Gabriel Moreno-Hagelsieb

Summary

Affiliation: Wilfrid Laurier University
Country: Canada

Publications

  1. pmc Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end illumina reads
    Andrea K Bartram
    Department of Biology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
    Appl Environ Microbiol 77:3846-52. 2011
  2. doi request reprint Phylogenomic clustering for selecting non-redundant genomes for comparative genomics
    Gabriel Moreno-Hagelsieb
    Department of Biology and Department of Mathematics, Wilfrid Laurier University, Waterloo, ON N2L 3C5, Canada
    Bioinformatics 29:947-9. 2013
  3. pmc The evolutionary dynamics of functional modules and the extraordinary plasticity of regulons: the Escherichia coli perspective
    Gabriel Moreno-Hagelsieb
    Department of Biology, Wilfrid Laurier University, 75 University Avenue West, Waterloo, ON, Canada N2L 3C5
    Nucleic Acids Res 40:7104-12. 2012
  4. pmc Understanding the evolutionary relationships and major traits of Bacillus through comparative genomics
    Luis David Alcaraz
    Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN Campus Guanajuato, Guanajuato, Mexico
    BMC Genomics 11:332. 2010
  5. ncbi request reprint Choosing BLAST options for better detection of orthologs as reciprocal best hits
    Gabriel Moreno-Hagelsieb
    Department of Biology, Wilfrid Laurier University, 75 University Avenue West, Waterloo, ON, Canada, N2L 3C5
    Bioinformatics 24:319-24. 2008
  6. ncbi request reprint Operons and the effect of genome redundancy in deciphering functional relationships using phylogenetic profiles
    Gabriel Moreno-Hagelsieb
    Department of Biology, Wilfrid Laurier University, 75 University Avenue West, Waterloo, ON N2L 3C5, Canada
    Proteins 70:344-52. 2008
  7. pmc The distinctive signatures of promoter regions and operon junctions across prokaryotes
    Sarath Chandra Janga
    Department of Biology, Wilfrid Laurier University, 75 University Avenue West, Waterloo, ON, Canada, N2L 3C5
    Nucleic Acids Res 34:3980-7. 2006
  8. pmc Bacterial biogeography of the human digestive tract
    Jennifer C Stearns
    Department of Biology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
    Sci Rep 1:170. 2011
  9. doi request reprint Beyond the bounds of orthology: functional inference from metagenomic context
    Gregory Vey
    Department of Biology, Wilfrid Laurier University, 75 University Avenue West, Waterloo ON, Canada
    Mol Biosyst 6:1247-54. 2010
  10. pmc Metagenomic annotation networks: construction and applications
    Gregory Vey
    Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
    PLoS ONE 7:e41283. 2012

Collaborators

  • Gregory Vey
  • Josh D Neufeld
  • Sarath Chandra Janga
  • Araceli M Huerta
  • Enrique Merino
  • Pablo Vinuesa
  • Miguel A Cevallos
  • Julio Collado-Vides
  • Jennifer C Stearns
  • Victor Gonzalez
  • Arturo Medrano-Soto
  • Michael D J Lynch
  • Andrea K Bartram
  • Luis David Alcaraz
  • Patricia Bustos
  • Guillermo Davila
  • Ismael Hernández-González
  • W F Warren F Lamboy
  • Ruy Jauregui
  • Esperanza Benítez-Bellón
  • Dennis G Cvitkovitch
  • Dilani B Senadheera
  • Kenneth Croitoru
  • Michael B Goldberg
  • Howard C Tenenbaum
  • Luis E Eguiarte
  • Valeria Souza
  • Gabriela Olmedo
  • Luis Herrera-Estrella
  • Veronica Jimenez-Jacinto
  • Rosa I Santamaría
  • Miguel A Ramirez
  • J Andrés Christen
  • Verónica Quintero
  • Juan Carlos Hernández-Celis
  • David Romero
  • Miguel A Ramírez-Romero
  • Cei Abreu-Goodger
  • Lourdes Girard
  • Margarita Flores
  • Heladia Salgado
  • Oscar Rodriguez

