Guillaume Bourque Ph.D.

Recent Publications

  1. Khuong-Quang DA, Buczkowicz P, Rakopoulos P, Liu XY, Fontebasso AM, Bouffet E, Bartels U, Albrecht S, Schwartzentruber J, Letourneau L, Bourgey M, Bourque G, Montpetit A, Bourret G, Lepage P, Fleming A, Lichter P, Kool M, von Deimling A, Sturm D, Korshunov A, Faury D, Jones DT, Majewski J, Pfister SM, Jabado N, Hawkins C. 2012. K27M mutation in histone H3.3 defines clinically and biologically distinct subgroups of pediatric diffuse intrinsic pontine gliomas. Acta Neuropathol. 124:439-47.
  2. Bard-Chapeau EA, Jeyakani J, Kok CH, Muller J, Chua BQ, Gunaratne J, Batagov A, Jenjaroenpun P, Kuznetsov VA, Wei CL, D'Andrea RJ, Bourque G, Jenkins NA, Copeland NG. 2012. Ecotopic viral integration site 1 (EVI1) regulates multiple cellular processes important for cancer and is a synergistic partner for FOS protein in invasive tumors. Proc Natl Acad Sci U S A. 109(6):2168-73.
  3. Handoko L, Xu H, Li G, Ngan CY, Chew E, Schnapp M, Lee CW, Ye C, Ping JL, Mulawadi F, Wong E, Sheng J, Zhang Y, Poh T, Chan CS, Kunarso G, Shahab A, Bourque G, Cacheux-Rataboul V, Sung WK, Ruan Y, Wei CL. 2011. CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet. 43(7):630-8.
  4. Hillmer AM, Yao F, Inaki K, Lee WH, Ariyaratne PN, Teo AS, Woo XY, Zhang Z, Zhao H, Ukil L, Chen JP, Zhu F, So JB, Salto-Tellez M, Poh WT, Zawack KF, Nagarajan N, Gao S, Li G, Kumar V, Lim HP, Sia YY, Chan CS, Leong ST, Neo SC, Choi PS, Thoreau H, Tan PB, Shahab A, Ruan X, Bergh J, Hall P, Cacheux-Rataboul V, Wei CL, Yeoh KG, Sung WK, Bourque G, Liu ET, Ruan Y. 2011. Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes. Genome Res. 21:665-675.
  5. Inaki K, Hillmer AM, Ukil L, Yao F, Woo XY, Vardy LA, Zawack KF, Lee CW, Ariyaratne PN, Chan YS, Desai KV, Bergh J, Hall P, Putti TC, Ong WL, Shahab A, Cacheux-Rataboul V, Karuturi RK, Sung WK, Ruan X, Bourque G, Ruan Y, Liu ET. 2011. Transcriptional consequences of genomic structural aberrations in breast cancer. Genome Res. 21:676-687.
  6. Aanes H, Winata CL, Lin CH, Chen JP, Srinivasan KG, Lee SG, Lim AY, Hajan HS, Collas P, Bourque G, Gong Z, Korzh V, Alestrm P, Mathavan S. 2011. Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition. Genome Res. 2011 21(8):1328-38.
  7. Lam SH, Lee SG, Lin CY, Thomsen JS, Fu PY, Murthy KR, Li H, Govindarajan KR, Nick LC, Bourque G, Gong Z, Lufkin T, Liu ET, Mathavan S. 2011. Molecular conservation of estrogen-response associ- ated with cell cycle regulation, hormonal carcinogenesis and cancer in zebrafish and human cancer cell lines. BMC Med Genomics 16;4:41.
  8. Cheong CY, Lon Ng PM, Ponnampalam R, Tsai HH, Bourque G, Lufkin T. 2011. In silico tandem affinity purification refines an Oct4 interaction list. Stem Cell Res Ther. 13;2(3):26.
  9. Kunarso G, Chia NY, Jeyakani J, Hwang C, Lu X, Chan YS, Ng HH, Bourque G*. 2010. Transposable Elements have Rewired the Core Regulatory Network of Human Embryonic Stem Cells. Nat. Genet. 42(7):631-634.
  10. Zheng Z, Schmidt B, Bourque G. 2010. Prediction of low coverage prone regions for Illumina se- quencing projects using a support vector machine. In Proceedings of IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010: 13-16.
  11. Lin CH, Zhao H, Lowcay SH, Shahab A, Bourque G*. 2010. webMGR: an online tool for multiple genome rearrangement. Bioinformatics. 26(3):408-10.
  12. Clarke ND, Bourque G. 2010. Success in the DREAM3 Signaling Response Challenge Using Simple Weighted-Average Imputation: Lessons for Community-Wide Experiments in Systems Biology. PLoS ONE. 5(1): e8417.
  13. Bourque G*. 2009. Transposable Elements in Gene Regulation and in the Evolution of Vertebrate Genomes. Currrent Opinions in Genetics & Development. 19:607-612.
