Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires
暂无分享,去创建一个
Scott F. Hickey | J. Banfield | C. Schadt | B. Woodcroft | B. Al-Shayeb | S. Juul | S. Gribaldo | Najwa Taib | J. Beaulaurier | N. Malvankar | R. Sachdeva | Ling-Dong Shi | Xiaoguang Dai | Christine He | Cong Shen | Jacob West-Roberts | M. C. Schoelmerich | L.T.N. Ly | C. Mozsary | M. Schoelmerich
[1] T. Sleutels,et al. Mechanisms of extracellular electron transfer in anaerobic methanotrophic archaea , 2023, bioRxiv.
[2] E. Egelman,et al. Extracellular cytochrome nanowires appear to be ubiquitous in prokaryotes , 2023, Cell.
[3] J. Söding,et al. Fast and accurate protein structure search with Foldseek , 2023, bioRxiv.
[4] Henrique Pondé de Oliveira Pinto,et al. GPT-4 Technical Report , 2023, 2303.08774.
[5] N. Kyrpides,et al. You can move, but you can’t hide: identification of mobile genetic elements with geNomad , 2023, bioRxiv.
[6] N. Malvankar,et al. Structure of Geobacter cytochrome OmcZ identifies mechanism of nanowire assembly and conductivity , 2023, Nature Microbiology.
[7] B. Woodcroft,et al. Anaerobic methanotroph ‘Candidatus Methanoperedens nitroreducens’ has a pleomorphic life cycle , 2023, Nature Microbiology.
[8] J. Banfield,et al. Tandem repeats in giant archaeal Borg elements undergo rapid evolution and create new intrinsically disordered regions in proteins , 2023, PLoS biology.
[9] K. Williams,et al. Borgs are giant genetic elements with potential to expand metabolic capacity , 2022, Nature.
[10] K. Corbett,et al. Structure and activity of a bacterial defense‐associated 3′‐5′ exonuclease , 2022, Protein science : a publication of the Protein Society.
[11] Petar I. Penev,et al. A widespread group of large plasmids in methanotrophic Methanoperedens archaea , 2022, bioRxiv.
[12] S. Ovchinnikov,et al. ColabFold: making protein folding accessible to all , 2022, Nature Methods.
[13] Oriol Vinyals,et al. Highly accurate protein structure prediction with AlphaFold , 2021, Nature.
[14] Elizabeth K. Eder,et al. Soil metabolome response to whole-ecosystem warming at the Spruce and Peatland Responses under Changing Environments experiment , 2021, Proceedings of the National Academy of Sciences.
[15] Takashi Okura,et al. Cell-to-Cell Transmission of Turkey Herpesvirus in Chicken Embryo Cells via Tunneling Nanotubes , 2021, Avian Diseases.
[16] J. Aury,et al. Hapo-G, haplotype-aware polishing of genome assemblies with accurate reads , 2020, bioRxiv.
[17] N. Kyrpides,et al. CheckV assesses the quality and completeness of metagenome-assembled viral genomes , 2020, Nature Biotechnology.
[18] Cameron L.M. Gilchrist,et al. clinker & clustermap.js: Automatic generation of gene cluster comparison figures , 2020, bioRxiv.
[19] T. Varga,et al. Electric field stimulates production of highly conductive microbial OmcZ nanowires , 2020, Nature Chemical Biology.
[20] M. Sullivan,et al. DRAM for distilling microbial metabolism to automate the curation of microbiome function , 2020, bioRxiv.
[21] K. Lewis,et al. Ureadepsipeptides as ClpP Activators. , 2019, ACS infectious diseases.
[22] P. Pevzner,et al. metaFlye: scalable long-read metagenome assembly using repeat graphs , 2019, Nature Methods.
[23] D. Charro,et al. Structural basis for assembly of vertical single β-barrel viruses , 2019, Nature Communications.
[24] S. Wolin,et al. Ro60 and Y RNAs: structure, functions, and roles in autoimmunity , 2019, Critical reviews in biochemistry and molecular biology.
[25] Konstantinos D. Tsirigos,et al. SignalP 5.0 improves signal peptide predictions using deep neural networks , 2019, Nature Biotechnology.
[26] Sudhir Kumar,et al. MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. , 2018, Molecular biology and evolution.
[27] Johannes Söding,et al. MMseqs2: sensitive protein sequence searching for the analysis of massive data sets , 2017, bioRxiv.
[28] R. Szczepaniak,et al. The Exonuclease Activity of Herpes Simplex Virus 1 UL12 Is Required for Production of Viral DNA That Can Be Packaged To Produce Infectious Virus , 2017, Journal of Virology.
[29] Heng Li,et al. Minimap2: pairwise alignment for nucleotide sequences , 2017, Bioinform..
