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Items: 1 to 20 of 24

1.
Phylogenomics of Prokaryotic Ribosomal Proteins
Natalya Yutin, Pere Puigbò, Eugene V. Koonin, Yuri I. Wolf
PLoS One. 2012; 7(5): e36972. Published online 2012 May 16. doi: 10.1371/journal.pone.0036972
PMCID:
PMC3353972
ArticlePubReaderPDF–3.0MCite
2.
Fitness costs limit influenza A virus hemagglutinin glycosylation as an immune evasion strategy
Suman R. Das, Scott E. Hensley, Alexandre David, Loren Schmidt, James S. Gibbs, Pere Puigbò, William L. Ince, Jack R. Bennink, Jonathan W. Yewdell
Proc Natl Acad Sci U S A. 2011 Dec 20; 108(51): E1417–E1422. Published online 2011 Nov 21. doi: 10.1073/pnas.1108754108
PMCID:
PMC3251056
ArticlePubReaderPDF–1.0MCite
3.
Comparison of Phylogenetic Trees and Search for a Central Trend in the “Forest of Life”
Eugene V. Koonin, Pere Puigbò, Yuri I. Wolf
J Comput Biol. 2011 Jul; 18(7): 917–924. doi: 10.1089/cmb.2010.0185
PMCID:
PMC3123530
ArticlePubReaderPDF–991KCite
4.
RCDI/eRCDI: a web-server to estimate codon usage deoptimization
Pere Puigbò, Lluís Aragonès, Santiago Garcia-Vallvé
BMC Res Notes. 2010; 3: 87. Published online 2010 Mar 31. doi: 10.1186/1756-0500-3-87
PMCID:
PMC2853550
ArticlePubReaderPDF–475KCite
5.
The Phylogenetic Forest and the Quest for the Elusive Tree of Life
E.V. Koonin, Y.I. Wolf, P. Puigbò
Cold Spring Harb Symp Quant Biol. Author manuscript; available in PMC 2012 Jun 21.
Published in final edited form as: Cold Spring Harb Symp Quant Biol. 2009; 74: 205–213. Published online 2009 Aug 17. doi: 10.1101/sqb.2009.74.006
PMCID:
PMC3380366
ArticlePubReaderPDF–2.0MCite
6.
Search for a 'Tree of Life' in the thicket of the phylogenetic forest
Pere Puigbò, Yuri I Wolf, Eugene V Koonin
J Biol. 2009; 8(6): 59. Published online 2009 Jul 13. doi: 10.1186/jbiol159
PMCID:
PMC2737373
ArticlePubReaderPDF–3.3MCite
7.
Towards reconstructing a metabolic tree of life
Marina Marcet-Houben, Pere Puigbò, Antoni Romeu, Santiago Garcia-Vallve
Bioinformation. 2007; 2(4): 135–144. Published online 2007 Dec 11. doi: 10.6026/97320630002135
PMCID:
PMC2255071
ArticlePubReaderPDF–130KCite
8.
OPTIMIZER: a web server for optimizing the codon usage of DNA sequences
Pere Puigbò, Eduard Guzmán, Antoni Romeu, Santiago Garcia-Vallvé
Nucleic Acids Res. 2007 Jul; 35(Web Server issue): W126–W131. Published online 2007 Apr 16. doi: 10.1093/nar/gkm219
PMCID:
PMC1933141
ArticlePubReaderPDF–4.3MCite
9.
An Unsupervised Algorithm for Host Identification in Flaviviruses
Phuoc Truong Nguyen, Santiago Garcia-Vallvé, Pere Puigbò
Life (Basel) 2021 May; 11(5): 442. Published online 2021 May 14. doi: 10.3390/life11050442
PMCID:
PMC8157105
ArticlePubReaderPDF–982KCite
10.
A Pilot Study for Metabolic Profiling of Obesity-Associated Microbial Gut Dysbiosis in Male Wistar Rats
Julia Hernandez-Baixauli, Pere Puigbò, Helena Torrell, Hector Palacios-Jordan, Vicent J. Ribas Ripoll, Antoni Caimari, Josep M Del Bas, Laura Baselga-Escudero, Miquel Mulero
Biomolecules. 2021 Feb; 11(2): 303. Published online 2021 Feb 18. doi: 10.3390/biom11020303
PMCID:
PMC7922951
ArticlePubReaderPDF–1.9MCite
11.
