Journals

Year of 2009

H. Zhao, G. Bourque. 2009. Recovering Genome Rearrangements in the Mammalian Phylogeny.Genome Res. In press. 19: 934-942. PubMed

Year of 2008

G. Bourque, B. Leong, V.B. Vega, X. Chen, K.G. Srinivasan, J.L. Chew, Y. Ruan, C.L. Wei, H.H. Ng, E.T. Liu. 2008. Evolution of the mammalian transcription factor binding repertoire via transposable elements. Genome Res. 18(11):1752-62. PubMed
Y.F. Pan, K.D.S.A. Wansa, M.H. Liu, B. Zhao, S.Z. Hong, P.Y. Tan, K.S. Lim, G. Bourque, E.T. Liu, E. Cheung. 2008. Regulation of estrogen receptor-mediated long-range transcription via evolutionarily conserved distal response elements. J. Biol. Chem. 283(47):32977-88. PubMed
X. Chen, X. Han, P. Yuan, F. Fang, E.M. Huss, V.B. Vega, E. Wong, Y.L. Orlov, W. Zhang, J. Jiang, Y.H. Loh, H.C. Yeo, Z.H. Yeo, V. Narang, K.R. Govindarajan, B. Leong, A. Shahab, Y. Ruan, G.Bourque, W.K. Sung, N. Clarke, C.L. Wei, H.H. Ng. 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. PubMed
C.H. Lin, G. Bourque*, P. Tan*. 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 (*corresponding authors). PubMed

Year of 2007

H. Zhao, G. Bourque. 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.
X.D. Zhao, J.L. Chew, X. Han, J. Liu, K.P. Chiu, A. Choo, A. Shahab, V.A. Kuznetsov, G. Bourque, S. Ho, Y. Ruan, H.H. Ng, C.L. Wei. 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. PubMed
J.U. Pontius, J.C. Mullikin, D. Smith, K. Lindblad Toh, S. Gnerre, M. Clamp, J. Chang, R. Stephens, B. Neelam, N. Volfovsky, A.A. Schffer, R. Agarwala, K. Narfstrm, W.J. Murphy, U. Giger, A.L. Roca, A. Antunes, M. Menotti Raymond, N. Yuhki, J. Pecon Slattery, W.E. Johnson, G. Bourque, G. Tesler, S.J. OBrien. 2007. The Domestic Cat Genome Sequence: Annotation and Comparative Inferences. Genome Res. 17:1675-1689. PubMed
Y. Ruan, H.S. Ooi, S.W. Choo, K.P. Chiu, X.D. Zhao, K.G. Srinivasan, F. Yao, C.Y. Choo, P. Nuwantha, R. Kalpana, W.G.W. Bin, A. Shahab, W.K. Sung, G. Bourque, N. Palanisamy, C.L. Wei 2007. Fusion Transcripts and Transcribed Retrotransposed Loci Discovered through Comprehensive Transcriptome Analysis using Paired-End diTagging (PET). Genome Res. 17(6):828-838. PubMed
C.Y. Lin, V.B.B. Vega, J.S. Thomsen, T. Zhang, S.L.L. Kong, M. Xie, K.P. Chiu, L. Lipovich, D.H. Barnett, F. Stossi, A. Yeo, J. George, V.A. Kuznetsov, Y.K. Lee, T.H. Charn, N. Palanisamy, L.D. Miller, E. Cheung, B. Katzenellenbogen, Y. Ruan, G. Bourque, C.L. Wei, E.T. Liu. 2007. Whole-Genome Cartography of Estrogen Receptor Binding Sites. PLoS Genetics 3(6):e87. PubMed

Year of 2006

V.B. Vega, C.Y. Lin, K.S. Lai, X. Su, H.F. Teh, J.S. Thomsen, S.L. Kong, M. Xie, A.L. Yeo., W.K. Sung, G. Bourque, E.T. Liu. 2006. Multi-platform genome-wide identification and modeling of functional human estrogen receptor binding sites. Genome Biol. 7(9):R8. PubMed
J. Xu, B.P. Srinivas, S.Y Tay, A. Mak, X. Yu, S.G.P. Lee, H. Yang, K.R. Govindarajan, B. Leong, G. Bourque, S. Mathavan, and S. Roy. 2006. Genome-wide expression profiling in the Zebrafish embryo identifies target genes regulated by hedgehog signaling during vertebrate development. Genetics 174: 735-752. PubMed
Y.H. Loh, W. Wu, J.L. Chew, V.B. Vega, W. Zhang, X. ChenLoh, G. Bourque, et al. 2006. The Oct4 and Nanog transcription network that regulates pluripotency in mouse embryonic stem cells. Nature Genetics 38(4):431-440. PubMed
G. Bourque, G. Tesler, P.A. Pevzner. 2006. The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction. Genome Res. 16(3):311-313. PubMed

