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PMID:28376755
PMCID:
Puigbo P, Makarova KS, Kristensen DM, Wolf YI, Koonin EV. (2017) Reconstruction of the evolution of microbial defense systems. BMC Evol Biol, 17:94
PMID:27503291
PMCID:
Iranzo J, Puigbo P, Lobkovsky AE, Wolf YI, Koonin EV. (2016) Inevitability of genetic parasites. Genome Biol Evol, 8:2856-2869
PMID:25141959
PMCID:4166000
Puigbo P, Lobkovsky AE, Kristensen DM, Wolf YI, Koonin EV. (2014) Genomes in turmoil: Quantification of genome dynamics in prokaryote supergenomes. BMC Biology, 12:66.
PMID:23587361
PMCID:3626908
Puigbo P, Wolf YI, Koonin EV. (2013) Seeing the Tree of Life behind the phylogenetic forest. BMC Biology, 11:46.
PMID:22882546
PMCID:3533761
Galperin MY, Mekhedov SL, Puigbo P, Smirnov S, Wolf YI, Rigden DJ. (2012) Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genesi. Environ Microbiol, 11:2870-90.
PMID:2615861
PMCID:3353972
Yutin N, Puigbo P, Koonin EV, Wolf YI (2012) Phylogenomics of prokaryotic ribosomal proteins. PLoS One, 7(5):e36972.
PMID:22399455
PMCID:22399455
Puigbo P, Wolf YI, Koonin EV. (2012) Genome-wide comparative analysis of phylogenetic trees: the prokaryotic forest of life. Methods Mol Biol., 856:53-79.
PMID:22106257
PMCID:3251056
Das SR, Hensley SE, David A, Schmidt L, Gibbs JS, Puigbo P, Ince WL, Bennink JR, Yewdell JW. (2011) Fitness costs limit influenza A virus hemagglutinin glycosylation as an immune evasion strategy. Proc Natl Acad Sci USA, 108(51):E1417-22.
PMID:2003006
PMCID:3233072
Gonzalez JM, Pinhassi J, Fernandez-Gomez B, Coll-Llado M, Gonzalez-Velazquez M, Puigbo P, Jaenicke S, Gomez-Consarnau L, Fernandez-Guerra A, Goesmann A, Pedros-Alio C. (2011) Genomics of the proteorhodopsin-containing marine flavobacterium Dokdonia sp. strain MED134. Appl Environ Microbiol, 77:8676-86
PMCID:3439026 Puigbo P, Mekhedov S, Wolf YI, Koonin EV. (2011) A comprehensive census of horizontal gene transfers from prokaryotes to unikonts. Genome Biol, 12(Suppl 1): P20.
PMID:21457008
PMCID:3123530
Koonin EV, Puigbo P, Wolf YI. (2011) Comparison of phylogenetic trees and search for a central trend in the "forest of life". J Comput Biol., 18:917-24
PMID:21124818
PMCID:2991263
Das SR*, Puigbo P*, Hensley SE, Hurt DE, Bennink JR, Yewdell JW. (2010) Glycosylation focuses sequence variation in the influenza A virus H1 hemagglutinin globular domain. PLoS Pathogens, 6:e1001211
(*Equal contribution)
PMID:20889655
PMCID:2997564
Puigbo P, Wolf YI, Koonin EV. (2010) The tree and net components of prokaryote evolution. Genom Biol Evol, 2:274-56
PMID:20356391
PMCID:2853550
Puigbo P, Aragones L, Garcia-Vallve S. (2010) RCDI/eRCDI: a web-server to estimate codon usage deoptimization. BMC Res Notes, 3:87
PMID:19687142
PMCID:3380366
Koonin EV, Wolf YI, Puigbo P. (2009) The phylogenetic forest and the quest for the elusive tree of life. Cold Spring Harb Symp Quant Biol, 74:205-13
PDF Garcia-Vallve S, Puigbo P (2009) Ciento cincuenta aņos tras el arbol de la vida. Nuevos retos sobre el origen de las especies., Revista de la SEBBM, 160:18-21
PMID:19594957
PMCID:2737373
Puigbo P, Wolf YI, Koonin EV. (2009) Search for a 'Tree of Life' in the thicket of the phylogenetic forest. J Biol, 8:59
PMID:18796141
PMCID:2553769
Puigbo P, Bravo IG, Garcia-Vallve S. (2008) CAIcal: a combined set of tools to assess codon usage adaptation. Biol Direct, 3:38
PMID:18230160
PMCID:2246156
Puigbo P, Bravo IG, Garcia-Vallve S. (2008) E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI). BMC Bioinformatics, 9:65
PMID:18054113 Puigbo P, Pasamontes A, Garcia-Vallve S. (2008) Gaining and losing the thermophilic adaptation in prokaryotes. Trends Genet, 24:10-4
PMID:17933767
PMCID:2238906
Puigbo P, Romeu A, Garcia-Vallve S. (2007) HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection. Nucleic Acids Res, 36:D524-7
PMID:17459965 Puigbo P, Garcia-Vallve S, McInerney JO. (2007) TOPD/FMTS: a new software to compare phylogenetic trees. Bioinformatics, 23:1556-58
PMID:17439967
PMCID:1933141
Puigbo P, Guzman E, Romeu A, Garcia-Vallve S. (2007) OPTIMIZER: a web server for optimizing the codon usage of DNA sequences. Nucleic Acids Res, 35:W126-31
PMID:21670791
PMCID:2255071
Marcet-Houben M, Puigbo P, Romeu A, Garcia-Vallve S. (2007) Towards reconstructing a metabolic tree of life. Bioinformation, 2:135-44
BOOK Rojas A, Montero MA, Guzman E, Palleja A, Puigbo P, Garcia-Vallve S and Romeu A. (2006) Thodosius Dobzhansky (1900-1975). El naixement de la teoria sintetica. Actes de la VIII trobada d'historia de la ciencia i de la tecnica, Barcelona, SCHCT, 2006. 349-354
PMID:12781983 Luis Villar J, Puigbo P, Riera-Codina M. (2003) Analysis of highly phosphorylated inositols in avian and crocodilian erythrocytes. Comp Biochem Physiol B Biochem Mol Biol, 135:169-75