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

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

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

Clades of huge phages from across Earth’s ecosystems

(2020) Basem Al-Shayeb et al.   NATURE

A complete domain-to-species taxonomy for Bacteria and Archaea

(2020) Donovan H. Parks et al.   NATURE BIOTECHNOLOGY

A new genomic blueprint of the human gut microbiota

(2019) Alexandre Almeida et al.   NATURE

Rapid Genetic Code Evolution in Green Algal Mitochondrial Genomes

(2019) Emmanuel Noutahi et al.   MOLECULAR BIOLOGY AND EVOLUTION

Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts

(2019) Jacob L. Steenwyk et al.   PLOS BIOLOGY

Evolution and Unprecedented Variants of the Mitochondrial Genetic Code in a Lineage of Green Algae

(2019) David Žihala et al.   Genome Biology and Evolution

Endogenous Stochastic Decoding of the CUG Codon by Competing Ser- and Leu-tRNAs in Ascoidea asiatica

(2018) Stefanie Mühlhausen et al.   CURRENT BIOLOGY

Evolutionary instability of CUG-Leu in the genetic code of budding yeasts

(2018) Tadeusz Krassowski et al.   Nature Communications

Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum

(2018) Xing-Xing Shen et al.   CELL

Mitogenomics Reveals a Novel Genetic Code in Hemichordata

(2018) Yuanning Li et al.   Genome Biology and Evolution

The expansion of Inosine at the wobble position of tRNAs, and its role in the evolution of proteomes

(2018) Àlbert Rafels-Ybern et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Pfam protein families database in 2019

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

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Genetic Codes with No Dedicated Stop Codon: Context-Dependent Translation Termination

(2016) Estienne Carl Swart et al.   CELL

An Unprecedented Non-canonical Nuclear Genetic Code with All Three Termination Codons Reassigned as Sense Codons

(2016) Kristína Záhonová et al.   CURRENT BIOLOGY

A novel nuclear genetic code alteration in yeasts and the evolution of codon reassignment in eukaryotes

(2016) Stefanie Mühlhausen et al.   GENOME RESEARCH

Novel Ciliate Genetic Code Variants Including the Reassignment of All Three Stop Codons to Sense Codons inCondylostoma magnum

(2016) Stephen M. Heaphy et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparative genomics of biotechnologically important yeasts

(2016) Robert Riley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reassignment of a rare sense codon to a non-canonical amino acid inEscherichia coli

(2015) Takahito Mukai et al.   NUCLEIC ACIDS RESEARCH

Genome expansion via lineage splitting and genome reduction in the cicada endosymbiontHodgkinia

(2015) Matthew A. Campbell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predicting the fungal CUG codon translation with Bagheera

(2014) Stefanie Mühlhausen et al.   BMC GENOMICS

Stop codon reassignments in the wild

(2014) N. N. Ivanova et al.   SCIENCE

Small, Smaller, Smallest: The Origins and Evolution of Ancient Dual Symbioses in a Phloem-Feeding Insect

(2013) Gordon M. Bennett et al.   Genome Biology and Evolution

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota

(2013) J. H. Campbell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TIGRFAMs and Genome Properties in 2013

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

Obligately Phagotrophic Aphelids Turned out to Branch with the Earliest-diverging Fungi

(2012) Sergey A. Karpov et al.   PROTIST

FACIL: Fast and Accurate Genetic Code Inference and Logo

(2011) Bas E. Dutilh et al.   BIOINFORMATICS

Extreme genome reduction in symbiotic bacteria

(2011) John P. McCutcheon et al.   NATURE REVIEWS MICROBIOLOGY

Across Bacterial Phyla, Distantly-Related Genomes with Similar Genomic GC Content Have Similar Patterns of Amino Acid Usage

(2011) John Lightfield et al.   PLoS One

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Functional Convergence in Reduced Genomes of Bacterial Symbionts Spanning 200 My of Evolution

(2010) John P. McCutcheon et al.   Genome Biology and Evolution

Deciphering synonymous codons in the three domains of life: Co-evolution with specific tRNA modification enzymes

(2009) Henri Grosjean et al.   FEBS LETTERS

Origin of an Alternative Genetic Code in the Extremely Small and GC–Rich Genome of a Bacterial Symbiont

(2009) John P. McCutcheon et al.   PLoS Genetics

The role of alternative genetic codes in viral evolution and emergence

(2008) Laura A. Shackelton et al.   JOURNAL OF THEORETICAL BIOLOGY