Preface
BMC Bioinformatics 2008 9(Suppl 2):S1
Published on: 26 March 2008
Volume 9 Supplement 2
Italian Society of Bioinformatics (BITS): Annual Meeting 2007
Research
Edited by Graziano Pesole
Italian Society of Bioinformatics (BITS): Annual Meeting 2007. Go to conference site.
Naples, Italy
26-28 April 2007
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Research
FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures
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...
BMC Bioinformatics 2008 9(Suppl 2):S2
Published on: 26 March 2008
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Research
CellExcite: an efficient simulation environment for excitable cells
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...
BMC Bioinformatics 2008 9(Suppl 2):S3
Published on: 26 March 2008
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Research
Discovering multi–level structures in bio-molecular data through the Bernstein inequality
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...
BMC Bioinformatics 2008 9(Suppl 2):S4
Published on: 26 March 2008
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Research
Gene expression profile of peripheral blood mononuclear cells in response to HIV-VLPs stimulation
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.
BMC Bioinformatics 2008 9(Suppl 2):S5
Published on: 26 March 2008
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Research
A three-state prediction of single point mutations on protein stability changes
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...
BMC Bioinformatics 2008 9(Suppl 2):S6
Published on: 26 March 2008
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Research
ISOL@: an Italian SOLAnaceae genomics resource
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 ...
BMC Bioinformatics 2008 9(Suppl 2):S7
Published on: 26 March 2008
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Research
In silico docking of urokinase plasminogen activator and integrins
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...
BMC Bioinformatics 2008 9(Suppl 2):S8
Published on: 26 March 2008
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Research
Version VI of the ESTree db: an improved tool for peach transcriptome analysis
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...
BMC Bioinformatics 2008 9(Suppl 2):S9
Published on: 26 March 2008
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Research
CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment
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...
BMC Bioinformatics 2008 9(Suppl 2):S10
Published on: 26 March 2008
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Research
The MoVIN server for the analysis of protein interaction networks
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...
BMC Bioinformatics 2008 9(Suppl 2):S11
Published on: 26 March 2008
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Research
Time-course analysis of genome-wide gene expression data from hormone-responsive human breast cancer cells
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 ...
BMC Bioinformatics 2008 9(Suppl 2):S12
Published on: 26 March 2008
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Research
SNPLims: a data management system for genome wide association studies
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...
BMC Bioinformatics 2008 9(Suppl 2):S13
Published on: 26 March 2008
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Research
Is plant mitochondrial RNA editing a source of phylogenetic incongruence? An answer from in silico and in vivo data sets
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...
BMC Bioinformatics 2008 9(Suppl 2):S14
Published on: 26 March 2008
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Research
SWS: accessing SRS sites contents through Web Services
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...
BMC Bioinformatics 2008 9(Suppl 2):S15
Published on: 26 March 2008
