Guillaume Bourque

Summary

Country: Singapore

Publications

  1. doi request reprint Computational tools for the analysis of rearrangements in mammalian genomes
    Glenn Tesler
    Department of Mathematics, University of California San Diego, La Jolla, CA
    Methods Mol Biol 422:145-70. 2008
  2. pmc In silico tandem affinity purification refines an Oct4 interaction list
    Clara Yujing Cheong
    Stem Cell and Developmental Biology Group, Genome Institute of Singapore, 60 Biopolis Street, 138672, Singapore
    Stem Cell Res Ther 2:26. 2011
  3. pmc Multiplatform genome-wide identification and modeling of functional human estrogen receptor binding sites
    Vinsensius B Vega
    Estrogen Receptor Biology Program, Genome Institute of Singapore, 60 Biopolis Street, Republic of Singapore 138672
    Genome Biol 7:R82. 2006
  4. pmc The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction
    Guillaume Bourque
    Information and Mathematical Sciences, Genome Institute of Singapore, 138672 Singapore
    Genome Res 16:311-3. 2006
  5. ncbi request reprint Transposable elements in gene regulation and in the evolution of vertebrate genomes
    Guillaume Bourque
    Genome Institute of Singapore, Singapore 138672, Singapore
    Curr Opin Genet Dev 19:607-12. 2009
  6. pmc Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages
    Guillaume Bourque
    Genome Institute of Singapore, Singapore 138672, Republic of Singapore
    Genome Res 15:98-110. 2005
  7. pmc Evolution of the mammalian transcription factor binding repertoire via transposable elements
    Guillaume Bourque
    Computational and Mathematical Biology, Genome Institute of Singapore, Singapore 138672, Singapore
    Genome Res 18:1752-62. 2008
  8. ncbi request reprint Improving gene network inference by comparing expression time-series across species, developmental stages or tissues
    Guillaume Bourque
    Centre de Recherches Mathématiques, Universite de Montreal, Montreal, Quebec, H3C 3J7, Canada
    J Bioinform Comput Biol 2:765-83. 2004
  9. pmc An oestrogen-receptor-alpha-bound human chromatin interactome
    Melissa J Fullwood
    Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672
    Nature 462:58-64. 2009
  10. doi request reprint webMGR: an online tool for the multiple genome rearrangement problem
    Chi Ho Lin
    Genome Institute of Singapore, 60 Biopolis Street, 02 01, Genome, Singapore 138672
    Bioinformatics 26:408-10. 2010

