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Volume 12 Supplement 1

Validation methods for functional genome annotation


Edited by Scott E Baker, Jon K Magnuson and Frank R Collart

  1. Identifying functions for all gene products in all sequenced organisms is a central challenge of the post-genomic era. However, at least 30-50% of the proteins encoded by any given genome are of unknown or vag...

    Authors: Svetlana Gerdes, Basma El Yacoubi, Marc Bailly, Ian K Blaby, Crysten E Blaby-Haas, Linda Jeanguenin, Aurora Lara-Núñez, Anne Pribat, Jeffrey C Waller, Andreas Wilke, Ross Overbeek, Andrew D Hanson and Valérie de Crécy-Lagard
    Citation: BMC Genomics 2011 12(Suppl 1):S2
  2. Genome-scale prediction of gene regulation and reconstruction of transcriptional regulatory networks in bacteria is one of the critical tasks of modern genomics. The Shewanella genus is comprised of metabolically...

    Authors: Dmitry A Rodionov, Pavel S Novichkov, Elena D Stavrovskaya, Irina A Rodionova, Xiaoqing Li, Marat D Kazanov, Dmitry A Ravcheev, Anna V Gerasimova, Alexey E Kazakov, Galina Yu Kovaleva, Elizabeth A Permina, Olga N Laikova, Ross Overbeek, Margaret F Romine, James K Fredrickson, Adam P Arkin…
    Citation: BMC Genomics 2011 12(Suppl 1):S3
  3. Recent advances in the field of metabolic engineering have been expedited by the availability of genome sequences and metabolic modelling approaches. The complete sequencing of the C. reinhardtii genome has made ...

    Authors: Lila Ghamsari, Santhanam Balaji, Yun Shen, Xinping Yang, Dawit Balcha, Changyu Fan, Tong Hao, Haiyuan Yu, Jason A Papin and Kourosh Salehi-Ashtiani
    Citation: BMC Genomics 2011 12(Suppl 1):S4
  4. In order to carry out experimental gene annotation, DNA encoding open reading frames (ORFs) derived from real genes (termed "genic") in the correct frame is required. When genes are correctly assigned, isolati...

    Authors: Sara D'Angelo, Nileena Velappan, Flavio Mignone, Claudio Santoro, Daniele Sblattero, Csaba Kiss and Andrew RM Bradbury
    Citation: BMC Genomics 2011 12(Suppl 1):S5
  5. Mass spectrometry-based metabolomics analyses have the potential to complement sequence-based methods of genome annotation, but only if raw mass spectral data can be linked to specific metabolic pathways. In u...

    Authors: Benjamin P Bowen, Curt R Fischer, Richard Baran, Jillian F Banfield and Trent Northen
    Citation: BMC Genomics 2011 12(Suppl 1):S6
  6. Correct annotation of function is essential if one is to take full advantage of the vast amounts of genomic sequence data. The accuracy of sequence-based functional annotations is often variable, particularly ...

    Authors: Yihong Chen, Ethel Apolinario, Libuse Brachova, Zvi Kelman, Zhuo Li, Basil J Nikolau, Lucas Showman, Kevin Sowers and John Orban
    Citation: BMC Genomics 2011 12(Suppl 1):S7
  7. Transporter proteins are one of an organism’s primary interfaces with the environment. The expressed set of transporters mediates cellular metabolic capabilities and influences signal transduction pathways and...

    Authors: Sarah E Giuliani, Ashley M Frank, Danielle M Corgliano, Catherine Seifert, Loren Hauser and Frank R Collart
    Citation: BMC Genomics 2011 12(Suppl 1):S8

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