Archaeal Clusters of Orthologous Genes (arCOGs): An Update and Application for Analysis of Shared Features between Thermococcales, Methanococcales, and Methanobacteriales
暂无分享,去创建一个
[1] B. Snel,et al. Toward Automatic Reconstruction of a Highly Resolved Tree of Life , 2006, Science.
[2] Natalia N. Ivanova,et al. Insights into the phylogeny and coding potential of microbial dark matter , 2013, Nature.
[3] Céline Brochier,et al. An emerging phylogenetic core of Archaea: phylogenies of transcription and translation machineries converge following addition of new genome sequences , 2005, BMC Evolutionary Biology.
[4] J. Einasto. Dark Matter , 2009, 0901.0632.
[5] Arcady R. Mushegian,et al. Computational methods for Gene Orthology inference , 2011, Briefings Bioinform..
[6] Hervé Philippe,et al. Archaeal phylogeny based on ribosomal proteins. , 2002, Molecular biology and evolution.
[7] P. Forterre,et al. Phylogeny and evolution of the Archaea: one hundred genomes later. , 2011, Current opinion in microbiology.
[8] Doug Hyatt,et al. Enigmatic, ultrasmall, uncultivated Archaea , 2010, Proceedings of the National Academy of Sciences.
[9] Natalya Yutin,et al. Phylogenomics of prokaryotic ribosomal proteins , 2011, Genome Biology.
[10] Claire O'Donovan,et al. Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data , 2014, Database J. Biol. Databases Curation.
[11] E. Koonin,et al. Two new families of the FtsZ-tubulin protein superfamily implicated in membrane remodeling in diverse bacteria and archaea , 2010, Biology Direct.
[12] Sean D. Hooper,et al. Genomic Characterization of Methanomicrobiales Reveals Three Classes of Methanogens , 2009, PloS one.
[13] L. Knowles,et al. How low can you go? The effects of mutation rate on the accuracy of species-tree estimation. , 2014, Molecular phylogenetics and evolution.
[14] R. Lewis,et al. RNA degradation in Bacillus subtilis: an interplay of essential endo‐ and exoribonucleases , 2012, Molecular microbiology.
[15] István Miklós,et al. Streamlining and Large Ancestral Genomes in Archaea Inferred with a Phylogenetic Birth-and-Death Model , 2009, Molecular biology and evolution.
[16] A. Force,et al. The probability of duplicate gene preservation by subfunctionalization. , 2000, Genetics.
[17] Dieter Söll,et al. The genome of Nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[18] Sagi Snir,et al. Defense Islands in Bacterial and Archaeal Genomes and Prediction of Novel Defense Systems , 2011, Journal of bacteriology.
[19] E. Koonin,et al. A korarchaeal genome reveals insights into the evolution of the Archaea , 2008, Proceedings of the National Academy of Sciences.
[20] N. Loman,et al. Calculating Orthologs in Bacteria and Archaea: A Divide and Conquer Approach , 2011, PloS one.
[21] Michael Y. Galperin,et al. Comparative genomic analysis of evolutionarily conserved but functionally uncharacterized membrane proteins in archaea: Prediction of novel components of secretion, membrane remodeling and glycosylation systems , 2015, Biochimie.
[22] Eugene V Koonin,et al. The CMG (CDC45/RecJ, MCM, GINS) complex is a conserved component of the DNA replication system in all archaea and eukaryotes , 2012, Biology Direct.
[23] Tsutomu Suzuki,et al. molecular mechanism of lysidine synthesis that determines tRNA identity and codon recognition. , 2005, Molecular cell.
[24] Maureen A. O’Malley,et al. Prokaryotic evolution and the tree of life are two different things , 2009, Biology Direct.
[25] E. Koonin,et al. Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park , 2013, Biology Direct.
[26] Haiwei Luo,et al. Gene Order Phylogeny and the Evolution of Methanogens , 2009, PloS one.
[27] Katsuhiko Murakami,et al. Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees , 2007, Nucleic Acids Res..
[28] K. Makarova,et al. The Complete Genome Sequence of Thermoproteus tenax: A Physiologically Versatile Member of the Crenarchaeota , 2011, PloS one.
[29] Thijs J. G. Ettema,et al. The archaeal 'TACK' superphylum and the origin of eukaryotes. , 2011, Trends in microbiology.
[30] Yue-qin Tang,et al. E. coli aconitase B structure reveals a HEAT-like domain with implications for protein–protein recognition , 2002, Nature Structural Biology.
