Volume 13 Supplement 4

Italian Society of Bioinformatics (BITS): Annual Meeting 2011


Edited by Paolo Romano and Manuela Helmer-Citterich

Eighth Annual Meeting of the Italian Society of Bioinformatics (BITS). Go to conference site.

Pisa, Italy

20-22 June 2011

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  1. Research

    Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee

    Transmembrane proteins (TMPs) constitute about 20~30% of all protein coding genes. The relative lack of experimental structure has so far made it hard to develop specific alignment methods and the current stat...

    Jia-Ming Chang, Paolo Di Tommaso, Jean-François Taly and Cedric Notredame

    BMC Bioinformatics 2012 13(Suppl 4):S1

    Published on: 28 March 2012

  2. Research

    GIDL: a rule based expert system for GenBank Intelligent Data Loading into the Molecular Biodiversity database

    In the scientific biodiversity community, it is increasingly perceived the need to build a bridge between molecular and traditional biodiversity studies. We believe that the information technology could have a...

    Paolo Pannarale, Domenico Catalano, Giorgio De Caro, Giorgio Grillo, Pietro Leo, Graziano Pappadà, Francesco Rubino, Gaetano Scioscia and Flavio Licciulli

    BMC Bioinformatics 2012 13(Suppl 4):S4

    Published on: 28 March 2012

  3. Research

    An ICT infrastructure to integrate clinical and molecular data in oncology research

    The ONCO-i2b2 platform is a bioinformatics tool designed to integrate clinical and research data and support translational research in oncology. It is implemented by the University of Pavia and the IRCCS Fonda...

    Daniele Segagni, Valentina Tibollo, Arianna Dagliati, Alberto Zambelli, Silvia G Priori and Riccardo Bellazzi

    BMC Bioinformatics 2012 13(Suppl 4):S5

    Published on: 28 March 2012

  4. Research

    OREMPdb: a semantic dictionary of computational pathway models

    The information coming from biomedical ontologies and computational pathway models is expanding continuously: research communities keep this process up and their advances are generally shared by means of dedic...

    Renato Umeton, Giuseppe Nicosia and C Forbes Dewey Jr

    BMC Bioinformatics 2012 13(Suppl 4):S6

    Published on: 28 March 2012

  5. Research

    Towards linked open gene mutations data

    With the advent of high-throughput technologies, a great wealth of variation data is being produced. Such information may constitute the basis for correlation analyses between genotypes and phenotypes and, in ...

    Achille Zappa, Andrea Splendiani and Paolo Romano

    BMC Bioinformatics 2012 13(Suppl 4):S7

    Published on: 28 March 2012

  6. Research

    Fine-tuning anti-tumor immunotherapies via stochastic simulations

    Anti-tumor therapies aim at reducing to zero the number of tumor cells in a host within their end or, at least, aim at leaving the patient with a sufficiently small number of tumor cells so that the residual t...

    Giulio Caravagna, Roberto Barbuti and Alberto d'Onofrio

    BMC Bioinformatics 2012 13(Suppl 4):S8

    Published on: 28 March 2012

  7. Research

    Characterization of the emergent properties of a synthetic quasi-cellular system

    The process of solutes entrapment during liposomes formation is interesting for the investigation of the relationship between the formation of compartments and the distribution of molecules inside them; a rele...

    Lorenzo Lazzerini-Ospri, Pasquale Stano, PierLuigi Luisi and Roberto Marangoni

    BMC Bioinformatics 2012 13(Suppl 4):S9

    Published on: 28 March 2012

  8. Research

    Stochastic simulations of minimal cells: the Ribocell model

    Over the last two decades, lipid compartments (liposomes, lipid-coated droplets) have been extensively used as in vitro "minimal" cell models. In particular, simple and complex biomolecular reactions have been...

    Fabio Mavelli

    BMC Bioinformatics 2012 13(Suppl 4):S10

    Published on: 28 March 2012

  9. Research

    Characterization of an inducible promoter in different DNA copy number conditions

    The bottom-up programming of living organisms to implement novel user-defined biological capabilities is one of the main goals of synthetic biology. Currently, a predominant problem connected with the construc...

