Breeze CE; Haugen E; Reynolds A; Teschendorff A; van Dongen J; Lan Q; Rothman N; Bourque G; Dunham I; Beck S; Stamatoyannopoulos J; Franceschini N; Berndt SI, 2022. Integrative analysis of 3604 GWAS reveals multiple novel cell type-specific regulatory associations.  Genome Biol 23(1):13

Povysil G; Butler-Laporte G; Shang N; Wang C; Khan A; Alaamery M; Nakanishi T; Zhou S; Forgetta V; Eveleigh RJ; Bourgey M; Aziz N; Jones SJ; Knoppers B; Scherer SW; Strug LJ; Lepage P; Ragoussis J; Bourque G; Alghamdi J; Aljawini N; Albes N; Al-Afghani HM; Alghamdi B; Almutairi MS; Mahmoud ES; Abu-Safieh L; El Bardisy H; Harthi FSA; Alshareef A; Suliman BA; Alqahtani SA; Almalik A; Alrashed MM; Massadeh S; Mooser V; Lathrop M; Fawzy M; Arabi YM; Mbarek H; Saad C; Al-Muftah W; Jung J; Mangul S; Badji R; Thani AA; Ismail SI; Gharavi AG; Abedalthagafi MS; Richards JB; Goldstein DB; Kiryluk K, 2021. Rare loss-of-function variants in type I IFN immunity genes are not associated with severe COVID-19.  J Clin Invest 131.

AlOgayil N; Bauermeister K; Galvez JH; Venkatesh VS; Zhuang QK; Chang ML; Davey RA; Zajac JD; Ida K; Kamiya A; Taketo T; Bourque G; Naumova AK, 2021. Author Correction: Distinct roles of androgen receptor, estrogen receptor alpha, and BCL6 in the establishment of sex-biased DNA methylation in mouse liver.  Sci Rep 11(1):22975

Dankner M; Caron M; Al-Saadi T; Yu W; Ouellet V; Ezzeddine R; Maritan SM; Annis MG; Le PU; Nadaf J; Neubarth NS; Savage P; Zuo D; Couturier CP; Monlong J; Djambazian H; Altoukhi H; Bourque G; Ragoussis J; Diaz RJ; Park M; Guiot MC; Lam S; Petrecca K; Siegel PM, 2021. Invasive growth associated with cold-inducible RNA-binding protein expression drives recurrence of surgically resected brain metastases.  Neuro Oncol 23(9):1470-1480

Cheng AP; Cheng MP; Gu W; Sesing Lenz J; Hsu E; Schurr E; Bourque G; Bourgey M; Ritz J; Marty FM; Chiu CY; Vinh DC; De Vlaminck I, 2021. Cell-free DNA tissues of origin by methylation profiling reveals significant cell, tissue, and organ-specific injury related to COVID-19 severity.  Med (N Y) 2(4):411-422.e5

Sanchez-Ferras O; Pacis A; Sotiropoulou M; Zhang Y; Wang YC; Bourgey M; Bourque G; Ragoussis J; Bouchard M, 2021. A coordinated progression of progenitor cell states initiates urinary tract development.  Nat Commun 12(1):2627

Liu P; Ewald J; Galvez JH; Head J; Crump D; Bourque G; Basu N; Xia J, 2021. Ultrafast functional profiling of RNA-seq data for nonmodel organisms.  Genome Res 31(4):713-720

Ferreira-Neto JRC; Borges ANDC; da Silva MD; Morais DAL; Bezerra-Neto JP; Bourque G; Kido EA; Benko-Iseppon AM, 2021. The Cowpea Kinome: Genomic and Transcriptomic Analysis Under Biotic and Abiotic Stresses.  Front Plant Sci 12:667013

AlOgayil N; Bauermeister K; Galvez JH; Venkatesh VS; Zhuang QK; Chang ML; Davey RA; Zajac JD; Ida K; Kamiya A; Taketo T; Bourque G; Naumova AK, 2021. Distinct roles of androgen receptor, estrogen receptor alpha, and BCL6 in the establishment of sex-biased DNA methylation in mouse liver.  Sci Rep 11(1):13766

Lambrot R; Chan D; Shao X; Aarabi M; Kwan T; Bourque G; Moskovtsev S; Librach C; Trasler J; Dumeaux V; Kimmins S, 2021. Whole-genome sequencing of H3K4me3 and DNA methylation in human sperm reveals regions of overlap linked to fertility and development.  Cell Rep 36(3):109418