Year of 2005

H.X. Yu, J.-M. Chia, G. Bourque, M.V. Wong, S.H. Chan, E.C. Ren. 2005. A population-based LD map of the human chromosome 6p. Immunogenetics. 57(8): 559-565. PubMed
G. Bourque, Y. Yacef, and N. El-Mabrouk. 2005. Maximizing synteny blocks to identify ancestral homologs. In Proceedings of RECOMB Comparative Genomics Satellite Workshop. LNBI 3678: 21-34.
W.J. Murphy, D.M. Larkin, A. Everts-van der Wind, G. Bourque, G. Tesler, L. Auvil, J.E. Beever, B.P. Chowdhary, F. Galibert, L. Gatzke, C. Hitte, S.N. Meyers, E.A. Ostrander, G. Pape, H.G. Parker, T. Raudsepp, M.B. Rogatcheva, L.B. Schook, L.C. Skow, M. Welge, J.E. Womack, S.J. OBrien, P.A. Pevzner, H.A. Lewin. 2005. Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 309(5734): 613-617. PubMed
G. Bourque, E. M. Zdobnov, P. Bork, P. A. Pevzner, and G. Tesler. 2005. Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages. Genome Res. 15: 98–110. PubMed

Year of 2004

International Chicken Genome Sequencing Consortium, (including G. Bourque). 2004. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432: 695–716. PubMed
G. Bourque and D. Sankoff. 2004. Improving gene network inference by comparing expression time-series across species, developmental stages or tissues. J Bioinform Comput Biol. 2(4):765–83. PubMed
Rat Genome Sequencing Project Consortium (including G. Bourque). 2004. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428(6982):493–521. PubMed
G. Bourque, P. A. Pevzner, and G. Tesler. 2004. Reconstructing the genomic architecture of ancestral mammals: Lessons from human, mouse, and rat genomes. Genome Res. 14(4):507–516. PubMed
G. Andelfinger, C. Hitte, R. Guyon, F. Galibert, G. Tesler, G. Bourque, P. Pevzner, E. Kirkness, L. Etter, D.W. Benson. 2004. Detailed comparative mapping and gene order analysis of the canine ctvm locus and syntenic regions in human, mouse, and rat genomes. Genomics 83(6): 1053–1062. PubMed

Year of 2003

W.J. Murphy, G. Bourque, G. Tesler, P.A. Pevzner, and S.J. OBrien. 2003. Reconstructing the genomic architecture of mammalian ancestors using multispecies comparative maps. Human Genomics 1(1): 30–40. PubMed

Year of 2002

G. Bourque. 2002. Algorithms for phylogenetic tree reconstruction based on genome rearrangements. PhD Thesis, Advisor P. Pevzner.
G. Bourque and P. Pevzner. 2002. Genome-Scale Evolution: Reconstructing Gene Orders in the Ancestral Species. Genome Res. 12(1): 26–36. PubMed
G. Bourque. 2002. MGR. Web tool at www-cse.ucsd.edu/groups/bioinformatics.
D. Sankoff, M. Blanchette and G. Bourque. 1997. Breakpoint Phylogenies. In Genome Informatics, Miyano, S., and Takagi, T., eds., Universal Academy Press, Tokyo, 25–34. PubMed

Book Chapters

H. Zhao, G. Bourque. 2009. Chromosomal Rearrangements in Evolution. In Evolutionary Genomics and Systems Biology, Caetano-Anolles G. ed, John Wiley & Sons.
G. Tesler, G. Bourque. 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.

G. Bourque, G. Tesler. 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.
G. Bourque and L. Zhang. 2006. Models and Methods in Comparative Genomics. In Advances in Computers, Special Volume: Computational Biology, C.-W. Tseng ed., Volume 68, Elsevier, ISBN-10: 0-12-012168-9.
G. Bourque. 2006. Analyzing genome rearrangements. In Bioinformatics: From Genomes to Therapies. Lengauer T. ed, Wiley-VCH. ISBN-10: 3-527-31278-1.
G. Bourque. 2005. Chromosome phylogeny. In Encyclopedia of Genomics, Proteomics and Bioinformatics. Dunn M., Jorde L., Little P. and Subramaniam S. eds., Wiley. Volume 7, Section 4.