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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 ...
Mascotâ„¢ is a commonly used protein identification program for MS as well as for tandem MS data. When analyzing huge shotgun proteomics datasets with Mascotâ„¢'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...
Numerous microarray analysis programs have been created through the efforts of Open Source software development projects. Providing browser-based interfaces that allow these programs to be executed over the In...
The completion of the Human Genome Project has resulted in large quantities of biological data which are proving difficult to manage and integrate effectively. There is a need for a system that is able to auto...
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...
NemaFootPrinter (Nematode Transcription Factor Scan Through Philogenetic Footprinting) is a web-based software for interactive identification of conserved, non-exonic DNA segments in the genomes of C. elegans and...
The application of high throughput approaches to the identification of protein interactions has offered for the first time a glimpse of the global interactome of some model organisms. Until now, however, such ...
Protein kinases are a well defined family of proteins, characterized by the presence of a common kinase catalytic domain and playing a significant role in many important cellular processes, such as proliferati...
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...
Analysis of inherited diseases and their associated phenotypes is of great importance to gain knowledge of underlying genetic interactions and could ultimately give clinically useful insights into disease proc...
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...
The ESTree db http://​www.​itb.​cnr.​it/​estree/​ represents a collection of Prunus persica expressed sequenced tags (ESTs) and is intended as a resource for peach...
Histones are short proteins involved in chromatin packaging; in eukaryotes, two H2a-H2b and H3-H4 histone dimers form the nucleosomal core, which acts as the fundamental DNA-packaging element. The double histo...
Routine application of gene expression microarray technology is rapidly producing large amounts of data that necessitate new approaches of analysis. The analysis of a specific microarray experiment profits eno...
The SH3 domain family is one of the most representative and widely studied cases of so-called Peptide Recognition Modules (PRM). The polyproline II motif PxxP that generally characterizes its ligands does not ...
Structure prediction of membrane proteins is still a challenging computational problem. Hidden Markov models (HMM) have been successfully applied to the problem of predicting membrane protein topology. In a pr...
Reconstructing regulatory networks from gene expression profiles is a challenging problem of functional genomics. In microarray studies the number of samples is often very limited compared to the number of gen...
The organic polychlorinated compounds like dichlorodiphenyltrichloroethane with its metabolites and polychlorinated biphenyls are a class of highly persistent environmental contaminants. They have been recogni...
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...
Secondary structure is used in hierarchical classification of protein structures, identification of protein features, such as helix caps and loops, for fold recognition, and as a precursor to ab initio structu...
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...
Improvements of bio-nano-technologies and biomolecular techniques have led to increasing production of high-throughput experimental data. Spotted cDNA microarray is one of the most diffuse technologies, used i...
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...
Population genetics studies based on the analysis of mtDNA and mitochondrial disease studies have produced a huge quantity of sequence data and related information. These data are at present worldwide distribu...
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...
The advent of the technology of DNA microarrays constitutes an epochal change in the classification and discovery of different types of cancer because the information provided by DNA microarrays allows an appr...
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...
One frequent application of microarray experiments is in the study of monitoring gene activities in a cell during cell cycle or cell division. A new challenge for analyzing the microarray experiments is to ide...
Biological Mass Spectrometry is used to analyse peptides and proteins. A mass spectrum generates a list of measured mass to charge ratios and intensities of ionised peptides, which is called a peak-list. In or...
Families of homologous enzymes evolved from common progenitors. The availability of multiple sequences representing each activity presents an opportunity for extracting information specifying the functionality...
Dehydrogenase enzymes belong to the oxidoreductase class and utilise the coenzymes NAD and NADP. Stereo-selectivity is focused on the C4 hydrogen atoms of the nicotinamide ring of NAD(P). Depending upon which ...
Detecting homology between remotely related protein families is an important problem in computational biology since the biological properties of uncharacterized proteins can often be inferred from those of hom...
Determination and quantification of nucleic acid components in a mixture is usually accomplished by microarray approaches, where the mixtures are hybridized against specific probes. As an alternative, we propo...
The identification of unique proteins at different taxonomic levels has both scientific and practical value. Strain-, species- and genus-specific proteins can provide insight into the criteria that define an o...
Sequence alignment is a common tool in bioinformatics and comparative genomics. It is generally assumed that multiple sequence alignment yields better results than pair wise sequence alignment, but this assump...
The development of high-throughput technologies such as yeast two-hybrid systems and mass spectrometry technologies has made it possible to generate large protein-protein interaction (PPI) datasets. Mining the...
The responses to interleukin 1 (IL-1) in human chondrocytes constitute a complex regulatory mechanism, where multiple transcription factors interact combinatorially to transcription-factor binding motifs (TFBM...
A major challenge in computational genomics is the development of methodologies that allow accurate genome-wide prediction of the regulatory targets of a transcription factor. We present a method for target id...
In two-channel competitive genomic hybridization microarray experiments, the ratio of the two fluorescent signal intensities at each spot on the microarray is commonly used to infer the relative amounts of the...
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