Six-Week Endurance Exercise Alters Gut Metagenome That Is not Reflected in Systemic Metabolism in Over-weight Women
Eveliina Munukka, Juha P. Ahtiainen, Pere Puigbó, Sirpa Jalkanen, Katja Pahkala, Anniina Keskitalo, Urho M. Kujala, Sami Pietilä, Maija Hollmén, Laura Elo, Pentti Huovinen, Giuseppe D'Auria, Satu Pekkala
Front Microbiol. 2018; 9: 2323. Published online 2018 Oct 3. doi: 10.3389/fmicb.2018.02323
PMCID:
PMC6178902
ArticlePubReaderPDF–2.2MCite
12.
Reconstruction of the evolution of microbial defense systems
Pere Puigbò, Kira S. Makarova, David M. Kristensen, Yuri I. Wolf, Eugene V. Koonin
BMC Evol Biol. 2017; 17: 94. Published online 2017 Apr 4. doi: 10.1186/s12862-017-0942-y
PMCID:
PMC5379612
ArticlePubReaderPDF–1.9MCite
13.
Inevitability of Genetic Parasites
Jaime Iranzo, Pere Puigbò, Alexander E. Lobkovsky, Yuri I. Wolf, Eugene V. Koonin
Genome Biol Evol. 2016 Sep; 8(9): 2856–2869. Published online 2016 Aug 8. doi: 10.1093/gbe/evw193
PMCID:
PMC5631039
ArticlePubReaderPDF–447KCite
14.
Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes
Pere Puigbò, Alexander E Lobkovsky, David M Kristensen, Yuri I Wolf, Eugene V Koonin
BMC Biol. 2014; 12: 66. Published online 2014 Aug 21. doi: 10.1186/s12915-014-0066-4
PMCID:
PMC4166000
ArticlePubReaderPDF–2.4MCite
15.
Seeing the Tree of Life behind the phylogenetic forest
Pere Puigbò, Yuri I Wolf, Eugene V Koonin
BMC Biol. 2013; 11: 46. Published online 2013 Apr 15. doi: 10.1186/1741-7007-11-46
PMCID:
PMC3626908
ArticlePubReaderPDF–335KCite
16.
Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes
Michael Y Galperin, Sergei L Mekhedov, Pere Puigbo, Sergey Smirnov, Yuri I Wolf, Daniel J Rigden
Environ Microbiol. 2012 Nov; 14(11): 2870–2890. doi: 10.1111/j.1462-2920.2012.02841.x
PMCID:
PMC3533761
ArticlePubReaderPDF–439KCite
17.
GENOME-WIDE COMPARATIVE ANALYSIS OF PHYLOGENETIC TREES: THE PROKARYOTIC FOREST OF LIFE
Pere Puigbò, Yuri I. Wolf, Eugene V. Koonin
Methods Mol Biol. Author manuscript; available in PMC 2013 Nov 28.
Published in final edited form as: Methods Mol Biol. 2012; 856: 10.1007/978-1-61779-585-5_3. doi: 10.1007/978-1-61779-585-5_3
PMCID:
PMC3842619
ArticlePubReaderPDF–2.6MCite
18.
Genomics of the Proteorhodopsin-Containing Marine Flavobacterium Dokdonia sp. Strain MED134
José M. González, Jarone Pinhassi, Beatriz Fernández-Gómez, Montserrat Coll-Lladó, Mónica González-Velázquez, Pere Puigbò, Sebastian Jaenicke, Laura Gómez-Consarnau, Antoni Fernàndez-Guerra, Alexander Goesmann, Carlos Pedrós-Alió
Appl Environ Microbiol. 2011 Dec; 77(24): 8676–8686. doi: 10.1128/AEM.06152-11
PMCID:
PMC3233072
ArticlePubReaderPDF–1.9MCite
19.
A comprehensive census of horizontal gene transfers from prokaryotes to unikonts
Pere Puigbò, Sergei Mekhedov, Yuri I Wolf, Eugene V Koonin
Genome Biol. 2011; 12(Suppl 1): P20. Published online 2011 Sep 19. doi: 10.1186/gb-2011-12-s1-p20
PMCID:
PMC3439026
ArticlePubReaderPDF–321KCite
20.
Glycosylation Focuses Sequence Variation in the Influenza A Virus H1 Hemagglutinin Globular Domain
Suman R. Das, Pere Puigbò, Scott E. Hensley, Darrell E. Hurt, Jack R. Bennink, Jonathan W. Yewdell
PLoS Pathog. 2010 Nov; 6(11): e1001211. Published online 2010 Nov 24. doi: 10.1371/journal.ppat.1001211
PMCID:
PMC2991263
ArticlePubReaderPDF–1.4MCite

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