B F Lang

Summary

Country: Canada

Publications

  1. pmc Comparative mitochondrial genomics in zygomycetes: bacteria-like RNase P RNAs, mobile elements and a close source of the group I intron invasion in angiosperms
    Elias Seif
    Program in Evolutionary Biology, Canadian Institute for Advanced Research, Montreal, Quebec, Canada H3T 1J4
    Nucleic Acids Res 33:734-44. 2005
  2. pmc Natural reassignment of CUU and CUA sense codons to alanine in Ashbya mitochondria
    Jiqiang Ling
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 8114, USA, Departement de Biochimie, Centre Robert Cedergren, Universite de Montreal, 2900 Boulevard Edouard Montpetit, Montreal, Quebec, H3C 3J7, Canada, Program in Chemical Biology, Harvard University, Cambridge, MA 02138, USA, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA and Department of Chemistry, Yale University, New Haven, CT 06520 8114, USA
    Nucleic Acids Res 42:499-508. 2014
  3. pmc Yeast mitochondrial RNase P, RNase Z and the RNA degradosome are part of a stable supercomplex
    Rachid Daoud
    Robert Cedergren Centre for Bioinformatics and Genomics, Department of Biochemistry, Universite de Montreal, 2900 Edouard Montpetit, Montreal, Quebec H3T 1J4, Canada
    Nucleic Acids Res 40:1728-36. 2012
  4. pmc Phylogenomic analyses predict sistergroup relationship of nucleariids and fungi and paraphyly of zygomycetes with significant support
    Yu Liu
    Robert Cedergren Centre, Departement de Biochimie, Universite de Montreal, Montreal, Quebec, Canada
    BMC Evol Biol 9:272. 2009
  5. pmc AnaBench: a Web/CORBA-based workbench for biomolecular sequence analysis
    Elarbi Badidi
    The Canadian Institute for Advanced Research, Program in Evolutionary Biology, Departement de Biochimie, Universite de Montreal, 2900, Boul, Edouard Montpetit, Montreal, QC H3T 1J4, Canada
    BMC Bioinformatics 4:63. 2003
  6. pmc AutoFACT: an automatic functional annotation and classification tool
    Liisa B Koski
    Robert Cedergren Center for Bioinformatics and Genomics, Universite de Montreal, Montreal, Quebec, Canada
    BMC Bioinformatics 6:151. 2005
  7. ncbi Purification of mitochondrial and plastid DNA
    B Franz Lang
    Departement de Biochimie, Robert Cedergren Center for Bioinformatics and Genomics, Canadian Institute for Advanced Research, Program in Evolutionary Biology, Universite de Montreal, CP 6128, Montreal, Quebec, Canada H3T 1J4
    Nat Protoc 2:652-60. 2007
  8. ncbi A comparative genomics approach to the evolution of eukaryotes and their mitochondria
    B F Lang
    Departement de Biochimie, Universite de Montreal, Quebec, Canada
    J Eukaryot Microbiol 46:320-6. 1999
  9. ncbi Mitochondrial introns: a critical view
    B Franz Lang
    Robert Cedergren Centre, Program in Evolutionary Biology, Canadian Institute for Advanced Research, Departement de Biochimie, Universite de Montreal, Montreal, Quebec, Canada
    Trends Genet 23:119-25. 2007
  10. pmc A comparison of three fission yeast mitochondrial genomes
    C E Bullerwell
    Program in Evolutionary Biology, Canadian Institute for Advanced Research, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
    Nucleic Acids Res 31:759-68. 2003

Collaborators

Detail Information

Publications71

  1. pmc Comparative mitochondrial genomics in zygomycetes: bacteria-like RNase P RNAs, mobile elements and a close source of the group I intron invasion in angiosperms
    Elias Seif
    Program in Evolutionary Biology, Canadian Institute for Advanced Research, Montreal, Quebec, Canada H3T 1J4
    Nucleic Acids Res 33:734-44. 2005
    ..Laforest,M.J., Forget,L., Roewer,I., Wang,Z., Longcore,J. and Lang,B.F. (1997) Curr. Genet., 31, 380-395]. The combined mtDNA-encoded proteins contain insufficient phylogenetic signal to demonstrate monophyly of zygomycetes...