Detail Information

Publications41

  1. doi request reprint Computational tools for the analysis of rearrangements in mammalian genomes
    Glenn Tesler
    Department of Mathematics, University of California San Diego, La Jolla, CA
    Methods Mol Biol 422:145-70. 2008
    ..We describe three computational tools (GRIMM-Synteny, GRIMM, and MGR) that can be used separately or in succession to contrast different organisms at the genome-level to exploit large-scale rearrangements as a phylogenetic character...
  2. pmc In silico tandem affinity purification refines an Oct4 interaction list
    Clara Yujing Cheong
    Stem Cell and Developmental Biology Group, Genome Institute of Singapore, 60 Biopolis Street, 138672, Singapore
    Stem Cell Res Ther 2:26. 2011
    ..Unearthing the interactions of Oct4 would provide insight into how this transcription factor is central to cell fate and stem cell pluripotency...
  3. pmc Multiplatform genome-wide identification and modeling of functional human estrogen receptor binding sites
    Vinsensius B Vega
    Estrogen Receptor Biology Program, Genome Institute of Singapore, 60 Biopolis Street, Republic of Singapore 138672
    Genome Biol 7:R82. 2006
    ..We posited that the inadequacy is due to limited input of empirically verified sites, and demonstrated a multiplatform approach to constructing a robust model...
  4. pmc The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction
    Guillaume Bourque
    Information and Mathematical Sciences, Genome Institute of Singapore, 138672 Singapore
    Genome Res 16:311-3. 2006
  5. ncbi request reprint Transposable elements in gene regulation and in the evolution of vertebrate genomes
    Guillaume Bourque
    Genome Institute of Singapore, Singapore 138672, Singapore
    Curr Opin Genet Dev 19:607-12. 2009
    ..I will also summarize results that show how transposable elements have been a major catalyst of structural rearrangements throughout evolution...
  6. pmc Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages
    Guillaume Bourque
    Genome Institute of Singapore, Singapore 138672, Republic of Singapore
    Genome Res 15:98-110. 2005
    ....
  7. pmc Evolution of the mammalian transcription factor binding repertoire via transposable elements
    Guillaume Bourque
    Computational and Mathematical Biology, Genome Institute of Singapore, Singapore 138672, Singapore
    Genome Res 18:1752-62. 2008
    ..Our results demonstrate that transcriptional regulatory networks are highly dynamic in eukaryotic genomes and that transposable elements play an important role in expanding the repertoire of binding sites...
  8. ncbi request reprint Improving gene network inference by comparing expression time-series across species, developmental stages or tissues
    Guillaume Bourque
    Centre de Recherches Mathématiques, Universite de Montreal, Montreal, Quebec, H3C 3J7, Canada
    J Bioinform Comput Biol 2:765-83. 2004
    ..We show how this comparative framework can facilitate the recovery of the networks and improve the quality of the solutions inferred...
  9. pmc An oestrogen-receptor-alpha-bound human chromatin interactome
    Melissa J Fullwood
    Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672
    Nature 462:58-64. 2009
    ..We propose that chromatin interactions constitute a primary mechanism for regulating transcription in mammalian genomes...
  10. doi request reprint webMGR: an online tool for the multiple genome rearrangement problem
    Chi Ho Lin
    Genome Institute of Singapore, 60 Biopolis Street, 02 01, Genome, Singapore 138672
    Bioinformatics 26:408-10. 2010
    ..Moreover, we have developed a web server (webMGR) that includes elaborate web output to facilitate navigation through the results...
  11. pmc Long span DNA paired-end-tag (DNA-PET) sequencing strategy for the interrogation of genomic structural mutations and fusion-point-guided reconstruction of amplicons
    Fei Yao
    Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
    PLoS ONE 7:e46152. 2012
    ..This provides a key advantage in studying rearrangements in cancer, and we show how it can be used in a fusion-point-guided-concatenation algorithm to study focally amplified regions in cancer...
  12. doi request reprint Transposable elements have rewired the core regulatory network of human embryonic stem cells
    Galih Kunarso
    Computational and Mathematical Biology, Genome Institute of Singapore, Singapore, Singapore
    Nat Genet 42:631-4. 2010
    ..These data indicate that species-specific transposable elements have substantially altered the transcriptional circuitry of pluripotent stem cells...
  13. pmc Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes
    Axel M Hillmer
    Genome Technology and Biology, Genome Institute of Singapore, Singapore 138672, Singapore
    Genome Res 21:665-75. 2011
    ....
  14. doi request reprint Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells
    Xiao Dong Zhao
    Genome Technology and Biology Group, Genome Institute of Singapore, 138672, Singapore
