Experimental validation that human microbiome phages use alternative genetic coding

[1]  Adair L. Borges,et al.  Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes , 2022, Nature Microbiology.

[2]  J. Banfield,et al.  Infant gut strain persistence is associated with maternal origin, phylogeny, and traits including surface adhesion and iron acquisition , 2021, Cell reports. Medicine.

[3]  Adair L. Borges,et al.  Closely related Lak megaphages replicate in the microbiomes of diverse animals , 2021, iScience.

[4]  Natalia N. Ivanova,et al.  Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome , 2021, Nature Microbiology.

[5]  J. Banfield,et al.  Accurate and complete genomes from metagenomes , 2019, bioRxiv.

[6]  Christine L. Sun,et al.  Clades of huge phages from across Earth’s ecosystems , 2019, bioRxiv.

[7]  C. Hill,et al.  Bacteriophages of the Human Gut: The "Known Unknown" of the Microbiome. , 2019, Cell host & microbe.

[8]  Brian C. Thomas,et al.  Megaphages infect Prevotella and variants are widespread in gut microbiomes , 2019, Nature Microbiology.

[9]  Ngoc Hieu Tran,et al.  Deep learning enables de novo peptide sequencing from data-independent-acquisition mass spectrometry , 2018, Nature Methods.

[10]  Tanveer S. Batth,et al.  Protein Aggregation Capture on Microparticles Enables Multipurpose Proteomics Sample Preparation , 2018, Molecular & Cellular Proteomics.

[11]  D. Hoyt,et al.  Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem , 2018, Nature Microbiology.

[12]  Lukas Zimmermann,et al.  A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core. , 2017, Journal of molecular biology.

[13]  E. Susko,et al.  Nuclear genetic codes with a different meaning of the UAG and the UAA codon , 2017, BMC Biology.

[14]  Brian C. Thomas,et al.  Measurement of bacterial replication rates in microbial communities , 2016, Nature Biotechnology.

[15]  Michael J E Sternberg,et al.  The Phyre2 web portal for protein modeling, prediction and analysis , 2015, Nature Protocols.

[16]  Michael C. Jewett,et al.  Non-standard amino acid incorporation into proteins using Escherichia coli cell-free protein synthesis , 2014, Front. Chem..

[17]  Axel Visel,et al.  Stop codon reassignments in the wild , 2014, Science.

[18]  J. Banfield,et al.  Recoding of the stop codon UGA to glycine by a BD1-5/SN-2 bacterium and niche partitioning between Alpha- and Gammaproteobacteria in a tidal sediment microbial community naturally selected in a laboratory chemostat , 2014, Front. Microbiol..

[19]  Jürgen Cox,et al.  A systematic investigation into the nature of tryptic HCD spectra. , 2012, Journal of proteome research.

[20]  Carrie D. Nicora,et al.  Proteomic Detection of Non-Annotated Protein-Coding Genes in Pseudomonas fluorescens Pf0-1 , 2009, PloS one.

[21]  M. Baudet,et al.  Proteomics-based Refinement of Deinococcus deserti Genome Annotation Reveals an Unwonted Use of Non-canonical Translation Initiation Codons , 2009, Molecular & Cellular Proteomics.

[22]  N. Moran,et al.  Origin of an Alternative Genetic Code in the Extremely Small and GC–Rich Genome of a Bacterial Symbiont , 2009, PLoS genetics.

[23]  Johannes Söding,et al.  Protein homology detection by HMM?CHMM comparison , 2005, Bioinform..

[24]  Jacob D. Jaffe,et al.  Proteogenomic mapping as a complementary method to perform genome annotation , 2004, Proteomics.

[25]  O. Fayet,et al.  Programmed translational frameshifting and initiation at an AUU codon in gene expression of bacterial insertion sequence IS911. , 1991, Journal of molecular biology.

[26]  He Fuchu,et al.  Integrated nr Database in Protein Annotation System and Its Localization , 2006 .