2017

  1. Hamdan, FF et al.. 2017. High Rate of Recurrent De Novo Mutations in Developmental and Epileptic Encephalopathies. Am. J. Hum. Genet. 101:664-685. doi: 10.1016/j.ajhg.2017.09.008.

  2. Bellenguez, C, Charbonnier, C, Grenier-Boley, B, Quenez, O, Le Guennec, K, Nicolas, G, Chauhan, G, Wallon, D, Rousseau, S, Richard, AC, Boland, A, Bourque, G, Munter, HM, Olaso, R, Meyer, V, Rollin-Sillaire, A, Pasquier, F, Letenneur, L, Redon, R, Dartigues, JF, Tzourio, C, Frebourg, T, Lathrop, M, Deleuze, JF, Hannequin, D, Genin, E, Amouyel, P, Debette, S, Lambert, JC, Campion, D, CNR MAJ collaborators. 2017. Contribution to Alzheimer's disease risk of rare variants in TREM2, SORL1, and ABCA7 in 1779 cases and 1273 controls. Neurobiol. Aging 59:220.e1-220.e9. doi: 10.1016/j.neurobiolaging.2017.07.001.

  3. Audet-Walsh, É, Dufour, CR, Yee, T, Zouanat, FZ, Yan, M, Kalloghlian, G, Vernier, M, Caron, M, Bourque, G, Scarlata, E, Hamel, L, Brimo, F, Aprikian, AG, Lapointe, J, Chevalier, S, Giguère, V. 2017. Nuclear mTOR acts as a transcriptional integrator of the androgen signaling pathway in prostate cancer. Genes Dev. :. doi: 10.1101/gad.299958.117.

  4. Arseneault, M, Monlong, J, Vasudev, NS, Laskar, RS, Safisamghabadi, M, Harnden, P, Egevad, L, Nourbehesht, N, Panichnantakul, P, Holcatova, I, Brisuda, A, Janout, V, Kollarova, H, Foretova, L, Navratilova, M, Mates, D, Jinga, V, Zaridze, D, Mukeria, A, Jandaghi, P, Brennan, P, Brazma, A, Tost, J, Scelo, G, Banks, RE, Lathrop, M, Bourque, G, Riazalhosseini, Y. 2017. Loss of chromosome Y leads to down regulation of KDM5D and KDM6C epigenetic modifiers in clear cell renal cell carcinoma. Sci Rep 7:44876. doi: 10.1038/srep44876.

  5. Oliazadeh, N, Gorman, KF, Eveleigh, R, Bourque, G, Moreau, A. 2017. Identification of Elongated Primary Cilia with Impaired Mechanotransduction in Idiopathic Scoliosis Patients. Sci Rep 7:44260. doi: 10.1038/srep44260.

  6. Cheung, WA, Shao, X, Morin, A, Siroux, V, Kwan, T, Ge, B, Aïssi, D, Chen, L, Vasquez, L, Allum, F, Guénard, F, Bouzigon, E, Simon, MM, Boulier, E, Redensek, A, Watt, S, Datta, A, Clarke, L, Flicek, P, Mead, D, Paul, DS, Beck, S, Bourque, G, Lathrop, M, Tchernof, A, Vohl, MC, Demenais, F, Pin, I, Downes, K, Stunnenberg, HG, Soranzo, N, Pastinen, T, Grundberg, E. 2017. Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome. Genome Biol. 18:50. doi: 10.1186/s13059-017-1173-7.

  7. Ramsay, L, Marchetto, MC, Caron, M, Chen, SH, Busche, S, Kwan, T, Pastinen, T, Gage, FH, Bourque, G. 2017. Conserved expression of transposon-derived non-coding transcripts in primate stem cells. BMC Genomics 18:214. doi: 10.1186/s12864-017-3568-y.

  8. Hocking, TD, Goerner-Potvin, P, Morin, A, Shao, X, Pastinen, T, Bourque, G. 2017. Optimizing ChIP-seq peak detectors using visual labels and supervised machine learning. Bioinformatics 33:491-499. doi: 10.1093/bioinformatics/btw672.

Search PubMed

2016

  1. Dyke, SO, Saulnier, KM, Pastinen, T, Bourque, G, Joly, Y. 2016. Evolving data access policy: The Canadian context. Facets (Ott) 1:138-147. doi: 10.1139/facets-2016-0002.