  2. pmc Natural reassignment of CUU and CUA sense codons to alanine in Ashbya mitochondria
    Jiqiang Ling
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 8114, USA, Departement de Biochimie, Centre Robert Cedergren, Universite de Montreal, 2900 Boulevard Edouard Montpetit, Montreal, Quebec, H3C 3J7, Canada, Program in Chemical Biology, Harvard University, Cambridge, MA 02138, USA, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA and Department of Chemistry, Yale University, New Haven, CT 06520 8114, USA
    Nucleic Acids Res 42:499-508. 2014
    ..Our work highlights the dynamic feature of natural genetic codes in mitochondria, and the relative simplicity by which tRNA identity may be switched. ..
  3. pmc Yeast mitochondrial RNase P, RNase Z and the RNA degradosome are part of a stable supercomplex
    Rachid Daoud
    Robert Cedergren Centre for Bioinformatics and Genomics, Department of Biochemistry, Universite de Montreal, 2900 Edouard Montpetit, Montreal, Quebec H3T 1J4, Canada
    Nucleic Acids Res 40:1728-36. 2012
    ..Finally, the question of mt-RNase P localization within mitochondria was investigated, by GFP-tracing of a known protein subunit (Rpm2p). We find that about equal fractions of RNase P are soluble versus membrane-attached...
  4. pmc Phylogenomic analyses predict sistergroup relationship of nucleariids and fungi and paraphyly of zygomycetes with significant support
    Yu Liu
    Robert Cedergren Centre, Departement de Biochimie, Universite de Montreal, Montreal, Quebec, Canada
    BMC Evol Biol 9:272. 2009
    ..Yet, published phylogenies with up to five genes are without compelling statistical support, and genome-level data should be used to resolve this question with confidence...
  5. pmc AnaBench: a Web/CORBA-based workbench for biomolecular sequence analysis
    Elarbi Badidi
    The Canadian Institute for Advanced Research, Program in Evolutionary Biology, Departement de Biochimie, Universite de Montreal, 2900, Boul, Edouard Montpetit, Montreal, QC H3T 1J4, Canada
    BMC Bioinformatics 4:63. 2003
    ....
  6. pmc AutoFACT: an automatic functional annotation and classification tool
    Liisa B Koski
    Robert Cedergren Center for Bioinformatics and Genomics, Universite de Montreal, Montreal, Quebec, Canada
    BMC Bioinformatics 6:151. 2005
    ..Assignment of function to new molecular sequence data is an essential step in genomics projects. The usual process involves similarity searches of a given sequence against one or more databases, an arduous process for large datasets...
  7. ncbi Purification of mitochondrial and plastid DNA
    B Franz Lang
    Departement de Biochimie, Robert Cedergren Center for Bioinformatics and Genomics, Canadian Institute for Advanced Research, Program in Evolutionary Biology, Universite de Montreal, CP 6128, Montreal, Quebec, Canada H3T 1J4
    Nat Protoc 2:652-60. 2007
    ..Procedures can be completed in 3-5 days, typically yielding a few micrograms of DNA-ample for sequencing complete genomes...
  8. ncbi A comparative genomics approach to the evolution of eukaryotes and their mitochondria
    B F Lang
    Departement de Biochimie, Universite de Montreal, Quebec, Canada
    J Eukaryot Microbiol 46:320-6. 1999
    ..Gene repertoire and gene order comparisons as well as multiple-gene phylogenies support the view of a single endosymbiotic origin of mitochondria, whose closest extant relatives are Rickettsia-type alpha-Proteobacteria...
  9. ncbi Mitochondrial introns: a critical view
    B Franz Lang
    Robert Cedergren Centre, Program in Evolutionary Biology, Canadian Institute for Advanced Research, Departement de Biochimie, Universite de Montreal, Montreal, Quebec, Canada
    Trends Genet 23:119-25. 2007
    ..On the basis of the results, we focus here on building a comprehensive picture of mitochondrial group I introns, including a modified (reduced) consensus RNA secondary structure and a concise phylogeny-based subclassification...
  10. pmc A comparison of three fission yeast mitochondrial genomes
    C E Bullerwell
    Program in Evolutionary Biology, Canadian Institute for Advanced Research, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
    Nucleic Acids Res 31:759-68. 2003
    ..The results of our phylogenetic analysis support the monophyly of the Schizosaccharomycetales, but question their grouping within the Archiascomycota...
