Pere Puigbò

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc Search for a 'Tree of Life' in the thicket of the phylogenetic forest
    Pere Puigbò
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Biol 8:59. 2009
  2. pmc Phylogenomics of prokaryotic ribosomal proteins
    Natalya Yutin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS ONE 7:e36972. 2012
  3. doi request reprint Genome-wide comparative analysis of phylogenetic trees: the prokaryotic forest of life
    Pere Puigbò
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Methods Mol Biol 856:53-79. 2012
  4. pmc Comparison of phylogenetic trees and search for a central trend in the "forest of life"
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
    J Comput Biol 18:917-24. 2011
  5. pmc CAIcal: a combined set of tools to assess codon usage adaptation
    Pere Puigbò
    Department of Biochemistry and Biotechnology, Rovira i Virgili University URV, Campus Sescelades, c Marcelli Domingo s n, 43007 Tarragona, Spain
    Biol Direct 3:38. 2008
  6. pmc RCDI/eRCDI: a web-server to estimate codon usage deoptimization
    Pere Puigbò
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Res Notes 3:87. 2010
  7. pmc Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Environ Microbiol 14:2870-90. 2012
  8. pmc The tree and net components of prokaryote evolution
    Pere Puigbò
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
    Genome Biol Evol 2:745-56. 2010

Collaborators

Detail Information

Publications8

  1. pmc Search for a 'Tree of Life' in the thicket of the phylogenetic forest
    Pere Puigbò
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Biol 8:59. 2009
    ..However, the possibility remains that a statistical central trend still exists in the phylogenetic 'forest of life'...
  2. pmc Phylogenomics of prokaryotic ribosomal proteins
    Natalya Yutin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
    PLoS ONE 7:e36972. 2012
    ..These alignments, available for download, can be used as search profiles to improve genome annotation of r-proteins and for further comparative genomics studies...
  3. doi request reprint Genome-wide comparative analysis of phylogenetic trees: the prokaryotic forest of life
    Pere Puigbò
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Methods Mol Biol 856:53-79. 2012
    ..These results support the concept of the Tree of Life (TOL) as a central evolutionary trend in the FOL as opposed to the traditional view of the TOL as a "species tree."..
  4. pmc Comparison of phylogenetic trees and search for a central trend in the "forest of life"
    Eugene V Koonin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
    J Comput Biol 18:917-24. 2011
    ..Despite the substantial amount of apparent HGT seen even among the NUTs, these gene transfers appear to be distributed randomly and do not obscure the central tree-like trend...
  5. pmc CAIcal: a combined set of tools to assess codon usage adaptation
    Pere Puigbò
    Department of Biochemistry and Biotechnology, Rovira i Virgili University URV, Campus Sescelades, c Marcelli Domingo s n, 43007 Tarragona, Spain
    Biol Direct 3:38. 2008
    ..The CAI quantifies the similarity between the synonymous codon usage of a gene and the synonymous codon frequency of a reference set...
  6. pmc RCDI/eRCDI: a web-server to estimate codon usage deoptimization
    Pere Puigbò
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Res Notes 3:87. 2010
    ..The Relative Codon Deoptimization Index (RCDI) was developed by Mueller et al. (2006) as measure of codon deoptimization by comparing how similar is the codon usage of a gene and the codon usage of a reference genome...
  7. pmc Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes
    Michael Y Galperin
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Environ Microbiol 14:2870-90. 2012
    ..These profiles should help further experimental studies of uncharacterized widespread sporulation genes, which would ultimately allow delineation of the minimal set(s) of sporulation-specific genes in Bacilli and Clostridia...
  8. pmc The tree and net components of prokaryote evolution
    Pere Puigbò
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
    Genome Biol Evol 2:745-56. 2010
    ..Evolutionary simulations indicate that the central tree-like signal cannot be realistically explained by a self-reinforcing pattern of biased HGT...