  2. Torchia, J et al.. 2016. Integrated (epi)-Genomic Analyses Identify Subgroup-Specific Therapeutic Targets in CNS Rhabdoid Tumors. Cancer Cell 30:891-908. doi: 10.1016/j.ccell.2016.11.003.

  3. Paul, DS, Teschendorff, AE, Dang, MA, Lowe, R, Hawa, MI, Ecker, S, Beyan, H, Cunningham, S, Fouts, AR, Ramelius, A, Burden, F, Farrow, S, Rowlston, S, Rehnstrom, K, Frontini, M, Downes, K, Busche, S, Cheung, WA, Ge, B, Simon, MM, Bujold, D, Kwan, T, Bourque, G, Datta, A, Lowy, E, Clarke, L, Flicek, P, Libertini, E, Heath, S, Gut, M, Gut, IG, Ouwehand, WH, Pastinen, T, Soranzo, N, Hofer, SE, Karges, B, Meissner, T, Boehm, BO, Cilio, C, Elding Larsson, H, Lernmark, Å, Steck, AK, Rakyan, VK, Beck, S, Leslie, RD. 2016. Increased DNA methylation variability in type 1 diabetes across three immune effector cell types. Nat Commun 7:13555. doi: 10.1038/ncomms13555.

  4. Bujold, D, Morais, DA, Gauthier, C, Côté, C, Caron, M, Kwan, T, Chen, KC, Laperle, J, Markovits, AN, Pastinen, T, Caron, B, Veilleux, A, Jacques, PÉ, Bourque, G. 2016. The International Human Epigenome Consortium Data Portal. Cell Syst 3:496-499.e2. doi: 10.1016/j.cels.2016.10.019.

  5. Astle, WJ, Elding, H, Jiang, T, Allen, D, Ruklisa, D, Mann, AL, Mead, D, Bouman, H, Riveros-Mckay, F, Kostadima, MA, Lambourne, JJ, Sivapalaratnam, S, Downes, K, Kundu, K, Bomba, L, Berentsen, K, Bradley, JR, Daugherty, LC, Delaneau, O, Freson, K, Garner, SF, Grassi, L, Guerrero, J, Haimel, M, Janssen-Megens, EM, Kaan, A, Kamat, M, Kim, B, Mandoli, A, Marchini, J, Martens, JH, Meacham, S, Megy, K, O'Connell, J, Petersen, R, Sharifi, N, Sheard, SM, Staley, JR, Tuna, S, van der Ent, M, Walter, K, Wang, SY, Wheeler, E, Wilder, SP, Iotchkova, V, Moore, C, Sambrook, J, Stunnenberg, HG, Di Angelantonio, E, Kaptoge, S, Kuijpers, TW, Carrillo-de-Santa-Pau, E, Juan, D, Rico, D, Valencia, A, Chen, L, Ge, B, Vasquez, L, Kwan, T, Garrido-Martín, D, Watt, S, Yang, Y, Guigo, R, Beck, S, Paul, DS, Pastinen, T, Bujold, D, Bourque, G, Frontini, M, Danesh, J, Roberts, DJ, Ouwehand, WH, Butterworth, AS, Soranzo, N. 2016. The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease. Cell 167:1415-1429.e19. doi: 10.1016/j.cell.2016.10.042.

  6. Chen, L, Ge, B, Casale, FP, Vasquez, L, Kwan, T, Garrido-Martín, D, Watt, S, Yan, Y, Kundu, K, Ecker, S, Datta, A, Richardson, D, Burden, F, Mead, D, Mann, AL, Fernandez, JM, Rowlston, S, Wilder, SP, Farrow, S, Shao, X, Lambourne, JJ, Redensek, A, Albers, CA, Amstislavskiy, V, Ashford, S, Berentsen, K, Bomba, L, Bourque, G, Bujold, D, Busche, S, Caron, M, Chen, SH, Cheung, W, Delaneau, O, Dermitzakis, ET, Elding, H, Colgiu, I, Bagger, FO, Flicek, P, Habibi, E, Iotchkova, V, Janssen-Megens, E, Kim, B, Lehrach, H, Lowy, E, Mandoli, A, Matarese, F, Maurano, MT, Morris, JA, Pancaldi, V, Pourfarzad, F, Rehnstrom, K, Rendon, A, Risch, T, Sharifi, N, Simon, MM, Sultan, M, Valencia, A, Walter, K, Wang, SY, Frontini, M, Antonarakis, SE, Clarke, L, Yaspo, ML, Beck, S, Guigo, R, Rico, D, Martens, JH, Ouwehand, WH, Kuijpers, TW, Paul, DS, Stunnenberg, HG, Stegle, O, Downes, K, Pastinen, T, Soranzo, N. 2016. Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells. Cell 167:1398-1414.e24. doi: 10.1016/j.cell.2016.10.026.

