Publications
2022
Original Articles
Butler-Laporte, G., Povysil, G., Kosmicki, J. A., Cirulli, E. T., Drivas, T., Furini, S., Saad, C., Schmidt, A., Olszewski, P., Korotko, U., Quinodoz, M., Celik, E., Kundu, K., Walter, K., Jung, J., Stockwell, A. D., Sloofman, L. G., Jordan, D. M., Thompson, R. C., Del Valle, D., Simons, N., Cheng, E., Sebra, R., Schadt, E. E., Kim-Schulze, S., Gnjatic, S., Merad, M., Buxbaum, J. D., Beckmann, N. D., Charney, A. W., Przychodzen, B., Chang, T., Pottinger, T. D., Shang, N., Brand, F., Fava, F., Mari, F., Chwialkowska, K., Niemira, M., Pula, S., Baillie, J. K., Stuckey, A., Salas, A., Bello, X., Pardo-Seco, J., Gomez-Carballa, A., Rivero-Calle, I., Martinon-Torres, F., Ganna, A., Karczewski, K. J., Veerapen, K., Bourgey, M., Bourque, G., Eveleigh, R. J., Forgetta, V., Morrison, D., Langlais, D., Lathrop, M., Mooser, V., Nakanishi, T., Frithiof, R., Hultstrom, M., Lipcsey, M., Marincevic-Zuniga, Y., Nordlund, J., Barrett, K. M. S., Lee, W., Bolze, A., White, S., Riffle, S., Tanudjaja, F., Sandoval, E., Neveux, I., Dabe, S., Casadei, N., Motameny, S., Alaamery, M., Massadeh, S., Aljawini, N., Almutairi, M. S., Arabi, Y. M., Alqahtani, S. A., Al Harthi, F. S., Almutairi, A., Alqubaishi, F., Alotaibi, S., Binowayn, A., Alsolm, E. A., El Bardisy, H., Fawzy, M., Cai, F., Soranzo, N., Butterworth, A., Geschwind, D. H., Arteaga, S., Stephens, A., Butte, M. J., Boutros, P. C., Yamaguchi, T. N., Tao, S., Eng, S., Sanders, T., Tung, P. J., Broudy, M. E., Pan, Y., Gonzalez, A., Chavan, N., Johnson, R., Pasaniuc, B., Yaspan, B., Smieszek, S., Rivolta, C., Bibert, S., Bochud, P. Y., Dabrowski, M., Zawadzki, P., Sypniewski, M., Kaja, E., Chariyavilaskul, P., Nilaratanakul, V., Hirankarn, N., Shotelersuk, V., Pongpanich, M., Phokaew, C., Chetruengchai, W., Tokunaga, K., Sugiyama, M., Kawai, Y., Hasegawa, T., Naito, T., Namkoong, H., Edahiro, R., Kimura, A., Ogawa, S., Kanai, T., Fukunaga, K., Okada, Y., Imoto, S., Miyano, S., Mangul, S., Abedalthagafi, M. S., Zeberg, H., Grzymski, J. J., Washington, N. L., Ossowski, S., Ludwig, K. U., Schulte, E. C., Riess, O., Moniuszko, M., Kwasniewski, M., Mbarek, H., Ismail, S. I., Verma, A., Goldstein, D. B., Kiryluk, K., Renieri, A., Ferreira, M. A. R., Richards, J. B., Initiative, C.-H. G., De, C. O. I. H. G. G., Study, G.-C. M., Mt Sinai Clinical Intelligence, C., Consortium, G.-C., Gen, O. C., Japan, C.-T. F., & Regeneron Genetics, C. (2022). Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative. Plos Genetics, 18(11). doi:10.1371/journal.pgen.1010367
2021
Original Papers
Caron, M., St-Onge, P., Sontag, T., Wang, Y. C., Richer, C., Ragoussis, I., Sinnett, D., & Bourque, G. (2021). Single-cell analysis of childhood leukemia reveals a link between developmental states and ribosomal protein expression as a source of intra-individual heterogeneity (vol 10, 8079, 2020). Scientific Reports, 11(1). https://doi.org/10.1038/s41598-021-85034-7
Cheng, A. P., Cheng, M. P., Gu, W., Sesing Lenz, J., Hsu, E., Schurr, E., Bourque, G., Bourgey, M., Ritz, J., Marty, F. M., Chiu, C. Y., Vinh, D. C., & DeVlaminck, 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.e415. https://doi.org/10.1016/j.medj.2021.01.001
