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Select item 60095811.

Methylation guide RNA evolution in archaea: structure, function and genomic organization of 110 C/D box sRNA families across six Pyrobaculum species

Lauren M Lui, Andrew V Uzilov, David L Bernick, Andrea Corredor, Todd M Lowe, Patrick P Dennis

Nucleic Acids Res. 2018 Jun 20; 46(11): 5678–5691. Published online 2018 May 16. doi: 10.1093/nar/gky284

PMCID:: PMC6009581

Abstract Article PDF–1.6M

Select item 57974282.

Candidatus Nitrosocaldus cavascurensis, an Ammonia Oxidizing, Extremely Thermophilic Archaeon with a Highly Mobile Genome

Sophie S. Abby, Michael Melcher, Melina Kerou, Mart Krupovic, Michaela Stieglmeier, Claudia Rossel, Kevin Pfeifer, Christa Schleper

Front Microbiol. 2018; 9: 28. Published online 2018 Jan 26. doi: 10.3389/fmicb.2018.00028

PMCID:: PMC5797428

Abstract Article PDF–4.2M

Select item 53899473.

Comparative Analysis of Predicted Gene Expression among Crenarchaeal Genomes

Shibsankar Das, Brajadulal Chottopadhyay, Satyabrata Sahoo

Genomics Inform. 2017 Mar; 15(1): 38–47. Published online 2017 Mar 29. doi: 10.5808/GI.2017.15.1.38

PMCID:: PMC5389947

Abstract Article PDF–549K

Select item 51733194.

Crenactin forms actin-like double helical filaments regulated by arcadin-2

Thierry Izoré, Danguole Kureisaite-Ciziene, Stephen H McLaughlin, Jan Löwe

eLife. 2016; 5: e21600. Published online 2016 Nov 17. doi: 10.7554/eLife.21600

PMCID:: PMC5173319

Abstract Article PDF–4.4M

Select item 51504145.

Proteomics and comparative genomics of Nitrososphaera viennensis reveal the core genome and adaptations of archaeal ammonia oxidizers

Melina Kerou, Pierre Offre, Luis Valledor, Sophie S. Abby, Michael Melcher, Matthias Nagler, Wolfram Weckwerth, Christa Schleper

Proc Natl Acad Sci U S A. 2016 Dec 6; 113(49): E7937–E7946. Published online 2016 Nov 18. doi: 10.1073/pnas.1601212113

PMCID:: PMC5150414

Abstract Article PDF–1.4M

Select item 50542226.

A Method for Identification of Selenoprotein Genes in Archaeal Genomes

Mingfeng Li, Yanzhao Huang, Yi Xiao

Genomics Proteomics Bioinformatics. 2009 Jun; 7(1-2): 62–70. Published online 2009 Jul 8. doi: 10.1016/S1672-0229(08)60034-0

PMCID:: PMC5054222

Abstract Article PDF–759K

Select item 43908877.

Phylogeny and Taxonomy of Archaea: A Comparison of the Whole-Genome-Based CVTree Approach with 16S rRNA Sequence Analysis

Guanghong Zuo, Zhao Xu, Bailin Hao

Life (Basel) 2015 Mar; 5(1): 949–968. Published online 2015 Mar 17. doi: 10.3390/life5010949

PMCID:: PMC4390887

Abstract Article PDF–1019K

Select item 41687028.

Assembly-free genome comparison based on next-generation sequencing reads and variable length patterns

Matteo Comin, Michele Schimd

BMC Bioinformatics. 2014; 15(Suppl 9): S1. Published online 2014 Sep 10. doi: 10.1186/1471-2105-15-S9-S1

PMCID:: PMC4168702

Abstract Article PDF–676K

Select item 35589659.

Complete genome sequence of Pyrobaculum oguniense

David L. Bernick, Kevin Karplus, Lauren M. Lui, Joanna K. C. Coker, Julie N. Murphy, Patricia P. Chan, Aaron E. Cozen, Todd M. Lowe

Stand Genomic Sci. 2012 Jul 30; 6(3): 336–345. Published online 2012 Jul 20. doi: 10.4056/sigs.2645906

PMCID:: PMC3558965

Abstract Article PDF–2.0M

Select item 339628510.

Comparative genomic and transcriptional analyses of CRISPR systems across the genus Pyrobaculum

David L. Bernick, Courtney L. Cox, Patrick P. Dennis, Todd M. Lowe

Front Microbiol. 2012; 3: 251. Prepublished online 2012 May 11. Published online 2012 Jul 13. doi: 10.3389/fmicb.2012.00251

PMCID:: PMC3396285

Abstract Article PDF–932K

Select item 338879411.