  11. pmc Genome structure and gene content in protist mitochondrial DNAs
    M W Gray
    Program in Evolutionary Biology, Canadian Institute for Advanced Research, Department of Biochemistry, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
    Nucleic Acids Res 26:865-78. 1998
    ..Comparative analysis of protist mtDNAs is providing a new perspective on mtDNA evolution: how the original mitochondrial genome was organized, what genes it contained, and in what ways it must have changed in different eukaryotic phyla...
  12. pmc The complete mitochondrial DNA sequences of Nephroselmis olivacea and Pedinomonas minor. Two radically different evolutionary patterns within green algae
    M Turmel
    Program in Evolutionary Biology, Canadian Institute for Advanced Research, Quebec, Quebec G1K 7P4, Canada
    Plant Cell 11:1717-30. 1999
    ..Our results confirm the existence of two radically different patterns of mitochondrial genome evolution within the green algae...
  13. ncbi The mitochondrial DNA of Allomyces macrogynus: the complete genomic sequence from an ancestral fungus
    B Paquin
    Departement de Biochimie, Universite de Montreal, Centre Ville, Canada
    J Mol Biol 255:688-701. 1996
    ....
  14. ncbi An ancestral mitochondrial DNA resembling a eubacterial genome in miniature
    B F Lang
    Departement de Biochimie, Universite de Montreal, Quebec, Canada
    Nature 387:493-7. 1997
    ..americana mtDNA more closely resembles the ancestral proto-mitochondrial genome than any other mtDNA investigated to date...
  15. pmc Interspecific transfer of mitochondrial genes in fungi and creation of a homologous hybrid gene
    B Paquin
    Departement de Biochimie, Universite de Montreal, PQ, Canada
    Proc Natl Acad Sci U S A 91:11807-10. 1994
    ..We present evidence that this insertion may have been acquired by interspecific transfer and we discuss the possible role of the endonuclease in this process...
  16. pmc Evolution of monoblepharidalean fungi based on complete mitochondrial genome sequences
    C E Bullerwell
    Program in Evolutionary Biology, Canadian Institute for Advanced Research, Departement de Biochimie, Universite de Montreal, 2900 Boulevard Edouard Montpetit, Montreal, Quebec H3T 1J4, Canada
    Nucleic Acids Res 31:1614-23. 2003
    ..Intriguingly, a similar interaction may also be involved in mitochondrial translation initiation in the sea anemone Metridium senile...
  17. ncbi Mitochondrial evolution
    M W Gray
    Department of Biochemistry, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
    Science 283:1476-81. 1999
    ....
  18. pmc Complete sequence of the mitochondrial DNA of the red alga Porphyra purpurea. Cyanobacterial introns and shared ancestry of red and green algae
    G Burger
    Program in Evolutionary Biology, Canadian Institute for Advanced Research, 180 Dundas Street West, Toronto, Ontario M5G 1Z8, Canada
    Plant Cell 11:1675-94. 1999
    ..Finally, phylogenetic analyses provide strong evidence that red algae share a common ancestry with green algae and plants...
  19. pmc Genes encoding the same three subunits of respiratory complex II are present in the mitochondrial DNA of two phylogenetically distant eukaryotes
    G Burger
    Program in Evolutionary Biology, Canadian Institute for Advanced Research, Departement de Biochimie, Universite de Montreal, Quebec, Canada
    Proc Natl Acad Sci U S A 93:2328-32. 1996
    ..The data presented here are consistent with the view that mitochondria constitute a monophyletic lineage...
  20. ncbi A novel motif for identifying rps3 homologs in fungal mitochondrial genomes
    C E Bullerwell
    Program in Evolutionary Biology, Canadian Institute for Advanced Research, Departement de Biochimie, Universite de Montreal, 2900 boul Edouard Montpetit, Montreal, Que, Canada H3T 1J4
    Trends Biochem Sci 25:363-5. 2000
  21. ncbi Hyaloraphidium curvatum: a linear mitochondrial genome, tRNA editing, and an evolutionary link to lower fungi
    Lise Forget
    Program in Evolutionary Biology, Departement de Biochimie, Canadian Institute for Advanced Research, Universite de Montreal, 2900 Boulevard Edouard Montpetit, Montreal, Quebec, Canada
    Mol Biol Evol 19:310-9. 2002
    ..Our phylogenetic analysis confirms with overwhelming support that H. curvatum is a member of the chytridiomycete fungi, specifically related to the Monoblepharidales...
