great impact on subsequent gene expression data analysis. Spiked-in cRNAs with known concentration are often used to assess t...
Various experimental techniques yield peptides that are biologically active but have unfavourable pharmacological properties. The design of structurally similar organic compounds, i.e. peptide mimetics, is a c...
Benchmarking algorithms in structural bioinformatics often involves the construction of datasets of proteins with given sequence and structural properties. The SCOP database is a manually curated structural cl...
It necessary to use highly accurate and statistics-based systems for viral and phage genome annotations. The GeneMark systems for gene-finding in virus and phage genomes suffer from some basic drawbacks. This ...
Single nucleotide polymorphisms (SNPs) are locations at which the genomic sequences of population members differ. Since these differences are known to follow patterns, disease association studies are facilitat...
Expressed sequence tag (EST) datasets represent perhaps the largest collection of genetic information. ESTs can be exploited in a variety of biological experiments and analysis. Here we are interested in the d...
Through the use of DNA microarrays it is now possible to obtain quantitative measurements of the expression of thousands of genes from a biological sample. This technology yields a global view of gene expressi...
Escherichia coli is the model organism for which our knowledge of its regulatory network is the most extensive. Over the last few years, our project has been collecting and curating the literature concerning E. c...
Single nucleotide polymorphisms (SNP) constitute more than 90% of the genetic variation, and hence can account for most trait differences among individuals in a given species. Polymorphism detection software P...
Selection of relevant genes for sample classification is a common task in most gene expression studies, where researchers try to identify the smallest possible set of genes that can still achieve good predicti...
Protein-protein interactions have traditionally been studied on a small scale, using classical biochemical methods to investigate the proteins of interest. More recently large-scale methods, such as two-hybrid...
Many vital biological processes, including transcription and splicing, require a combination of short, degenerate sequence patterns, or motifs, adjacent to defined sequence features. Although these motifs occu...
Type 1 diabetes mellitus (T1DM) is a autoimmune disease caused by a long-term negative balance between immune-mediated beta-cell damage and beta-cell repair/regeneration. Following immune-mediated damage the b...
MicroRNAs (miRNAs) are a group of short (~22 nt) non-coding RNAs that play important regulatory roles. MiRNA precursors (pre-miRNAs) are characterized by their hairpin structures. However, a large amount of si...
The quality of microarray data can seriously affect the accuracy of downstream analyses. In order to reduce variability and enhance signal reproducibility in these data, many normalization methods have been pr...
Through genetic engineering it is possible to introduce targeted genetic changes and hereby engineer the metabolism of microbial cells with the objective to obtain desirable phenotypes. However, owing to the c...
Significant inconsistencies between probe-to-gene annotations between different releases of probe set identifiers by commercial microarray platform solutions have been reported. Such inconsistencies lead to mi...
Many cutting-edge microarray analysis tools and algorithms, including commonly used limma and affy packages in Bioconductor, need sophisticated knowledge of mathematics, statistics and computer skills for impl...
In bioinformatics and genomics, there are many applications designed to investigate the common properties for a set of genes. Often, these multi-gene analysis tools attempt to reveal sequential, functional, an...
Translational research requires taking basic science observations and developing them into clinically useful tests and therapeutics. We have developed a process to develop molecular biomarkers for diagnosis an...
Different classes of haplotype block algorithms exist and the ideal dataset to assess their performance would be to comprehensively re-sequence a large genomic region in a large population. Such data sets are ...
One of the most evident achievements of bioinformatics is the development of methods that transfer biological knowledge from characterised proteins to uncharacterised sequences. This mode of protein function a...
Estimators of free energies are routinely used to judge the quality of protein structural models. As these estimators still present inaccuracies, they are frequently evaluated by discriminating native or nativ...
In expressed sequence tag (EST) sequencing, we are often interested in how many genes we can capture in an EST sample of a targeted size. This information provides insights to sequencing efficiency in experime...
