Josee Dostie

Summary

Affiliation: McGill University
Country: Canada

Publications

  1. pmc Shaping the Genome with Non-Coding RNAs
    Xue Q D Wang
    Department of Biochemistry, and Goodman Cancer Research Center, McGill University, 3655 Promenade Sir William Osler, Room 815A, Montreal, Quebec, H3G1Y6, Canada
    Curr Genomics 12:307-21. 2011
  2. pmc Clustering of tissue-specific sub-TADs accompanies the regulation of HoxA genes in developing limbs
    Soizik Berlivet
    Unité de génétique et développement, Institut de Recherches Cliniques de Montreal, Montreal, Quebec, Canada Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal, Quebec, Canada
    PLoS Genet 9:e1004018. 2013
  3. doi request reprint Computing chromosome conformation
    James Fraser
    Department of Biochemistry, Goodman Cancer Research Center, McGill University, Montreal, QC, Canada
    Methods Mol Biol 674:251-68. 2010
  4. pmc Hox in motion: tracking HoxA cluster conformation during differentiation
    Mathieu Rousseau
    Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal, Quebec, H3G 1Y6, Canada and School of Computer Science and McGill Centre for Bioinformatics, McGill University, Montreal, Quebec, H3A 0E9, Canada
    Nucleic Acids Res 42:1524-40. 2014
  5. doi request reprint A Torrent of data: mapping chromatin organization using 5C and high-throughput sequencing
    James Fraser
    Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal, Quebec, Canada
    Methods Enzymol 513:113-41. 2012
  6. pmc From cells to chromatin: capturing snapshots of genome organization with 5C technology
    Maria A Ferraiuolo
    Department of Biochemistry and Goodman Cancer Research Center, McGill University, 3655 Promenade Sir William Osler, Room 815A, Montreal, Quebec, Canada H3G1Y6
    Methods 58:255-67. 2012
  7. pmc Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling
    Mathieu Rousseau
    McGill Centre for Bioinformatics, Bellini Building, Life Sciences Complex, 3649 Promenade Sir William Osler, Montreal, Quebec, H3G 0B1, Canada
    BMC Bioinformatics 12:414. 2011
  8. pmc The three-dimensional architecture of Hox cluster silencing
    Maria A Ferraiuolo
    Department of Biochemistry, and Goodman Cancer Research Center, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec, Canada
    Nucleic Acids Res 38:7472-84. 2010
  9. doi request reprint Chromatin conformation signatures: ideal human disease biomarkers?
    Jennifer L Crutchley
    Department of Biochemistry, McGill University, Montreal, Quebec, Canada
    Biomark Med 4:611-29. 2010
  10. pmc Chromatin conformation signatures of cellular differentiation
    James Fraser
    Department of Biochemistry and McGill Cancer Center, McGill University, 3655 Promenade Sir William Osler, Montreal, H3G1Y6, Canada
    Genome Biol 10:R37. 2009

