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Volume 15 Supplement 1

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


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, Italy14-16 November 2012

  1. 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...

    Authors: Paolo Romano, Frédérique Lisacek and Marco Masseroli
    Citation: BMC Bioinformatics 2014 15(Suppl 1):S1
  2. 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 ...

    Authors: Marco Masseroli, Barend Mons, Erik Bongcam-Rudloff, Stefano Ceri, Alexander Kel, François Rechenmann, Frederique Lisacek and Paolo Romano
    Citation: BMC Bioinformatics 2014 15(Suppl 1):S2
  3. The huge amount of biomedical-molecular data increasingly produced is providing scientists with potentially valuable information. Yet, such data quantity makes difficult to find and extract those data that are...

    Authors: Marco Masseroli, Matteo Picozzi, Giorgio Ghisalberti and Stefano Ceri
    Citation: BMC Bioinformatics 2014 15(Suppl 1):S3
  4. 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...

    Authors: Gianvito Pio, Donato Malerba, Domenica D'Elia and Michelangelo Ceci
    Citation: BMC Bioinformatics 2014 15(Suppl 1):S4
  5. 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.

    Authors: Paolo Cremaschi, Sergio Rovida, Lucia Sacchi, Antonella Lisa, Francesca Calvi, Alessandra Montecucco, Giuseppe Biamonti, Silvia Bione and Gianni Sacchi
    Citation: BMC Bioinformatics 2014 15(Suppl 1):S6
  6. 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...

    Authors: Francesca Finotello, Enrico Lavezzo, Luca Bianco, Luisa Barzon, Paolo Mazzon, Paolo Fontana, Stefano Toppo and Barbara Di Camillo
    Citation: BMC Bioinformatics 2014 15(Suppl 1):S7
  7. 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...

    Authors: Luca Zammataro, Rita DeMolfetta, Gabriele Bucci, Arnaud Ceol and Heiko Muller
    Citation: BMC Bioinformatics 2014 15(Suppl 1):S8
  8. 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 ...

    Authors: 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…
    Citation: BMC Bioinformatics 2014 15(Suppl 1):S9
  9. 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...

    Authors: Andrea Manconi, Alessandro Orro, Emanuele Manca, Giuliano Armano and Luciano Milanesi
    Citation: BMC Bioinformatics 2014 15(Suppl 1):S10
  10. 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...

    Authors: Alejandra González-Beltrán, Steffen Neumann, Eamonn Maguire, Susanna-Assunta Sansone and Philippe Rocca-Serra
    Citation: BMC Bioinformatics 2014 15(Suppl 1):S11
  11. 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 ...

    Authors: Sarah Cohen-Boulakia, Jiuqiang Chen, Paolo Missier, Carole Goble, Alan R Williams and Christine Froidevaux
    Citation: BMC Bioinformatics 2014 15(Suppl 1):S12
  12. 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...

    Authors: Piergiorgio Palla, Gianfranco Frau, Laura Vargiu and Patricia Rodriguez-Tomé
    Citation: BMC Bioinformatics 2014 15(Suppl 1):S13
  13. In the last decades, a wide number of researchers/clinicians involved in tissue engineering field published several works about the possibility to induce a tissue regeneration guided by the use of biomaterials...

    Authors: Federica Viti, Silvia Scaglione, Alessandro Orro and Luciano Milanesi
    Citation: BMC Bioinformatics 2014 15(Suppl 1):S14
  14. 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...

    Authors: Emilie Pasche, Julien Gobeill, Olivier Kreim, Fatma Oezdemir-Zaech, Therese Vachon, Christian Lovis and Patrick Ruch
    Citation: BMC Bioinformatics 2014 15(Suppl 1):S15

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