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P. Puigbò · SciRah

Researcher profile · Semantic Scholar

P. Puigbò

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P. Puigbò — researcher profile on SciRah

h-index: 26
Works: 56
Citations: 4,049

Most-cited papers

CAIcal: A combined set of tools to assess codon usage adaptation
P. Puigbò, I. Bravo, S. García-Vallvé
2008Biology Direct564 citations Open access
Semantic Scholar
Working toward a new NIOSH.
P. Puigbò, E. Guzmán, A. Romeu, S. García-Vallvé
1996Nucleic Acids Res.496 citations Open access
Semantic Scholar
Search for a 'Tree of Life' in the thicket of the phylogenetic forest
P. Puigbò, Y. Wolf, E. Koonin
2009Journal of Biology268 citations Open access
Semantic Scholar
Phylogenomics of Prokaryotic Ribosomal Proteins
N. Yutin, P. Puigbò, E. Koonin, Y. Wolf
2012PLoS ONE258 citations Open access
Semantic Scholar
Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes
Michael Y. Galperin, S. Mekhedov, P. Puigbò, S. Smirnov +2 more
2012Environmental Microbiology245 citations Open access
Semantic Scholar
Six-Week Endurance Exercise Alters Gut Metagenome That Is not Reflected in Systemic Metabolism in Over-weight Women
E. Munukka, J. Ahtiainen, P. Puigbò, S. Jalkanen +9 more
2018Frontiers in Microbiology209 citations Open access
Semantic Scholar
Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes
P. Puigbò, A. Lobkovsky, D. Kristensen, Y. Wolf +1 more
2014BMC Biology206 citations Open access
Semantic Scholar
E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI)
P. Puigbò, I. Bravo, S. García-Vallvé
2008BMC Bioinformatics184 citations Open access
Semantic Scholar
Ecosystem consequences of herbicides: the role of microbiome.
S. Ruuskanen, B. Fuchs, R. Nissinen, P. Puigbò +3 more
2022Trends in Ecology & Evolution154 citations Open access
Semantic Scholar
The Tree and Net Components of Prokaryote Evolution
P. Puigbò, Y. Wolf, E. Koonin
2010Genome Biology and Evolution152 citations Open access
Semantic Scholar
Fitness costs limit influenza A virus hemagglutinin glycosylation as an immune evasion strategy
S. Das, Scott E. Hensley, A. David, Loren M. Schmidt +5 more
2011Proceedings of the National Academy of Sciences of the United States of America151 citations Open access
Semantic Scholar
TOPD/FMTS: a new software to compare phylogenetic trees
P. Puigbò, S. García-Vallvé, J. McInerney
2007Bioinform.140 citations Open access
Semantic Scholar
Classification of the glyphosate target enzyme (5-enolpyruvylshikimate-3-phosphate synthase)
L. Leino, Tuomas Tall, M. Helander, I. Saloniemi +3 more
2020bioRxiv125 citations Open access
Semantic Scholar
Glycosylation Focuses Sequence Variation in the Influenza A Virus H1 Hemagglutinin Globular Domain
Suman R. Das, P. Puigbò, Scott E. Hensley, D. Hurt +2 more
2010PLoS Pathogens107 citations Open access
Semantic Scholar
Inevitability of Genetic Parasites
Jaime Iranzo, P. Puigbò, A. Lobkovsky, Y. Wolf +1 more
2016Genome Biology and Evolution90 citations Open access
Semantic Scholar
HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection
P. Puigbò, A. Romeu, S. García-Vallvé
2007Nucleic Acids Res.80 citations Open access
Semantic Scholar
RCDI/eRCDI: a web-server to estimate codon usage deoptimization
P. Puigbò, L. Aragonès, S. García-Vallvé
2010BMC Research Notes78 citations Open access
Semantic Scholar
Genomics of the Proteorhodopsin-Containing Marine Flavobacterium Dokdonia sp. Strain MED134
José M. Gónzalez, J. Pinhassi, Beatriz Fernández-Gómez, M. Coll-Lladó +7 more
2011Applied and Environmental Microbiology61 citations Open access
Semantic Scholar
Reconstruction of the evolution of microbial defense systems
P. Puigbò, K. Makarova, D. Kristensen, Y. Wolf +1 more
2017BMC Evolutionary Biology56 citations Open access
Semantic Scholar
Seeing the Tree of Life behind the phylogenetic forest
P. Puigbò, Y. Wolf, E. Koonin
2013BMC Biology54 citations Open access
Semantic Scholar
Does Glyphosate Affect the Human Microbiota?
P. Puigbò, L. Leino, M. Rainio, K. Saikkonen +2 more
2022Life47 citations Open access
Semantic Scholar
Comparison of Phylogenetic Trees and Search for a Central Trend in the “Forest of Life”
E. Koonin, P. Puigbò, Y. Wolf
2011J. Comput. Biol.34 citations Open access
Semantic Scholar
Adaptation of bacteria to glyphosate: a microevolutionary perspective of the enzyme 5-enolpyruvylshikimate-3-phosphate synthase.
M. Rainio, S. Ruuskanen, M. Helander, K. Saikkonen +2 more
2021Environmental Microbiology Reports33 citations Open access
Semantic Scholar
The Phylogenetic Forest and the Quest for the Elusive Tree of Life
E. Koonin, Y. Wolf, P. Puigbò
2009Cold Spring Harbor Symposia on Quantitative Biology30 citations Open access
Semantic Scholar
Phylobone: a comprehensive database of bone extracellular matrix proteins in human and model organisms
Margalida Fontcuberta-Rigo, Miho Nakamura, P. Puigbò
2023bioRxiv29 citations Open access
Semantic Scholar