    Cell Stem Cell 1:286-98. 2007
    ..These global histone methylation maps provide an epigenetic framework that enables the discovery of novel transcriptional networks and delineation of different genetic compartments of the pluripotent cell genome...
  15. pmc Recovering genome rearrangements in the mammalian phylogeny
    Hao Zhao
    Computational and Mathematical Biology, Genome Institute of Singapore, Singapore
    Genome Res 19:934-42. 2009
    ..Together, this substantiates the model that regions of high sequence identity have been associated with rearrangement events throughout the mammalian phylogeny...
  16. pmc Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes
    Guillaume Bourque
    Centre de Recherches Mathématiques, Universite de Montreal, Canada H3C 3J7
    Genome Res 14:507-16. 2004
    ..Our analysis implies that the rate of rearrangements is much higher in murid rodents than in the human lineage and confirms the existence of rearrangement hot-spots in all three lineages...
  17. doi request reprint Inferring direct regulatory targets of a transcription factor in the DREAM2 challenge
    Vinsensius B Vega
    Genome Institute of Singapore, Singapore
    Ann N Y Acad Sci 1158:215-23. 2009
    ....
  18. ncbi request reprint The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity
    Xinyi Lu
    Gene Regulation Laboratory, Genome Institute of Singapore, Singapore
    Nat Struct Mol Biol 21:423-5. 2014
    ..Furthermore, HERVH is associated with OCT4, coactivators and Mediator subunits. Together, these results uncover a new role of species-specific transposable elements in hESCs. ..
  19. pmc Molecular conservation of estrogen-response associated with cell cycle regulation, hormonal carcinogenesis and cancer in zebrafish and human cancer cell lines
    Siew Hong Lam
    Genome Institute of Singapore, 02 01Genome, 60 Biopolis Street, 138672 Singapore
    BMC Med Genomics 4:41. 2011
    ..In order to determine the potential of zebrafish model for estrogen-related cancer research, we investigated the molecular conservation of estrogen responses operating in both zebrafish and human cancer cell lines...
  20. doi request reprint Regulation of estrogen receptor-mediated long range transcription via evolutionarily conserved distal response elements
    You Fu Pan
    Cancer Biology and Pharmacology, Genome Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis St, 02 01 Genome, Singapore 138672
    J Biol Chem 283:32977-88. 2008
    ....
  21. ncbi request reprint Integration of external signaling pathways with the core transcriptional network in embryonic stem cells
    Xi Chen
    Gene Regulation Laboratory, Genome Institute of Singapore, Singapore 138672
    Cell 133:1106-17. 2008
    ..Collectively, the comprehensive mapping of TF-binding sites identifies important features of the transcriptional regulatory networks that define ES-cell identity...
  22. pmc Conserved and non-conserved enhancers direct tissue specific transcription in ancient germ layer specific developmental control genes
    Sumantra Chatterjee
    Stem Cell and Developmental Biology, Genome Institute of Singapore, 60 Biopolis Street, 138672, Singapore
    BMC Dev Biol 11:63. 2011
    ..The pressing need is to integrate the tools of comparative genomics with knowledge of developmental biology to validate enhancers for developmental transcription factors in greater detail..
  23. pmc Transcriptional consequences of genomic structural aberrations in breast cancer
    Koichiro Inaki
    Cancer Biology and Pharmacology, Genome Institute of Singapore, Genome, Singapore 138672, Singapore
    Genome Res 21:676-87. 2011
    ..This gene fusion is caused by tandem duplication on 17q23 and appears to be an indicator of local genomic instability altering the expression of oncogenic components such as MIR21 and RPS6KB1...
  24. ncbi request reprint The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells
    Yuin Han Loh
    Gene Regulation Laboratory, Genome Institute of Singapore, Singapore 138672
    Nat Genet 38:431-40. 2006
    ..The emerging picture is one in which Oct4 and Nanog control a cascade of pathways that are intricately connected to govern pluripotency, self-renewal, genome surveillance and cell fate determination...
  25. pmc PPARG binding landscapes in macrophages suggest a genome-wide contribution of PU.1 to divergent PPARG binding in human and mouse
    Sebastian Pott
    Cancer Biology and Pharmacology 2, Genome Institute of Singapore, Singapore, Singapore
    PLoS ONE 7:e48102. 2012
    ....
  26. pmc Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs)
    Yijun Ruan
    Genome Technology and Biology Group, Genome Institute of Singapore, Singapore 138672, Singapore
    Genome Res 17:828-38. 2007
    ..The PET mapping strategy presented here promises to be a useful tool in annotating the human genome, especially aberrations in human cancer genomes...
  27. pmc CTCF-mediated functional chromatin interactome in pluripotent cells
    Lusy Handoko
