PMID: Saldivar-Espinoza B, Garcia-Segura P, Novau-Ferré N, Macip G, Martínez R, Puigbo P, Cereto-Massagué A, Pujadas G, Garcia-Vallve S. (2023) The Mutational Landscape of SARS-CoV-2. International Journal of Molecular Sciences, In press
BIORXIV Fontcuberta-Rigo M, Nakamura M, Puigbo P. (2023) Phylobone: A comprehensive database of bone extracellular matrix proteins in human and model organisms. Biorxiv (pre-print),
Mathew SA, Fuchs B, Nissinen R, Helander M, Puigbo P, Saikkonen K, Muola A. (2023)Glyphosate-based herbicide use affects individual microbial taxa in strawberry endosphere but not the microbial community composition. J Appl Microbiol, lxad006. doi: 10.1093/jambio/lxad006.
PMID:36243622 Ruuskanen S, Fuchs B, Nissinen R, Puigbo P, Rainio M, Saikkonen K, Helander M. (2023) Ecosystem consequences of herbicides: the role of microbiome. Trends in Ecology and Evolution,
Saldivar-Espinoza B, Macip G, Garcia-Segura P, Mestres-Truyol J, Puigbo P, Cereto-Massague A, Pujadas G, Garcia-Vallve S. (2022) Prediction of recurrent mutations in SARS-CoV-2 using artificial neural networks. International Journal of Molecular Sciences, 23(23):14683. doi: 10.3390/ijms232314683.
Tall T, Puigbo P. (2022) Rethinking the Intrinsic Sensitivity of Fungi to Glyphosate. BioTech, 11(3), 28;
Pensem PDF Puigbo P (2022) Com pot afectar el glifosat a la salut humana?. Pensem, 08.06.2022
Puigbo P, Leino LI, Rainio MJ, Saikkonen K, Saloniemi I, Helander M. (2022) Does Glyphosate Affect the Human Microbiota?. Life, 12(5), 707;
Belin D, Puigbo P. (2022) Why Is the UAG (Amber) Stop Codon Almost Absent in Highly Expressed Bacterial Genes?. Life, 12(3), 431;
PMID:35068479 Mathew SA, Muola A, Saikkonen A, Saloniemi I, Helander M, Puigbo P. (2022) Quantification of the potential impact of glyphosate-based products on microbiomes. J. Vis. Exp., e63109, doi:10.3791/63109 (2022)
Hernandez-Baixauli J, Puigbo P, Abasolo N, Palacios-Jordan H, Foguet-Romero E, Suñol D, Galofré M, Caimari A, Baselga-Escudero L, Bas JMD, Mulero M. (2021) Alterations in Metabolome and Microbiome Associated with an Early Stress Stage in Male Wistar Rats: A Multi-Omics Approach. Int J Mol Sci., Int J Mol Sci. 22(23):12931.
Truong Nguyen P, Garcia-Vallve S, Puigbo P. (2021) An unsupervised algorithm for host identification in flaviviruses. Life, 11(5):442.
Hernandez-Baixauli J, Puigbo P, Torrell H, Palacios-Jordan H, Ribas Ripoll VJ, Caimari T, Del Bas JM, Baselga-Escudero L, Mulero M. (2021) A Pilot Study for Metabolic Profiling of Obesity-Associated Microbial Gut Dysbiosis in Male Wistar Rats. Biomolecules, accepted in press.
PMID:33530134 (*HIGHLY CITED*) Rainio MJ, Ruuskanen S, Helander M, Saikkonen K, Saloniemi I, Puigbo P. (2021) Adaptation of bacteria to glyphosate: a microevolutionary perspective of the enzyme 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase. Environmental Microbiology Reports, doi: 10.1111/1758-2229.12931. Online ahead of print.
Leino L, Tall T, Helander M, Saloniemi I, Saikkonen K, Ruuskanen S, Puigbo P. (2021) Classification of the glyphosate target enzyme (5-enolpyruvylshikimate-3-phosphate synthase) for assessing sensitivity of organisms to the herbicide. Journal of Hazardous Materials, 408:124556
PROCEEDINGS PDF Tall T, Puigbo P. (2020) The glyphosate target enzyme 5-enolpyruvylshikimate 3-phosphate synthase (EPSPS) contains several EPSPS-associated domains in fungi. MDPI in 1st International Electronic Conference on Genes: Theoretical and Applied Genomics session Applications of Genomic Technologies, doi:10.3390/IECGE-07146
BIORXIV Rainio MJ, Ruuskanen S, Helander M, Saikkonen K, Saloniemi I, Puigbo P. (2020) Adaptation of bacteria to glyphosate: a microevolutionary perspective of the enzyme 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase. Biorxiv (pre-print),
BIORXIV Leino L, Tall T, Helander M, Saloniemi I, Saikkonen K, Ruuskanen S, Puigbo P. (2020) Classification of the glyphosate target enzyme (5-enolpyruvylshikimate-3-phosphate synthase). Biorxiv (pre-print),
BIORXIV Truong P, Garcia-Vallve S, Puigbo P. (2020) An unsupervised algorithm for host identification in flaviviruses. Biorxiv (pre-print),
Puigbo P, Wolf YI, Koonin EV. (2019) Genome-Wide Comparative Analysis of Phylogenetic Trees: The Prokaryotic Forest of Life. Methods Mol Biol., 1910:241-269.
Munukka E, Ahtiainen J, Puigbo P, Jalkanen S, Pahkala K, Keskitalo A, Kujala UM, Hollmén M, Elo L, Huovinen P, D'Auria G, Pekkala S. (2018) Six-week endurance exercise alters gut metagenome that is not reflected in systemic metabolism in over-weight women. Front Microbiol, doi: 10.3389/fmicb.2018.02323
Puigbo P, Makarova KS, Kristensen DM, Wolf YI, Koonin EV. (2017) Reconstruction of the evolution of microbial defense systems. BMC Evol Biol, 17:94
Iranzo J, Puigbo P, Lobkovsky AE, Wolf YI, Koonin EV. (2016) Inevitability of genetic parasites. Genome Biol Evol, 8:2856-2869
PeerJ PrePrints Puigbo P, Major JM. (2015) GPT: a web-server to map phylogenetic trees on a virtual globe. PeerJ PrePrints 3:e1040.
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.
Puigbo P, Wolf YI, Koonin EV. (2013) Seeing the Tree of Life behind the phylogenetic forest. BMC Biology, 11:46.
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.
Yutin N, Puigbo P, Koonin EV, Wolf YI (2012) Phylogenomics of prokaryotic ribosomal proteins. PLoS One, 7(5):e36972.
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.
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.
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.
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
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)
Puigbo P, Wolf YI, Koonin EV. (2010) The tree and net components of prokaryote evolution. Genom Biol Evol, 2:274-56
Puigbo P, Aragones L, Garcia-Vallve S. (2010) RCDI/eRCDI: a web-server to estimate codon usage deoptimization. BMC Res Notes, 3:87
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 años tras el arbol de la vida. Nuevos retos sobre el origen de las especies., Revista de la SEBBM, 160:18-21
Puigbo P, Wolf YI, Koonin EV. (2009) Search for a 'Tree of Life' in the thicket of the phylogenetic forest. J Biol, 8:59
Puigbo P, Bravo IG, Garcia-Vallve S. (2008) CAIcal: a combined set of tools to assess codon usage adaptation. Biol Direct, 3:38
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
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
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
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