  7. Breeze, CE, Paul, DS, van Dongen, J, Butcher, LM, Ambrose, JC, Barrett, JE, Lowe, R, Rakyan, VK, Iotchkova, V, Frontini, M, Downes, K, Ouwehand, WH, Laperle, J, Jacques, PÉ, Bourque, G, Bergmann, AK, Siebert, R, Vellenga, E, Saeed, S, Matarese, F, Martens, JHA, Stunnenberg, HG, Teschendorff, AE, Herrero, J, Birney, E, Dunham, I, Beck, S. 2016. eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data. Cell Rep 17:2137-2150. doi: 10.1016/j.celrep.2016.10.059.

  8. Tahmasebi, S, Jafarnejad, SM, Tam, IS, Gonatopoulos-Pournatzis, T, Matta-Camacho, E, Tsukumo, Y, Yanagiya, A, Li, W, Atlasi, Y, Caron, M, Braunschweig, U, Pearl, D, Khoutorsky, A, Gkogkas, CG, Nadon, R, Bourque, G, Yang, XJ, Tian, B, Stunnenberg, HG, Yamanaka, Y, Blencowe, BJ, Giguère, V, Sonenberg, N. 2016. Control of embryonic stem cell self-renewal and differentiation via coordinated alternative splicing and translation of YY2. Proc. Natl. Acad. Sci. U.S.A. 113:12360-12367. doi: 10.1073/pnas.1615540113.

  9. Morin, A, Kwan, T, Ge, B, Letourneau, L, Ban, M, Tandre, K, Caron, M, Sandling, JK, Carlsson, J, Bourque, G, Laprise, C, Montpetit, A, Syvanen, AC, Ronnblom, L, Sawcer, SJ, Lathrop, MG, Pastinen, T. 2016. Immunoseq: the identification of functionally relevant variants through targeted capture and sequencing of active regulatory regions in human immune cells. BMC Med Genomics 9:59. doi: 10.1186/s12920-016-0220-7.

  10. Panichnantakul, P, Bourgey, M, Montpetit, A, Bourque, G, Riazalhosseini, Y. 2016. RNA-Seq as a Tool to Study the Tumor Microenvironment. Methods Mol. Biol. 1458:311-37. doi: 10.1007/978-1-4939-3801-8_22.

  11. Deblois, G, Smith, HW, Tam, IS, Gravel, SP, Caron, M, Savage, P, Labbé, DP, Bégin, LR, Tremblay, ML, Park, M, Bourque, G, St-Pierre, J, Muller, WJ, Giguère, V. 2016. ERRα mediates metabolic adaptations driving lapatinib resistance in breast cancer. Nat Commun 7:12156. doi: 10.1038/ncomms12156.

  12. Le Guennec, K, Nicolas, G, Quenez, O, Charbonnier, C, Wallon, D, Bellenguez, C, Grenier-Boley, B, Rousseau, S, Richard, AC, Rovelet-Lecrux, A, Bacq, D, Garnier, JG, Olaso, R, Boland, A, Meyer, V, Deleuze, JF, Amouyel, P, Munter, HM, Bourque, G, Lathrop, M, Frebourg, T, Redon, R, Letenneur, L, Dartigues, JF, Pasquier, F, Rollin-Sillaire, A, Génin, E, Lambert, JC, Hannequin, D, Campion, D, CNR-MAJ collaborators. 2016. ABCA7 rare variants and Alzheimer disease risk. Neurology 86:2134-7. doi: 10.1212/WNL.0000000000002627.