Detail Information

Publications21

  1. pmc Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end illumina reads
    Andrea K Bartram
    Department of Biology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
    Appl Environ Microbiol 77:3846-52. 2011
    ....
  2. doi request reprint Phylogenomic clustering for selecting non-redundant genomes for comparative genomics
    Gabriel Moreno-Hagelsieb
    Department of Biology and Department of Mathematics, Wilfrid Laurier University, Waterloo, ON N2L 3C5, Canada
    Bioinformatics 29:947-9. 2013
    ....
  3. pmc The evolutionary dynamics of functional modules and the extraordinary plasticity of regulons: the Escherichia coli perspective
    Gabriel Moreno-Hagelsieb
    Department of Biology, Wilfrid Laurier University, 75 University Avenue West, Waterloo, ON, Canada N2L 3C5
    Nucleic Acids Res 40:7104-12. 2012
    ....
  4. pmc Understanding the evolutionary relationships and major traits of Bacillus through comparative genomics
    Luis David Alcaraz
    Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN Campus Guanajuato, Guanajuato, Mexico
    BMC Genomics 11:332. 2010
    ..By distinguishing between core and pan-genome, we determined the evolutionary and functional relationships of known Bacillus...
  5. ncbi request reprint Choosing BLAST options for better detection of orthologs as reciprocal best hits
    Gabriel Moreno-Hagelsieb
    Department of Biology, Wilfrid Laurier University, 75 University Avenue West, Waterloo, ON, Canada, N2L 3C5
    Bioinformatics 24:319-24. 2008
    ..Thus, we decided to test whether such options would help better detect orthologs...
  6. ncbi request reprint Operons and the effect of genome redundancy in deciphering functional relationships using phylogenetic profiles
    Gabriel Moreno-Hagelsieb
    Department of Biology, Wilfrid Laurier University, 75 University Avenue West, Waterloo, ON N2L 3C5, Canada
    Proteins 70:344-52. 2008
    ..Confidence values as those presented here should help compare other strategies and scoring systems to use phylogenetic profiles and other genomic context methods for predicting functional interactions...
  7. pmc The distinctive signatures of promoter regions and operon junctions across prokaryotes
    Sarath Chandra Janga
    Department of Biology, Wilfrid Laurier University, 75 University Avenue West, Waterloo, ON, Canada, N2L 3C5
    Nucleic Acids Res 34:3980-7. 2006
    ..Oligonucleotide signatures should expand the number of tools available to identify operons even in poorly characterized genomes...
  8. pmc Bacterial biogeography of the human digestive tract
    Jennifer C Stearns
    Department of Biology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
    Sci Rep 1:170. 2011
    ..This first comprehensive characterization of the abundant and rare microflora found along the healthy human digestive tract represents essential groundwork to investigate further how the human microbiome relates to health and disease...
  9. doi request reprint Beyond the bounds of orthology: functional inference from metagenomic context
    Gregory Vey
    Department of Biology, Wilfrid Laurier University, 75 University Avenue West, Waterloo ON, Canada
    Mol Biosyst 6:1247-54. 2010
    ..Because metagenomes allow access to previously unreachable microorganisms, this will result in expanding the universe of known functional interactions thus furthering our understanding of functional organization...
  10. pmc Metagenomic annotation networks: construction and applications
    Gregory Vey
    Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
    PLoS ONE 7:e41283. 2012
    ..Applications to biocatalyst discovery and human health issues are discussed, as well as the limitations of the current implementation...
  11. doi request reprint Inferring functional relationships from conservation of gene order
    Gabriel Moreno-Hagelsieb
    Department of Biology, Wilfrid Laurier University, Waterloo, Ontario, Canada
    Methods Mol Biol 453:181-99. 2008
    ..The final step is to determine whether the orthologs of each original pair of genes are also adjacent in the informative genome...
  12. ncbi request reprint Operon conservation from the point of view of Escherichia coli, and inference of functional interdependence of gene products from genome context
    Gabriel Moreno-Hagelsieb
    Laboratory of Computational Genomics, CIFN, UNAM, Cuernavaca, Morelos, Mexico
