Combining multiple functional annotation tools increases coverage of metabolic annotation

Confronting the catalytic dark matter encoded by sequenced genomes

(2017) Kenneth W. Ellens et al.   NUCLEIC ACIDS RESEARCH

Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction

(2016) Christopher S. Henry et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

(2016) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

BRENDA in 2017: new perspectives and new tools in BRENDA

(2016) Sandra Placzek et al.   NUCLEIC ACIDS RESEARCH

The EcoCyc database: reflecting new knowledge aboutEscherichia coliK-12

(2016) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life

(2016) Liam D. H. Elbourne et al.   NUCLEIC ACIDS RESEARCH

Insights from 20 years of bacterial genome sequencing

(2015) Miriam Land et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Sequence-based Network Completion Reveals the Integrality of Missing Reactions in Metabolic Networks

(2015) Elias W. Krumholz et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2015) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Illuminating the dark matter in metabolomics: Fig. 1.

(2015) Ricardo R. da Silva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exometabolite niche partitioning among sympatric soil bacteria

(2015) Richard Baran et al.   Nature Communications

Big Data: Astronomical or Genomical?

(2015) Zachary D. Stephens et al.   PLOS BIOLOGY

Annotation and curation of uncharacterized proteins- challenges

(2015) Johny Ijaq et al.   Frontiers in Genetics

Consistency Analysis of Genome-Scale Models of Bacterial Metabolism: A Metamodel Approach

(2015) Miguel Ponce-de-Leon et al.   PLoS One

Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models

(2014) Matthew N. Benedict et al.   PLoS Computational Biology

Fifty-five years of enzyme classification: advances and difficulties

(2013) Andrew G. McDonald et al.   FEBS Journal

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

EFICAz2.5: application of a high-precision enzyme function predictor to 396 proteomes

(2012) Narendra Kumar et al.   BIOINFORMATICS

MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases

(2012) Akhil Kumar et al.   BMC BIOINFORMATICS

Reconciliation of metabolites and biochemical reactions for metabolic networks

(2012) T. Bernard et al.   BRIEFINGS IN BIOINFORMATICS

BKM-react, an integrated biochemical reaction database

(2011) Maren Lang et al.   BMC BIOCHEMISTRY

EnzymeDetector: an integrated enzyme function prediction tool and database

(2011) Susanne Quester et al.   BMC BIOINFORMATICS

Improved genome annotation through untargeted detection of pathway-specific metabolites

(2011) Benjamin P Bowen et al.   BMC GENOMICS

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

‘Unknown’ proteins and ‘orphan’ enzymes: the missing half of the engineering parts list – and how to find it

(2009) Andrew D. Hanson et al.   BIOCHEMICAL JOURNAL

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

(2009) Nikos C Kyrpides   NATURE BIOTECHNOLOGY

GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions

(2009) Vinay Satish Kumar et al.   PLoS Computational Biology

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

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

The future of biocuration

(2008) Doug Howe et al.   NATURE

PEDANT covers all complete RefSeq genomes

(2008) M. C. Walter et al.   NUCLEIC ACIDS RESEARCH