  13. Ramsay, L, Bourque, G. 2016. In Silico Methods to Identify Exapted Transposable Element Families. Methods Mol. Biol. 1400:33-45. doi: 10.1007/978-1-4939-3372-3_3.

  14. Audet-Walsh, É, Papadopoli, DJ, Gravel, SP, Yee, T, Bridon, G, Caron, M, Bourque, G, Giguère, V, St-Pierre, J. 2016. The PGC-1α/ERRα Axis Represses One-Carbon Metabolism and Promotes Sensitivity to Anti-folate Therapy in Breast Cancer. Cell Rep 14:920-931. doi: 10.1016/j.celrep.2015.12.086.

  15. Nicolas, G, Wallon, D, Charbonnier, C, Quenez, O, Rousseau, S, Richard, AC, Rovelet-Lecrux, A, Coutant, S, Le Guennec, K, Bacq, D, Garnier, JG, Olaso, R, Boland, A, Meyer, V, Deleuze, JF, Munter, HM, Bourque, G, Auld, D, Montpetit, A, Lathrop, M, Guyant-Maréchal, L, Martinaud, O, Pariente, J, Rollin-Sillaire, A, Pasquier, F, Le Ber, I, Sarazin, M, Croisile, B, Boutoleau-Bretonnière, C, Thomas-Antérion, C, Paquet, C, Sauvée, M, Moreaud, O, Gabelle, A, Sellal, F, Ceccaldi, M, Chamard, L, Blanc, F, Frebourg, T, Campion, D, Hannequin, D. 2016. Screening of dementia genes by whole-exome sequencing in early-onset Alzheimer disease: input and lessons. Eur. J. Hum. Genet. 24:710-6. doi: 10.1038/ejhg.2015.173.

Search PubMed

2015

  1. Busche, S, Shao, X, Caron, M, Kwan, T, Allum, F, Cheung, WA, Ge, B, Westfall, S, Simon, MM, Multiple Tissue Human Expression Resource, Barrett, A, Bell, JT, McCarthy, MI, Deloukas, P, Blanchette, M, Bourque, G, Spector, TD, Lathrop, M, Pastinen, T, Grundberg, E. 2015. Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation. Genome Biol. 16:290. doi: 10.1186/s13059-015-0856-1.

  2. Aarabi, M, San Gabriel, MC, Chan, D, Behan, NA, Caron, M, Pastinen, T, Bourque, G, MacFarlane, AJ, Zini, A, Trasler, J. 2015. High-dose folic acid supplementation alters the human sperm methylome and is influenced by the MTHFR C677T polymorphism. Hum. Mol. Genet. 24:6301-13. doi: 10.1093/hmg/ddv338.

  3. Hoen, DR, Hickey, G, Bourque, G, Casacuberta, J, Cordaux, R, Feschotte, C, Fiston-Lavier, AS, Hua-Van, A, Hubley, R, Kapusta, A, Lerat, E, Maumus, F, Pollock, DD, Quesneville, H, Smit, A, Wheeler, TJ, Bureau, TE, Blanchette, M. 2015. A call for benchmarking transposable element annotation methods. Mob DNA 6:13. doi: 10.1186/s13100-015-0044-6.

  4. Nicolas, G, Wallon, D, Charbonnier, C, Quenez, O, Rousseau, S, Richard, AC, Rovelet-Lecrux, A, Coutant, S, Le Guennec, K, Bacq, D, Garnier, JG, Olaso, R, Boland, A, Meyer, V, Deleuze, JF, Munter, HM, Bourque, G, Auld, D, Montpetit, A, Lathrop, M, Guyant-Maréchal, L, Martinaud, O, Pariente, J, Rollin-Sillaire, A, Pasquier, F, Le Ber, I, Sarazin, M, Croisile, B, Boutoleau-Bretonnière, C, Thomas-Antérion, C, Paquet, C, Sauvée, M, Moreaud, O, Gabelle, A, Sellal, F, Ceccaldi, M, Chamard, L, Blanc, F, Frebourg, T, Campion, D, Hannequin, D. 2016. Screening of dementia genes by whole-exome sequencing in early-onset Alzheimer disease: input and lessons. Eur. J. Hum. Genet. 24:710-6. doi: 10.1038/ejhg.2015.173.

