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1.

Response to "In vivo attenuation and genetic evolution of a ST247-SCCmecI MRSA clone after 13 years of pathogenic bronchopulmonary colonization in a patient with cystic fibrosis: implications of the innate immune response".

López-Collazo E, Jurado T, de Dios Caballero J, Pérez-Vázquez M, Vindel A, Hernández-Jiménez E, Tamames J, Cubillos-Zapata C, Manrique M, Tobes R, Máiz L, Cantón R, Baquero F, del Campo R.

Mucosal Immunol. 2015 May;8(3):697-8. doi: 10.1038/mi.2015.10. Epub 2015 Mar 4. No abstract available.

PMID:
25736458
2.

Bacteria dialog with Santa Rosalia: Are aggregations of cosmopolitan bacteria mainly explained by habitat filtering or by ecological interactions?

Pascual-García A, Tamames J, Bastolla U.

BMC Microbiol. 2014 Dec 4;14:284. doi: 10.1186/s12866-014-0284-5.

3.

In vivo attenuation and genetic evolution of a ST247-SCCmecI MRSA clone after 13 years of pathogenic bronchopulmonary colonization in a patient with cystic fibrosis: implications of the innate immune response.

López-Collazo E, Jurado T, de Dios Caballero J, Pérez-Vázquez M, Vindel A, Hernández-Jiménez E, Tamames J, Cubillos-Zapata C, Manrique M, Tobes R, Máiz L, Cantón R, Baquero F, Del Campo R.

Mucosal Immunol. 2015 Mar;8(2):362-71. doi: 10.1038/mi.2014.73. Epub 2014 Aug 13.

PMID:
25118167
4.

Analyses of cobalt-ligand and potassium-ligand bond lengths in metalloproteins: trends and patterns.

Brás NF, Ribeiro AJ, Oliveira M, Paixão NM, Tamames JA, Fernandes PA, Ramos MJ.

J Mol Model. 2014 Jun;20(6):2271. doi: 10.1007/s00894-014-2271-z. Epub 2014 May 22.

PMID:
24850495
5.

Complete Genome Sequence of Bacillus toyonensis BCT-7112T, the Active Ingredient of the Feed Additive Preparation Toyocerin.

Jiménez G, Blanch AR, Tamames J, Rosselló-Mora R.

Genome Announc. 2013 Dec 19;1(6). pii: e01080-13. doi: 10.1128/genomeA.01080-13.

6.

Volarea - a bioinformatics tool to calculate the surface area and the volume of molecular systems.

Ribeiro JV, Tamames JA, Cerqueira NM, Fernandes PA, Ramos MJ.

Chem Biol Drug Des. 2013 Dec;82(6):743-55. doi: 10.1111/cbdd.12197. Epub 2013 Oct 25.

PMID:
24164915
7.

Description of Bacillus toyonensis sp. nov., a novel species of the Bacillus cereus group, and pairwise genome comparisons of the species of the group by means of ANI calculations.

Jiménez G, Urdiain M, Cifuentes A, López-López A, Blanch AR, Tamames J, Kämpfer P, Kolstø AB, Ramón D, Martínez JF, Codoñer FM, Rosselló-Móra R.

Syst Appl Microbiol. 2013 Sep;36(6):383-91. doi: 10.1016/j.syapm.2013.04.008. Epub 2013 Jun 19.

PMID:
23791203
8.

COVER: a priori estimation of coverage for metagenomic sequencing.

Tamames J, de la Peña S, de Lorenzo V.

Environ Microbiol Rep. 2012 Jun;4(3):335-41. doi: 10.1111/j.1758-2229.2012.00338.x. Epub 2012 Apr 17.

PMID:
23760797
9.

Taxonomy becoming a driving force in genome sequencing projects.

Tamames J, Durante-Rodríguez G.

Syst Appl Microbiol. 2013 Jun;36(4):215-7. doi: 10.1016/j.syapm.2013.01.002. Epub 2013 Mar 1.