  22. ncbi Mitochondrial genomes of two demosponges provide insights into an early stage of animal evolution
    Dennis V Lavrov
    Departement de Biochimie, Universite de Montreal, Montreal, Quebec, Canada
    Mol Biol Evol 22:1231-9. 2005
    ....
  23. ncbi Monophyly of primary photosynthetic eukaryotes: green plants, red algae, and glaucophytes
    Naiara Rodriguez-Ezpeleta
    Canadian Institute for Advanced Research, Centre Robert Cedergren, Departement de Biochimie, Universite de Montreal, 2900 Boulevard Edouard Montpetit, Montreal, Quebec, H3T 1J4, Canada
    Curr Biol 15:1325-30. 2005
    ....
  24. ncbi Mitochondria of protists
    Michael W Gray
    Robert Cedergren Center, Program in Evolutionary Biology, Canadian Institute for Advanced Research, Canada
    Annu Rev Genet 38:477-524. 2004
    ..This comparative genomics approach has also revealed unique and fascinating aspects of mitochondrial gene expression, highlighting the mitochondrion as an evolutionary playground par excellence...
  25. ncbi The closest unicellular relatives of animals
    B F Lang
    The Canadian Institute for Advanced Research Program in Evolutionary Biology, Departement de Biochimie, Universite de Montreal, Succursale Centre Ville, Quebec, Canada
    Curr Biol 12:1773-8. 2002
    ..Our findings provide insight into the nature of the animal ancestor and have broad implications for our understanding of the evolutionary transition from unicellular protists to multicellular animals...
  26. ncbi Early eukaryote evolution based on mitochondrial gene order breakpoints
    D Sankoff
    Centre de Recherches Mathématiques, Universite de Montreal, Quebec
    J Comput Biol 7:521-35. 2000
    ....
  27. doi Construction of cDNA libraries: focus on protists and fungi
    Naiara Rodriguez-Ezpeleta
    Robert Cedergren Centre for Bioinformatics and Genomics, Departement de Biochimie, Universite de Montreal, Montreal, Quebec, Canada
    Methods Mol Biol 533:33-47. 2009
    ....
  28. ncbi The origins of multicellularity: a multi-taxon genome initiative
    Inaki Ruiz-Trillo
    Canadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    Trends Genet 23:113-8. 2007
    ..Here, we introduce this initiative and the biological questions that underpin it, summarize the rationale guiding the choice of organisms and discuss the anticipated benefits to the broader scientific community...
  29. pmc TBestDB: a taxonomically broad database of expressed sequence tags (ESTs)
    Emmet A O'Brien
    Departement de Biochimie, Canadian Institute for Advanced Research, Robert Cedergren Centre for Research in Bioinformatics and Genomics, Universite de Montreal, 2900 Edouard Montpetit, Montreal, QC, Canada H3T 1J4
    Nucleic Acids Res 35:D445-51. 2007
    ..For instructions on submission to TBestDB, contact tbestdb@bch.umontreal.ca. The database can be queried at http://tbestdb.bcm.umontreal.ca/...
  30. ncbi Molecular phylogeny of Allomyces macrogynus: congruency between nuclear ribosomal RNA- and mitochondrial protein-based trees
    B Paquin
    Departement de Biochimie, Universite de Montreal, Canada
    J Mol Evol 41:657-65. 1995
    ..In addition, our trees support a monophyletic origin of mitochondria for the range of analyzed eukaryotes...
  31. doi EST databases and web tools for EST projects
    Yao Qing Shen
    Robert Cedergren Centre for Bioinformatics and Genomics, Departement de Biochimie, Universite de Montreal, Montreal, Quebec, Canada
    Methods Mol Biol 533:241-56. 2009
    ..We discuss these in comparison to other available technologies and tools, and explain the reasons for our choices...
  32. ncbi Poriferan mtDNA and animal phylogeny based on mitochondrial gene arrangements
    Dennis V Lavrov
    Departement de Biochimie, Universite de Montreal, Succursale Centre Ville, Montreal, Que, H3C 3J7, Canada
    Syst Biol 54:651-9. 2005
    ..However, due to the remarkable stability of mitochondrial gene arrangements in Deuterostomia and the Ecdysozoa, conclusions on their evolutionary history cannot be drawn...
