‘ARMAN’ archaea depend on association with euryarchaeal host in culture and in situ

[1]  P. Pevzner,et al.  metaSPAdes: a new versatile metagenomic assembler. , 2017, Genome research.

[2]  Philipp C. Münch,et al.  Laboratory cultivation of acidophilic nanoorganisms. Physiological and bioinformatic dissection of a stable laboratory co-culture , 2017, bioRxiv.

[3]  T. Nechitaylo,et al.  Biology of archaea from a novel family Cuniculiplasmataceae (Thermoplasmata) ubiquitous in hyperacidic environments , 2016, Scientific Reports.

[4]  Eric P. Skaar,et al.  Heme Synthesis and Acquisition in Bacterial Pathogens. , 2016, Journal of Molecular Biology.

[5]  Richard J. Giannone,et al.  Genomics-informed isolation and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment , 2016, Nature Communications.

[6]  Daniel H. Huson,et al.  MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data , 2016, PLoS Comput. Biol..

[7]  E. Koonin,et al.  Diversity and Evolution of Type IV pili Systems in Archaea , 2016, Front. Microbiol..

[8]  Bonnie Berger,et al.  Enabling Privacy Preserving GWAS in Heterogeneous Human Populations , 2016, RECOMB.

[9]  K. Holmfeldt,et al.  Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations , 2015, The ISME Journal.

[10]  Patrick Forterre,et al.  The universal tree of life: an update , 2015, Front. Microbiol..

[11]  M. Ferrer,et al.  Microbial diversity and metabolic networks in acid mine drainage habitats , 2015, Front. Microbiol..

[12]  L. Sazanov.  A giant molecular proton pump: structure and mechanism of respiratory complex I , 2015, Nature Reviews Molecular Cell Biology.

[13]  Matthew R. Laird,et al.  IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis , 2015, Nucleic Acids Res..

[14]  Kenneth H. Williams,et al.  Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling , 2015, Current Biology.

[15]  Kira S. Makarova,et al.  Archaeal Clusters of Orthologous Genes (arCOGs): An Update and Application for Analysis of Shared Features between Thermococcales, Methanococcales, and Methanobacteriales , 2015, Life.

[16]  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.

[17]  Chao Xie,et al.  Fast and sensitive protein alignment using DIAMOND , 2014, Nature Methods.

[18]  A. Ducluzeau,et al.  The evolution of respiratory O2/NO reductases: an out-of-the-phylogenetic-box perspective , 2014, Journal of The Royal Society Interface.

[19]  E. Koonin,et al.  Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes , 2014, BMC Biology.

[20]  E. Koonin,et al.  Dark matter in archaeal genomes: a rich source of novel mobile elements, defense systems and secretory complexes , 2014, Extremophiles.

[21]  B. Siebers,et al.  Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation , 2014, Microbiology and Molecular Reviews.

[22]  S. Ferguson,et al.  Recent advances in the biosynthesis of modified tetrapyrroles: the discovery of an alternative pathway for the formation of heme and heme d1 , 2014, Cellular and Molecular Life Sciences.

[23]  S. Bräuer,et al.  Southern Appalachian Peatlands Support High Archaeal Diversity , 2014, Microbial Ecology.

[24]  Richard M. Leggett,et al.  NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries , 2013, Bioinform..

[25]  Michael Y. Galperin,et al.  Evolution of cytochrome bc complexes: from membrane-anchored dehydrogenases of ancient bacteria to triggers of apoptosis in vertebrates. , 2013, Biochimica et biophysica acta.

[26]  Natalia N. Ivanova,et al.  Insights into the phylogeny and coding potential of microbial dark matter , 2013, Nature.

[27]  Brian C. Thomas,et al.  Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea , 2013, BMC Genomics.

[28]  H. Huber,et al.  Microbial syntrophy: interaction for the common good. , 2013, FEMS microbiology reviews.

[29]  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.

[30]  E. Koonin,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.

[31]  Patrícia N. Refojo,et al.  The Alternative complex III: properties and possible mechanisms for electron transfer and energy conservation. , 2012, Biochimica et biophysica acta.

[32]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[33]  R. Gennis,et al.  The cytochrome bd respiratory oxygen reductases. , 2011, Biochimica et biophysica acta.

[34]  Natalya Yutin,et al.  Phylogenomics of prokaryotic ribosomal proteins , 2011, Genome Biology.