PMID:
23453737
10.

New insights into the archaeal diversity of a hypersaline microbial mat obtained by a metagenomic approach.

López-López A, Richter M, Peña A, Tamames J, Rosselló-Móra R.

Syst Appl Microbiol. 2013 May;36(3):205-14. doi: 10.1016/j.syapm.2012.11.008. Epub 2013 Jan 23.

PMID:
23352736
11.

On the fitness of microbial taxonomy.

Tamames J, Rosselló-Móra R.

Trends Microbiol. 2012 Nov;20(11):514-6. doi: 10.1016/j.tim.2012.08.012. Epub 2012 Sep 4.

PMID:
22959411
12.

Metaproteogenomic insights beyond bacterial response to naphthalene exposure and bio-stimulation.

Guazzaroni ME, Herbst FA, Lores I, Tamames J, Peláez AI, López-Cortés N, Alcaide M, Del Pozo MV, Vieites JM, von Bergen M, Gallego JL, Bargiela R, López-López A, Pieper DH, Rosselló-Móra R, Sánchez J, Seifert J, Ferrer M.

ISME J. 2013 Jan;7(1):122-36. doi: 10.1038/ismej.2012.82. Epub 2012 Jul 26.

13.

The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene.

Silva-Rocha R, de Jong H, Tamames J, de Lorenzo V.

BMC Syst Biol. 2011 Nov 11;5:191. doi: 10.1186/1752-0509-5-191.

14.

The logicome of environmental bacteria: merging catabolic and regulatory events with Boolean formalisms.

Silva-Rocha R, Tamames J, dos Santos VM, de Lorenzo V.

Environ Microbiol. 2011 Sep;13(9):2389-402. doi: 10.1111/j.1462-2920.2011.02455.x. Epub 2011 Mar 16. Review.

PMID:
21410625
15.

EnvMine: a text-mining system for the automatic extraction of contextual information.

Tamames J, de Lorenzo V.

BMC Bioinformatics. 2010 Jun 1;11:294. doi: 10.1186/1471-2105-11-294.

16.

Metals in proteins: cluster analysis studies.

Tamames JA, Ramos MJ.

J Mol Model. 2011 Mar;17(3):429-42. doi: 10.1007/s00894-010-0733-5. Epub 2010 May 21.

PMID:
20490881
17.

Environmental distribution of prokaryotic taxa.

Tamames J, Abellán JJ, Pignatelli M, Camacho A, Moya A.

BMC Microbiol. 2010 Mar 22;10:85. doi: 10.1186/1471-2180-10-85.

18.

Immunity and other defenses in pea aphids, Acyrthosiphon pisum.

Gerardo NM, Altincicek B, Anselme C, Atamian H, Barribeau SM, de Vos M, Duncan EJ, Evans JD, Gabaldón T, Ghanim M, Heddi A, Kaloshian I, Latorre A, Moya A, Nakabachi A, Parker BJ, Pérez-Brocal V, Pignatelli M, Rahbé Y, Ramsey JS, Spragg CJ, Tamames J, Tamarit D, Tamborindeguy C, Vincent-Monegat C, Vilcinskas A.

Genome Biol. 2010;11(2):R21. doi: 10.1186/gb-2010-11-2-r21. Epub 2010 Feb 23.

19.

High diversity of the viral community from an Antarctic lake.

López-Bueno A, Tamames J, Velázquez D, Moya A, Quesada A, Alcamí A.

Science. 2009 Nov 6;326(5954):858-61. doi: 10.1126/science.1179287.

20.

EnvDB, a database for describing the environmental distribution of prokaryotic taxa.

Pignatelli M, Moya A, Tamames J.

Environ Microbiol Rep. 2009 Jun;1(3):191-7. doi: 10.1111/j.1758-2229.2009.00030.x. Epub 2009 Apr 29.

PMID:
23765793
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