Volume 15 Supplement 1

Integrated Bio-Search: Selected Works from the 12th International Workshop on Network Tools and Applications in Biology (NETTAB 2012)

Research

Edited by Paolo Romano and Marco Masseroli

Publication of this supplement has not been supported by sponsorship. The source of funding used to cover the open access charges is declared by the authors in each article. Articles have undergone the journal's standard peer-review process for supplements. The Supplement Editors declare that they have no competing interests.

Integrated Bio-Search: 12th International Workshop on Network Tools and Applications in Biology (NETTAB 2012). Go to conference site.

Como, Italy

14-16 November 2012

  1. Introduction

    NETTAB 2012 on "Integrated Bio-Search"

    The NETTAB 2012 workshop, held in Como on November 14-16, 2012, was devoted to "Integrated Bio-Search", that is to technologies, methods, architectures, systems and applications for searching, retrieving, inte...

    Paolo Romano, Frédérique Lisacek and Marco Masseroli

    BMC Bioinformatics 2014 15(Suppl 1):S1

    Published on: 10 January 2014

  2. Review

    Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information

    Many efforts exist to design and implement approaches and tools for data capture, integration and analysis in the life sciences. Challenges are not only the heterogeneity, size and distribution of information ...

    Marco Masseroli, Barend Mons, Erik Bongcam-Rudloff, Stefano Ceri, Alexander Kel, François Rechenmann, Frederique Lisacek and Paolo Romano

    BMC Bioinformatics 2014 15(Suppl 1):S2

    Published on: 10 January 2014

  3. Research

    Integrating microRNA target predictions for the discovery of gene regulatory networks: a semi-supervised ensemble learning approach

    MicroRNAs (miRNAs) are small non-coding RNAs which play a key role in the post-transcriptional regulation of many genes. Elucidating miRNA-regulated gene networks is crucial for the understanding of mechanisms...

    Gianvito Pio, Donato Malerba, Domenica D'Elia and Michelangelo Ceci

    BMC Bioinformatics 2014 15(Suppl 1):S4

    Published on: 10 January 2014

  4. Software

    CorrelaGenes: a new tool for the interpretation of the human transcriptome

    The amount of gene expression data available in public repositories has grown exponentially in the last years, now requiring new data mining tools to transform them in information easily accessible to biologists.

    Paolo Cremaschi, Sergio Rovida, Lucia Sacchi, Antonella Lisa, Francesca Calvi, Alessandra Montecucco, Giuseppe Biamonti, Silvia Bione and Gianni Sacchi

    BMC Bioinformatics 2014 15(Suppl 1):S6

    Published on: 10 January 2014

  5. Research

    Reducing bias in RNA sequencing data: a novel approach to compute counts

    In the last decade, Next-Generation Sequencing technologies have been extensively applied to quantitative transcriptomics, making RNA sequencing a valuable alternative to microarrays for measuring and comparin...

    Francesca Finotello, Enrico Lavezzo, Luca Bianco, Luisa Barzon, Paolo Mazzon, Paolo Fontana, Stefano Toppo and Barbara Di Camillo

    BMC Bioinformatics 2014 15(Suppl 1):S7

    Published on: 10 January 2014

  6. Software

    AnnotateGenomicRegions: a web application

    Modern genomic technologies produce large amounts of data that can be mapped to specific regions in the genome. Among the first steps in interpreting the results is annotation of genomic regions with known fea...

    Luca Zammataro, Rita DeMolfetta, Gabriele Bucci, Arnaud Ceol and Heiko Muller

    BMC Bioinformatics 2014 15(Suppl 1):S8

    Published on: 10 January 2014

  7. Research

    Toolboxes for a standardised and systematic study of glycans

    Recent progress in method development for characterising the branched structures of complex carbohydrates has now enabled higher throughput technology. Automation of structure analysis then calls for software ...

    Matthew P Campbell, René Ranzinger, Thomas Lütteke, Julien Mariethoz, Catherine A Hayes, Jingyu Zhang, Yukie Akune, Kiyoko F Aoki-Kinoshita, David Damerell, Giorgio Carta, Will S York, Stuart M Haslam, Hisashi Narimatsu, Pauline M Rudd, Niclas G Karlsson, Nicolle H Packer…

    BMC Bioinformatics 2014 15(Suppl 1):S9

    Published on: 10 January 2014

  8. Research

    A tool for mapping Single Nucleotide Polymorphisms using Graphics Processing Units

    Single Nucleotide Polymorphism (SNP) genotyping analysis is very susceptible to SNPs chromosomal position errors. As it is known, SNPs mapping data are provided along the SNP arrays without any necessary infor...

    Andrea Manconi, Alessandro Orro, Emanuele Manca, Giuliano Armano and Luciano Milanesi

    BMC Bioinformatics 2014 15(Suppl 1):S10

    Published on: 10 January 2014

  9. Research

    The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again

    The ISA-Tab format and software suite have been developed to break the silo effect induced by technology-specific formats for a variety of data types and to better support experimental metadata tracking. Exper...

    Alejandra González-Beltrán, Steffen Neumann, Eamonn Maguire, Susanna-Assunta Sansone and Philippe Rocca-Serra

    BMC Bioinformatics 2014 15(Suppl 1):S11

    Published on: 10 January 2014

  10. Research

    Distilling structure in Taverna scientific workflows: a refactoring approach

    Scientific workflows management systems are increasingly used to specify and manage bioinformatics experiments. Their programming model appeals to bioinformaticians, who can use them to easily specify complex ...

    Sarah Cohen-Boulakia, Jiuqiang Chen, Paolo Missier, Carole Goble, Alan R Williams and Christine Froidevaux

    BMC Bioinformatics 2014 15(Suppl 1):S12

    Published on: 10 January 2014

  11. Software

    QTREDS: a Ruby on Rails-based platform for omics laboratories

    In recent years, the experimental aspects of the laboratory activities have been growing in complexity in terms of amount and diversity of data produced, equipment used, of computer-based workflows needed to p...

    Piergiorgio Palla, Gianfranco Frau, Laura Vargiu and Patricia Rodriguez-Tomé

    BMC Bioinformatics 2014 15(Suppl 1):S13

    Published on: 10 January 2014

  12. Research

    Development and tuning of an original search engine for patent libraries in medicinal chemistry

    The large increase in the size of patent collections has led to the need of efficient search strategies. But the development of advanced text-mining applications dedicated to patents of the biomedical field re...

    Emilie Pasche, Julien Gobeill, Olivier Kreim, Fatma Oezdemir-Zaech, Therese Vachon, Christian Lovis and Patrick Ruch

    BMC Bioinformatics 2014 15(Suppl 1):S15

    Published on: 10 January 2014