Bioinformatics in Italy: BITS2007, the fourth annual meeting of the Italian Society of Bioinformatics

Authors: Graziano Pesole and Manuela Helmer-Citterich

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...

Authors: Gabriele Ausiello, Pier Federico Gherardini, Paolo Marcatili, Anna Tramontano, Allegra Via and Manuela Helmer-Citterich

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...

Authors: Ezio Bartocci, Flavio Corradini, Emilia Entcheva, Radu Grosu and Scott A Smolka

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...

Authors: Alberto Bertoni and Giorgio Valentini

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.

Authors: Luigi Buonaguro, Alessandro Monaco, Eleonora Aricò, Ena Wang, Maria Lina Tornesello, George K Lewis, Franco M Marincola and Franco M Buonaguro

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...

Authors: Emidio Capriotti, Piero Fariselli, Ivan Rossi and Rita Casadio

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 ...

Authors: Maria Luisa Chiusano, Nunzio D'Agostino, Alessandra Traini, Concetta Licciardello, Enrico Raimondo, Mario Aversano, Luigi Frusciante and Luigi Monti

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...

Authors: Bernard Degryse, Juan Fernandez-Recio, Valentina Citro, Francescol Blasi and Maria Vittoria Cubellis

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...

Authors: Barbara Lazzari, Andrea Caprera, Alberto Vecchietti, Ivan Merelli, Francesca Barale, Luciano Milanesi, Alessandra Stella and Carlo Pozzi

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...

Authors: Svetlin A Manavski and Giorgio Valle

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...

Authors: Paolo Marcatili, Giovanni Bussotti and Anna Tramontano

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 ...

Authors: Margherita Mutarelli, Luigi Cicatiello, Lorenzo Ferraro, Olì MV Grober, Maria Ravo, Angelo M Facchiano, Claudia Angelini and Alessandro Weisz

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...

Authors: Alessandro Orro, Guia Guffanti, Erika Salvi, Fabio Macciardi and Luciano Milanesi

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...

Authors: Ernesto Picardi and Carla Quagliariello

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...

Authors: Paolo Romano and Domenico Marra