Gaining and losing the thermophilic adaptation in prokaryotes.
P. Puigbò, A. Pasamontes, S. García-Vallvé
2008Trends in Genetics28 citations
Semantic Scholar
GENOME-WIDE COMPARATIVE ANALYSIS OF PHYLOGENETIC TREES: THE PROKARYOTIC FOREST OF LIFE
P. Puigbò, Y. Wolf, E. Koonin
2012Methods in molecular biology26 citations Open access
Semantic Scholar
The Mutational Landscape of SARS-CoV-2
Bryan Saldivar-Espinoza, Pol Garcia-Segura, Nil Novau-Ferré, Guillem Macip +5 more
2023International Journal of Molecular Sciences25 citations Open access
Semantic Scholar
Glyphosate and a glyphosate-based herbicide affect bumblebee gut microbiota
M. Helander, Aditya Jeevannavar, Kimmo Kaakinen, S. Mathew +5 more
2023FEMS Microbiology Ecology25 citations Open access
Semantic Scholar
Prediction of Recurrent Mutations in SARS-CoV-2 Using Artificial Neural Networks
Bryan Saldivar-Espinoza, Guillem Macip, Pol Garcia-Segura, Júlia Mestres-Truyol +4 more
2022International Journal of Molecular Sciences13 citations Open access
Semantic Scholar
Why Is the UAG (Amber) Stop Codon Almost Absent in Highly Expressed Bacterial Genes?
D. Belin, P. Puigbò
2022Life12 citations Open access
Semantic Scholar
Alterations in Metabolome and Microbiome Associated with an Early Stress Stage in Male Wistar Rats: A Multi-Omics Approach
Julia Hernández-Baixauli, P. Puigbò, Nerea Abasolo, Hector Palacios-Jordan +7 more
2021International Journal of Molecular Sciences11 citations Open access
Semantic Scholar
Glyphosate-based herbicide use affects individual microbial taxa in strawberry endosphere but not the microbial community composition.
S. Mathew, B. Fuchs, R. Nissinen, M. Helander +3 more
2023Journal of Applied Microbiology9 citations Open access
Semantic Scholar
Use of Live Biopreservatives and Bacteriophages to Enhance the Safety of Meat Products
Cristina Rodríguez-Marca, Cristina Domenech-Coca, Miho Nakamura, Nàdia Ortega-Olivé +1 more
2025Life7 citations Open access
Semantic Scholar
The Glyphosate Target Enzyme 5-Enolpyruvyl Shikimate 3-Phosphate Synthase (EPSPS) Contains Several EPSPS-Associated Domains in Fungi
Tuomas Tall, P. Puigbò
2020Proceedings7 citations Open access
Semantic Scholar
Quantification of the Potential Impact of Glyphosate-Based Products on Microbiomes.
S. Mathew, A. Muola, K. Saikkonen, I. Saloniemi +2 more
2022Journal of Visualized Experiments6 citations Open access
Semantic Scholar
A Pilot Study for Metabolic Profiling of Obesity-Associated Microbial Gut Dysbiosis in Male Wistar Rats
Julia Hernández-Baixauli, P. Puigbò, H. Torrell, Hector Palacios-Jordan +5 more
2021Biomolecules6 citations Open access
Semantic Scholar
Rethinking the Intrinsic Sensitivity of Fungi to Glyphosate
Tuomas Tall, P. Puigbò
2022BioTech5 citations Open access
Semantic Scholar
Towards reconstructing a metabolic tree of life
M. Marcet-Houben, P. Puigbò, A. Romeu, S. García-Vallvé
2007Bioinformation5 citations Open access
Semantic Scholar
An Unsupervised Algorithm for Host Identification in Flaviviruses
Phuoc T. Truong Nguyen, S. García-Vallvé, P. Puigbò
2020bioRxiv4 citations Open access
Semantic Scholar
Adaptation of bacteria to glyphosate: a microevolutionary perspective of the enzyme 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase
M. Rainio, S. Ruuskanen, M. Helander, K. Saikkonen +2 more
2020bioRxiv4 citations Open access
Semantic Scholar
Reconstruction of the evolution of microbial defense systems
P. Puigbò, K. Makarova, D. Kristensen, Y. Wolf +1 more
2017BMC Evolutionary Biology3 citations Open access
Semantic Scholar
Bone mechano-response is driven by locomotion transitions during vertebrate evolution
Saeka Shimochi, C. Brunet, Margalida Fontcuberta-Rigo, K. Hrovat +2 more
2024bioRxiv2 citations Open access
Semantic Scholar
The evolution of microbial defense systems
P. Puigbò, K. Makarova, D. Kristensen, Y. Wolf +1 more
20211 citations
Semantic Scholar
GPT: a web-server to map phylogenetic trees on a virtual globe
P. Puigbò, J. M. Major
20151 citations Open access
Semantic Scholar
Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes
P. Puigbò, A. Lobkovsky, D. Kristensen, Y. Wolf +1 more
2014BMC Biology1 citations Open access
Semantic Scholar
A comprehensive census of horizontal gene transfers from prokaryotes to unikonts
P. Puigbò, S. Mekhedov, Y. Wolf, E. Koonin
2011Genome Biology1 citations Open access
Semantic Scholar
Low Light and Thermal Imaging Systems
P. Puigbò
19751 citations
Semantic Scholar
Use of the Phylobone database for the annotation of bone extracellular matrix proteins in reindeer (Rangifer tarandus)
Alba Sánchez-Reverté, Margalida Fontcuberta-Rigo, Miho Nakamura, P. Puigbò
2024Science in progress0 citations Open access
Semantic Scholar
Genome-Wide Comparative Analysis of Phylogenetic Trees: The Prokaryotic Forest of Life.
P. Puigbò, Y. Wolf, E. Koonin
2019Methods in molecular biology0 citations Open access
Semantic Scholar

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