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Items: 1 to 20 of 23


Reconstruction of the evolution of microbial defense systems.

Puigbò P, Makarova KS, Kristensen DM, Wolf YI, Koonin EV.

BMC Evol Biol. 2017 Apr 4;17(1):94. doi: 10.1186/s12862-017-0942-y.


Inevitability of Genetic Parasites.

Iranzo J, Puigbò P, Lobkovsky AE, Wolf YI, Koonin EV.

Genome Biol Evol. 2016 Sep 26;8(9):2856-2869.


Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes.

Puigbò P, Lobkovsky AE, Kristensen DM, Wolf YI, Koonin EV.

BMC Biol. 2014 Aug 21;12:66. doi: 10.1186/s12915-014-0066-4.


Seeing the Tree of Life behind the phylogenetic forest.

Puigbò P, Wolf YI, Koonin EV.

BMC Biol. 2013 Apr 15;11:46. doi: 10.1186/1741-7007-11-46. No abstract available.


Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes.

Galperin MY, Mekhedov SL, Puigbo P, Smirnov S, Wolf YI, Rigden DJ.

Environ Microbiol. 2012 Nov;14(11):2870-90. doi: 10.1111/j.1462-2920.2012.02841.x. Epub 2012 Aug 13.


Phylogenomics of prokaryotic ribosomal proteins.

Yutin N, Puigbò P, Koonin EV, Wolf YI.

PLoS One. 2012;7(5):e36972. doi: 10.1371/journal.pone.0036972. Epub 2012 May 16.


Genome-wide comparative analysis of phylogenetic trees: the prokaryotic forest of life.

Puigbò P, Wolf YI, Koonin EV.

Methods Mol Biol. 2012;856:53-79. doi: 10.1007/978-1-61779-585-5_3.


Fitness costs limit influenza A virus hemagglutinin glycosylation as an immune evasion strategy.

Das SR, Hensley SE, David A, Schmidt L, Gibbs JS, Puigbò P, Ince WL, Bennink JR, Yewdell JW.

Proc Natl Acad Sci U S A. 2011 Dec 20;108(51):E1417-22. doi: 10.1073/pnas.1108754108. Epub 2011 Nov 21.


Genomics of the proteorhodopsin-containing marine flavobacterium Dokdonia sp. strain MED134.

González JM, Pinhassi J, Fernández-Gómez B, Coll-Lladó M, González-Velázquez M, Puigbò P, Jaenicke S, Gómez-Consarnau L, Fernàndez-Guerra A, Goesmann A, Pedrós-Alió C.

Appl Environ Microbiol. 2011 Dec;77(24):8676-86. doi: 10.1128/AEM.06152-11. Epub 2011 Oct 14.


Comparison of phylogenetic trees and search for a central trend in the "forest of life".

Koonin EV, Puigbò P, Wolf YI.

J Comput Biol. 2011 Jul;18(7):917-24. doi: 10.1089/cmb.2010.0185. Epub 2011 Apr 1.


Glycosylation focuses sequence variation in the influenza A virus H1 hemagglutinin globular domain.

Das SR, Puigbò P, Hensley SE, Hurt DE, Bennink JR, Yewdell JW.

PLoS Pathog. 2010 Nov 24;6(11):e1001211. doi: 10.1371/journal.ppat.1001211.


The tree and net components of prokaryote evolution.

Puigbò P, Wolf YI, Koonin EV.

Genome Biol Evol. 2010;2:745-56. doi: 10.1093/gbe/evq062. Epub 2010 Oct 1.


RCDI/eRCDI: a web-server to estimate codon usage deoptimization.

Puigbò P, Aragonès L, Garcia-Vallvé S.

BMC Res Notes. 2010 Mar 31;3:87. doi: 10.1186/1756-0500-3-87.


The phylogenetic forest and the quest for the elusive tree of life.

Koonin EV, Wolf YI, Puigbò P.

Cold Spring Harb Symp Quant Biol. 2009;74:205-13. doi: 10.1101/sqb.2009.74.006. Epub 2009 Aug 17. Review.


Search for a 'Tree of Life' in the thicket of the phylogenetic forest.

Puigbò P, Wolf YI, Koonin EV.

J Biol. 2009;8(6):59. doi: 10.1186/jbiol159. Epub 2009 Jul 13.


CAIcal: a combined set of tools to assess codon usage adaptation.

Puigbò P, Bravo IG, Garcia-Vallve S.

Biol Direct. 2008 Sep 16;3:38. doi: 10.1186/1745-6150-3-38.


E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI).

Puigbò P, Bravo IG, Garcia-Vallvé S.

BMC Bioinformatics. 2008 Jan 29;9:65. doi: 10.1186/1471-2105-9-65.


Gaining and losing the thermophilic adaptation in prokaryotes.

Puigbò P, Pasamontes A, Garcia-Vallve S.

Trends Genet. 2008 Jan;24(1):10-4. Epub 2007 Dec 3.


HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection.

Puigbò P, Romeu A, Garcia-Vallvé S.

Nucleic Acids Res. 2008 Jan;36(Database issue):D524-7. Epub 2007 Oct 11.


TOPD/FMTS: a new software to compare phylogenetic trees.

Puigbò P, Garcia-Vallvé S, McInerney JO.

Bioinformatics. 2007 Jun 15;23(12):1556-8. Epub 2007 Apr 25.


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