Solving the Problem: Genome Annotation Standards before the Data Deluge

Meeting Report: Towards a Critical Assessment of Functional Annotation Experiment (CAFAE) for bacterial genome annotation

(2011) Owen White et al.   Standards in Genomic Sciences

Complete Genome Sequences of Yersinia pestis from Natural Foci in China

(2010) X. Shen et al.   JOURNAL OF BACTERIOLOGY

The European Nucleotide Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

COMBREX: a project to accelerate the functional annotation of prokaryotic genomes

(2010) R. J. Roberts et al.   NUCLEIC ACIDS RESEARCH

GenBank

(2010) D. A. Benson et al.   NUCLEIC ACIDS RESEARCH

EcoCyc: a comprehensive database of Escherichia coli biology

(2010) I. M. Keseler et al.   NUCLEIC ACIDS RESEARCH

Database resources of the National Center for Biotechnology Information

(2010) E. W. Sayers et al.   NUCLEIC ACIDS RESEARCH

Towards BioDBcore: a community-defined information specification for biological databases

(2010) Pascale Gaudet et al.   NUCLEIC ACIDS RESEARCH

Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop

(2010) James Rodney Brister et al.   Viruses-Basel

The annotation and the usage of scientific databases could be improved with public issue tracker software

(2010) Giovanni Marco Dall'Olio et al.   Database-The Journal of Biological Databases and Curation

The Extinction Dynamics of Bacterial Pseudogenes

(2010) Chih-Horng Kuo et al.   PLoS Genetics

GENETACK: FRAMESHIFT IDENTIFICATION IN PROTEIN-CODING SEQUENCES BY THE VITERBI ALGORITHM

(2010) IVAN ANTONOV et al.   Journal of Bioinformatics and Computational Biology

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes

(2009) K. D. Pruitt et al.   GENOME RESEARCH

Genome Sequences of Escherichia coli B strains REL606 and BL21(DE3)

(2009) Haeyoung Jeong et al.   JOURNAL OF MOLECULAR BIOLOGY

Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream

(2009) Nikos C Kyrpides   NATURE BIOTECHNOLOGY

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

The Gene Ontology in 2010: extensions and refinements

(2009)   NUCLEIC ACIDS RESEARCH

DDBJ launches a new archive database with analytical tools for next-generation sequence data

(2009) Eli Kaminuma et al.   NUCLEIC ACIDS RESEARCH

The Protein Naming Utility: a rules database for protein nomenclature

(2009) Johannes Goll et al.   NUCLEIC ACIDS RESEARCH

ACLAME: A CLAssification of Mobile genetic Elements, update 2010

(2009) Raphaël Leplae et al.   NUCLEIC ACIDS RESEARCH

The Dynamics and Time Scale of Ongoing Genomic Erosion in Symbiotic Bacteria

(2009) N. A. Moran et al.   SCIENCE

Protein function prediction – the power of multiplicity

(2009) Robert Rentzsch et al.   TRENDS IN BIOTECHNOLOGY

Data reporting standards: making the things we use better

(2009) John Quackenbush   Genome Medicine

Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies

(2009) Alexandra M. Schnoes et al.   PLoS Computational Biology

Origin of an Alternative Genetic Code in the Extremely Small and GC–Rich Genome of a Bacterial Symbiont

(2009) John P. McCutcheon et al.   PLoS Genetics

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

The minimum information about a genome sequence (MIGS) specification

(2008) Dawn Field et al.   NATURE BIOTECHNOLOGY

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

(2008) Chris F Taylor et al.   NATURE BIOTECHNOLOGY

Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world

(2008) E. V. Koonin et al.   NUCLEIC ACIDS RESEARCH

The National Center for Biotechnology Information's Protein Clusters Database

(2008) William Klimke et al.   NUCLEIC ACIDS RESEARCH

The Universal Protein Resource (UniProt) 2009

(2008)   NUCLEIC ACIDS RESEARCH

HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot

(2008) T. Lima et al.   NUCLEIC ACIDS RESEARCH

Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes

(2008) G. L. Winsor et al.   NUCLEIC ACIDS RESEARCH

NCBI Reference Sequences: current status, policy and new initiatives

(2008) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

InterPro: the integrative protein signature database

(2008) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

Toward an Online Repository of Standard Operating Procedures (SOPs) for (Meta)genomic Annotation

(2008) Samuel V. Angiuoli et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Revised nomenclature for transposable genetic elements

(2008) Adam P. Roberts et al.   PLASMID