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Items: 1 to 20 of 21

1.
MEBS, a software platform to evaluate large (meta)genomic collections according to their metabolic machinery: unraveling the sulfur cycle
Valerie De Anda, Icoquih Zapata-Peñasco, Augusto Cesar Poot-Hernandez, Luis E Eguiarte, Bruno Contreras-Moreira, Valeria Souza
Gigascience. 2017 Nov; 6(11): 1–17. Published online 2017 Oct 23. doi: 10.1093/gigascience/gix096
PMCID:
PMC5737871
AbstractArticlePDF–2.5M
2.
A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling
Rosalinda D’Amore, Umer Zeeshan Ijaz, Melanie Schirmer, John G. Kenny, Richard Gregory, Alistair C. Darby, Migun Shakya, Mircea Podar, Christopher Quince, Neil Hall
BMC Genomics. 2016; 17: 55. Published online 2016 Jan 14. doi: 10.1186/s12864-015-2194-9
PMCID:
PMC4712552
AbstractArticlePDF–1.2M
3.
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
4.
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
5.
Structural Features of the Regulatory ACT Domain of Phenylalanine Hydroxylase
Carla Carluccio, Franca Fraternali, Francesco Salvatore, Arianna Fornili, Adriana Zagari
PLoS One. 2013; 8(11): e79482. Published online 2013 Nov 14. doi: 10.1371/journal.pone.0079482
PMCID:
PMC3828330
AbstractArticlePDF–7.8M
6.
Structures of Open (R) and Close (T) States of Prephenate Dehydratase (PDT) - Implication of Allosteric Regulation by L-Phenylalanine
Kemin Tan, Hui Li, Rongguang Zhang, Minyi Gu, Shonda T. Clancy, Andrzej Joachimiak
J Struct Biol. Author manuscript; available in PMC 2012 Jun 4.
Published in final edited form as: J Struct Biol. 2008 Apr; 162(1): 94–107. Published online 2007 Nov 29. doi: 10.1016/j.jsb.2007.11.009
PMCID:
PMC3366492
AbstractArticlePDF–3.4M
7.
Structure of the pilus assembly protein TadZ from Eubacterium rectale: Implications for polar localization
Qingping Xu, Beat Christen, Hsiu-Ju Chiu, Lukasz Jaroszewski, Heath E. Klock, Mark W. Knuth, Mitchell D. Miller, Marc-André Elsliger, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, David H. Figurski, Lucy Shapiro, Ian A. Wilson
Mol Microbiol. Author manuscript; available in PMC 2013 Feb 1.
Published in final edited form as: Mol Microbiol. 2012 Feb; 83(4): 712–727. Published online 2012 Jan 18. doi: 10.1111/j.1365-2958.2011.07954.x
PMCID:
PMC3272108
AbstractArticlePDF–3.5M
8.
Distribution Analysis of Hydrogenases in Surface Waters of Marine and Freshwater Environments
Martin Barz, Christian Beimgraben, Torsten Staller, Frauke Germer, Friederike Opitz, Claudia Marquardt, Christoph Schwarz, Kirstin Gutekunst, Klaus Heinrich Vanselow, Ruth Schmitz, Julie LaRoche, Rüdiger Schulz, Jens Appel
PLoS One. 2010; 5(11): e13846. Published online 2010 Nov 5. doi: 10.1371/journal.pone.0013846
PMCID:
PMC2974642
AbstractArticlePDF–850K
9.
Functional Promiscuity of Homologues of the Bacterial ArsA ATPases
Rostislav Castillo, Milton H. Saier, Jr.
Int J Microbiol. 2010; 2010: 187373. Published online 2010 Oct 20. doi: 10.1155/2010/187373
PMCID:
PMC2963123
AbstractArticlePDF–1.5M
10.
Apo and Nickel-bound Forms of the Pyrococcus Horikoshii Species of the Metalloregulatory Protein: NikR Characterized by Molecular Dynamics Simulations
Daniel J. Sindhikara, Adrian E. Roitberg, Kenneth M. Merz
Biochemistry. Author manuscript; available in PMC 2010 Dec 22.
Published in final edited form as: Biochemistry. 2009 Dec 22; 48(50): 12024–12033. doi: 10.1021/bi9013352
PMCID:
PMC2795120
AbstractArticlePDF–4.9M
11.
The effect of sequencing errors on metagenomic gene prediction
Katharina J Hoff
BMC Genomics. 2009; 10: 520. Published online 2009 Nov 12. doi: 10.1186/1471-2164-10-520
PMCID:
PMC2781827
AbstractArticlePDF–285K
12.
Flavin Nucleotide Metabolism in Plants: MONOFUNCTIONAL ENZYMES SYNTHESIZE FAD IN PLASTIDS
Francisco J. Sandoval, Yi Zhang, Sanja Roje
J Biol Chem. 2008 Nov 7; 283(45): 30890–30900. doi: 10.1074/jbc.M803416200
PMCID:
PMC2662166
AbstractArticlePDF–1.7M
13.
Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications
Jorge Valdés, Inti Pedroso, Raquel Quatrini, Robert J Dodson, Herve Tettelin, Robert Blake, II, Jonathan A Eisen, David S Holmes
BMC Genomics. 2008; 9: 597. Published online 2008 Dec 11. doi: 10.1186/1471-2164-9-597
PMCID:
PMC2621215
AbstractArticlePDF–6.1M
14.
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
15.
Identification of Prophages in Bacterial Genomes by Dinucleotide Relative Abundance Difference
K. V. Srividhya, V. Alaguraj, G. Poornima, Dinesh Kumar, G. P. Singh, L. Raghavenderan, A. V. S. K. Mohan Katta, Preeti Mehta, S. Krishnaswamy
PLoS One. 2007; 2(11): e1193. Published online 2007 Nov 21. doi: 10.1371/journal.pone.0001193
PMCID:
PMC2075365
AbstractArticlePDF–295K
16.
Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species
Radhey S Gupta, Emily Lorenzini
BMC Evol Biol. 2007; 7: 71. Published online 2007 May 8. doi: 10.1186/1471-2148-7-71
PMCID:
PMC1887533
AbstractArticlePDF–1.5M
17.
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
18.
OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups
Feng Chen, Aaron J. Mackey, Christian J. Stoeckert, Jr, David S. Roos
Nucleic Acids Res. 2006 Jan 1; 34(Database issue): D363–D368. Published online 2005 Dec 28. doi: 10.1093/nar/gkj123
PMCID:
PMC1347485
AbstractArticlePDF–373K
19.
Diversity in domain architectures of Ser/Thr kinases and their homologues in prokaryotes
A Krupa, N Srinivasan
BMC Genomics. 2005; 6: 129. Published online 2005 Sep 19. doi: 10.1186/1471-2164-6-129
PMCID:
PMC1262709
AbstractArticlePDF–746K
20.
Different patterns of evolution for duplicated DNA repair genes in bacteria of the Xanthomonadales group
Marinalva Martins-Pinheiro, Rodrigo S Galhardo, Claudia Lage, Keronninn M Lima-Bessa, Karina A Aires, Carlos FM Menck
BMC Evol Biol. 2004; 4: 29. Published online 2004 Aug 27. doi: 10.1186/1471-2148-4-29
PMCID:
PMC518961
AbstractArticlePDF–350K

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