  33. doi Group I-intron trans-splicing and mRNA editing in the mitochondria of placozoan animals
    Gertraud Burger
    Robert Cedergren Centre for Bioinformatics and Genomics, Departement de Biochimie, Universite de Montreal, C P 6128, Montreal, Quebec, H3T 1J4, Canada
    Trends Genet 25:381-6. 2009
    ..These atypical features qualify placozoan mitochondrial gene and genome organization as derived rather than primitive. Whether the Placozoa diverged early or late during metazoan evolution remains unresolved by mitochondrial phylogeny...
  34. ncbi FLOSYS--a web-accessible workflow system for protocol-driven biomolecular sequence analysis
    E Badidi
    The Canadian Institute for Advanced Research, Program in Evolutionary Biology Département de Biochimie, Universite de Montreal, 2900, boul Edouard Montpetit, local G 312, Montreal, QC H3T 1J4, Canada
    Cell Mol Biol (Noisy-le-grand) 50:785-93. 2004
    ..bcm.umontreal.ca: 8091/anabench. The entire package is available on request to academic groups who wish to have a customized local analysis environment for research or teaching...
  35. ncbi Analysis of genes encoding highly conserved lysine-rich proteins in Aplysia californica and Saccharomyces cerevisiae
    D Auclair
    Department of Biochemistry, University of Montreal, Canada
    Eur J Biochem 220:997-1003. 1994
    ..Northern blotting experiments revealed that the expression of the gene is strongly repressed at 39 degrees C...
  36. ncbi Intron-encoded open reading frame of the GIY-YIG subclass in a plastid gene
    B Paquin
    Departement de Biochimie, Universite de Montreal, Canada
    Curr Genet 28:97-9. 1995
    ..These results suggest that GIY-YIG ORFs have a longer evolutionary history than previously assumed...
  37. ncbi Intra-isolate genome variation in arbuscular mycorrhizal fungi persists in the transcriptome
    E Boon
    Departement de sciences biologiques, Institut de recherche en biologie végétale, Universite de Montreal, Montreal, QC H1X 2B2, Canada
    J Evol Biol 23:1519-27. 2010
    ..This is the first study that investigates AMF intra-isolate variation at the transcriptome level. In conclusion, it is possible that, in AMF, multiple nuclear genomes contribute to a single phenotype...
  38. pmc Origin, evolution, and mechanism of 5' tRNA editing in chytridiomycete fungi
    Marie Josée Laforest
    Departement de Biochimie, Universite de Montreal, 2900, Boulevard Edouard Montpetit, C P 6128, Succursale Centre Ville, Quebec H3C 3J7, Canada
    RNA 10:1191-9. 2004
    ..brooksianum raises the possibility that 5' tRNA editing may have evolved twice independently within Chytridiomycota, once in the lineage leading to S. punctatus and once in the lineage leading to the Monoblepharidales...
  39. ncbi Sequencing complete mitochondrial and plastid genomes
    Gertraud Burger
    Departement de Biochimie, Robert Cedergren Centre, Program in Evolutionary Biology, Canadian Institute for Advanced Research, Universite de Montreal, 2900 Boulevard Edouard Montpetit, CP 6128, Montreal, Quebec, H3T 1J4 Canada
    Nat Protoc 2:603-14. 2007
    ..Library construction by either protocol can be completed within 1 week...
  40. ncbi Building a genome database using an object-oriented approach
    Anna Barbasiewicz
    Universite de Montreal, Département de Biochimie 2900 Blvd Edouard Montpetit, Montreal, Quebec Canada, H3C 3J7
    In Silico Biol 2:213-7. 2002
    ..Subsequently, the UML diagrams were used as templates for writing object-oriented automation programs in the Java programming language...
  41. pmc GOBASE--a database of mitochondrial and chloroplast information
    Emmet A O'Brien
    Program in Evolutionary Biology, Canadian Institute for Advanced Research, Departement de Biochimie, Universite de Montreal, 2900 Boulevard Edouard Montpetit, Montreal, Quebec H3T 1J4, Canada
    Nucleic Acids Res 31:176-8. 2003
    ..We have also implemented a more powerful and flexible user interface using the PHP programming language. http://megasun.bch.umontreal.ca/gobase/gobase.html...
  42. ncbi Toward resolving the eukaryotic tree: the phylogenetic positions of jakobids and cercozoans
    Naiara Rodriguez-Ezpeleta
    Centre Robert Cedergren, Departement de Biochimie, Universite de Montreal, 2900 Boulevard Edouard Montpetit, Montreal, Quebec H3T 1J4, Canada
    Curr Biol 17:1420-5. 2007
    ..We discuss the implications of these results for the concept of "excavates" and for the elucidation of eukaryotic phylogeny in general...