Collaborators

Detail Information

Publications17

  1. pmc Shaping the Genome with Non-Coding RNAs
    Xue Q D Wang
    Department of Biochemistry, and Goodman Cancer Research Center, McGill University, 3655 Promenade Sir William Osler, Room 815A, Montreal, Quebec, H3G1Y6, Canada
    Curr Genomics 12:307-21. 2011
    ..We also discuss potential mechanisms by which ncRNAs might exert three-dimensional transcriptional control and what recent studies have revealed about their role in shaping our genome...
  2. pmc Clustering of tissue-specific sub-TADs accompanies the regulation of HoxA genes in developing limbs
    Soizik Berlivet
    Unité de génétique et développement, Institut de Recherches Cliniques de Montreal, Montreal, Quebec, Canada Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal, Quebec, Canada
    PLoS Genet 9:e1004018. 2013
    ..From an evolutionary standpoint, our data points to the convergent evolution of HoxA and HoxD regulation in the fin-to-limb transition, one of the major morphological innovations in vertebrates. ..
  3. doi request reprint Computing chromosome conformation
    James Fraser
    Department of Biochemistry, Goodman Cancer Research Center, McGill University, Montreal, QC, Canada
    Methods Mol Biol 674:251-68. 2010
    ..This chapter explains how 5C studies are performed and describes stepwise how to use currently available bioinformatics tools for experimental design, data analysis, and interpretation...
  4. pmc Hox in motion: tracking HoxA cluster conformation during differentiation
    Mathieu Rousseau
    Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal, Quebec, H3G 1Y6, Canada and School of Computer Science and McGill Centre for Bioinformatics, McGill University, Montreal, Quebec, H3A 0E9, Canada
    Nucleic Acids Res 42:1524-40. 2014
    ....
  5. doi request reprint A Torrent of data: mapping chromatin organization using 5C and high-throughput sequencing
    James Fraser
    Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montreal, Quebec, Canada
    Methods Enzymol 513:113-41. 2012
    ....
  6. pmc From cells to chromatin: capturing snapshots of genome organization with 5C technology
    Maria A Ferraiuolo
    Department of Biochemistry and Goodman Cancer Research Center, McGill University, 3655 Promenade Sir William Osler, Room 815A, Montreal, Quebec, Canada H3G1Y6
    Methods 58:255-67. 2012
    ..We believe that this detailed protocol will help guide researchers in probing spatial genome organization and its role in various biological processes...
  7. pmc Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling
    Mathieu Rousseau
    McGill Centre for Bioinformatics, Bellini Building, Life Sciences Complex, 3649 Promenade Sir William Osler, Montreal, Quebec, H3G 0B1, Canada
    BMC Bioinformatics 12:414. 2011
    ..Our goal is to use the IF data generated by these experiments to computationally model and analyze three-dimensional chromatin organization...
  8. pmc The three-dimensional architecture of Hox cluster silencing
    Maria A Ferraiuolo
    Department of Biochemistry, and Goodman Cancer Research Center, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec, Canada
    Nucleic Acids Res 38:7472-84. 2010
    ..Our data suggest that Hox cluster looping may represent an evolutionarily conserved structural mechanism of transcription regulation...
  9. doi request reprint Chromatin conformation signatures: ideal human disease biomarkers?
    Jennifer L Crutchley
    Department of Biochemistry, McGill University, Montreal, Quebec, Canada
    Biomark Med 4:611-29. 2010
    ..We also summarize how chromatin conformation signatures can be identified and discuss why they might represent ideal biomarkers of human disease in such genetically diverse populations...
  10. pmc Chromatin conformation signatures of cellular differentiation
    James Fraser
    Department of Biochemistry and McGill Cancer Center, McGill University, 3655 Promenade Sir William Osler, Montreal, H3G1Y6, Canada
    Genome Biol 10:R37. 2009
    ..Genome-wide chromatin conformation signature identification might uniquely identify disease-associated states and represent an entirely novel class of human disease biomarkers...
  11. pmc PAM multiplicity marks genomic target sites as inhibitory to CRISPR-Cas9 editing
    Abba Malina
    Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
    Nat Commun 6:10124. 2015
    ..Thus we refine which substrates should be avoided in gRNA design, implicating PAM density as a novel sequence-specific feature that inhibits in vivo Cas9-driven DNA modification. ..
  12. pmc Protospacer adjacent motif (PAM)-distal sequences engage CRISPR Cas9 DNA target cleavage
    Regina Cencic
    Department of Biochemistry, McGill University, Montreal, Quebec, Canada
    PLoS ONE 9:e109213. 2014
    ....
  13. doi request reprint Discovering genome regulation with 3C and 3C-related technologies
    Sylvain D Ethier
    Department of Biochemistry, McGill University, Quebec, Canada
    Biochim Biophys Acta 1819:401-10. 2012
    ..In this review, we report on the biological questions addressed with 3C and 3C-related techniques and what has been uncovered to date. We also explore what these methods may further reveal about the regulation of genomic DNA activities...
  14. pmc Pharmacological inhibition of DNA-PK stimulates Cas9-mediated genome editing
    Francis Robert
    Department of Biochemistry, McGill University, Montreal, Quebec, H3G 1Y6, Canada
    Genome Med 7:93. 2015
    ..Homology-directed recombination (HDR) is far less efficient than NHEJ and makes screening of clones containing directed changes time-consuming and labor-intensive...
  15. pmc Repurposing CRISPR/Cas9 for in situ functional assays
    Abba Malina
    Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6 Canada
    Genes Dev 27:2602-14. 2013
    ..Taken together, these results establish Cas9 genome editing as a powerful and practical approach for positive in situ genetic screens...
  16. pmc An Overview of Genome Organization and How We Got There: from FISH to Hi-C
    James Fraser
    Department of Biochemistry, and Goodman Cancer Research Center, McGill University, Montreal, Quebec, Canada
    Microbiol Mol Biol Rev 79:347-72. 2015
    ..In this review, we present key methodologies used to study genome organization and discuss what they reveal about chromosome conformation as it relates to transcription regulation across genomic scales in mammals. ..
  17. doi request reprint p53 inhibits angiogenesis by inducing the production of Arresten
    Sarah Assadian
    Goodman Cancer Research Center, Department of Biochemistry, McGill University, Montreal, Quebec, Canada
    Cancer Res 72:1270-9. 2012
    ..Our findings, therefore, link the production of Arresten to the p53 tumor suppressor pathway and show a novel mechanism through which p53 can inhibit angiogenesis...