  14. Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, Orlov YL, Velkov S, Ho A, Mei PH, Chew EG, Huang PY, Welboren WJ, Han Y, Ooi HS, Ariyaratne PN, Vega VB, Luo Y, Tan PY, Choy PY, Wansa KD, Zhao B, Lim KS, Leow SC, Yow JS, Joseph R, Li H, Desai KV, Thomsen JS, Lee YK, Karuturi RK, Herve T, Bourque G, Stunnenberg HG, Ruan X, Cacheux-Rataboul V, Sung WK, Liu ET, Wei CL, Cheung E, Ruan Y. 2009. An oestrogen-receptor-α-bound human chromatin interactome. Nature. 462(7269):58-64.
  15. Zhao H, Bourque G*. 2009. Recovering genome rearrangements in the mammalian phylogeny. Genome Res. 19(5):934-42.
  16. Vega VB, Woo XY, Hamidi H, Yeo HC, Yeo ZX, Bourque G, Clarke ND. 2009. Inferring direct regulatory targets of a transcription factor in the DREAM2 challenge. Ann N Y Acad Sci. 1158:215- 23.
  17. Bourque G*, Leong B, Vega VB, Chen X, Lee YL, Srinivasan KG, Chew JL, Ruan Y, Wei CL, Ng HH, Liu ET. 2008. Evolution of the mammalian transcription factor binding repertoire via transposable elements. Genome Res. 18(11):1752-62.
  18. Pan YF, Wansa KD, Liu MH, Zhao B, Hong SZ, Tan PY, Lim KS, Bourque G, Liu ET, Cheung E. 2008. Regulation of estrogen receptor-mediated long-range transcription via evolutionarily conserved distal response elements. J. Biol. Chem. 283(47):32977-88.
  19. Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, Wong E, Orlov YL, Zhang W, Jiang J, Loh YH, Yeo HC, Yeo ZX, Narang V, Govindarajan KR, Leong B, Shahab A, Ruan Y, Bourque G, Sung WK, Clarke ND, Wei CL, Ng HH. 2008. Integration of external signaling pathways with the core transcriptional network through transcription factor colocalization hotspots in embryonic stem cells. Cell 133(6):1106-17.
  20. Lin CH, Bourque G*, Tan P. 2008. A comparative synteny map of Burkholderia species links large-scale genome rearrangements to fine-scale nucleotide variation in prokaryotes. Mol. Biol. Evol. 25(3):549-58.
  21. Zhao H, Bourque G*. 2007. Recovering true evolutionary events on phylogenetic trees. In Proceedings of the 5th RECOMB Workshop on Comparative Genomics, San Diego, USA, LNCS 4751:149-161.
  22. Zhao XD, Han X, Chew JL, Liu J, Chiu KP, Choo A, Orlov YL, Sung WK, Shahab A, Kuznetsov VA, Bourque G, Oh S, Ruan Y, Ng HH, Wei CL. 2007. Whole Genome Mapping of Histone H3 Lys 4 and 27 Trimethylation Reveals Distinct Genomic Compartments in Human Embryonic Stem Cells. Cell Stem Cell 1(3):286.
  23. Pontius JU, Mullikin JC, Smith DR; Agencourt Sequencing Team, Lindblad-Toh K, Gnerre S, Clamp M, Chang J, Stephens R, Neelam B, Volfovsky N, Schffer AA, Agarwala R, Narfstrm K, Murphy WJ, Giger U, Roca AL, Antunes A, Menotti-Raymond M, Yuhki N, Pecon-Slattery J, Johnson WE, Bourque G, Tesler G; NISC Comparative Sequencing Program, O'Brien SJ. 2007. The Domestic Cat Genome Sequence: Annotation and Comparative Inferences. Genome Res. 17:1675-1689.
  24. Ruan Y, Ooi HS, Choo SW, Chiu KP, Zhao XD, Srinivasan KG, Yao F, Choo CY, Liu J, Ariyaratne P, Bin WG, Kuznetsov VA, Shahab A, Sung WK, Bourque G, Palanisamy N, Wei CL. 2007. Fusion Transcripts and Transcribed Retrotransposed Loci Discovered through Comprehensive Transcriptome Analysis using Paired-End diTagging (PET). Genome Res. 17(6):828-838.
  25. Lin CY, Vega VB, Thomsen JS, Zhang T, Kong SL, Xie M, Chiu KP, Lipovich L, Barnett DH, Stossi F, Yeo A, George J, Kuznetsov VA, Lee YK, Charn TH, Palanisamy N, Miller LD, Cheung E, Katzenel- lenbogen BS, Ruan Y, Bourque G, Wei CL, Liu ET. 2007. Whole-Genome Cartography of Estrogen Receptor α Binding Sites. PLoS Genetics 3(6):e87.

Book Chapters

  1. Zhao H, Bourque G. 2010. Chromosomal Rearrangements in Evolution. In Evolutionary Genomics and Systems Biology, Caetano-Anolles G. ed, John Wiley & Sons. ISBN: 9780470195147.
  2. Tesler G, Bourque G. 2008. Computational tools for the analysis of rearrangements in mammalian genomes. In Phylogenomics. Series: Methods in Molecular Biology, Murphy W.J. ed, Humana Press, 422 : 145-70.
  3. Bourque G, Tesler G. 2008. Computational tools for the analysis of rearrangements in mammalian genomes. In Bioinformatics: Data, Sequence Analysis and Evolution. Series: Methods in Molecular Biology, Keith J.M. ed, Humana Press, 452 : 431-55.