MgCod: Gene Prediction in Phage Genomes with Multiple Genetic Codes

Experimental validation that human microbiome phages use alternative genetic coding

(2022) Samantha L. Peters et al.   Nature Communications

Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features

(2021) Natalya Yutin et al.   Nature Communications

Thousands of previously unknown phages discovered in whole-community human gut metagenomes

(2021) Sean Benler et al.   Microbiome

tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes

(2021) Patricia P Chan et al.   NUCLEIC ACIDS RESEARCH

A computational screen for alternative genetic codes in over 250,000 genomes

(2021) Yekaterina Shulgina et al.   eLife

The crAss-like Phage Group: How Metagenomics Reshaped the Human Virome

(2020) Eugene V. Koonin et al.   TRENDS IN MICROBIOLOGY

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

(2019) Robert A. Edwards et al.   Nature Microbiology

Biology and Taxonomy of crAss-like Bacteriophages, the Most Abundant Virus in the Human Gut

(2018) Emma Guerin et al.   Cell Host & Microbe

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data

(2017) Jie Ren et al.   Microbiome

Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut

(2017) Natalya Yutin et al.   Nature Microbiology

Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation

(2016) Ana Laura Grazziotin et al.   NUCLEIC ACIDS RESEARCH

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Predicting the fungal CUG codon translation with Bagheera

(2014) Stefanie Mühlhausen et al.   BMC GENOMICS

A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes

(2014) Bas E. Dutilh et al.   Nature Communications

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

(2013) Jaina Mistry et al.   NUCLEIC ACIDS RESEARCH

FACIL: Fast and Accurate Genetic Code Inference and Logo

(2011) Bas E. Dutilh et al.   BIOINFORMATICS

Ab initio gene identification in metagenomic sequences

(2010) Wenhan Zhu et al.   NUCLEIC ACIDS RESEARCH