Affiliation: Wilfrid Laurier University
- Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end illumina readsAndrea K Bartram
Department of Biology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
Appl Environ Microbiol 77:3846-52. 2011....
- Inferring Functional Relationships from Conservation of Gene OrderGabriel Moreno-Hagelsieb
Department of Biology, Wilfrid Laurier University, 75 University Ave W, Waterloo, ON, Canada, N2L 3C5
Methods Mol Biol 1526:41-63. 2017..The final step is to verify if the mapped orthologs are also pairs of adjacent genes in the informative genomes...
- Predicting Functional Interactions Among Genes in Prokaryotes by Genomic ContextG Moreno-Hagelsieb
Department of Biology, Wilfrid Laurier University, 75 University Ave W, Waterloo, ON, N2L 3C5, Canada
Adv Exp Med Biol 883:97-106. 2015..We present here a view of genomic context methods for predicting functional interactions, with simple examples of their implementation as compared and evaluated using genes whose products are known to functionally interact. ..
- The loose evolutionary relationships between transcription factors and other gene products across prokaryotesMarc Del Grande
Department of Biology, Wilfrid Laurier University, 75 University Ave, W, N2L 3C5 Waterloo, Ontario, Canada
BMC Res Notes 7:928. 2014..We then used genes predicted to code for TFs to compare their most conserved interactions against the most conserved interactions for the rest of the genes within each prokaryotic genome available...
- Estimating overannotation across prokaryotic genomes using BLAST+, UBLAST, LAST and BLATGabriel Moreno-Hagelsieb
Department of Biology, Wilfrid Laurier University, 75 University Ave, W, N2L 3C5 Waterloo, ON, Canada
BMC Res Notes 7:651. 2014....
- Nebulon: a system for the inference of functional relationships of gene products from the rearrangement of predicted operonsSarath Chandra Janga
Program of Computational Genomics, CCG UNAM Apdo Postal 565 A, Cuernavaca, Morelos, 62100 Mexico
Nucleic Acids Res 33:2521-30. 2005....
- Phylogenomic clustering for selecting non-redundant genomes for comparative genomicsGabriel Moreno-Hagelsieb
Department of Biology and Department of Mathematics, Wilfrid Laurier University, Waterloo, ON N2L 3C5, Canada
Bioinformatics 29:947-9. 2013....
- The evolutionary dynamics of functional modules and the extraordinary plasticity of regulons: the Escherichia coli perspectiveGabriel Moreno-Hagelsieb
Department of Biology, Wilfrid Laurier University, 75 University Avenue West, Waterloo, ON, Canada N2L 3C5
Nucleic Acids Res 40:7104-12. 2012....
- Understanding the evolutionary relationships and major traits of Bacillus through comparative genomicsLuis 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...
- Operons and the effect of genome redundancy in deciphering functional relationships using phylogenetic profilesGabriel 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...
- Choosing BLAST options for better detection of orthologs as reciprocal best hitsGabriel 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...
- The distinctive signatures of promoter regions and operon junctions across prokaryotesSarath 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...
- Operon conservation from the point of view of Escherichia coli, and inference of functional interdependence of gene products from genome contextGabriel 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...
- Evaluation of thresholds for the detection of binding sites for regulatory proteins in Escherichia coli K12 DNAEsperanza 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...
- Inferring functional relationships from conservation of gene orderGabriel 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...
- A powerful non-homology method for the prediction of operons in prokaryotesGabriel 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...
- Bacterial biogeography of the human digestive tractJennifer 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...
- Conservation of adjacency as evidence of paralogous operonsSarath 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...
- Beyond the bounds of orthology: functional inference from metagenomic contextGregory 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...
- The mosaic structure of the symbiotic plasmid of Rhizobium etli CFN42 and its relation to other symbiotic genome compartmentsVictor 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...
- Successful lateral transfer requires codon usage compatibility between foreign genes and recipient genomesArturo 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...
- Global functional atlas of Escherichia coli encompassing previously uncharacterized proteinsPingzhao Hu
Banting and Best Department of Medical Research, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
PLoS Biol 7:e96. 2009..This resource provides a "systems-wide" functional blueprint of a model microbe, with insights into the biological and evolutionary significance of previously uncharacterized proteins...
- Evaluating bias of illumina-based bacterial 16S rRNA gene profilesKatherine Kennedy
University of Waterloo, Department of Biology, Waterloo, Ontario, Canada
Appl Environ Microbiol 80:5717-22. 2014....
- Probing teichoic acid genetics with bioactive molecules reveals new interactions among diverse processes in bacterial cell wall biogenesisMichael A D'Elia
Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
Chem Biol 16:548-56. 2009..Furthermore, the new reporter assay represents an exciting avenue for the discovery of antibacterial molecules...
- Metagenomic annotation networks: construction and applicationsGregory 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...
- A new method of solution for the occupancy problem and its application to operon size predictionW 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...
- Conservation of DNA curvature signals in regulatory regions of prokaryotic genesRuy 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...
- The partitioned Rhizobium etli genome: genetic and metabolic redundancy in seven interacting repliconsVictor 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...