MacDonald A; Lu B; Caron M; Caporicci-Dinucci N; Hatrock D; Petrecca K; Bourque G; Stratton JA, 2021. Single Cell Transcriptomics of Ependymal Cells Across Age, Region and Species Reveals Cilia-Related and Metal Ion Regulatory Roles as Major Conserved Ependymal Cell Functions.  Front Cell Neurosci 15:703951

Kuzmin E; Monlong J; Martinez C; Kuasne H; Kleinman CL; Ragoussis J; Bourque G; Park M, 2021. Inferring Copy Number from Triple-Negative Breast Cancer Patient Derived Xenograft scRNAseq Data Using scCNA.  Methods Mol Biol 2381:285-303

Murall CL; Fournier E; Galvez JH; N'Guessan A; Reiling SJ; Quirion PO; Naderi S; Roy AM; Chen SH; Stretenowich P; Bourgey M; Bujold D; Gregoire R; Lepage P; St-Cyr J; Willet P; Dion R; Charest H; Lathrop M; Roger M; Bourque G; Ragoussis J; Shapiro BJ; Moreira S, 2021. A small number of early introductions seeded widespread transmission of SARS-CoV-2 in Québec, Canada.  Genome Med 13(1):169

Yokobayashi S; Yabuta Y; Nakagawa M; Okita K; Hu B; Murase Y; Nakamura T; Bourque G; Majewski J; Yamamoto T; Saitou M, 2021. Inherent genomic properties underlie the epigenomic heterogeneity of human induced pluripotent stem cells.  Cell Rep 37(5):109909

Groza C; Kwan T; Soranzo N; Pastinen T; Bourque G, 2020. Personalized and graph genomes reveal missing signal in epigenomic data.  Genome Biol 21(1):124

Rodriguez-Martin B; Alvarez EG; Baez-Ortega A; Zamora J; Supek F; Demeulemeester J; Santamarina M; Ju YS; Temes J; Garcia-Souto D; Detering H; Li Y; Rodriguez-Castro J; Dueso-Barroso A; Bruzos AL; Dentro SC; Blanco MG; Contino G; Ardeljan D; Tojo M; Roberts ND; Zumalave S; Edwards PAW; Weischenfeldt J; Puiggròs M; Chong Z; Chen K; Lee EA; Wala JA; Raine K; Butler A; Waszak SM; Navarro FCP; Schumacher SE; Monlong J; Maura F; Bolli N; Bourque G; Gerstein M; Park PJ; Wedge DC; Beroukhim R; Torrents D; Korbel JO; Martincorena I; Fitzgerald RC; Van Loo P; Kazazian HH; Burns KH; Campbell PJ; Tubio JMC, 2020. Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition.  Nat Genet 52(3):306-319

2020. Pan-cancer analysis of whole genomes.  Nature 578(7793):82-93

Vijay J; Gauthier MF; Biswell RL; Louiselle DA; Johnston JJ; Cheung WA; Belden B; Pramatarova A; Biertho L; Gibson M; Simon MM; Djambazian H; Staffa A; Bourque G; Laitinen A; Nystedt J; Vohl MC; Fraser JD; Pastinen T; Tchernof A; Grundberg E, 2020. Single-cell analysis of human adipose tissue identifies depot and disease specific cell types.  Nat Metab 2(1):97-109

Bogdan L; Barreiro L; Bourque G, 2020. Transposable elements have contributed human regulatory regions that are activated upon bacterial infection.  Philos Trans R Soc Lond B Biol Sci 375(1795):20190332

Caron M; St-Onge P; Sontag T; Wang YC; Richer C; Ragoussis I; Sinnett D; Bourque G, 2020. Single-cell analysis of childhood leukemia reveals a link between developmental states and ribosomal protein expression as a source of intra-individual heterogeneity.  Sci Rep 10(1):8079

Chehboun S; Leiva-Torres GA; Charbonneau B; Eveleigh R; Bourque G; Vidal SM, 2020. A point mutation in the linker domain of mouse STAT5A is associated with impaired NK-cell regulation.  Genes Immun 21(2):136-141

Zhuang QK; Galvez JH; Xiao Q; AlOgayil N; Hyacinthe J; Taketo T; Bourque G; Naumova AK, 2020. Sex Chromosomes and Sex Phenotype Contribute to Biased DNA Methylation in Mouse Liver.  Cells 9.