[30] Ryan R. Wick,et al. Completing bacterial genome assemblies with multiplex MinION sequencing , 2017, bioRxiv.
[31] A. von Haeseler,et al. UFBoot2: Improving the Ultrafast Bootstrap Approximation , 2017, bioRxiv.
[32] T. Schulz,et al. Kaposi's Sarcoma-Associated Herpesvirus Latency-Associated Nuclear Antigen: Replicating and Shielding Viral DNA during Viral Persistence , 2017, Journal of Virology.
[33] I. Ahel,et al. The Toxin-Antitoxin System DarTG Catalyzes Reversible ADP-Ribosylation of DNA , 2016, Molecular cell.
[34] Brian C. Thomas,et al. Measurement of bacterial replication rates in microbial communities , 2016, Nature Biotechnology.
[35] Itay Mayrose,et al. ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules , 2016, Nucleic Acids Res..
[36] Peer Bork,et al. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees , 2016, Nucleic Acids Res..
[37] H. O. D. op den Camp,et al. A Metagenomics-Based Metabolic Model of Nitrate-Dependent Anaerobic Oxidation of Methane by Methanoperedens-Like Archaea , 2015, Front. Microbiol..
[38] L. Aravind,et al. Comparative genomic analyses reveal a vast, novel network of nucleotide-centric systems in biological conflicts, immunity and signaling , 2015, Nucleic acids research.
[39] A. Boetius,et al. Intercellular wiring enables electron transfer between methanotrophic archaea and bacteria , 2015, Nature.
[40] Brian C. Thomas,et al. Unusual biology across a group comprising more than 15% of domain Bacteria , 2015, Nature.
[41] Raven H. Huang,et al. Reconstitution and structure of a bacterial Pnkp1–Rnl–Hen1 RNA repair complex , 2015, Nature Communications.
[42] A. von Haeseler,et al. IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies , 2014, Molecular biology and evolution.
[43] Christopher J. Oldfield,et al. Classification of Intrinsically Disordered Regions and Proteins , 2014, Chemical reviews.
[44] Brian Bushnell,et al. BBMap: A Fast, Accurate, Splice-Aware Aligner , 2014 .
[45] Shihu Hu,et al. Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage , 2013, Nature.
[46] Wei Shi,et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features , 2013, Bioinform..
[47] K. Katoh,et al. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.
[48] Pelin Yilmaz,et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools , 2012, Nucleic Acids Res..
[49] S. Weller,et al. Herpes simplex viruses: mechanisms of DNA replication. , 2012, Cold Spring Harbor perspectives in biology.
[50] G. Rákhely,et al. Relationship between PHA and hydrogen metabolism in the purple sulfur phototrophic bacterium Thiocapsa roseopersicina BBS , 2012 .
[51] A. Biegert,et al. HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment , 2011, Nature Methods.
[52] D. Higgins,et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega , 2011, Molecular systems biology.
[53] Alexis Criscuolo,et al. BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments , 2010, BMC Evolutionary Biology.
[54] Colin R. Parrish,et al. Presence and role of cytosine methylation in DNA viruses of animals , 2008, Nucleic acids research.
[55] E. Birney,et al. Pfam: the protein families database , 2013, Nucleic Acids Res..
[56] M. Dyall-Smith,et al. Constituents of SH1, a Novel Lipid-Containing Virus Infecting the Halophilic Euryarchaeon Haloarcula hispanica , 2005, Journal of Virology.
[57] Yuan-ming Luo,et al. Sulfolobus tengchongensis Spindle-Shaped Virus STSV1: Virus-Host Interactions and Genomic Features , 2005, Journal of Virology.
[58] Johannes Söding,et al. Protein homology detection by HMM?CHMM comparison , 2005, Bioinform..
[59] K Henrick,et al. Electronic Reprint Biological Crystallography Secondary-structure Matching (ssm), a New Tool for Fast Protein Structure Alignment in Three Dimensions Biological Crystallography Secondary-structure Matching (ssm), a New Tool for Fast Protein Structure Alignment in Three Dimensions , 2022 .
[60] J. Christopher Fromme,et al. Structure of a trapped endonuclease III–DNA covalent intermediate , 2003, The EMBO journal.
[61] R. Myers,et al. Bacteriophage SPP1 Chu Is an Alkaline Exonuclease in the SynExo Family of Viral Two-Component Recombinases , 2003, Journal of Bacteriology.
[62] P. Sung,et al. DNA.RNA helicase activity of RAD3 protein of Saccharomyces cerevisiae. , 1991, Proceedings of the National Academy of Sciences of the United States of America.
[63] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[64] R. Levitz,et al. Bacteriophage T4 anticodon nuclease, polynucleotide kinase and RNA ligase reprocess the host lysine tRNA. , 1987, The EMBO journal.
[65] W. Delano. The PyMOL Molecular Graphics System , 2002 .