Guillaume Bourque

Summary

Country: Singapore

Publications

  1. ncbi 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. ncbi 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. ncbi 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. ncbi 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
  5. ncbi 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. ncbi 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. ncbi 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
  8. ncbi 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
  9. ncbi 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. ncbi 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

Detail Information

Publications37

  1. ncbi 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. ncbi 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. ncbi 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
    ..Other factors, in addition to primary nucleotide sequence, will ultimately determine binding site selection...
  4. ncbi 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...
  5. ncbi 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. ncbi 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. ncbi 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...
  8. ncbi 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
  9. ncbi 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. ncbi 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...
  11. ncbi 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...
  12. ncbi 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
    ....
  13. ncbi 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...
  14. ncbi 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...
  15. ncbi 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
    ....
  16. ncbi 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...
  17. ncbi 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...
  18. ncbi 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...
  19. ncbi 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
    ....
  20. ncbi Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes
    Guillaume Bourque
    , , 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...
  21. ncbi 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..
  22. ncbi 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...
  23. ncbi 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...
  24. ncbi 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...
  25. ncbi 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...
  26. ncbi 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
    ....
  27. ncbi 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 Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
    PLoS ONE 7:e48102. 2012
    ....
  28. ncbi 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...
  29. ncbi 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
    ....
  30. ncbi 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...
  31. ncbi 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 <http://www.hgsc.bcm.tmc.edu
    Nature 428:493-521. 2004
    ....
  32. ncbi Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
    Ladeana W Hillier
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 432:695-716. 2004
    ..The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture...
  33. ncbi 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
    ....
  34. ncbi 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...
  35. ncbi 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...
  36. ncbi 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...
  37. ncbi 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...