    In Silico Biol 2:87-95. 2002
    ..coli, is the same in any other prokaryote whose genome is currently available. We also show the relationship between our analyses of conservation and the inference of functional relationships from genomic context...
  13. ncbi request reprint A powerful non-homology method for the prediction of operons in prokaryotes
    Gabriel Moreno-Hagelsieb
    Program of Computational Genomics, CIFN, UNAM, A P 565 A, Cuernavaca, Morelos 62100, Mexico
    Bioinformatics 18:S329-36. 2002
    ..Log-likelihoods derived from inter-genic distance distributions work surprisingly well to predict operons in Escherichia coli and are available for any genome as soon as the gene sets are predicted...
  14. pmc Evaluation of thresholds for the detection of binding sites for regulatory proteins in Escherichia coli K12 DNA
    Esperanza Benítez-Bellón
    Program of Computational Genomics, CIFN, UNAM, A, P, 565 A, Cuernavaca, Morelos 62100, Mexico
    Genome Biol 3:RESEARCH0013. 2002
    ..Detailed evaluation also helps to improve and understand the behavior of the different methods and computational strategies...
  15. pmc The mosaic structure of the symbiotic plasmid of Rhizobium etli CFN42 and its relation to other symbiotic genome compartments
    Victor Gonzalez
    Centro de Investigacion Sobre Fijacion de Nitrogeno, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, Mexico 62210
    Genome Biol 4:R36. 2003
    ..We report the complete sequence of the symbiotic plasmid of Rhizobium etli CFN42, a microsymbiont of beans, and a comparison with other SGC sequences available...
  16. pmc Conservation of DNA curvature signals in regulatory regions of prokaryotic genes
    Ruy Jauregui
    Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Av Universidad 2001, Chamilpa, Cuernavaca Mor, 62210 Mexico
    Nucleic Acids Res 31:6770-7. 2003
    ..It is currently an open question whether these diverse systems are part of an integrated global regulatory response in different microorganisms...
  17. ncbi request reprint A new method of solution for the occupancy problem and its application to operon size prediction
    W F Warren F Lamboy
    Center for Agricultural Bioinformatics, United States Department of Agriculture, Agricultural Research Service, Cornell Theory Center, Rhodes Hall, Cornell University, Ithaca, NY 14853, USA
    J Theor Biol 227:315-22. 2004
    ..Since these predictions can be made for any completely sequenced and annotated prokaryotic genome, they provide a starting point for the comparison of regulatory complexity across such genomes...
  18. pmc The partitioned Rhizobium etli genome: genetic and metabolic redundancy in seven interacting replicons
    Victor Gonzalez
    Centro de Ciencias Genomicas, Universidad Nacional Autonoma de Mexico, AP565 A Cuernavaca, Morelos, 62210, Mexico
    Proc Natl Acad Sci U S A 103:3834-9. 2006
    ..Twenty-three putative sigma factors, numerous isozymes, and paralogous families attest to the metabolic redundancy and the genomic plasticity necessary to sustain the lifestyle of R. etli in symbiosis and in the soil...
  19. pmc Nebulon: a system for the inference of functional relationships of gene products from the rearrangement of predicted operons
    Sarath Chandra Janga
    Program of Computational Genomics, CCG UNAM Apdo Postal 565 A, Cuernavaca, Morelos, 62100 Mexico
    Nucleic Acids Res 33:2521-30. 2005
    ....
  20. pmc Conservation of adjacency as evidence of paralogous operons
    Sarath Chandra Janga
    Program of Computational Genomics, CIFN UNAM, Apdo Postal 565 A, Cuernavaca, Morelos, 62100 Mexico
    Nucleic Acids Res 32:5392-7. 2004
    ..The use of evidence from the conservation of adjacency of paralogous genes can improve the prediction of operons in E.coli K12 by approximately 0.27 over predictions using conservation of adjacency of orthologous genes alone...
  21. ncbi request reprint Successful lateral transfer requires codon usage compatibility between foreign genes and recipient genomes
    Arturo Medrano-Soto
    Program of Computational Genomics, Centro de Investigación sobre Fijación de Nitrógeno UNAM, Cuernavaca, Morelos, Mexico
    Mol Biol Evol 21:1884-94. 2004
    ..Our approach makes no assumptions about the CU of foreign genes being typical or atypical within the recipient genome, thus providing a novel unbiased framework to study the evolutionary dynamics of HGT...