    Genome Institute of Singapore, Singapore
    Nat Genet 43:630-8. 2011
    ..This highly complex nuclear organization offers insights toward the unifying principles that govern genome plasticity and function...
  28. ncbi request reprint Computational tools for the analysis of rearrangements in mammalian genomes
    Guillaume Bourque
    Genome Institute of Singapore, Singapore, Republic of Singapore
    Methods Mol Biol 452:431-55. 2008
    ....
  29. pmc Whole-genome cartography of estrogen receptor alpha binding sites
    Chin Yo Lin
    Genome Institute of Singapore, Singapore, Republic of Singapore
    PLoS Genet 3:e87. 2007
    ..Taken together, this genome-scale analysis suggests complex but definable rules governing ERalpha binding and gene regulation...
  30. pmc The majority of primate-specific regulatory sequences are derived from transposable elements
    Pierre Etienne Jacques
    Computational and Systems Biology, Genome Institute of Singapore, Singapore, Singapore
    PLoS Genet 9:e1003504. 2013
    ..Taken together, these results demonstrate that TEs, and in particular ERVs, have contributed hundreds of thousands of novel regulatory elements to the primate lineage and reshaped the human transcriptional landscape...
  31. doi request reprint Molecular and genetic crosstalks between mTOR and ERRα are key determinants of rapamycin-induced nonalcoholic fatty liver
    Cédric Chaveroux
    Rosalind and Morris Goodman Cancer Research Centre, McGill University, 1160 Pine Avenue West, Montreal, QC H3A 1A3, Canada
    Cell Metab 17:586-98. 2013
    ..Our work expands the role of mTOR action in metabolism and highlights the existence of a potent mTOR/ERRα regulatory axis with significant clinical impact...
  32. ncbi request reprint A comparative synteny map of Burkholderia species links large-scale genome rearrangements to fine-scale nucleotide variation in prokaryotes
    Chi Ho Lin
    Genome Institute of Singapore, Singapore
    Mol Biol Evol 25:549-58. 2008
    ..Our results suggest that in prokaryotes, genome rearrangements may influence functional diversity through the enhanced divergence of boundary genes and the creation of foci for acquiring and deleting species-specific genes...
  33. pmc K27M mutation in histone H3.3 defines clinically and biologically distinct subgroups of pediatric diffuse intrinsic pontine gliomas
    Dong Anh Khuong-Quang
    Department of Human Genetics, McGill University, Montreal, QC, Canada
    Acta Neuropathol 124:439-47. 2012
    ..Based on prognostic and therapeutic implications, our findings argue for H3.3-mutation testing at diagnosis, which should be rapidly integrated into the clinical decision-making algorithm, particularly in atypical DIPG...
  34. pmc Success in the DREAM3 signaling response challenge using simple weighted-average imputation: lessons for community-wide experiments in systems biology
    Neil D Clarke
    Genome Institute of Singapore, Singapore
    PLoS ONE 5:e8417. 2010
    ....
  35. ncbi request reprint Genome sequence of the Brown Norway rat yields insights into mammalian evolution
    Richard A Gibbs
    Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA lt http www hgsc bcm tmc edu
    Nature 428:493-521. 2004
    ....
  36. pmc Reconstructing the genomic architecture of mammalian ancestors using multispecies comparative maps
    William J Murphy
    Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702, USA
    Hum Genomics 1:30-40. 2003
    ....
  37. pmc Genome-scale evolution: reconstructing gene orders in the ancestral species
    Guillaume Bourque
    Department of Mathematics, University of Southern California, California 90089, USA
    Genome Res 12:26-36. 2002
    ..In particular, our analysis suggests a new improved rearrangement scenario for a very difficult Campanulaceae cpDNA dataset and a putative rearrangement scenario for human, mouse and cat genomes...
  38. ncbi request reprint Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps
    William J Murphy
    Department of Veterinary Integrative Biosciences, Texas A and M University, College Station, TX 77843, USA
    Science 309:613-7. 2005
    ..We found that segmental duplications populate the majority of primate-specific breakpoints and often flank inverted chromosome segments, implicating their role in chromosomal rearrangement...
  39. pmc Initial sequence and comparative analysis of the cat genome
    Joan U Pontius
    Laboratory of Genomic Diversity, SAIC Frederick, Inc, NCI Frederick, Frederick, Maryland 21702, USA
    Genome Res 17:1675-89. 2007
    ..9-fold) coverage mammal genome sequence...
  40. pmc Genomewide expression profiling in the zebrafish embryo identifies target genes regulated by Hedgehog signaling during vertebrate development
    Jun Xu
    Institute of Molecular and Cell Biology, Singapore
    Genetics 174:735-52. 2006
    ..Our data also demonstrate for the first time the functionality of the Gli-binding motif in the control of Hedgehog signaling-induced gene expression in the zebrafish embryo...