  43. pmc GOBASE: an organelle genome database
    Emmet A O'Brien
    Robert Cedergren Center for Bioinformatics and Genomics, Departement de Biochimie, Pavillon Roger Gaudry, Universite de Montreal, 2900 Edouard Montpetit, Montreal QC, Canada H3T 1J4
    Nucleic Acids Res 37:D946-50. 2009
    ..The GOBASE database can be found at http://gobase.bcm.umontreal.ca/. Queries about custom and large-scale data retrievals should be addressed to gobase@bch.umontreal.ca...
  44. ncbi The protein kinase ERK3 is encoded by a single functional gene: genomic analysis of the ERK3 gene family
    Benjamin Turgeon
    Institut de Recherches Cliniques de Montreal, Department of Pharmacology, Universite de Montreal, Montreal, Quebec, H2W 1R7, Canada
    Genomics 80:673-80. 2002
    ..Our analysis demonstrates that the ERK3 subfamily of MAP kinase genes is composed of two functional genes, MAPK6 and MAPK4, and several pseudogenes...
  45. pmc Diversity and dispersal of a ubiquitous protein family: acyl-CoA dehydrogenases
    Yao Qing Shen
    Robert Cedergren Center for Bioinformatics and Genomics, Biochemistry Department, Universite de Montreal, 2900 Edouard Montpetit, Montreal, QC, H3T 1J4, Canada
    Nucleic Acids Res 37:5619-31. 2009
    ..Through these unorthodox expansion strategies, the ACAD family is proficient in utilizing a large range of fatty acids and amino acids-strategies that could have shaped the evolutionary history of many other ancient protein families...
  46. ncbi Phylogenomic evidence for separate acquisition of plastids in cryptophytes, haptophytes, and stramenopiles
    Denis Baurain
    Departement de Biochimie, Centre Robert Cedergren, Universite de Montreal, Montreal, Quebec, Canada
    Mol Biol Evol 27:1698-709. 2010
    ..Therefore, we reject the chromalveolate hypothesis as falsified in favor of more complex evolutionary scenarios involving multiple higher order eukaryote-eukaryote endosymbioses...
  47. pmc Unique mitochondrial genome architecture in unicellular relatives of animals
    Gertraud Burger
    Program in Evolutionary Biology, Canadian Institute for Advanced Research, Departement de Biochimie, Universite de Montreal, Succursale Centre Ville, Montreal, QC, Canada H3C 3J7
    Proc Natl Acad Sci U S A 100:892-7. 2003
    ....
  48. ncbi Parallels in genome evolution in mitochondria and bacterial symbionts
    Gertraud Burger
    Canarian Institute for Advanced Research, Program in Evolutionary Biology, Department of Biochemistry, Universite de Montreal, Montreal, Quebec, Canada
    IUBMB Life 55:205-12. 2003
    ..New insights into early mitochondrial genome evolution come from the investigation of primitive mitochondriate eukaryotes, as well as the comparison between mitochondria and intracellular bacterial symbionts...
  49. ncbi Mitochondrial genomes: anything goes
    Gertraud Burger
    Canadian Institute for Advanced Research, Programme in Evolutionary Biology, Department de Biochimie, Universite de Montreal, 2900 Boulevard Edouard Montpetit, Montreal, Quebec, Canada H3T 1J4
    Trends Genet 19:709-16. 2003
  50. pmc GOBASE--a database of organelle and bacterial genome information
    Emmet A O'Brien
    Center Robert Cedergren for Bioinformatics and Genomics, Departement de Biochimie, Pavillon Roger Gaudry, Universite de Montreal, 2900 Edouard Montpetit, Montreal, QC, Canada H3T 1J4
    Nucleic Acids Res 34:D697-9. 2006
    ..The GOBASE database can be queried at http://gobase.bcm.umontreal.ca/ and inquiries should be directed to gobase@bch.umontreal.ca...
  51. pmc The Rhodomonas salina mitochondrial genome: bacteria-like operons, compact gene arrangement and complex repeat region
    Amy M Hauth
    Departement de Biochimie, Robert Cedergren Research Center for Bioinformatics and Genomics, Canadian Institute for Advanced Research, Université de Montréal 2900 Boulevard Edouard Montpetit, Montreal, Quebec, Canada H3T 1J4
    Nucleic Acids Res 33:4433-42. 2005
    ....
