Volume 12 Supplement 1

Validation methods for functional genome annotation


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

  1. Research

    Synergistic use of plant-prokaryote comparative genomics for functional annotations

    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...

    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

    BMC Genomics 2011 12(Suppl 1):S2

    Published on: 15 June 2011

  2. Research

    Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus

    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...

    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…

    BMC Genomics 2011 12(Suppl 1):S3

    Published on: 15 June 2011

  3. Research

    Genome-wide functional annotation and structural verification of metabolic ORFeome of Chlamydomonas reinhardtii

    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 ...

    Lila Ghamsari, Santhanam Balaji, Yun Shen, Xinping Yang, Dawit Balcha, Changyu Fan, Tong Hao, Haiyuan Yu, Jason A Papin and Kourosh Salehi-Ashtiani

    BMC Genomics 2011 12(Suppl 1):S4

    Published on: 15 June 2011

  4. Research

    Filtering "genic" open reading frames from genomic DNA samples for advanced annotation

    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...

    Sara D'Angelo, Nileena Velappan, Flavio Mignone, Claudio Santoro, Daniele Sblattero, Csaba Kiss and Andrew RM Bradbury

    BMC Genomics 2011 12(Suppl 1):S5

    Published on: 15 June 2011

  5. Research

    A nuclear magnetic resonance based approach to accurate functional annotation of putative enzymes in the methanogen Methanosarcina acetivorans

    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 ...

    Yihong Chen, Ethel Apolinario, Libuse Brachova, Zvi Kelman, Zhuo Li, Basil J Nikolau, Lucas Showman, Kevin Sowers and John Orban

    BMC Genomics 2011 12(Suppl 1):S7

    Published on: 15 June 2011

  6. Research

    Environment sensing and response mediated by ABC transporters

    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...

    Sarah E Giuliani, Ashley M Frank, Danielle M Corgliano, Catherine Seifert, Loren Hauser and Frank R Collart

    BMC Genomics 2011 12(Suppl 1):S8

    Published on: 15 June 2011

Portable peer review

 The editors of BMC Genomics support initiatives that expedite the peer review process and are happy to consider manuscripts that have been reviewed in Axios Review or Peerage of Science. Please indicate in your cover letter if this applies to your manuscript.

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