Elucidating the dynamic behaviour of genetic regulatory networks is one of the most significant challenges in systems biology. However, conventional quantitative predictions have been limited to small networks...
The alignment of multiple protein sequences is a fundamental step in the analysis of biological data. It has traditionally been applied to analyzing protein families for conserved motifs, phylogeny, structural...
Good statistical models for analyzing and simulating multilocus recombination data exist but are not accessible to many biologists because their use requires reasonably sophisticated mathematical and computati...
Protein-protein association is essential for a variety of cellular processes and hence a large number of investigations are being carried out to understand the principles of protein-protein interactions. In th...
MEDLINE/PubMed (hereinafter called PubMed) is one of the most important literature databases for the biological and medical sciences, but it is impossible to read all related records due to the sheer size of t...
Microscopists are familiar with many blemishes that fluorescence images can have due to dust and debris, glass flaws, uneven distribution of fluids or surface coatings, etc. Microarray scans do show similar ar...
Although DNA microarray technologies are very powerful for the simultaneous quantitative characterization of thousands of genes, the quality of the obtained experimental data is often far from ideal. The measu...
Recent advances in sequencing technologies promise to provide a better understanding of the genetics of human disease as well as the evolution of microbial populations. Single Nucleotide Polymorphisms (SNPs) a...
The large gap between the number of protein sequences in databases and the number of functionally characterized proteins calls for the development of a fast computational tool for the prediction of subnuclear ...
Mascot™ is a commonly used protein identification program for MS as well as for tandem MS data. When analyzing huge shotgun proteomics datasets with Mascot™'s native tools, limits of computing resources are ea...
Clustering is a key step in the analysis of gene expression data, and in fact, many classical clustering algorithms are used, or more innovative ones have been designed and validated for the task. Despite the ...
Synthetic lethality experiments identify pairs of genes with complementary function. More direct functional associations (for example greater probability of membership in a single protein complex) may be infer...
Biological resources are essential tools for biomedical research. Their availability is promoted through on-line catalogues. Common Access to Biological Resources and Information (CABRI) is a service for distr...
This article is part of a Supplement: Volume 6 Supplement 4
This study concerns the development of a high performance workflow that, using grid technology, correlates different kinds of Bioinformatics data, starting from the base pairs of the nucleotide sequence to the...
This article is part of a Supplement: Volume 6 Supplement 4
In our studies of genetically isolated populations in a remote mountain area in the center of Sardinia (Italy), we found that 80–85% of the inhabitants of each village belong to a single huge pedigree with fam...
This article is part of a Supplement: Volume 6 Supplement 4
The organic polychlorinated compounds like dichlorodiphenyltrichloroethane with its metabolites and polychlorinated biphenyls are a class of highly persistent environmental contaminants. They have been recogni...
This article is part of a Supplement: Volume 6 Supplement 4
Expressed Sequence Tags (ESTs) are short and error-prone DNA sequences generated from the 5' and 3' ends of randomly selected cDNA clones. They provide an important resource for comparative and functional geno...
This article is part of a Supplement: Volume 6 Supplement 4
Neoplastic transformation is a multistep process in which distinct gene products of specific cell regulatory pathways are involved at each stage. Identification of overexpressed genes provides an unprecedented...
This article is part of a Supplement: Volume 6 Supplement 4
The identification of local similarities between two protein structures can provide clues of a common function. Many different methods exist for searching for similar subsets of residues in proteins of known s...
This article is part of a Supplement: Volume 6 Supplement 4
Due to the strict relation between protein function and structure, the prediction of protein 3D-structure has become one of the most important tasks in bioinformatics and proteomics. In fact, notwithstanding t...
This article is part of a Supplement: Volume 6 Supplement 4
The BITS2005 Conference brought together about 200 Italian scientists working in the field of Bioinformatics, students in Biology, Computer Science and Bioinformatics on March 17–19 2005, in Milan. This Editor...
This article is part of a Supplement: Volume 6 Supplement 4
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