Cheng AP; Cheng MP; Gu W; Lenz JS; Hsu E; Schurr E; Bourque G; Bourgey M; Ritz J; Marty F; Chiu CY; Vinh DC; Vlaminck I, 2020. Cell-Free DNA in Blood Reveals Significant Cell, Tissue and Organ Specific injury and Predicts COVID-19 Severity.  medRxiv.

Couturier CP; Ayyadhury S; Le PU; Nadaf J; Monlong J; Riva G; Allache R; Baig S; Yan X; Bourgey M; Lee C; Wang YCD; Yong VW; Guiot MC; Najafabadi H; Misic B; Antel J; Bourque G; Ragoussis J; Petrecca K, 2020. Author Correction: Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy.  Nat Commun 11(1):4041

Li CH; Prokopec SD; Sun RX; Yousif F; Schmitz N; Boutros PC, 2020. Sex differences in oncogenic mutational processes.  Nat Commun 11(1):4330

Bailey MH; Meyerson WU; Dursi LJ; Wang LB; Dong G; Liang WW; Weerasinghe A; Li S; Li Y; Kelso S; Saksena G; Ellrott K; Wendl MC; Wheeler DA; Getz G; Simpson JT; Gerstein MB; Ding L, 2020. Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.  Nat Commun 11(1):4748

Chen L; Yang R; Kwan T; Tang C; Watt S; Zhang Y; Bourque G; Ge B; Downes K; Frontini M; Ouwehand WH; Lin JW; Soranzo N; Pastinen T; Chen L, 2020. Paired rRNA-depleted and polyA-selected RNA sequencing data and supporting multi-omics data from human T cells.  Sci Data 7(1):376

Bailey MH; Meyerson WU; Dursi LJ; Wang LB; Dong G; Liang WW; Weerasinghe A; Li S; Li Y; Kelso S; Saksena G; Ellrott K; Wendl MC; Wheeler DA; Getz G; Simpson JT; Gerstein MB; Ding L, 2020. Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.  Nat Commun 11(1):6232

Couturier CP; Ayyadhury S; Le PU; Nadaf J; Monlong J; Riva G; Allache R; Baig S; Yan X; Bourgey M; Lee C; Wang YCD; Wee Yong V; Guiot MC; Najafabadi H; Misic B; Antel J; Bourque G; Ragoussis J; Petrecca K, 2020. Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy.  Nat Commun 11(1):3406

Povysil G; Butler-Laporte G; Shang N; Weng C; Khan A; Alaamery M; Nakanishi T; Zhou S; Forgetta V; Eveleigh R; Bourgey M; Aziz N; Jones S; Knoppers B; Scherer S; Strug L; Lepage P; Ragoussis J; Bourque G; Alghamdi J; Aljawini N; Albes N; Al-Afghani HM; Alghamdi B; Almutair M; Mahmoud ES; Safie LA; Bardisy HE; Al Harthi FS; Alshareef A; Suliman BA; Alqahtani S; AlMalik A; Alrashed MM; Massadeh S; Mooser V; Lathrop M; Arabi Y; Mbarek H; Saad C; Al-Muftah W; Badji R; Al Thani A; Ismail SI; Gharavi AG; Abedalthagafi MS; Richards JB; Goldstein DB; Kiryluk K, 2020. Failure to replicate the association of rare loss-of-function variants in type I IFN immunity genes with severe COVID-19.  medRxiv.

Breeze CE; Reynolds AP; van Dongen J; Dunham I; Lazar J; Neph S; Vierstra J; Bourque G; Teschendorff AE; Stamatoyannopoulos JA; Beck S, 2019. eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data.  Bioinformatics 35(22):4767-4769

Shokoohi F; Stephens DA; Bourque G; Pastinen T; Greenwood CMT; Labbe A, 2019. A hidden markov model for identifying differentially methylated sites in bisulfite sequencing data.  Biometrics 75(1):210-221

Page DJ; Miossec MJ; Williams SG; Monaghan RM; Fotiou E; Cordell HJ; Sutcliffe L; Topf A; Bourgey M; Bourque G; Eveleigh R; Dunwoodie SL; Winlaw DS; Bhattacharya S; Breckpot J; Devriendt K; Gewillig M; Brook JD; Setchfield KJ; Bu'Lock FA; O'Sullivan J; Stuart G; Bezzina CR; Mulder BJM; Postma AV; Bentham JR; Baron M; Bhaskar SS; Black GC; Newman WG; Hentges KE; Lathrop GM; Santibanez-Koref M; Keavney BD, 2019. Whole Exome Sequencing Reveals the Major Genetic Contributors to Nonsyndromic Tetralogy of Fallot.  Circ Res 124(4):553-563