  5. Dyke, SO, Cheung, WA, Joly, Y, Ammerpohl, O, Lutsik, P, Rothstein, MA, Caron, M, Busche, S, Bourque, G, Rönnblom, L, Flicek, P, Beck, S, Hirst, M, Stunnenberg, H, Siebert, R, Walter, J, Pastinen, T. 2015. Epigenome data release: a participant-centered approach to privacy protection. Genome Biol. 16:142. doi: 10.1186/s13059-015-0723-0.

  6. Tang, QL, Julien, C, Eveleigh, R, Bourque, G, Franco, A, Labelle, H, Grimard, G, Parent, S, Ouellet, J, Mac-Thiong, JM, Gorman, KF, Moreau, A. 2015. A replication study for association of 53 single nucleotide polymorphisms in ScoliScore test with adolescent idiopathic scoliosis in French-Canadian population. Spine 40:537-43. doi: 10.1097/BRS.0000000000000807.

  7. McGraw, S, Zhang, JX, Farag, M, Chan, D, Caron, M, Konermann, C, Oakes, CC, Mohan, KN, Plass, C, Pastinen, T, Bourque, G, Chaillet, JR, Trasler, JM. 2015. Transient DNMT1 suppression reveals hidden heritable marks in the genome. Nucleic Acids Res. 43:1485-97. doi: 10.1093/nar/gku1386.

Search PubMed

2014

  1. Scelo, G, Riazalhosseini, Y, Greger, L, Letourneau, L, Gonzàlez-Porta, M, Wozniak, MB, Bourgey, M, Harnden, P, Egevad, L, Jackson, SM, Karimzadeh, M, Arseneault, M, Lepage, P, How-Kit, A, Daunay, A, Renault, V, Blanché, H, Tubacher, E, Sehmoun, J, Viksna, J, Celms, E, Opmanis, M, Zarins, A, Vasudev, NS, Seywright, M, Abedi-Ardekani, B, Carreira, C, Selby, PJ, Cartledge, JJ, Byrnes, G, Zavadil, J, Su, J, Holcatova, I, Brisuda, A, Zaridze, D, Moukeria, A, Foretova, L, Navratilova, M, Mates, D, Jinga, V, Artemov, A, Nedoluzhko, A, Mazur, A, Rastorguev, S, Boulygina, E, Heath, S, Gut, M, Bihoreau, MT, Lechner, D, Foglio, M, Gut, IG, Skryabin, K, Prokhortchouk, E, Cambon-Thomsen, A, Rung, J, Bourque, G, Brennan, P, Tost, J, Banks, RE, Brazma, A, Lathrop, GM. 2014. Variation in genomic landscape of clear cell renal cell carcinoma across Europe. Nat Commun 5:5135. doi: 10.1038/ncomms6135.

  2. Chen, ES, Gigek, CO, Rosenfeld, JA, Diallo, AB, Maussion, G, Chen, GG, Vaillancourt, K, Lopez, JP, Crapper, L, Poujol, R, Shaffer, LG, Bourque, G, Ernst, C. 2014. Molecular convergence of neurodevelopmental disorders. Am. J. Hum. Genet. 95:490-508. doi: 10.1016/j.ajhg.2014.09.013.

  3. Caignard, G, Eva, MM, van Bruggen, R, Eveleigh, R, Bourque, G, Malo, D, Gros, P, Vidal, SM. 2014. Mouse ENU Mutagenesis to Understand Immunity to Infection: Methods, Selected Examples, and Perspectives. Genes (Basel) 5:887-925. doi: 10.3390/genes5040887.

  4. Salem, S, Langlais, D, Lefebvre, F, Bourque, G, Bigley, V, Haniffa, M, Casanova, JL, Burk, D, Berghuis, A, Butler, KM, Leahy, TR, Hambleton, S, Gros, P. 2014. Functional characterization of the human dendritic cell immunodeficiency associated with the IRF8(K108E) mutation. Blood 124:1894-904. doi: 10.1182/blood-2014-04-570879.

