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Volume 10 Supplement 6

European Molecular Biology Network (EMBnet) Conference 2008: 20th Anniversary Celebration. Leading applications and technologies in bioinformatics

Proceedings

Edited by Erik Bongcam-Rudloff, Domenica D'Elia, Andreas Gisel, Sophia Kossida, Kimmo Mattila and Lubos Klucar

European Molecular Biology Network (EMBnet) Conference 2008: 20th Anniversary Celebration. Go to conference site.

Martina Franca, Italy18-20 September 2008

  1. The EMBnet Conference 2008, focusing on 'Leading Applications and Technologies in Bioinformatics', was organized by the European Molecular Biology network (EMBnet) to celebrate its 20th anniversary. Since its fou...

    Authors: Domenica D'Elia, Andreas Gisel, Nils-Einar Eriksson, Sophia Kossida, Kimmo Mattila, Lubos Klucar and Erik Bongcam-Rudloff
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S1
  2. The identification of protein coding elements in sets of mammalian conserved elements is one of the major challenges in the current molecular biology research. Many features have been proposed for automaticall...

    Authors: Teresa M Creanza, David S Horner, Annarita D'Addabbo, Rosalia Maglietta, Flavio Mignone, Nicola Ancona and Graziano Pesole
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S2
  3. Comparative genomics is a central step in many sequence analysis studies, from gene annotation and the identification of new functional regions in genomes, to the study of evolutionary processes at the molecul...

    Authors: Simon Penel, Anne-Muriel Arigon, Jean-François Dufayard, Anne-Sophie Sertier, Vincent Daubin, Laurent Duret, Manolo Gouy and Guy Perrière
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S3
  4. The rapid accumulation of genomic information in databases necessitates rapid and specific algorithms for extracting biologically meaningful information. More or less complete retroviral sequences, also called...

    Authors: Göran Sperber, Anders Lövgren, Nils-Einar Eriksson, Farid Benachenhou and Jonas Blomberg
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S4
  5. The comparative genomic analysis of a large number of orthologous promoter regions of the chordate and plant genes from the DoOP databases shows thousands of conserved motifs. Most of these motifs differ from ...

    Authors: Endre Sebestyén, Tibor Nagy, Sándor Suhai and Endre Barta
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S6
  6. The mollicute Mycoplasma conjunctivae is the etiological agent leading to infectious keratoconjunctivitis (IKC) in domestic sheep and wild caprinae. Although this pathogen is relatively benign for domestic animal...

    Authors: Sandra P Calderon-Copete, George Wigger, Christof Wunderlin, Tobias Schmidheini, Joachim Frey, Michael A Quail and Laurent Falquet
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S7
  7. Genome-wide duplication is ubiquitous during diversification of the angiosperms, and gene duplication is one of the most important mechanisms for evolutionary novelties. As an indicator of functional evolution...

    Authors: Zhe Li, He Zhang, Song Ge, Xiaocheng Gu, Ge Gao and Jingchu Luo
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S8
  8. Time-course microarray experiments study the progress of gene expression along time across one or several experimental conditions. Most developed analysis methods focus on the clustering or the differential ex...

    Authors: María José Nueda, Patricia Sebastián, Sonia Tarazona, Francisco García-García, Joaquín Dopazo, Alberto Ferrer and Ana Conesa
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S9
  9. ESTs and full-length cDNAs represent an invaluable source of evidence for inferring reliable gene structures and discovering potential alternative splicing events. In newly sequenced genomes, these tasks may n...

    Authors: Ernesto Picardi, Flavio Mignone and Graziano Pesole
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S10
  10. During the last years, high throughput experimental methods have been developed which generate large datasets of protein – protein interactions (PPIs). However, due to the experimental methodologies these data...

    Authors: Charalampos N Moschopoulos, Georgios A Pavlopoulos, Reinhard Schneider, Spiridon D Likothanassis and Sophia Kossida
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S11
  11. Liquid Chromatography-Mass Spectrometry (LC-MS) is a commonly used technique to resolve complex protein mixtures. Visualization of large data sets produced from LC-MS, namely the chromatogram and the mass spec...

    Authors: Dimosthenis Tsagkrasoulis, Panagiotis Zerefos, George Loudos, Antonia Vlahou, Marc Baumann and Sophia Kossida
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S12
  12. Chemogenomics is an emerging inter-disciplinary approach to drug discovery that combines traditional ligand-based approaches with biological information on drug targets and lies at the interface of chemistry, ...