Diversity of Antisense and Other Non-Coding RNAs in Archaea Revealed by Comparative Small RNA Sequencing in Four Pyrobaculum Species

David L. Bernick, Patrick P. Dennis, Lauren M. Lui, Todd M. Lowe

Front Microbiol. 2012; 3: 231. Published online 2012 Jul 2. doi: 10.3389/fmicb.2012.00231

PMCID:: PMC3388794

Abstract Article PDF–834K

Select item 327883612.

Novel base triples in RNA structures revealed by graph theoretical searching methods

Mohd Firdaus-Raih, Anne-Marie Harrison, Peter Willett, Peter J Artymiuk

BMC Bioinformatics. 2011; 12(Suppl 13): S2. Published online 2011 Nov 30. doi: 10.1186/1471-2105-12-S13-S2

PMCID:: PMC3278836

Abstract Article PDF–1.3M

Select item 287300213.

The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods

Peter G. Foster, Cymon J. Cox, T. Martin Embley

Philos Trans R Soc Lond B Biol Sci. 2009 Aug 12; 364(1527): 2197–2207. doi: 10.1098/rstb.2009.0034

PMCID:: PMC2873002

Abstract Article PDF–500K

Select item 273596714.

Estimating the Fraction of Non-Coding RNAs in Mammalian Transcriptomes

Yurong Xin, Giulio Quarta, Hin Hark Gan, Tamar Schlick

Bioinform Biol Insights. 2008; 2: 75–94. Published online 2008 Mar 1. doi: 10.4137/bbi.s443

PMCID:: PMC2735967

Abstract Article PDF–670K

Select item 270149315.

Fine-structured multi-scaling long-range correlations in completely sequenced genomes—features, origin, and classification

Tobias A. Knoch, Markus Göker, Rudolf Lohner, Anis Abuseiris, Frank G. Grosveld

Eur Biophys J. 2009 Jul; 38(6): 757–779. Published online 2009 Jun 17. doi: 10.1007/s00249-009-0489-y

PMCID:: PMC2701493

Abstract Article PDF–1.5M

Select item 268558516.

A putative viral defence mechanism in archaeal cells

Reidun Lillestøl, Peter Redder, Roger A. Garrett, Kim Brügger

Archaea. 2006 Aug; 2(1): 59–72. Published online 2006 Jul 10. doi: 10.1155/2006/542818

PMCID:: PMC2685585

Abstract Article PDF–1.2M

Select item 268554817.

Identification of replication origins in archaeal genomes based on the Z-curve method

Ren Zhang, Chun-Ting Zhang

Archaea. 2005 May; 1(5): 335–346. Published online 2004 Nov 9. doi: 10.1155/2005/509646

PMCID:: PMC2685548

Abstract Article PDF–228K

Select item 265032618.

Tri-split tRNA is a transfer RNA made from 3 transcripts that provides insight into the evolution of fragmented tRNAs in archaea

Kosuke Fujishima, Junichi Sugahara, Kaoru Kikuta, Reiko Hirano, Asako Sato, Masaru Tomita, Akio Kanai

Proc Natl Acad Sci U S A. 2009 Feb 24; 106(8): 2683–2687. Published online 2009 Feb 3. doi: 10.1073/pnas.0808246106

PMCID:: PMC2650326

Abstract Article PDF–876K

Select item 256622019.

Stygiolobus Rod-Shaped Virus and the Interplay of Crenarchaeal Rudiviruses with the CRISPR Antiviral System

Gisle Vestergaard, Shiraz A. Shah, Ariane Bize, Werner Reitberger, Monika Reuter, Hien Phan, Ariane Briegel, Reinhard Rachel, Roger A. Garrett, David Prangishvili

J Bacteriol. 2008 Oct; 190(20): 6837–6845. Published online 2008 Aug 22. doi: 10.1128/JB.00795-08

PMCID:: PMC2566220

Abstract Article PDF–1.0M

Select item 223790020.

Sequence Evidence in the Archaeal Genomes that tRNAs Emerged Through the Combination of Ancestral Genes as 5′ and 3′ tRNA Halves

Kosuke Fujishima, Junichi Sugahara, Masaru Tomita, Akio Kanai

PLoS One. 2008; 3(2): e1622. Published online 2008 Feb 20. doi: 10.1371/journal.pone.0001622

PMCID:: PMC2237900

Abstract Article PDF–541K

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