  5. Buczkowicz, P, Hoeman, C, Rakopoulos, P, Pajovic, S, Letourneau, L, Dzamba, M, Morrison, A, Lewis, P, Bouffet, E, Bartels, U, Zuccaro, J, Agnihotri, S, Ryall, S, Barszczyk, M, Chornenkyy, Y, Bourgey, M, Bourque, G, Montpetit, A, Cordero, F, Castelo-Branco, P, Mangerel, J, Tabori, U, Ho, KC, Huang, A, Taylor, KR, Mackay, A, Bendel, AE, Nazarian, J, Fangusaro, JR, Karajannis, MA, Zagzag, D, Foreman, NK, Donson, A, Hegert, JV, Smith, A, Chan, J, Lafay-Cousin, L, Dunn, S, Hukin, J, Dunham, C, Scheinemann, K, Michaud, J, Zelcer, S, Ramsay, D, Cain, J, Brennan, C, Souweidane, MM, Jones, C, Allis, CD, Brudno, M, Becher, O, Hawkins, C. 2014. Genomic analysis of diffuse intrinsic pontine gliomas identifies three molecular subgroups and recurrent activating ACVR1 mutations. Nat. Genet. 46:451-6. doi: 10.1038/ng.2936.

  6. Lu, X, Sachs, F, Ramsay, L, Jacques, PÉ, Göke, J, Bourque, G, Ng, HH. 2014. The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity. Nat. Struct. Mol. Biol. 21:423-5. doi: 10.1038/nsmb.2799.

  7. Magnus, N, Garnier, D, Meehan, B, McGraw, S, Lee, TH, Caron, M, Bourque, G, Milsom, C, Jabado, N, Trasler, J, Pawlinski, R, Mackman, N, Rak, J. 2014. Tissue factor expression provokes escape from tumor dormancy and leads to genomic alterations. Proc. Natl. Acad. Sci. U.S.A. 111:3544-9. doi: 10.1073/pnas.1314118111.

Search PubMed

2013

  1. Lu, X, Göke, J, Sachs, F, Jacques, PÉ, Liang, H, Feng, B, Bourque, G, Bubulya, PA, Ng, HH. 2013. SON connects the splicing-regulatory network with pluripotency in human embryonic stem cells. Nat. Cell Biol. 15:1141-1152. doi: 10.1038/ncb2839.

  2. Jacques, PÉ, Jeyakani, J, Bourque, G. 2013. The majority of primate-specific regulatory sequences are derived from transposable elements. PLoS Genet. 9:e1003504. doi: 10.1371/journal.pgen.1003504.

  3. Kapusta, A, Kronenberg, Z, Lynch, VJ, Zhuo, X, Ramsay, L, Bourque, G, Yandell, M, Feschotte, C. 2013. Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs. PLoS Genet. 9:e1003470. doi: 10.1371/journal.pgen.1003470.

  4. Chaveroux, C, Eichner, LJ, Dufour, CR, Shatnawi, A, Khoutorsky, A, Bourque, G, Sonenberg, N, Giguère, V. 2013. Molecular and genetic crosstalks between mTOR and ERRα are key determinants of rapamycin-induced nonalcoholic fatty liver. Cell Metab. 17:586-98. doi: 10.1016/j.cmet.2013.03.003.

Search PubMed

2012

  1. Nagarajan, N, Bertrand, D, Hillmer, AM, Zang, ZJ, Yao, F, Jacques, PÉ, Teo, AS, Cutcutache, I, Zhang, Z, Lee, WH, Sia, YY, Gao, S, Ariyaratne, PN, Ho, A, Woo, XY, Veeravali, L, Ong, CK, Deng, N, Desai, KV, Khor, CC, Hibberd, ML, Shahab, A, Rao, J, Wu, M, Teh, M, Zhu, F, Chin, SY, Pang, B, So, JB, Bourque, G, Soong, R, Sung, WK, Tean Teh, B, Rozen, S, Ruan, X, Yeoh, KG, Tan, PB, Ruan, Y. 2012. Whole-genome reconstruction and mutational signatures in gastric cancer. Genome Biol. 13:R115. doi: 10.1186/gb-2012-13-12-r115.

  2. Pott, S, Kamrani, NK, Bourque, G, Pettersson, S, Liu, ET. 2012. PPARG binding landscapes in macrophages suggest a genome-wide contribution of PU.1 to divergent PPARG binding in human and mouse. PLoS ONE 7:e48102. doi: 10.1371/journal.pone.0048102.