    Susanna Zucca, Lorenzo Pasotti, Giuliano Mazzini, Maria Gabriella Cusella De Angelis and Paolo Magni

    BMC Bioinformatics 2012 13(Suppl 4):S11

    Published on: 28 March 2012

  10. Research

    In-silico and in-vivo analyses of EST databases unveil conserved miRNAs from Carthamus tinctorius and Cynara cardunculus

    MicroRNAs (miRNAs) are small RNAs (21-24 bp) providing an RNA-based system of gene regulation highly conserved in plants and animals. In plants, miRNAs control mRNA degradation or restrain translation, affecti...

    Domenico Catalano, Domenico Pignone, Gabriella Sonnante and Mariella M Finetti-Sialer

    BMC Bioinformatics 2012 13(Suppl 4):S12

    Published on: 28 March 2012

  11. Research

    Design of a multi-signature ensemble classifier predicting neuroblastoma patients' outcome

    Neuroblastoma is the most common pediatric solid tumor of the sympathetic nervous system. Development of improved predictive tools for patients stratification is a crucial requirement for neuroblastoma therapy...

    Andrea Cornero, Massimo Acquaviva, Paolo Fardin, Rogier Versteeg, Alexander Schramm, Alessandra Eva, Maria Carla Bosco, Fabiola Blengio, Sara Barzaghi and Luigi Varesio

    BMC Bioinformatics 2012 13(Suppl 4):S13

    Published on: 28 March 2012

  12. Research

    Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms

    Predicting protein function has become increasingly demanding in the era of next generation sequencing technology. The task to assign a curator-reviewed function to every single sequence is impracticable. Bioi...

    Marco Falda, Stefano Toppo, Alessandro Pescarolo, Enrico Lavezzo, Barbara Di Camillo, Andrea Facchinetti, Elisa Cilia, Riccardo Velasco and Paolo Fontana

    BMC Bioinformatics 2012 13(Suppl 4):S14

    Published on: 28 March 2012

  13. Research

    Primates and mouse NumtS in the UCSC Genome Browser

    NumtS (N uclear M iT ochondrial S equences) are mitochondrial DNA sequences that, after stress events involving the mitochondrion, colonized the nuclear genome. Accurate mapping of NumtS avoids contamination duri...

    Francesco Maria Calabrese, Domenico Simone and Marcella Attimonelli

    BMC Bioinformatics 2012 13(Suppl 4):S15

    Published on: 28 March 2012

  14. Research

    Intuitive representation of surface properties of biomolecules using BioBlender

    In living cells, proteins are in continuous motion and interaction with the surrounding medium and/or other proteins and ligands. These interactions are mediated by protein features such as electrostatic and l...

    Raluca Mihaela Andrei, Marco Callieri, Maria Francesca Zini, Tiziana Loni, Giuseppe Maraziti, Mike Chen Pan and Monica Zoppè

    BMC Bioinformatics 2012 13(Suppl 4):S16

    Published on: 28 March 2012

  15. Research

    Identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities

    The identification of ligand binding sites is a key task in the annotation of proteins with known structure but uncharacterized function. Here we describe a knowledge-based method exploiting the observation th...

    Valerio Bianchi, Pier Federico Gherardini, Manuela Helmer-Citterich and Gabriele Ausiello

    BMC Bioinformatics 2012 13(Suppl 4):S17

    Published on: 28 March 2012

  16. Research

    Bluues: a program for the analysis of the electrostatic properties of proteins based on generalized Born radii

    The Poisson-Boltzmann (PB) equation and its linear approximation have been widely used to describe biomolecular electrostatics. Generalized Born (GB) models offer a convenient computational approximation for t...

    Federico Fogolari, Alessandra Corazza, Vijaylakshmi Yarra, Anusha Jalaru, Paolo Viglino and Gennaro Esposito

    BMC Bioinformatics 2012 13(Suppl 4):S18

    Published on: 28 March 2012

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