  52. pmc Mitochondrial RNase P RNAs in ascomycete fungi: lineage-specific variations in RNA secondary structure
    Elias R Seif
    Program in Evolutionary Biology, Canadian Institute for Advanced Research, Departement de Biochimie, Universite de Montreal, Montreal, Quebec H3T 1J4, Canada
    RNA 9:1073-83. 2003
    ..The evolutionary implications of the reduction of mtP-RNA structures in ascomycetes will be discussed...
  53. pmc Distribution and phylogeny of EFL and EF-1alpha in Euglenozoa suggest ancestral co-occurrence followed by differential loss
    Gillian H Gile
    Department of Botany, Canadian Institute for Advanced Research, University of British Columbia, Vancouver, British Columbia, Canada
    PLoS ONE 4:e5162. 2009
    ..However, differential loss may play a role in EFL evolution, and this possibility has been less widely discussed...
  54. ncbi Accounting for gene rate heterogeneity in phylogenetic inference
    Rachel B Bevan
    McGill Centre for Bioinformatics, McGill University, Duff Medical Building, 3775 University Street, Montreal, Quebec, H3A 2B4, Canada
    Syst Biol 56:194-205. 2007
    ..Furthermore, improved model fit over the concatenated model is highly correlated with the presence of a gene with a slow relative rate of evolution...
  55. doi Phylogenomic analyses support the monophyly of Taphrinomycotina, including Schizosaccharomyces fission yeasts
    Yu Liu
    Robert Cedergren Centre, Departement de Biochimie, Universite de Montreal, Montreal, Quebec, Canada
    Mol Biol Evol 26:27-34. 2009
    ....
  56. ncbi Detecting and overcoming systematic errors in genome-scale phylogenies
    Naiara Rodriguez-Ezpeleta
    Canadian Institute for Advanced Research, Centre Robert Cedergren, Departement de Biochimie, Universite de Montreal, 2900 Boulevard Edouard Montpetit, Montreal, Quebec, H3T 1J4, Canada
    Syst Biol 56:389-99. 2007
    ..Finally, our results allow us to formulate guidelines for detecting and overcoming phylogenetic artefacts in genome-scale phylogenetic analyses...
  57. pmc Hybrid E. coli--Mitochondrial ribonuclease P RNAs are catalytically active
    Elias Seif
    Canadian Institute for Advanced Research, Robert Cedergren Centre for Bioinformatics and Genomics, Departement de Biochimie, Universite de Montreal, Montreal, Quebec, H3T 1J4, Canada
    RNA 12:1661-70. 2006
    ..Finally, we will discuss reasons for the failure of mtP-RNAs to show catalytic activity in the absence of P-proteins based on our mutagenesis analysis...
  58. pmc Mitochondrial 3' tRNA editing in the jakobid Seculamonas ecuadoriensis: a novel mechanism and implications for tRNA processing
    Jessica Leigh
    Departement de Biochimie, Universite de Montreal, Montreal Quebec, H3T 1J4, Canada
    RNA 10:615-21. 2004
    ..This 3' tRNA editing mechanism is likely distinct from that of L. forficatus, despite the apparent similarities between the two systems...
  59. ncbi Calculating the evolutionary rates of different genes: a fast, accurate estimator with applications to maximum likelihood phylogenetic analysis
    Rachel B Bevan
    McGill Centre for Bioinformatics, Duff Medical Building, 3775 University Street, Montreal, Quebec, H3A 2B4, Canada
    Syst Biol 54:900-15. 2005
    ..e., without protein rates) were corrected. [Bayesian credible intervals; DistR method; multigene phylogeny; PHYML; rate heterogeneity.]...
  60. ncbi Transfer RNA gene recruitment in mitochondrial DNA
    Dennis V Lavrov
    Program in Evolutionary Biology, Canadian Institute for Advanced Research, Centre Robert Cedergren, Departement de Biochimie, Universite de Montreal, 2900 Boulevard Edouard Montpetit, Montreal, Quebec, Canada, H3T 1J4
    Trends Genet 21:129-33. 2005
    ....
