Volume 10 Supplement 12

Bioinformatics Methods for Biomedical Complex System Applications

Research

Edited by Luciano Milanesi and Paolo Romano

Bioinformatics Methods for Biomedical Complex Systems Applications (NETTAB2008). Go to conference site.

Varenna, Italy

19-21 May 2008

  1. Research

    Data recovery and integration from public databases uncovers transformation-specific transcriptional downregulation of cAMP-PKA pathway-encoding genes

    The integration of data from multiple genome-wide assays is essential for understanding dynamic spatio-temporal interactions within cells. Such integration, which leads to a more complete view of cellular proc...

    Chiara Balestrieri, Lilia Alberghina, Marco Vanoni and Ferdinando Chiaradonna

    BMC Bioinformatics 2009 10(Suppl 12):S1

    Published on: 15 October 2009

  2. Introduction

    Trends in modeling Biomedical Complex Systems

    In this paper we provide an introduction to the techniques for multi-scale complex biological systems, from the single bio-molecule to the cell, combining theoretical modeling, experiments, informatics tools a...

    Luciano Milanesi, Paolo Romano, Gastone Castellani, Daniel Remondini and Pietro Liò

    BMC Bioinformatics 2009 10(Suppl 12):I1

    Published on: 15 October 2009

  3. Research

    The Human EST Ontology Explorer: a tissue-oriented visualization system for ontologies distribution in human EST collections

    The NCBI dbEST currently contains more than eight million human Expressed Sequenced Tags (ESTs). This wide collection represents an important source of information for gene expression studies, provided it can ...

    Ivan Merelli, Andrea Caprera, Alessandra Stella, Marcello Del Corvo, Luciano Milanesi and Barbara Lazzari

    BMC Bioinformatics 2009 10(Suppl 12):S2

    Published on: 15 October 2009

  4. Research

    In silico saturation mutagenesis and docking screening for the analysis of protein-ligand interaction: the Endothelial Protein C Receptor case study

    The design of mutants in protein functional regions, such as the ligand binding sites, is a powerful approach to recognize the determinants of specific protein activities in cellular pathways. For an exhaustiv...

    Federica Chiappori, Pasqualina D'Ursi, Ivan Merelli, Luciano Milanesi and Ermanna Rovida

    BMC Bioinformatics 2009 10(Suppl 12):S3

    Published on: 15 October 2009

  5. Research

    Developing optimal input design strategies in cancer systems biology with applications to microfluidic device engineering

    Mechanistic models are becoming more and more popular in Systems Biology; identification and control of models underlying biochemical pathways of interest in oncology is a primary goal in this field. Unfortuna...

    Filippo Menolascina, Domenico Bellomo, Thomas Maiwald, Vitoantonio Bevilacqua, Caterina Ciminelli, Angelo Paradiso and Stefania Tommasi

    BMC Bioinformatics 2009 10(Suppl 12):S4

    Published on: 15 October 2009

  6. Research

    Clinical bioinformatics for complex disorders: a schizophrenia case study

    In the diagnosis of complex diseases such as neurological pathologies, a wealth of clinical and molecular information is often available to help the interpretation. Yet, the pieces of information are usually c...

    Emanuel Schwarz, F Markus Leweke, Sabine Bahn and Pietro Liò

    BMC Bioinformatics 2009 10(Suppl 12):S6

    Published on: 15 October 2009

  7. Research

    XML-based approaches for the integration of heterogeneous bio-molecular data

    The today's public database infrastructure spans a very large collection of heterogeneous biological data, opening new opportunities for molecular biology, bio-medical and bioinformatics research, but raising ...

    Marco Mesiti, Ernesto Jiménez-Ruiz, Ismael Sanz, Rafael Berlanga-Llavori, Paolo Perlasca, Giorgio Valentini and David Manset

    BMC Bioinformatics 2009 10(Suppl 12):S7

    Published on: 15 October 2009

  8. Research

    Identification of functionally related genes using data mining and data integration: a breast cancer case study

    The identification of the organisation and dynamics of molecular pathways is crucial for the understanding of cell function. In order to reconstruct the molecular pathways in which a gene of interest is involv...

    Ettore Mosca, Gloria Bertoli, Eleonora Piscitelli, Laura Vilardo, Rolland A Reinbold, Ileana Zucchi and Luciano Milanesi

    BMC Bioinformatics 2009 10(Suppl 12):S8

    Published on: 15 October 2009

  9. Research

    Survival Online: a web-based service for the analysis of correlations between gene expression and clinical and follow-up data

    Complex microarray gene expression datasets can be used for many independent analyses and are particularly interesting for the validation of potential biomarkers and multi-gene classifiers. This article presen...

    Luca Corradi, Valentina Mirisola, Ivan Porro, Livia Torterolo, Marco Fato, Paolo Romano and Ulrich Pfeffer

    BMC Bioinformatics 2009 10(Suppl 12):S10

    Published on: 15 October 2009

  10. Research

    A Perl procedure for protein identification by Peptide Mass Fingerprinting

    One of the topics of major interest in proteomics is protein identification. Protein identification can be achieved by analyzing the mass spectrum of a protein sample through different approaches. One of them,...

    Alessandra Tiengo, Nicola Barbarini, Sonia Troiani, Luisa Rusconi and Paolo Magni

    BMC Bioinformatics 2009 10(Suppl 12):S11

    Published on: 15 October 2009

  11. Research

    Analysis and modelling of motility of cell populations with MotoCell

    Cell motility plays a central role in development, wound-healing and tumour invasion. Cultures of eucariotic cells are a complex system where most cells move according to 'random' patterns, but may also be ind...

    Concita Cantarella, Leandra Sepe, Francesca Fioretti, Maria Carla Ferrari and Giovanni Paolella

    BMC Bioinformatics 2009 10(Suppl 12):S12

    Published on: 15 October 2009

  12. Research

    Conditional independence relations among biological markers may improve clinical decision as in the case of triple negative breast cancers

    The associations existing among different biomarkers are important in clinical settings because they contribute to the characterisation of specific pathways related to the natural history of the disease, genet...

    Federico M Stefanini, Danila Coradini and Elia Biganzoli

    BMC Bioinformatics 2009 10(Suppl 12):S13

    Published on: 15 October 2009

  13. Research

    Towards a systems biology approach to mammalian cell cycle: modeling the entrance into S phase of quiescent fibroblasts after serum stimulation

    The cell cycle is a complex process that allows eukaryotic cells to replicate chromosomal DNA and partition it into two daughter cells. A relevant regulatory step is in the G0/G1 phase, a point called the restric...

    Roberta Alfieri, Matteo Barberis, Ferdinando Chiaradonna, Daniela Gaglio, Luciano Milanesi, Marco Vanoni, Edda Klipp and Lilia Alberghina

    BMC Bioinformatics 2009 10(Suppl 12):S16

    Published on: 15 October 2009

  14. Research

    Protopia: a protein-protein interaction tool

    Protein-protein interactions can be considered the basic skeleton for living organism self-organization and homeostasis. Impressive quantities of experimental data are being obtained and computational tools ar...

    Alejandro Real-Chicharro, Iván Ruiz-Mostazo, Ismael Navas-Delgado, Amine Kerzazi, Othmane Chniber, Francisca Sánchez-Jiménez, Miguel Ángel Medina and José F Aldana-Montes

    BMC Bioinformatics 2009 10(Suppl 12):S17

    Published on: 15 October 2009