Dankner, M., Caron, M., Al-Saadi, T., Yu, W., Ouellet, V., Ezzeddine, R., Maritan, S. M., Annis, M.G., Le, P. U., Nadaf, J., Neubarth, N. S., Savage, P., Zuo, D., Couturier, C.P., Monlong, J., Djambazian, H., Altoukhi, H., Bourque, G., Ragoussis, J., Diaz, R. J., Park, M., Guiot, M. C., Lam, S., Petrecca, K., & Siegel, P. M.(2021). Invasive growth associated with Cold-Inducible RNA-Binding Protein expression drives recurrence of surgically resected brain metastases. NeuroOncol. https://doi.org/10.1093/neuonc/noab002
2020
Original Papers
Gordon, M. G., Inoue, F., Martin, B., Schubach, M.,Agarwal, V., Whalen, S., Feng, S. Y., Zhao, J. J., Ashuach, T., Ziffra, R., Kreimer,A., Georgakopoulos-Soares, I., Yosef, N., Ye, C. J., Pollard, K. S., Shendure,J., Kircher, M., & Ahituv, N. lentiMPRA and MPRAflow for high-throughputfunctional characterization of gene regulatory elements (vol 15, 2387, 2020). NatureProtocols. https://doi.org/10.1038/s41596-020-00422-z
Klein, J. C., Agarwal, V., Inoue, F., Keith, A.,Martin, B., Kircher, M., Ahituv, N., & Shendure, J. (2020). A systematicevaluation of the design and context dependencies of massively parallelreporter assays. Nature Methods, 17(11), 1083-+. https://doi.org/10.1038/s41592-020-0965-y
Groza, C., Kwan, T., Soranzo, N., Pastinen, T., & Bourque,G. (2020). Personalized and graph genomes reveal missing signal inepigenomic data. Genome Biology, 21(1). https://doi.org/10.1186/s13059-020-02038-8
Bogdan, L., Barreiro, L., & Bourque, G. (2020).Transposable elements have contributed human regulatory regions that areactivated upon bacterial infection. Philosophical Transactions of the RoyalSociety B-Biological Sciences, 375(1795). https://doi.org/10.1098/rstb.2019.0332
Caron, M., St-Onge, P., Sontag, T., Wang, Y. C., Richer,C., Ragoussis, I., Sinnett, D., & Bourque, G. (2020). Single-cellanalysis of childhood leukemia reveals a link between developmental states andribosomal protein expression as a source of intra-individual heterogeneity. ScientificReports, 10(1). https://doi.org/10.1038/s41598-020-64929-x
Hocking, T. D., & Bourque, G. (2020). Machinelearning algorithms for simultaneous supervised detection of peaks in multiplesamples and cell types. Pac Symp Biocomput, 25, 367-378.
Zhuang, Q. K. W., Galvez, J. H., Xiao, Q., AlOgayil, N.,Hyacinthe, J., Taketo, T., Bourque, G., & Naumova, A. K. (2020). SexChromosomes and Sex Phenotype Contribute to Biased DNA Methylation in MouseLiver. Cells, 9(6). https://doi.org/10.3390/cells9061436
2019
Original Papers
Bourgey, M., Dali, R., Eveleigh, R., Chen, K. C., Letourneau, L., Fillon, J., Michaud, M., Caron, M., Sandoval, J., Lefebvre, F., Leveque, G., Mercier, E., Bujold, D., Marquis, P., Van, P. T., Morais, D. A. D., Tremblay, J., Shao, X. J., Henrion, E., Gonzalez, E., Quirion, P. O., Caron, B., & Bourque, G. (2019). GenPipes: an open-source framework for distributed and scalable genomicanalyses. Gigascience, 8(6). https://doi.org/10.1093/gigascience/giz037
Breeze, C. E., Reynolds, A. P., van Dongen, J., Dunham, I., Lazar, J., Neph, S., Vierstra, J., Bourque, G., Teschendorff, A. E., Stamatoyannopoulos, J. A., & Beck, S. (2019). eFORGE v2.0: updated analysis of cell type-specificsignal in epigenomic data. Bioinformatics, 35(22), 4767-4769. https://doi.org/10.1093/bioinformatics/btz456