  61. pmc Whirly proteins maintain plastid genome stability in Arabidopsis
    Alexandre Maréchal
    Department of Biochemistry, Universite de Montreal, Station Centre Ville, Montreal, QC, Canada
    Proc Natl Acad Sci U S A 106:14693-8. 2009
    ..We propose a model where Whirlies contribute to plastid genome stability by protecting against illegitimate repeat-mediated recombination...
  62. pmc Loss of the mRNA-like region in mitochondrial tmRNAs of jakobids
    Yannick Jacob
    Departement de Biochimie, Universite de Montreal, Montreal, Quebec, Canada H3T 1J4
    RNA 10:605-14. 2004
    ..Our results strongly support the functionality of these reduced mitochondrial tmRNAs...
  63. pmc The enigmatic mitochondrial ORF ymf39 codes for ATP synthase chain b
    Gertraud Burger
    Canadian Institute for Advanced Research, Departement de Biochimie, Universite de Montreal, 2900 Boulevard Edouard Montpetit, Montreal, Quebec H3T 1J4, Canada
    Nucleic Acids Res 31:2353-60. 2003
    ..This analysis provides clear evidence that ymf39 is an atpF homolog, while ATP4/ATP5F appears to be a highly diverged form of ymf39 that has migrated to the nucleus. We propose to designate ymf39 from now on atp4...
  64. ncbi MetR and CRP bind to the Vibrio harveyi lux promoters and regulate luminescence
    Jaidip Chatterjee
    Department of Biochemistry, Room 813, McIntyre Medical Sciences Building, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec, H3G 1Y6, Canada
    Mol Microbiol 46:101-11. 2002
    ....
  65. ncbi Phylogenetic relationships of non-mitochondrial nucleotide transport proteins in bacteria and eukaryotes
    Nicole Linka
    Universitat Kaiserslautern, Pflanzenphysiologie, Postfach 3049, D 67653 Kaiserslautern, Germany
    Gene 306:27-35. 2003
    ..The tree topology indicates that some bacterial NTT paralogs have arisen by gene duplications and others by horizontal transfer...
  66. ncbi Fungal evolution: the case of the vanishing mitochondrion
    Charles E Bullerwell
    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 1X5, Canada
    Curr Opin Microbiol 8:362-9. 2005
    ..These organisms have organelles derived from mitochondria that retain traces of their mitochondrial ancestry...
  67. pmc Transcription and RNA-processing in fission yeast mitochondria
    Bernd Schafer
    Department of Biology IV Microbiology, RWTH Aachen University, Worringer Weg, 52056 Aachen, Germany
    RNA 11:785-95. 2005
    ..Similar 3'-RNA-processing motifs are present in species of the genus Schizosaccharomyces, but not in budding yeasts that have functionally analogous A+T-rich dodecamer processing signals...
  68. ncbi Structure of the bc1 complex from Seculamonas ecuadoriensis, a jakobid flagellate with an ancestral mitochondrial genome
    Stefanie Marx
    Institut für Angewandte Genetik, Universitat Hannover, Hannover, Germany
    Mol Biol Evol 20:145-53. 2003
    ..We posit that the recruitment of additional subunits in mitochondrial respiratory complexes is a consequence of the migration of originally alpha-proteobacterial genes to the nucleus...
  69. doi A phylogenomic investigation into the origin of metazoa
    Inaki Ruiz-Trillo
    Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
    Mol Biol Evol 25:664-72. 2008
    ..Understanding the function of "metazoan-specific" proteins we have identified in these protists will clarify the evolutionary steps that led to the emergence of the Metazoa...
  70. ncbi Glass sponges and bilaterian animals share derived mitochondrial genomic features: a common ancestry or parallel evolution?
    Karri M Haen
    Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa, USA
    Mol Biol Evol 24:1518-27. 2007
    ..Thus, it remains an open question whether shared mitochondrial genomic features in glass sponges and bilaterian animals reflect their close phylogenetic affinity or provide a remarkable example of parallel evolution...
  71. ncbi Translocation of an 89-kDa periplasmic protein is associated with Holospora infection
    Koichi Iwatani
    Biological Institute, Faculty of Science, Yamaguchi University, Yoshida 1677 1, Yamaguchi 753 8512, Japan
    Biochem Biophys Res Commun 337:1198-205. 2005
    ..Our findings suggest that the 89-kDa protein plays a role in Holospora's escape from the host digestive vacuole, the migration through the host cytoplasm, and the invasion into the macronucleus...