[35]  O. Golyshina.  Environmental, Biogeographic, and Biochemical Patterns of Archaea of the Family Ferroplasmaceae , 2011, Applied and Environmental Microbiology.

[36]  Sonja J. Prohaska,et al.  Proteinortho: Detection of (Co-)orthologs in large-scale analysis , 2011, BMC Bioinformatics.

[37]  Miklós Csuös,et al.  Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood , 2010, Bioinform..

[38]  Doug Hyatt,et al.  Enigmatic, ultrasmall, uncultivated Archaea , 2010, Proceedings of the National Academy of Sciences.

[39]  Paramvir S. Dehal,et al.  FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.

[40]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[41]  Kenneth H Downing,et al.  Three-dimensional analysis of the structure and ecology of a novel, ultra-small archaeon , 2009, The ISME Journal.

[42]  S. Juutinen,et al.  Seasonality of rDNA- and rRNA-derived archaeal communities and methanogenic potential in a boreal mire , 2008, The ISME Journal.

[43]  Michael Y. Galperin,et al.  Evolutionary primacy of sodium bioenergetics , 2008, Biology Direct.

[44]  M. F. Drincovich,et al.  Escherichia coli Malic Enzymes: Two Isoforms with Substantial Differences in Kinetic Properties, Metabolic Regulation, and Structure , 2007, Journal of bacteriology.

[45]  Philip Hugenholtz,et al.  Lineages of Acidophilic Archaea Revealed by Community Genomic Analysis , 2006, Science.

[46]  Carsten Damm,et al.  Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models , 2006, BMC Bioinformatics.

[47]  C. Baker-Austin,et al.  Molecular insight into extreme copper resistance in the extremophilic archaeon 'Ferroplasma acidarmanus' Fer1. , 2005, Microbiology.

[48]  Eric P. Skaar,et al.  Iron-Source Preference of Staphylococcus aureus Infections , 2004, Science.

[49]  Robert C. Edgar,et al.  MUSCLE: a multiple sequence alignment method with reduced time and space complexity , 2004, BMC Bioinformatics.

[50]  T. Reinthaler,et al.  Combining Catalyzed Reporter Deposition-Fluorescence In Situ Hybridization and Microautoradiography To Detect Substrate Utilization by Bacteria and Archaea in the Deep Ocean , 2004, Applied and Environmental Microbiology.

[51]  G. Cecchini,et al.  Function and structure of complex II of the respiratory chain. , 2003, Annual review of biochemistry.

[52]  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.

[53]  Steven J. M. Jones,et al.  IslandPath: aiding detection of genomic islands in prokaryotes , 2003, Bioinform..

[54]  Junichi Takagi,et al.  Archaeal Surface Layer Proteins Contain β Propeller, PKD, and β Helix Domains and Are Related to Metazoan Cell Surface Proteins , 2002 .

[55]  Harald Huber,et al.  A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont , 2002, Nature.

[56]  K. Schleifer,et al.  The domain-specific probe EUB338 is insufficient for the detection of all Bacteria: development and evaluation of a more comprehensive probe set. , 1999, Systematic and applied microbiology.

[57]  E. Conway de Macario,et al.  Structure, organization, and expression of genes coding for envelope components in the archaeon Methanosarcina mazei S-6 , 1998, Archives of Microbiology.

[58]  D A Stahl,et al.  Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology , 1990, Journal of bacteriology.

[59]  P. Golyshin,et al.  The novel extremely acidophilic, cell-wall-deficient archaeon Cuniculiplasma divulgatum gen. nov., sp. nov. represents a new family, Cuniculiplasmataceae fam. nov., of the order Thermoplasmatales. , 2016, International journal of systematic and evolutionary microbiology.

[60]  Michail M. Yakimov,et al.  Genomic Analysis of Pure Cultures and Communities , 2015 .

[61]  Ricardo Amils,et al.  Microbial community structure across the tree of life in the extreme Río Tinto , 2011, The ISME Journal.

[62]  R. Kolter,et al.  In-depth Characterization via Complementing Culture-Independent Approaches of the Microbial Community in an Acidic Hot Spring of the Colombian Andes , 2011, Microbial Ecology.

[63]  C. Baker-Austin,et al.  Molecular insight into extreme copper resistance in the extremophilic archaeon ‘ Ferroplasma acidarmanus ’ Fer 1 , 2005 .

[64]  K. Johnson.  An Update. , 1984, Journal of food protection.