[31] Rolf Bernander,et al. Archaeal Signal Transduction: Impact of Protein Phosphatase Deletions on Cell Size, Motility, and Energy Metabolism in Sulfolobus acidocaldarius* , 2013, Molecular & Cellular Proteomics.
[32] Boris G. Mirkin,et al. Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell , 2005, Nucleic acids research.
[33] A. Krogh,et al. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. , 2001, Journal of molecular biology.
[34] Andrew M. Smith,et al. The UCSC Archaeal Genome Browser: 2012 update , 2011, Nucleic Acids Res..
[35] E. Koonin,et al. Search for a 'Tree of Life' in the thicket of the phylogenetic forest , 2009, Journal of biology.
[36] P. Bork,et al. A P‐loop‐like motif in a widespread ATP pyrophosphatase domain: Implications for the evolution of sequence motifs and enzyme activity , 1994, Proteins.
[37] Eugene V Koonin,et al. CRISPR-Cas , 2013, RNA biology.
[38] E. Koonin. Carl Woese's vision of cellular evolution and the domains of life , 2014, RNA biology.
[39] P. Wright,et al. Change of carbon source causes dramatic effects in the phospho-proteome of the archaeon Sulfolobus solfataricus. , 2012, Journal of proteome research.
[40] Eric Bapteste,et al. INAUGURAL ARTICLE by a Recently Elected Academy Member:Pattern pluralism and the Tree of Life hypothesis , 2007 .
[41] Maryse Condé. Tree of Life , 1992 .
[42] Peer Bork,et al. A Phylogeny-Based Benchmarking Test for Orthology Inference Reveals the Limitations of Function-Based Validation , 2014, PloS one.
[43] W. Doolittle,et al. Alternative methods for concatenation of core genes indicate a lack of resolution in deep nodes of the prokaryotic phylogeny. , 2007, Molecular biology and evolution.
[44] Tomasello,et al. A congruent phylogenomic signal places eukaryotes within the Archaea , 2012, Proceedings of the Royal Society B: Biological Sciences.
[45] E. Koonin,et al. Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea , 2007, Biology Direct.
[46] Natalia N. Ivanova,et al. A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans , 2008, Genome Biology.
[47] Paramvir S. Dehal,et al. FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.
[48] Daniel N. Wilson,et al. Proteomic characterization of archaeal ribosomes reveals the presence of novel archaeal-specific ribosomal proteins. , 2011, Journal of molecular biology.
[49] Harald Huber,et al. A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont , 2002, Nature.
[50] E. Koonin,et al. Seeing the Tree of Life behind the phylogenetic forest , 2013, BMC Biology.
[51] Robert C. Edgar,et al. MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.
[52] Eugene V Koonin,et al. The basic building blocks and evolution of CRISPR-CAS systems. , 2013, Biochemical Society transactions.
[53] Rolf Bernander,et al. A unique cell division machinery in the Archaea , 2008, Proceedings of the National Academy of Sciences.
[54] N. Kyrpides,et al. Integration of phenotypic metadata and protein similarity in Archaea using a spectral bipartitioning approach , 2009, Nucleic acids research.
[55] E. Birney,et al. Pfam: the protein families database , 2013, Nucleic Acids Res..
[56] Alexander Goncearenco,et al. Exploring the evolution of protein function in Archaea , 2012, BMC Evolutionary Biology.
[57] E. Koonin,et al. GINS, a central nexus in the archaeal DNA replication fork , 2006, EMBO reports.
[58] William J. Kelly,et al. The Genome Sequence of the Rumen Methanogen Methanobrevibacter ruminantium Reveals New Possibilities for Controlling Ruminant Methane Emissions , 2010, PloS one.
[59] Darren A. Natale,et al. The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[60] E. Koonin,et al. Dark matter in archaeal genomes: a rich source of novel mobile elements, defense systems and secretory complexes , 2014, Extremophiles.
[61] Natalya Yutin,et al. Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer , 2012, Biology Direct.
[62] K. Katoh,et al. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.
[63] Narmada Thanki,et al. CDD: specific functional annotation with the Conserved Domain Database , 2008, Nucleic Acids Res..
[64] E. Koonin,et al. The Deep Archaeal Roots of Eukaryotes , 2008, Molecular biology and evolution.
[65] E V Koonin,et al. Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. , 1999, Genome research.
[66] Céline Brochier,et al. Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox , 2004, Genome Biology.