Chan, D., Shao, X., Dumargne, M. C., Aarabi, M., Simon, M. M., Kwan, T., Bailey, J. L., Robaire, B., Kimmins, S., San Gabriel, M. C., Zini, A., Librach, C., Moskovtsev, S., Grundberg, E., Bourque, G., Pastinen, T., & Trasler, J. M. (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. https://doi.org/10.1289/EHP4812
Chehboun, S., Leiva-Torres, G. A., Charbonneau, B., Eveleigh, R., Bourque, G., &Vidal, S. M. (2020). A point mutation in the linker domain of mouse STAT5A is associated with impaired NK-cell regulation. Genes Immun, 21(2), 136-141. https://doi.org/10.1038/s41435-019-0088-6
Grajcarek, J., Monlong, J., Nishinaka-Arai, Y., Nakamura, M., Nagai, M., Matsuo, S., Lougheed, D., Sakurai, H., Saito, M. K., Bourque, G., & Woltjen, K. (2019). Genome-wide microhomologies enable precise template-free editing ofbiologically relevant deletion mutations. Nature Communications, 10. https://doi.org/10.1038/s41467-019-12829-8
Jessa, S., Blanchet-Cohen, A., Krug, B., Vladoiu, M., Coutelier, M., Faury, D., Poreau, B., De Jay, N., Hebert, S., Monlong, J., Farmer, W. T., Donovan, L. K., Hu, Y. X., McConechy, M. K., Cavalli, F. M. G., Mikael, L. G., Ellezam, B., Richer, M., Allaire, A., Weil, A. G., Atkinson, J., Farmer, J. P., Dudley, R.W. R., Larouche, V., Crevier, L., Albrecht, S., Filbin, M. G., Sartelet, H., Lutz, P. E., Nagy, C., Turecki, G., Costantino, S., Dirks, P. B., Murai, K. K., Bourque, G., Ragoussis, J., Garzia, L., Taylor, M. D., Jabado, N., &Kleinman, C. L. (2019). Stalled developmental programs at the root of pediatricbrain tumors. Nature Genetics, 51(12), 1702-+. https://doi.org/10.1038/s41588-019-0531-7
Laperle, J., Hebert-Deschamps, S., Raby, J., Morais, D. A. D., Barrette, M., Bujold, D., Bastin, C., Robert, M. A., Nadeau, J. F., Harel, M., Nordell-Markovits, A., Veilleux, A., Bourque, G., & Jacques, P. E. (2019). The epiGenomic Efficient Correlator (epiGeEC) tool allows fast comparison of user datasets with thousands of public epigenomic datasets. Bioinformatics, 35(4), 674-676. https://doi.org/10.1093/bioinformatics/bty655
Page, D. J., Miossec, M. J., Williams, S. G., Monaghan, R. M., Fotiou, E., Cordell, H. J., Sutcliffe, L., Topf, A., Bourgey, M., Bourque, G., Eveleigh, R., Dunwoodie, S. L., Winlaw, D. S., Bhattacharya, S., Breckpot, J., Devriendt, K., Gewillig, M., Brook, J. D., Setchfield, K. J., Bu’Lock, F. A., O’Sullivan, J., Stuart, G., Bezzina, C. R., Mulder, B. J. M., Postma, A. V., Bentham, J. R., Baron, M., Bhaskar, S. S., Black, G. C., Newman, W. G., Hentges, K. E., Lathrop, G. M., Santibanez-Koref, M., & Keavney, B. D. (2019). Whole Exome Sequencing Reveals the Major Genetic Contributors to Nonsyndromic Tetralogy of Fallot. CirculationResearch, 124(4), 553-563. https://doi.org/10.1161/circresaha.118.313250
Saulnier, K. M., Bujold, D., Dyke, S. O. M., Dupras, C., Beck, S., Bourque, G., &Joly, Y. (2019). Benefits and barriers in the design of harmonized access agreements for international data sharing. ScientificData, 6. https://doi.org/10.1038/s41597-019-0310-4
Shokoohi, F., Stephens, D. A., Bourque, G., Pastinen, T., Greenwood, C. M. T., &Labbe, A. (2019). A hidden markov model for identifying differentially methylated sites in bisulfite sequencing data. Biometrics, 75(1), 210-221. https://doi.org/10.1111/biom.12965