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Items: 1 to 20 of 23

1.
A Reexamination of Thioredoxin Reductase from Thermoplasma acidophilum, a Thermoacidophilic Euryarchaeon, Identifies It as an NADH-Dependent Enzyme
Dwi Susanti, Usha Loganathan, Austin Compton, Biswarup Mukhopadhyay
ACS Omega. 2017 Aug 31; 2(8): 4180–4187. Published online 2017 Aug 3. doi: 10.1021/acsomega.7b00640
PMCID:
PMC5579543
AbstractArticlePDF–3.5M
2.
Conservation of coevolving protein interfaces bridges prokaryote–eukaryote homologies in the twilight zone
Juan Rodriguez-Rivas, Simone Marsili, David Juan, Alfonso Valencia
Proc Natl Acad Sci U S A. 2016 Dec 27; 113(52): 15018–15023. Published online 2016 Dec 13. doi: 10.1073/pnas.1611861114
PMCID:
PMC5206536
AbstractArticlePDF–1.0M
3.
Conditions for duality between fluxes and concentrations in biochemical networks
Ronan M.T. Fleming, Nikos Vlassis, Ines Thiele, Michael A. Saunders
J Theor Biol. Author manuscript; available in PMC 2017 Nov 21.
Published in final edited form as: J Theor Biol. 2016 Nov 21; 409: 1–10. Published online 2016 Jun 23. doi: 10.1016/j.jtbi.2016.06.033
PMCID:
PMC5048525
AbstractArticlePDF–625K
4.
Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer
Raquel Bromberg, Nick V. Grishin, Zbyszek Otwinowski
PLoS Comput Biol. 2016 Jun; 12(6): e1004985. Published online 2016 Jun 23. doi: 10.1371/journal.pcbi.1004985
PMCID:
PMC4918981
AbstractArticlePDF–1.6M
5.
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
AbstractArticlePDF–1019K
6.
Genome-wide gene order distances support clustering the gram-positive bacteria
Christopher H. House, Matteo Pellegrini, Sorel T. Fitz-Gibbon
Front Microbiol. 2014; 5: 785. Published online 2015 Jan 20. doi: 10.3389/fmicb.2014.00785
PMCID:
PMC4299520
AbstractArticlePDF–8.7M
7.
The First Complete Genome Sequence of the Class Fimbriimonadia in the Phylum Armatimonadetes
Zi-Ye Hu, Yue-Zhu Wang, Wan-Taek Im, Sheng-Yue Wang, Guo-Ping Zhao, Hua-Jun Zheng, Zhe-Xue Quan
PLoS One. 2014; 9(6): e100794. Published online 2014 Jun 26. doi: 10.1371/journal.pone.0100794
PMCID:
PMC4072686
AbstractArticlePDF–953K
8.
Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms
Arshan Nasir, Aisha Naeem, Muhammad Jawad Khan, Horacio D. Lopez-Nicora, Gustavo Caetano-Anollés
Genes (Basel) 2011 Dec; 2(4): 869–911. Published online 2011 Nov 8. doi: 10.3390/genes2040869
PMCID:
PMC3927607
AbstractArticlePDF–2.0M
9.
Argonaute protein as a linker to command center of physiological processes
Kaifa Wei, Lingjuan Wu, Yanhui Chen, Yina Lin, Yanmei Wang, Xiaoyao Liu, Daoxin Xie
Chin J Cancer Res. 2013 Aug; 25(4): 430–441. doi: 10.3978/j.issn.1000-9604.2013.08.13
PMCID:
PMC3752357
AbstractArticlePDF–1.3M
10.
On the Distribution of Protein Refractive Index Increments
Huaying Zhao, Patrick H. Brown, Peter Schuck
Biophys J. 2011 May 4; 100(9): 2309–2317. doi: 10.1016/j.bpj.2011.03.004
PMCID:
PMC3149238
AbstractArticlePDF–491K
11.
Archaeal RNA polymerase and transcription regulation
Sung-Hoon Jun, Matthew J. Reichlen, Momoko Tajiri, Katsuhiko S. Murakami
Crit Rev Biochem Mol Biol. Author manuscript; available in PMC 2012 Feb 1.
Published in final edited form as: Crit Rev Biochem Mol Biol. 2011 Feb; 46(1): 27–40. doi: 10.3109/10409238.2010.538662
PMCID:
PMC3076279
AbstractArticlePDF–1.4M
12.
Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans
Vinay Satish Kumar, James G Ferry, Costas D Maranas
BMC Syst Biol. 2011; 5: 28. Published online 2011 Feb 15. doi: 10.1186/1752-0509-5-28
PMCID:
PMC3048526
AbstractArticlePDF–365K
13.
An ancient family of SelB elongation factor-like proteins with a broad but disjunct distribution across archaea
Gemma C Atkinson, Vasili Hauryliuk, Tanel Tenson
BMC Evol Biol. 2011; 11: 22. Published online 2011 Jan 21. doi: 10.1186/1471-2148-11-22
PMCID:
PMC3037878
AbstractArticlePDF–1.2M
14.
A transposon toolkit for gene transfer and mutagenesis in protozoan parasites
Jeziel D. Damasceno, Stephen M. Beverley, Luiz R. O. Tosi
Genetica. Author manuscript; available in PMC 2010 Mar 1.
Published in final edited form as: Genetica. 2010 Mar; 138(3): 301. Published online 2009 Sep 10. doi: 10.1007/s10709-009-9406-7
PMCID:
PMC2813944
AbstractArticlePDF–1.2M
15.
Uncovering metabolic pathways relevant to phenotypic traits of microbial genomes
Gabi Kastenmüller, Maria Elisabeth Schenk, Johann Gasteiger, Hans-Werner Mewes
Genome Biol. 2009; 10(3): R28. Published online 2009 Mar 10. doi: 10.1186/gb-2009-10-3-r28
PMCID:
PMC2690999
AbstractArticlePDF–705K
16.
tRNAdb 2009: compilation of tRNA sequences and tRNA genes
Frank Jühling, Mario Mörl, Roland K. Hartmann, Mathias Sprinzl, Peter F. Stadler, Joern Pütz
Nucleic Acids Res. 2009 Jan; 37(Database issue): D159–D162. Published online 2008 Oct 28. doi: 10.1093/nar/gkn772
PMCID:
PMC2686557
AbstractArticlePDF–75K
17.
Minimum Contradiction Matrices in Whole Genome Phylogenies
Marc Thuillard
Evol Bioinform Online. 2008; 4: 237–247. Published online 2008 Jul 21. doi: 10.4137/ebo.s909
PMCID:
PMC2614196
AbstractArticlePDF–498K
18.
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
AbstractArticlePDF–541K
19.
Three-Dimensional Phylogeny Explorer: Distinguishing paralogs, lateral transfer, and violation of "molecular clock" assumption with 3D visualization
Namshin Kim, Christopher Lee
BMC Bioinformatics. 2007; 8: 213. Published online 2007 Jun 20. doi: 10.1186/1471-2105-8-213
PMCID:
PMC1906840
AbstractArticlePDF–919K
20.
Transcriptional regulatory network discovery via multiple method integration: application to e. coli K12
Jingjun Sun, Kagan Tuncay, Alaa Abi Haidar, Lisa Ensman, Frank Stanley, Michael Trelinski, Peter Ortoleva
Algorithms Mol Biol. 2007; 2: 2. Published online 2007 Mar 30. doi: 10.1186/1748-7188-2-2
PMCID:
PMC1852316
AbstractArticlePDF–707K

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