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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

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. Gene regulatory networks are widely used by biologists to describe the interactions among genes, proteins and other components at the intra-cellular level. Recently, a great effort has been devoted to give gen...

    Authors: Fabio Fioravanti, Manuela Helmer-Citterich and Enrico Nardelli
    Citation: BMC Bioinformatics 2012 13(Suppl 4):S20
  20. It is known from recent studies that more than 90% of human multi-exon genes are subject to Alternative Splicing (AS), a key molecular mechanism in which multiple transcripts may be generated from a single gen...

    Authors: Arianna Consiglio, Massimo Carella, Giorgio De Caro, Gianfranco Delle Foglie, Candida Giovannelli, Giorgio Grillo, Massimo Ianigro, Flavio Licciulli, Orazio Palumbo, Ada Piepoli, Elena Ranieri and Sabino Liuni
    Citation: BMC Bioinformatics 2012 13(Suppl 4):S21
  21. The identification of robust lists of molecular biomarkers related to a disease is a fundamental step for early diagnosis and treatment. However, methodologies for biomarker discovery using microarray data oft...

    Authors: Tiziana Sanavia, Fabio Aiolli, Giovanni Da San Martino, Andrea Bisognin and Barbara Di Camillo
    Citation: BMC Bioinformatics 2012 13(Suppl 4):S22

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