AnnoTree: visualization and exploration of a functionally annotated microbial tree of life

Bioinformatic discovery of a toxin family in Chryseobacterium piperi with sequence similarity to botulinum neurotoxins

(2019) Michael James Mansfield et al.   Scientific Reports

Identification of a diphtheria toxin-like gene family beyond the Corynebacterium genus

(2018) Michael J. Mansfield et al.   FEBS LETTERS

Gene annotation bias impedes biomedical research

(2018) Winston A. Haynes et al.   Scientific Reports

Lateral Gene Transfer Dynamics in the Ancient Bacterial Genus Streptomyces

(2017) Bradon R. McDonald et al.   mBio

Diversity and function of prevalent symbiotic marine bacteria in the genus Endozoicomonas

(2016) Matthew J. Neave et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Aquerium: A web application for comparative exploration of domain-based protein occurrences on the taxonomically clustered genome tree

(2016) Ogun Adebali et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer

(2016) Raquel Bromberg et al.   PLoS Computational Biology

A new view of the tree of life

(2016) Laura A. Hug et al.   Nature Microbiology

Complete nitrification by a single microorganism

(2015) Maartje A. H. J. van Kessel et al.   NATURE

Complete nitrification by Nitrospira bacteria

(2015) Holger Daims et al.   NATURE

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Toward a standard in structural genome annotation for prokaryotes

(2015) H. James Tripp et al.   Standards in Genomic Sciences

Inferring Horizontal Gene Transfer

(2015) Matt Ravenhall et al.   PLoS Computational Biology

Compact graphical representation of phylogenetic data and metadata with GraPhlAn

(2015) Francesco Asnicar et al.   PeerJ

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

Botulinum neurotoxin homologs in non-Clostridiumspecies

(2014) Michael J. Mansfield et al.   FEBS LETTERS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Overview of organohalide-respiring bacteria and a proposal for a classification system for reductive dehalogenases

(2013) L. A. Hug et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya

(2012) Arshan Nasir et al.   BMC EVOLUTIONARY BIOLOGY

Phylogenetic conservatism of functional traits in microorganisms

(2012) Adam C Martiny et al.   ISME Journal

The NCBI Taxonomy database

(2011) S. Federhen   NUCLEIC ACIDS RESEARCH

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

The life and death of gene families

(2009) Jeffery P. Demuth et al.   BIOESSAYS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The Evolutionary History of Protein Domains Viewed by Species Phylogeny

(2009) Song Yang et al.   PLoS One

Database resources of the National Center for Biotechnology Information

(2008) E. W. Sayers et al.   NUCLEIC ACIDS RESEARCH