Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification

Genome annotation of disease-causing microorganisms

(2021) Yibo Dong et al.   BRIEFINGS IN BIOINFORMATICS

An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants

(2021) Fei Xie et al.   Microbiome

Post-weaning shifts in microbiome composition and metabolism revealed by over 25 000 pig gut metagenome-assembled genomes

(2021) Daniela Gaio et al.   Microbial Genomics

ASA3P: An automatic and scalable pipeline for the assembly, annotation and higher level analysis of closely related bacterial isolates

(2020) Oliver Schwengers et al.   PLoS Computational Biology

An assessment of genome annotation coverage across the bacterial tree of life

(2020) Briallen Lobb et al.   Microbial Genomics

Accurate and complete genomes from metagenomes

(2020) Lin-Xing Chen et al.   GENOME RESEARCH

Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes

(2020) Robert A. Petit et al.   mSystems

Universal whole-sequence-based plasmid typing and its utility to prediction of host range and epidemiological surveillance

(2020) James Robertson et al.   Microbial Genomics

Automated Prediction and Annotation of Small Open Reading Frames in Microbial Genomes

(2020) Matthew G. Durrant et al.   Cell Host & Microbe

RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation

(2020) Wenjun Li et al.   NUCLEIC ACIDS RESEARCH

The Gene Ontology resource: enriching a GOld mine

(2020) et al.   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase in 2021

(2020) et al.   NUCLEIC ACIDS RESEARCH

Rfam 14: expanded coverage of metagenomic, viral and microRNA families

(2020) Ioanna Kalvari et al.   NUCLEIC ACIDS RESEARCH

TORMES: an automated pipeline for whole bacterial genome analysis

(2019) Narciso M Quijada et al.   BIOINFORMATICS

Validating the NCBI AMRFinder Tool and Resistance Gene Database Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of NARMS Isolates

(2019) Michael Feldgarden et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Taxonomic reassessment of the genus Pseudocitrobacter using whole genome sequencing: Pseudocitrobacter anthropi is a later heterotypic synonym of Pseudocitrobacter faecalis and description of Pseudocitrobacter vendiensis sp. nov.

(2019) Peter Kämpfer et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

OUP accepted manuscript

(2018)   BIOINFORMATICS

VFDB 2019: a comparative pathogenomic platform with an interactive web interface

(2018) Bo Liu et al.   NUCLEIC ACIDS RESEARCH

DoriC 10.0: an updated database of replication origins in prokaryotic genomes including chromosomes and plasmids

(2018) Hao Luo et al.   NUCLEIC ACIDS RESEARCH

The European Nucleotide Archive in 2018

(2018) Peter W Harrison et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

RefSeq: an update on prokaryotic genome annotation and curation

(2017) Daniel H Haft et al.   NUCLEIC ACIDS RESEARCH

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

The FAIR Guiding Principles for scientific data management and stewardship

(2016) Mark D. Wilkinson et al.   Scientific Data

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Anatomy of BioJS, an open source community for the life sciences

(2015) Guy Yachdav et al.   eLife

Small Proteins Can No Longer Be Ignored

(2014) Gisela Storz et al.   Annual Review of Biochemistry

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Thepsmα Locus Regulates Production of Staphylococcus aureus Alpha-Toxin during Infection

(2014) Bryan J. Berube et al.   INFECTION AND IMMUNITY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Improving prokaryotic transposable elements identification using a combination of de novo and profile HMM methods

(2013) Choumouss Kamoun et al.   BMC GENOMICS

Small proteins link coat and cortex assembly during sporulation in Bacillus subtilis

(2012) Sarah E. Ebmeier et al.   MOLECULAR MICROBIOLOGY

ExPASy: SIB bioinformatics resource portal

(2012) P. Artimo et al.   NUCLEIC ACIDS RESEARCH

AntiFam: a tool to help identify spurious ORFs in protein annotation

(2012) R. Y. Eberhardt et al.   Database-The Journal of Biological Databases and Curation

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

MetaGeneAnnotator: Detecting Species-Specific Patterns of Ribosomal Binding Site for Precise Gene Prediction in Anonymous Prokaryotic and Phage Genomes

(2008) H. Noguchi et al.   DNA RESEARCH