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, 2019. Correction to: Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome.  Genome Biol 20(1):89

Laperle J; Hébert-Deschamps S; Raby J; de Lima Morais DA; Barrette M; Bujold D; Bastin C; Robert MA; Nadeau JF; Harel M; Nordell-Markovits A; Veilleux A; Bourque G; Jacques PÉ, 2019. The epiGenomic Efficient Correlator (epiGeEC) tool allows fast comparison of user datasets with thousands of public epigenomic datasets.  Bioinformatics 35(4):674-676

Bourgey M; Dali R; Eveleigh R; Chen KC; Letourneau L; Fillon J; Michaud M; Caron M; Sandoval J; Lefebvre F; Leveque G; Mercier E; Bujold D; Marquis P; Van PT; Anderson de Lima Morais D; Tremblay J; Shao X; Henrion E; Gonzalez E; Quirion PO; Caron B; Bourque G, 2019. GenPipes: an open-source framework for distributed and scalable genomic analyses.  Gigascience 8.

Grajcarek J; Monlong J; Nishinaka-Arai Y; Nakamura M; Nagai M; Matsuo S; Lougheed D; Sakurai H; Saito MK; Bourque G; Woltjen K, 2019. Genome-wide microhomologies enable precise template-free editing of biologically relevant deletion mutations.  Nat Commun 10(1):4856

Chan D; Shao X; Dumargne MC; Aarabi M; Simon MM; Kwan T; Bailey JL; Robaire B; Kimmins S; San Gabriel MC; Zini A; Librach C; Moskovtsev S; Grundberg E; Bourque G; Pastinen T; Trasler JM, 2019. Customized MethylC-Capture Sequencing to Evaluate Variation in the Human Sperm DNA Methylome Representative of Altered Folate Metabolism.  Environ Health Perspect 127(8):87002

Jessa S; Blanchet-Cohen A; Krug B; Vladoiu M; Coutelier M; Faury D; Poreau B; De Jay N; Hébert S; Monlong J; Farmer WT; Donovan LK; Hu Y; McConechy MK; Cavalli FMG; Mikael LG; Ellezam B; Richer M; Allaire A; Weil AG; Atkinson J; Farmer JP; Dudley RWR; Larouche V; Crevier L; Albrecht S; Filbin MG; Sartelet H; Lutz PE; Nagy C; Turecki G; Costantino S; Dirks PB; Murai KK; Bourque G; Ragoussis J; Garzia L; Taylor MD; Jabado N; Kleinman CL, 2019. Stalled developmental programs at the root of pediatric brain tumors.  Nat Genet 51(12):1702-1713

Saulnier KM; Bujold D; Dyke SOM; Dupras C; Beck S; Bourque G; Joly Y, 2019. Benefits and barriers in the design of harmonized access agreements for international data sharing.  Sci Data 6(1):297

Chong J; Soufan O; Li C; Caraus I; Li S; Bourque G; Wishart DS; Xia J, 2018. MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis.  Nucleic Acids Res 46(W1):W486-W494

Venuto D; Bourque G, 2018. Identifying co-opted transposable elements using comparative epigenomics.  Dev Growth Differ 60(1):53-62

Kanagaratham C; Chiwara V; Ho B; Moussette S; Youssef M; Venuto D; Jeannotte L; Bourque G; de Sanctis JB; Radzioch D; Naumova AK, 2018. Loss of the zona pellucida-binding protein 2 (Zpbp2) gene in mice impacts airway hypersensitivity and lung lipid metabolism in a sex-dependent fashion.  Mamm Genome 29(3-4):281-298

Monlong J; Girard SL; Meloche C; Cadieux-Dion M; Andrade DM; Lafreniere RG; Gravel M; Spiegelman D; Dionne-Laporte A; Boelman C; Hamdan FF; Michaud JL; Rouleau G; Minassian BA; Bourque G; Cossette P, 2018. Global characterization of copy number variants in epilepsy patients from whole genome sequencing.  PLoS Genet 14(4):e1007285

Hirukawa A; Smith HW; Zuo D; Dufour CR; Savage P; Bertos N; Johnson RM; Bui T; Bourque G; Basik M; Giguère V; Park M; Muller WJ, 2018. Targeting EZH2 reactivates a breast cancer subtype-specific anti-metastatic transcriptional program.  Nat Commun 9(1):2547

Bourque G, 2018. Comparing Apples to Apples and Oranges to Oranges.  Trends Genet 34(8):571-572