    Authors: Helena Strömbergsson and Gerard J Kleywegt
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S13
  13. DNA sequences have become a primary source of information in biodiversity analysis. For example, short standardized species-specific genomic regions, DNA barcodes, are being used as a global standard for speci...

    Authors: Gregory AC Singer and Mehrdad Hajibabaei
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S14
  14. A standardized and cost-effective molecular identification system is now an urgent need for Fungi owing to their wide involvement in human life quality. In particular the potential use of mitochondrial DNA spe...

    Authors: Monica Santamaria, Saverio Vicario, Graziano Pappadà, Gaetano Scioscia, Claudio Scazzocchio and Cecilia Saccone
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S15
  15. To allow the survival of the population in the absence of nitrogen, some cyanobacteria strains have developed the capability of differentiating into nitrogen fixing cells, forming a characteristic pattern. In ...

    Authors: Ziomara P Gerdtzen, J Cristian Salgado, Axel Osses, Juan A Asenjo, Ivan Rapaport and Barbara A Andrews
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S16
  16. As biological networks often show complex topological features, mathematical methods are required to extract meaningful information. Clustering methods are useful in this setting, as they allow the summary of ...

    Authors: Franck Picard, Vincent Miele, Jean-Jacques Daudin, Ludovic Cottret and Stéphane Robin
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S17
  17. The Distributed Annotation System (DAS) is a widely used network protocol for sharing biological information. The distributed aspects of the protocol enable the use of various reference and annotation servers ...

    Authors: Álvaro Martínez Barrio, Erik Lagercrantz, Göran O Sperber, Jonas Blomberg and Erik Bongcam-Rudloff
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S18
  18. In the biological sciences, the need to analyse vast amounts of information has become commonplace. Such large-scale analyses often involve drawing together data from a variety of different databases, held rem...

    Authors: Steve Pettifer, David Thorne, Philip McDermott, James Marsh, Alice Villéger, Douglas B Kell and Teresa K Attwood
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S19
  19. microRNAs (miRNAs) are single-stranded RNA molecules of about 20–23 nucleotides length found in a wide variety of organisms. miRNAs regulate gene expression, by interacting with target mRNAs at specific sites ...

    Authors: Maria G Roubelakis, Pantelis Zotos, Georgios Papachristoudis, Ioannis Michalopoulos, Kalliopi I Pappa, Nicholas P Anagnou and Sophia Kossida
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S20
  20. Grid technology is the computing model which allows users to share a wide pletora of distributed computational resources regardless of their geographical location. Up to now, the high security policy requested in...

    Authors: Roberto Barbera, Giacinto Donvito, Alberto Falzone, Giuseppe La Rocca, Luciano Milanesi, Giorgio Pietro Maggi and Saverio Vicario
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S21
  21. The number of natural proteins represents a small fraction of all the possible protein sequences and there is an enormous number of proteins never sampled by nature, the so called "never born proteins" (NBPs)....

    Authors: Giovanni Minervini, Giuseppe Evangelista, Laura Villanova, Debora Slanzi, Davide De Lucrezia, Irene Poli, Pier Luigi Luisi and Fabio Polticelli
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S22
  22. A fundamental activity in biomedical research is Knowledge Discovery which has the ability to search through large amounts of biomedical information such as documents and data. High performance computational i...

    Authors: Marcello Castellano, Giuseppe Mastronardi, Roberto Bellotti and Gianfranco Tarricone
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S23
  23. Recent technological advances in DNA sequencing and genotyping have led to the accumulation of a remarkable quantity of data on genetic polymorphisms. However, the development of new statistical and computatio...

    Authors: Vincenzo Lagani, Alberto Montesanto, Fausta Di Cianni, Victor Moreno, Stefano Landi, Domenico Conforti, Giuseppina Rose and Giuseppe Passarino
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S24
  24. Many studies report about detection and functional characterization of cis-regulatory motifs in untranslated regions (UTRs) of mRNAs but little is known about the nature and functional role of their distributi...

    Authors: Antonio Turi, Corrado Loglisci, Eliana Salvemini, Giorgio Grillo, Donato Malerba and Domenica D'Elia
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S25

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