  3. Yao, F, Ariyaratne, PN, Hillmer, AM, Lee, WH, Li, G, Teo, AS, Woo, XY, Zhang, Z, Chen, JP, Poh, WT, Zawack, KF, Chan, CS, Leong, ST, Neo, SC, Choi, PS, Gao, S, Nagarajan, N, Thoreau, H, Shahab, A, Ruan, X, Cacheux-Rataboul, V, Wei, CL, Bourque, G, Sung, WK, Liu, ET, Ruan, Y. 2012. Long span DNA paired-end-tag (DNA-PET) sequencing strategy for the interrogation of genomic structural mutations and fusion-point-guided reconstruction of amplicons. PLoS ONE 7:e46152. doi: 10.1371/journal.pone.0046152.

  4. 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. doi: 10.1007/s00401-012-0998-0.

  5. 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. 109:2168-73. doi: 10.1073/pnas.1119229109.

Search PubMed

2011

  1. Zemojtel, T, Kielbasa, SM, Arndt, PF, Behrens, S, Bourque, G, Vingron, M. 2011. CpG deamination creates transcription factor-binding sites with high efficiency. Genome Biol Evol 3:1304-11. doi: 10.1093/gbe/evr107.

  2. Chatterjee, S, Bourque, G, Lufkin, T. 2011. Conserved and non-conserved enhancers direct tissue specific transcription in ancient germ layer specific developmental control genes. BMC Dev. Biol. 11:63. doi: 10.1186/1471-213X-11-63.

  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. 43:630-8. doi: 10.1038/ng.857.

  4. 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 associated with cell cycle regulation, hormonal carcinogenesis and cancer in zebrafish and human cancer cell lines. BMC Med Genomics 4:41. doi: 10.1186/1755-8794-4-41.

  5. 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 2:26. doi: 10.1186/scrt67.

  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, Aleström, P, Mathavan, S. 2011. Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition. Genome Res. 21:1328-38. doi: 10.1101/gr.116012.110.

  7. 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. 21:665-75. doi: 10.1101/gr.113555.110.

  8. 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. 21:676-87. doi: 10.1101/gr.113225.110.

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2002-2010

  1. 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. 42:631-4. doi: 10.1038/ng.600.

  2. 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:e8417. doi: 10.1371/journal.pone.0008417.

  3. Lin, CH, Zhao, H, Lowcay, SH, Shahab, A, Bourque, G. 2010. webMGR: an online tool for the multiple genome rearrangement problem. Bioinformatics 26:408-10. doi: 10.1093/bioinformatics/btp689.

  4. Bourque, G. 2009. Transposable elements in gene regulation and in the evolution of vertebrate genomes. Curr. Opin. Genet. Dev. 19:607-12. doi: 10.1016/j.gde.2009.10.013.

  5. 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-alpha-bound human chromatin interactome. Nature 462:58-64. doi: 10.1038/nature08497.

  6. Zhao, H, Bourque, G. 2009. Recovering genome rearrangements in the mammalian phylogeny. Genome Res. 19:934-42. doi: 10.1101/gr.086009.108.

  7. 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. doi: 10.1111/j.1749-6632.2008.03759.x.

  8. 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. 283:32977-88. doi: 10.1074/jbc.M802024200.

  9. 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. 18:1752-62. doi: 10.1101/gr.080663.108.

  10. Tesler, G, Bourque, G. 2008. Computational tools for the analysis of rearrangements in mammalian genomes. Methods Mol. Biol. 422:145-70. doi: 10.1007/978-1-59745-581-7_10.

  11. Bourque, G, Tesler, G. 2008. Computational tools for the analysis of rearrangements in mammalian genomes. Methods Mol. Biol. 452:431-55. doi: 10.1007/978-1-60327-159-2_20.

  12. 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 in embryonic stem cells. Cell 133:1106-17. doi: 10.1016/j.cell.2008.04.043.

  13. 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 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells. Cell Stem Cell 1:286-98. doi: 10.1016/j.stem.2007.08.004.

  14. 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. 25:549-58. doi: 10.1093/molbev/msm282.

