GapMind: Automated Annotation of Amino Acid Biosynthesis

Metabolic and genetic basis for auxotrophies in Gram-negative species

(2020) Yara Seif et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Oxidative Pathways of Deoxyribose and Deoxyribonate Catabolism

(2019) Morgan N. Price et al.   mSystems

Clostridium scindens ATCC 35704: Integration of Nutritional Requirements, the Complete Genome Sequence, and Global Transcriptional Responses to Bile Acids

(2019) Saravanan Devendran et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Curated BLAST for Genomes

(2019) Morgan N. Price et al.   mSystems

Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics

(2018) Morgan N. Price et al.   PLoS Genetics

Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies

(2018) Melanie Tramontano et al.   Nature Microbiology

Mutant phenotypes for thousands of bacterial genes of unknown function

(2018) Morgan N. Price et al.   NATURE

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Parallel evolution of non-homologous isofunctional enzymes in methionine biosynthesis

(2017) Karine Bastard et al.   Nature Chemical Biology

Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota

(2017) Ilya V. Kublanov et al.   Frontiers in Microbiology

A metabolic pathway for catabolizing levulinic acid in bacteria

(2017) Jacqueline M. Rand et al.   Nature Microbiology

PaperBLAST: Text Mining Papers for Information about Homologs

(2017) Morgan N. Price et al.   mSystems

BRENDA in 2017: new perspectives and new tools in BRENDA

(2016) Sandra Placzek et al.   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

Reconstruction of diaminopimelic acid biosynthesis allows characterisation of Mycobacterium tuberculosis N-succinyl-L,L-diaminopimelic acid desuccinylase

(2016) Veeraraghavan Usha et al.   Scientific Reports

The essential gene set of a photosynthetic organism

(2015) Benjamin E. Rubin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Harnessing the landscape of microbial culture media to predict new organism–media pairings

(2015) Matthew A. Oberhardt et al.   Nature Communications

Using a Genome-Scale Metabolic Model of Enterococcus faecalis V583 To Assess Amino Acid Uptake and Its Impact on Central Metabolism

(2014) Nadine Veith et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

LESS IS MORE: SELECTIVE ADVANTAGES CAN EXPLAIN THE PREVALENT LOSS OF BIOSYNTHETIC GENES IN BACTERIA

(2014) Glen D'Souza et al.   EVOLUTION

REBASE—a database for DNA restriction and modification: enzymes, genes and genomes

(2014) Richard J. Roberts et al.   NUCLEIC ACIDS RESEARCH

CDD: NCBI's conserved domain database

(2014) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Variations in metabolic pathways create challenges for automated metabolic reconstructions: Examples from the tetrahydrofolate synthesis pathway

(2014) Valérie de Crécy-Lagard   Computational and Structural Biotechnology Journal

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Improving Microbial Genome Annotations in an Integrated Database Context

(2013) I-Min A. Chen et al.   PLoS One

Distribution of nitrogen fixation and nitrogenase-like sequences amongst microbial genomes

(2012) Patricia C Dos Santos et al.   BMC GENOMICS

Nutrient requirements for growth of the extreme oligotroph ‘Candidatus Pelagibacter ubique’ HTCC1062 on a defined medium

(2012) Paul Carini et al.   ISME Journal

TIGRFAMs and Genome Properties in 2013

(2012) Daniel H. Haft et al.   NUCLEIC ACIDS RESEARCH

Phenylalanine Hydroxylase from Legionella pneumophila Is a Thermostable Enzyme with a Major Functional Role in Pyomelanin Synthesis

(2012) Marte I. Flydal et al.   PLoS One

CharProtDB: a database of experimentally characterized protein annotations

(2011) R. Madupu et al.   NUCLEIC ACIDS RESEARCH

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

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

(2009) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

MicrobesOnline: an integrated portal for comparative and functional genomics

(2009) P. S. Dehal et al.   NUCLEIC ACIDS RESEARCH

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

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