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BMC Bioinformatics

Volume 13 Supplement 4

Italian Society of Bioinformatics (BITS): Annual Meeting 2011

Research

Edited by Paolo Romano and Manuela Helmer-Citterich

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

Pisa, Italy20-22 June 2011

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  1. Content type: Research

    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...

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

    Citation: BMC Bioinformatics 2012 13(Suppl 4):S1

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  2. Content type: Research

    In recent years, an exponential growing number of tools for protein sequence analysis, editing and modeling tasks have been put at the disposal of the scientific community. Despite the vast majority of these t...

    Authors: Emanuele Bramucci, Alessandro Paiardini, Francesco Bossa and Stefano Pascarella

    Citation: BMC Bioinformatics 2012 13(Suppl 4):S2

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  3. Content type: Research

    Tandem repeats are multiple duplications of substrings in the DNA that occur contiguously, or at a short distance, and may involve some mutations (such as substitutions, insertions, and deletions). Tandem repe...

    Authors: Marco Pellegrini, Maria Elena Renda and Alessio Vecchio

    Citation: BMC Bioinformatics 2012 13(Suppl 4):S3

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  4. Content type: Research

    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...

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

    Citation: BMC Bioinformatics 2012 13(Suppl 4):S4

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  5. Content type: 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...

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

    Citation: BMC Bioinformatics 2012 13(Suppl 4):S5

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  6. Content type: Research

    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...

    Authors: Renato Umeton, Giuseppe Nicosia and C Forbes Dewey Jr

    Citation: BMC Bioinformatics 2012 13(Suppl 4):S6

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  7. Content type: Research

    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 ...

    Authors: Achille Zappa, Andrea Splendiani and Paolo Romano

    Citation: BMC Bioinformatics 2012 13(Suppl 4):S7

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  8. Content type: Research

    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...

    Authors: Giulio Caravagna, Roberto Barbuti and Alberto d'Onofrio

    Citation: BMC Bioinformatics 2012 13(Suppl 4):S8

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  9. Content type: Research

    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...

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

    Citation: BMC Bioinformatics 2012 13(Suppl 4):S9

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  10. Content type: Research

    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...

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

    Citation: BMC Bioinformatics 2012 13(Suppl 4):S11

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  11. Content type: Research

    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...

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

    Citation: BMC Bioinformatics 2012 13(Suppl 4):S12

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  12. Content type: Research

    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...

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

    Citation: BMC Bioinformatics 2012 13(Suppl 4):S13

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  13. Content type: Research

    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...

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

    Citation: BMC Bioinformatics 2012 13(Suppl 4):S14

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  14. Content type: Research

    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...

    Authors: Francesco Maria Calabrese, Domenico Simone and Marcella Attimonelli

    Citation: BMC Bioinformatics 2012 13(Suppl 4):S15

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  15. Content type: Research

    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...

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

    Citation: BMC Bioinformatics 2012 13(Suppl 4):S16

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  16. Content type: Research

    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...

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

    Citation: BMC Bioinformatics 2012 13(Suppl 4):S17

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  17. Content type: Research

    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...

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

    Citation: BMC Bioinformatics 2012 13(Suppl 4):S18

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  18. Content type: Research

    The development of accurate protein-protein docking programs is making this kind of simulations an effective tool to predict the 3D structure and the surface of interaction between the molecular partners in ma...

    Authors: Anna Vangone, Romina Oliva and Luigi Cavallo

    Citation: BMC Bioinformatics 2012 13(Suppl 4):S19

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