Bourque Group


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).

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.

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.


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.

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-+.

Groza, C., Kwan, T., Soranzo, N., Pastinen, T., & Bourque,G. (2020). Personalized and graph genomes reveal missing signal inepigenomic data. Genome Biology, 21(1).

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).

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).

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).


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).

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.

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.

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.

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.

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-+.

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.

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.

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.

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.