Volume 10 Supplement 6

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


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, Italy

18-20 September 2008

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  1. Introduction

    The 20th anniversary of EMBnet: 20 years of bioinformatics for the Life Sciences community

    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...

    Domenica D'Elia, Andreas Gisel, Nils-Einar Eriksson, Sophia Kossida, Kimmo Mattila, Lubos Klucar and Erik Bongcam-Rudloff

    BMC Bioinformatics 2009 10(Suppl 6):S1

    Published on: 16 June 2009

  2. Proceedings

    Statistical assessment of discriminative features for protein-coding and non coding cross-species conserved sequence elements

    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...

    Teresa M Creanza, David S Horner, Annarita D'Addabbo, Rosalia Maglietta, Flavio Mignone, Nicola Ancona and Graziano Pesole

    BMC Bioinformatics 2009 10(Suppl 6):S2

    Published on: 16 June 2009

  3. Proceedings

    Databases of homologous gene families for comparative genomics

    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...

    Simon Penel, Anne-Muriel Arigon, Jean-François Dufayard, Anne-Sophie Sertier, Vincent Daubin, Laurent Duret, Manolo Gouy and Guy Perrière

    BMC Bioinformatics 2009 10(Suppl 6):S3

    Published on: 16 June 2009

  4. Proceedings

    RetroTector online, a rational tool for analysis of retroviral elements in small and medium size vertebrate genomic sequences

    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...

    Göran Sperber, Anders Lövgren, Nils-Einar Eriksson, Farid Benachenhou and Jonas Blomberg

    BMC Bioinformatics 2009 10(Suppl 6):S4

    Published on: 16 June 2009

  5. Proceedings

    DoOPSearch: a web-based tool for finding and analysing common conserved motifs in the promoter regions of different chordate and plant genes

    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 ...

    Endre Sebestyén, Tibor Nagy, Sándor Suhai and Endre Barta

    BMC Bioinformatics 2009 10(Suppl 6):S6

    Published on: 16 June 2009

  6. Proceedings

    The Mycoplasma conjunctivae genome sequencing, annotation and analysis

    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...

    Sandra P Calderon-Copete, George Wigger, Christof Wunderlin, Tobias Schmidheini, Joachim Frey, Michael A Quail and Laurent Falquet

    BMC Bioinformatics 2009 10(Suppl 6):S7

    Published on: 16 June 2009

  7. Proceedings

    Expression pattern divergence of duplicated genes in rice

    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...

    Zhe Li, He Zhang, Song Ge, Xiaocheng Gu, Ge Gao and Jingchu Luo

    BMC Bioinformatics 2009 10(Suppl 6):S8

    Published on: 16 June 2009

  8. Proceedings

    Functional assessment of time course microarray data

    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...

    María José Nueda, Patricia Sebastián, Sonia Tarazona, Francisco García-García, Joaquín Dopazo, Alberto Ferrer and Ana Conesa

    BMC Bioinformatics 2009 10(Suppl 6):S9

    Published on: 16 June 2009

  9. Proceedings

    GIBA: a clustering tool for detecting protein complexes

    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...

    Charalampos N Moschopoulos, Georgios A Pavlopoulos, Reinhard Schneider, Spiridon D Likothanassis and Sophia Kossida

    BMC Bioinformatics 2009 10(Suppl 6):S11

    Published on: 16 June 2009

  10. Proceedings

    'Brukin2D': a 2D visualization and comparison tool for LC-MS data

    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...

    Dimosthenis Tsagkrasoulis, Panagiotis Zerefos, George Loudos, Antonia Vlahou, Marc Baumann and Sophia Kossida

    BMC Bioinformatics 2009 10(Suppl 6):S12

    Published on: 16 June 2009

  11. Proceedings

    A chemogenomics view on protein-ligand spaces

    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, ...

    Helena Strömbergsson and Gerard J Kleywegt

    BMC Bioinformatics 2009 10(Suppl 6):S13

    Published on: 16 June 2009

  12. Proceedings

    iBarcode.org: web-based molecular biodiversity analysis

    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...

    Gregory AC Singer and Mehrdad Hajibabaei

    BMC Bioinformatics 2009 10(Suppl 6):S14

    Published on: 16 June 2009

  13. Proceedings

    Towards barcode markers in Fungi: an intron map of Ascomycota mitochondria

    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...

    Monica Santamaria, Saverio Vicario, Graziano Pappadà, Gaetano Scioscia, Claudio Scazzocchio and Cecilia Saccone

    BMC Bioinformatics 2009 10(Suppl 6):S15

    Published on: 16 June 2009

  14. Proceedings

    Modeling heterocyst pattern formation in cyanobacteria

    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 ...

    Ziomara P Gerdtzen, J Cristian Salgado, Axel Osses, Juan A Asenjo, Ivan Rapaport and Barbara A Andrews

    BMC Bioinformatics 2009 10(Suppl 6):S16

    Published on: 16 June 2009

  15. Proceedings

    Deciphering the connectivity structure of biological networks using MixNet

    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 ...

    Franck Picard, Vincent Miele, Jean-Jacques Daudin, Ludovic Cottret and Stéphane Robin

    BMC Bioinformatics 2009 10(Suppl 6):S17

    Published on: 16 June 2009

  16. Proceedings

    Annotation and visualization of endogenous retroviral sequences using the Distributed Annotation System (DAS) and eBioX

    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 ...

    Álvaro Martínez Barrio, Erik Lagercrantz, Göran O Sperber, Jonas Blomberg and Erik Bongcam-Rudloff

    BMC Bioinformatics 2009 10(Suppl 6):S18

    Published on: 16 June 2009

  17. Proceedings

    Visualising biological data: a semantic approach to tool and database integration

    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...

    Steve Pettifer, David Thorne, Philip McDermott, James Marsh, Alice Villéger, Douglas B Kell and Teresa K Attwood

    BMC Bioinformatics 2009 10(Suppl 6):S19

    Published on: 16 June 2009

  18. Proceedings

    Human microRNA target analysis and gene ontology clustering by GOmir, a novel stand-alone application

    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 ...

    Maria G Roubelakis, Pantelis Zotos, Georgios Papachristoudis, Ioannis Michalopoulos, Kalliopi I Pappa, Nicholas P Anagnou and Sophia Kossida

    BMC Bioinformatics 2009 10(Suppl 6):S20

    Published on: 16 June 2009

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