Monlong J; Cossette P; Meloche C; Rouleau G; Girard SL; Bourque G, 2018. Human copy number variants are enriched in regions of low mappability.  Nucleic Acids Res 46(14):7236-7249

Goerner-Potvin P; Bourque G, 2018. Computational tools to unmask transposable elements.  Nat Rev Genet 19(11):688-704

Caron M; St-Onge P; Drouin S; Richer C; Sontag T; Busche S; Bourque G; Pastinen T; Sinnett D, 2018. Very long intergenic non-coding RNA transcripts and expression profiles are associated to specific childhood acute lymphoblastic leukemia subtypes.  PLoS One 13(11):e0207250

Bourque G; Burns KH; Gehring M; Gorbunova V; Seluanov A; Hammell M; Imbeault M; Izsvák Z; Levin HL; Macfarlan TS; Mager DL; Feschotte C, 2018. Ten things you should know about transposable elements.  Genome Biol 19(1):199

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(1):50

Ecker S; Chen L; Pancaldi V; Bagger FO; Fernández JM; Carrillo de Santa Pau E; Juan D; Mann AL; Watt S; Casale FP; Sidiropoulos N; Rapin N; Merkel A; Stunnenberg HG; Stegle O; Frontini M; Downes K; Pastinen T; Kuijpers TW; Rico D; Valencia A; Beck S; Soranzo N; Paul DS, 2017. Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types.  Genome Biol 18(1):18

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(1):214

Hamdan FF; Myers CT; Cossette P; Lemay P; Spiegelman D; Laporte AD; Nassif C; Diallo O; Monlong J; Cadieux-Dion M; Dobrzeniecka S; Meloche C; Retterer K; Cho MT; Rosenfeld JA; Bi W; Massicotte C; Miguet M; Brunga L; Regan BM; Mo K; Tam C; Schneider A; Hollingsworth G; FitzPatrick DR; Donaldson A; Canham N; Blair E; Kerr B; Fry AE; Thomas RH; Shelagh J; Hurst JA; Brittain H; Blyth M; Lebel RR; Gerkes EH; Davis-Keppen L; Stein Q; Chung WK; Dorison SJ; Benke PJ; Fassi E; Corsten-Janssen N; Kamsteeg EJ; Mau-Them FT; Bruel AL; Verloes A; Õunap K; Wojcik MH; Albert DVF; Venkateswaran S; Ware T; Jones D; Liu YC; Mohammad SS; Bizargity P; Bacino CA; Leuzzi V; Martinelli S; Dallapiccola B; Tartaglia M; Blumkin L; Wierenga KJ; Purcarin G; O'Byrne JJ; Stockler S; Lehman A; Keren B; Nougues MC; Mignot C; Auvin S; Nava C; Hiatt SM; Bebin M; Shao Y; Scaglia F; Lalani SR; Frye RE; Jarjour IT; Jacques S; Boucher RM; Riou E; Srour M; Carmant L; Lortie A; Major P; Diadori P; Dubeau F; D'Anjou G; Bourque G; Berkovic SF; Sadleir LG; Campeau PM; Kibar Z; Lafrenière RG; Girard SL; Mercimek-Mahmutoglu S; Boelman C; Rouleau GA; Scheffer IE; Mefford HC; Andrade DM; Rossignol E; Minassian BA; Michaud JL, 2017. High Rate of Recurrent De Novo Mutations in Developmental and Epileptic Encephalopathies.  Am J Hum Genet 101(5):664-685

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

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

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 31(12):1228-1242

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, 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

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(4):491-499

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(5):710-6

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(4):920-931

Ramsay L; Bourque G, 2016. In Silico Methods to Identify Exapted Transposable Element Families.  Methods Mol Biol 1400:33-45

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, 2016. ABCA7 rare variants and Alzheimer disease risk.  Neurology 86(23):2134-7