  15. Pontius, JU, Mullikin, JC, Smith, DR, Agencourt Sequencing Team, Lindblad-Toh, K, Gnerre, S, Clamp, M, Chang, J, Stephens, R, Neelam, B, Volfovsky, N, Schäffer, AA, Agarwala, R, Narfström, 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. Initial sequence and comparative analysis of the cat genome. Genome Res. 17:1675-89. doi: 10.1101/gr.6380007.

  16. 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 diTags (PETs). Genome Res. 17:828-38. doi: 10.1101/gr.6018607.

  17. 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, Katzenellenbogen, BS, Ruan, Y, Bourque, G, Wei, CL, Liu, ET. 2007. Whole-genome cartography of estrogen receptor alpha binding sites. PLoS Genet. 3:e87. doi: 10.1371/journal.pgen.0030087.

  18. Vega, VB, Lin, CY, Lai, KS, Kong, SL, Xie, M, Su, X, Teh, HF, Thomsen, JS, Yeo, AL, Sung, WK, Bourque, G, Liu, ET. 2006. Multiplatform genome-wide identification and modeling of functional human estrogen receptor binding sites. Genome Biol. 7:R82. doi: 10.1186/gb-2006-7-9-r82.

  19. Xu, J, Srinivas, BP, Tay, SY, Mak, A, Yu, X, Lee, SG, Yang, H, Govindarajan, KR, Leong, B, Bourque, G, Mathavan, S, Roy, S. 2006. Genomewide expression profiling in the zebrafish embryo identifies target genes regulated by Hedgehog signaling during vertebrate development. Genetics 174:735-52. doi: 10.1534/genetics.106.061523.

  20. Loh, YH, Wu, Q, Chew, JL, Vega, VB, Zhang, W, Chen, X, Bourque, G, George, J, Leong, B, Liu, J, Wong, KY, Sung, KW, Lee, CW, Zhao, XD, Chiu, KP, Lipovich, L, Kuznetsov, VA, Robson, P, Stanton, LW, Wei, CL, Ruan, Y, Lim, B, Ng, HH. 2006. The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nat. Genet. 38:431-40. doi: 10.1038/ng1760.

  21. Bourque, G, Tesler, G, Pevzner, PA. 2006. The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction. Genome Res. 16:311-3. doi: 10.1101/gr.4631806.

  22. Yu, HX, Chia, JM, Bourque, G, Wong, MV, Chan, SH, Ren, EC. 2005. A population-based LD map of the human chromosome 6p. Immunogenetics 57:559-65. doi: 10.1007/s00251-005-0002-4.

  23. Murphy, WJ, Larkin, DM, Everts-van der Wind, A, Bourque, G, Tesler, G, Auvil, L, Beever, JE, Chowdhary, BP, Galibert, F, Gatzke, L, Hitte, C, Meyers, SN, Milan, D, Ostrander, EA, Pape, G, Parker, HG, Raudsepp, T, Rogatcheva, MB, Schook, LB, Skow, LC, Welge, M, Womack, JE, O'brien, SJ, Pevzner, PA, Lewin, HA. 2005. Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 309:613-7. doi: 10.1126/science.1111387.

  24. Bourque, G, Sankoff, D. 2004. Improving gene network inference by comparing expression time-series across species, developmental stages or tissues. J Bioinform Comput Biol 2:765-83.

  25. Murphy, WJ, Bourque, G, Tesler, G, Pevzner, P, O'Brien, SJ. 2003. Reconstructing the genomic architecture of mammalian ancestors using multispecies comparative maps. Hum. Genomics 1:30-40.

  26. Bourque, G, Zdobnov, EM, Bork, P, Pevzner, PA, Tesler, G. 2005. Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages. Genome Res. 15:98-110. doi: 10.1101/gr.3002305.

  27. Bourque, G, Pevzner, PA, Tesler, G. 2004. Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes. Genome Res. 14:507-16. doi: 10.1101/gr.1975204.

  28. Gibbs, RA et al.. 2004. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428:493-521. doi: 10.1038/nature02426.

  29. Bourque, G, Pevzner, PA. 2002. Genome-scale evolution: reconstructing gene orders in the ancestral species. Genome Res. 12:26-36.

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