[67] Christophe Dessimoz,et al. Inferring orthology and paralogy. , 2012, Methods in molecular biology.
[68] P. Forterre,et al. Global Phylogenomic Analysis Disentangles the Complex Evolutionary History of DNA Replication in Archaea , 2014, Genome biology and evolution.
[69] Fan Yang,et al. TIGRFAMs: a protein family resource for the functional identification of proteins , 2001, Nucleic Acids Res..
[70] S. Gribaldo,et al. Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine , 2014, BMC Genomics.
[71] Purificación López-García,et al. Rooting the Domain Archaea by Phylogenomic Analysis Supports the Foundation of the New Kingdom Proteoarchaeota , 2014, Genome biology and evolution.
[72] Johannes Söding,et al. The HHpred interactive server for protein homology detection and structure prediction , 2005, Nucleic Acids Res..
[73] V. Kaberdin,et al. Unraveling new roles for minor components of the E. coli RNA degradosome , 2009, RNA biology.
[74] Michael Y. Galperin,et al. Expanded microbial genome coverage and improved protein family annotation in the COG database , 2014, Nucleic Acids Res..
[75] S. Brunak,et al. SignalP 4.0: discriminating signal peptides from transmembrane regions , 2011, Nature Methods.
[76] R. DeSalle,et al. Phylogeny of genes for secretion NTPases: Identification of the widespread tadA subfamily and development of a diagnostic key for gene classification , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[77] P. Lockhart,et al. A reality check for alignments and trees. , 2007, Trends in genetics : TIG.
[78] P. Forterre,et al. Nanoarchaea: representatives of a novel archaeal phylum or a fast-evolving euryarchaeal lineage related to Thermococcales? , 2005, Genome Biology.
[79] M. Paddy,et al. NCL1, a novel gene for a non-essential nuclear protein in Saccharomyces cerevisiae. , 1998, Gene.
[80] Antoine Danchin,et al. Re-annotation of genome microbial CoDing-Sequences: finding new genes and inaccurately annotated genes , 2002, BMC Bioinformatics.
[81] F. Lapointe,et al. Of woods and webs: possible alternatives to the tree of life for studying genomic fluidity in E. coli , 2011, Biology Direct.
[82] Eugene V Koonin,et al. Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems , 2011, Biology Direct.
[83] M. F. White,et al. CARF and WYL domains: ligand-binding regulators of prokaryotic defense systems , 2014, Front. Genet..
[84] John Gatesy,et al. Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum. , 2014, Molecular phylogenetics and evolution.
[85] E. Koonin,et al. Evolution of diverse cell division and vesicle formation systems in Archaea , 2010, Nature Reviews Microbiology.
[86] E. Koonin,et al. Evolution of replicative DNA polymerases in archaea and their contributions to the eukaryotic replication machinery , 2014, Front. Microbiol..
[87] L. Regan,et al. Structure and function of KH domains , 2008, The FEBS journal.
[88] W. Martin,et al. The tree of one percent , 2006, Genome Biology.
[89] Eugene V Koonin,et al. Connected gene neighborhoods in prokaryotic genomes. , 2002, Nucleic acids research.
[90] J. Kissinger,et al. Identification of Diverse Archaeal Proteins with Class III Signal Peptides Cleaved by Distinct Archaeal Prepilin Peptidases , 2006, Journal of bacteriology.
[91] E. Koonin,et al. Archaeology of eukaryotic DNA replication. , 2013, Cold Spring Harbor perspectives in medicine.
[92] E. Koonin,et al. Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world , 2008, Nucleic acids research.
[93] Filipa L. Sousa,et al. Origins of major archaeal clades correspond to gene acquisitions from bacteria , 2014, Nature.
[94] Eugene V Koonin,et al. The fundamental units, processes and patterns of evolution, and the Tree of Life conundrum , 2009, Biology Direct.
[95] Tom A. Williams,et al. Archaeal “Dark Matter” and the Origin of Eukaryotes , 2014, Genome biology and evolution.
[96] Nicola J. Mulder,et al. The use of semantic similarity measures for optimally integrating heterogeneous Gene Ontology data from large scale annotation pipelines , 2014, Front. Genet..
[97] P. Bork,et al. Orthology prediction methods: A quality assessment using curated protein families , 2011, BioEssays : news and reviews in molecular, cellular and developmental biology.
[98] V. Lyubetsky,et al. Modeling RNA polymerase competition: the effect of σ-subunit knockout and heat shock on gene transcription level , 2011, Biology Direct.