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

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

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(1):59

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(44):12360-12367

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(8):2137-2150

Torchia J; Golbourn B; Feng S; Ho KC; Sin-Chan P; Vasiljevic A; Norman JD; Guilhamon P; Garzia L; Agamez NR; Lu M; Chan TS; Picard D; de Antonellis P; Khuong-Quang DA; Planello AC; Zeller C; Barsyte-Lovejoy D; Lafay-Cousin L; Letourneau L; Bourgey M; Yu M; Gendoo DMA; Dzamba M; Barszczyk M; Medina T; Riemenschneider AN; Morrissy AS; Ra YS; Ramaswamy V; Remke M; Dunham CP; Yip S; Ng HK; Lu JQ; Mehta V; Albrecht S; Pimentel J; Chan JA; Somers GR; Faria CC; Roque L; Fouladi M; Hoffman LM; Moore AS; Wang Y; Choi SA; Hansford JR; Catchpoole D; Birks DK; Foreman NK; Strother D; Klekner A; Bognár L; Garami M; Hauser P; Hortobágyi T; Wilson B; Hukin J; Carret AS; Van Meter TE; Hwang EI; Gajjar A; Chiou SH; Nakamura H; Toledano H; Fried I; Fults D; Wataya T; Fryer C; Eisenstat DD; Scheinemann K; Fleming AJ; Johnston DL; Michaud J; Zelcer S; Hammond R; Afzal S; Ramsay DA; Sirachainan N; Hongeng S; Larbcharoensub N; Grundy RG; Lulla RR; Fangusaro JR; Druker H; Bartels U; Grant R; Malkin D; McGlade CJ; Nicolaides T; Tihan T; Phillips J; Majewski J; Montpetit A; Bourque G; Bader GD; Reddy AT; Gillespie GY; Warmuth-Metz M; Rutkowski S; Tabori U; Lupien M; Brudno M; Schüller U; Pietsch T; Judkins AR; Hawkins CE; Bouffet E; Kim SK; Dirks PB; Taylor MD; Erdreich-Epstein A; Arrowsmith CH; De Carvalho DD; Rutka JT; Jabado N; Huang A, 2016. Integrated (epi)-Genomic Analyses Identify Subgroup-Specific Therapeutic Targets in CNS Rhabdoid Tumors.  Cancer Cell 30(6):891-908

Gross JA; Lefebvre F; Lutz PE; Bacot F; Vincent D; Bourque G; Turecki G, 2016. Variations in 5-methylcytosine and 5-hydroxymethylcytosine among human brain, blood, and saliva using oxBS and the Infinium MethylationEPIC array.  Biol Methods Protoc 1(1):1-8

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

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

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 JHA; 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(5):1415-1429.e19

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 JHA; 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(5):1398-1414.e24

Bujold D; Morais DAL; 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(5):496-499.e2

Busche S; Shao X; Caron M; Kwan T; Allum F; Cheung WA; Ge B; Westfall S; Simon MM; 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

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(22):6301-13

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

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

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 (Phila Pa 1976) 40(8):537-43

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(3):1485-97

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(12):1894-904

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(9):3544-9

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(4):423-5

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(5):451-6

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(4):887-925

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

Singh PK; Bourque G; Craig NL; Dubnau JT; Feschotte C; Flasch DA; Gunderson KL; Malik HS; Moran JV; Peters JE; Slotkin RK; Levin HL, 2014. Mobile genetic elements and genome evolution 2014.  Mob DNA 5:26

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(5):490-508

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(10):1141-1152

Jacques PÉ; Jeyakani J; Bourque G, 2013. The majority of primate-specific regulatory sequences are derived from transposable elements.  PLoS Genet 9(5):e1003504

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(4):e1003470

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(4):586-98

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(12):R115

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(9):e46152

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(3):439-47

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

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(8):1328-38

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(5):676-87

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(5):665-75

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

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(3):26

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

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

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):631-4

Lin CH; Zhao H; Lowcay SH; Shahab A; Bourque G, 2010. webMGR: an online tool for the multiple genome rearrangement problem.  Bioinformatics 26(3):408-10

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

Zhao H; Bourque G, 2009. Recovering genome rearrangements in the mammalian phylogeny.  Genome Res 19(5):934-42

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(7269):58-64

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

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

Tesler G; Bourque G, 2008. Computational tools for the analysis of rearrangements in mammalian genomes.  Methods Mol Biol 422:145-70

Bourque G; Tesler G, 2008. Computational tools for the analysis of rearrangements in mammalian genomes.  Methods Mol Biol 452:431-55

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(6):1106-17

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(6):e87

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(3):286-98

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(6):828-38

Pontius JU; Mullikin JC; Smith DR; 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; O'Brien SJ, 2007. Initial sequence and comparative analysis of the cat genome.  Genome Res 17(11):1675-89

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(9):R82

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(2):735-52

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(4):431-40

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(8):559-65

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(5734):613-7

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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(1):30-40

Bourque G; Pevzner PA, 2002. Genome-scale evolution: reconstructing gene orders in the ancestral species.  Genome Res 12(1):26-36

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