| PMID:37580331 |
Fontcuberta-Rigo M, Nakamura M, Puigbo P. (2023) Phylobone: A comprehensive database of bone extracellular matrix proteins in human and model organisms. Bone Research, 11, 44. https://doi.org/10.1038/s41413-023-00281-w |
PMID:37316439
PMCID:10306328 |
Helander M, Jeevannavar A, Kaakinen K, Mathew SA,Saikkonen K, Fuchs B, Puigbò P; Loukola O, Tamminen M. (2023)Glyphosate and a glyphosate-based herbicide affect bumblebee gut microbiota. FEMS Microbiology Ecology., In press.
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| PMID:37240420 |
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, 24(10):9072. doi: 10.3390/ijms24109072 |
| 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), https://www.biorxiv.org/content/10.1101/2023.03.28.534628v2 |
PMID:36639128
PMCID: |
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.
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| 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, https://doi.org/10.1016/j.tree.2022.09.009.
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PMID:36499005
PMCID:9736107 |
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.
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PMID:35892933
PMCID:9394408 |
Tall T, Puigbo P. (2022) Rethinking the Intrinsic Sensitivity of Fungi to Glyphosate. BioTech, 11(3), 28; https://doi.org/10.3390/biotech11030028 |
| Pensem PDF |
Puigbo P (2022) Com pot afectar el glifosat a la salut humana?. Pensem, 08.06.2022 |
PMID:35629374
PMCID:9145961 |
Puigbo P, Leino LI, Rainio MJ, Saikkonen K, Saloniemi I, Helander M. (2022) Does Glyphosate Affect the Human Microbiota?. Life, 12(5), 707; https://doi.org/10.3390/life12050707 |
PMID:35330182
PMCID:8954436 |
Belin D, Puigbo P. (2022) Why Is the UAG (Amber) Stop Codon Almost Absent in Highly Expressed Bacterial Genes?. Life, 12(3), 431; https://doi.org/10.3390/life12030431 |
| 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) |
PMID:34884735
PMCID:8657954 |
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. |
PMID:34069049
PMCID:8157105 |
Truong Nguyen P, Garcia-Vallve S, Puigbo P. (2021) An unsupervised algorithm for host identification in flaviviruses. Life, 11(5):442. https://doi.org/10.3390/life11050442 |
PMID:33670496
PMCID:7922951 |
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. |
PMID:33243645
PRESS |
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), https://doi.org/10.1101/2020.06.16.154005 |
| 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), https://doi.org/10.1101/2020.05.27.118265 |
| BIORXIV |
Truong P, Garcia-Vallve S, Puigbo P. (2020) An unsupervised algorithm for host identification in flaviviruses. Biorxiv (pre-print), https://doi.org/10.1101/2020.04.20.050047 |
PMID:31278667
PMCID: |
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. |
PMID:30337914
PMCID:6178902 |
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 |
PMID:28376755
PMCID:5379612 |
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:5631039 |
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.
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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 años 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 |
