• Laisné, M., Lupien, M. & Vallot, C. (2024) Epigenomic heterogeneity as a source of tumour evolution. Nat Rev Cancer. https://doi.org/10.1038/s41568-024-00757-9.
• Zhao SG, Bootsma M, Zhou S, Shrestha R, Moreno-Rodriguez T, Lundberg A, Pan C, Arlidge C, Hawley JR, Foye A, Weinstein AS, Sjöström M, Zhang M, Li H, Chesner LN, Rydzewski NR, Helzer KT, Shi Y; West Coast Dream Team Consortium; Lynch M, Dehm SM, Lang JM, Alumkal JJ, He HH, Wyatt AW, Aggarwal R, Zwart W, Small EJ, Quigley DA, Lupien M, Feng FY. (2024). Integrated analyses highlight interactions between the three-dimensional genome and DNA, RNA and epigenomic alterations in metastatic prostate cancer. Nat Genet. doi: 10.1038/s41588-024-01826-3. PMID: 39020220.
• Grillo G, Keshavarzian T, Linder S, Arlidge C, Mout L, Nand A, Teng M, Qamra A, Zhou S, Kron KJ, Murison A, Hawley JR, Fraser M, van der Kwast TH, Raj GV, He HH, Zwart W, Lupien M. (2023). Transposable elements are co-opted as oncogenic regulatory elements by lineage-specific transcription factors in prostate cancer. Cancer Discov.13(11):2470-2487. doi: 10.1158/2159-8290.CD-23-0331. PMID: 37694973.
• Wu Q, Nie DY, Ba-Alawi W, Ji Y, Zhang Z, Cruickshank J, Haight J, Ciamponi FE, Chen J, Duan S, Shen Y, Liu J, Marhon SA, Mehdipour P, Szewczyk MM, Dogan-Artun N, Chen W, Zhang LX, Deblois G, Prinos P, Massirer KB, Barsyte-Lovejoy D, Jin J, De Carvalho DD, Haibe-Kains B, Wang X, Cescon DW, Lupien M, Arrowsmith CH. (2022). PRMT inhibition induces a viral mimicry response in triple-negative breast cancer. Nat Chem Biol. doi: 10.1038/s41589-022-01024-4. PMID: 35578032.
• Takayama N, Murison A, Takayanagi SI, Arlidge C, Zhou S, Garcia-Prat L, Chan-Seng-Yue M, Zandi S, Gan OI, Boutzen H, Kaufmann KB, Trotman-Grant A, Schoof E, Kron K, Díaz N, Lee JJY, Medina T, De Carvalho DD, Taylor MD, Vaquerizas JM, Xie SZ, Dick JE, Lupien M. (2021). The Transition from Quiescent to Activated States in Human Hematopoietic Stem Cells Is Governed by Dynamic 3D Genome Reorganization. Cell Stem Cell, 28(3), 488-501.e10. doi: 10.1016/j.stem.2020.11.001. PMID: 33242413.
• Deblois G, Madani Tonekaboni SA, Grillo G, Martinez C, Kao TI, Tai F, Ettayebi I, Fortier A-M, Savage P, Fedor AN, Liu X, Guilhamon P, Lima Fernandes E, Murison A, Kuasne H, Ba-alawi W, Cescon DW, Arrowsmith CH, De Carvalho DD, Haibe-Kains B, Locasale JW, Park M and Lupien M. (2020). Epigenetic switch-induced viral mimicry evasion in chemotherapy resistant breast cancer. Cancer Discovery. doi: 10.1158/2159-8290.CD-19-1493. PMID: 32546577.
• Mazrooei P, Kron KJ, Zhu Y, Zhou S, Grillo G, Mehdi T, Ahmed M, Severson TM, Guilhamon P, Sinnott-Armstrong N, Huang V, Yamaguchi TN, Fraser M, van der Kwast T, Boutros PC, He HH, Bergman AM, Bristow RG, Zwart W and Lupien M. (2019) Cistrome partitioning reveals convergence of somatic mutations and risk variants on master transcription regulators in primary prostate tumors. Cancer Cell. 36:674-689. doi: https: //doi.org/10.1016/j.ccell.2019.10.005. PMID: 31735626.
• Bailey SD, Desai K, Kron KJ, Mazrooei P, Sinnott-Armstrong NA, Treloar AE, Dowar M, Thu KL, Cescon DW, Silvester J, Yang SY, Wu X, Pezo RC, Haibe-Kains B, Mak TW, Bedard PL, Pugh TJ, Sallari RC, Lupien M. (2016). Noncoding somatic and inherited single-nucleotide variants converge to promoter ESR1 expression in breast cancer. Nat Genet. 48: 1260-1266. doi: 10.1038/ng.3650. PMID: 27571262.

See Dr. Lupien’s recent publications on PubMed or on Google Scholar.

• Cross Cell-type Correlation in DNA accessibility (C3D)
• Variant Set Enrichment (VSE)
• Allele-specific Bias in Binding from ChIP-seq (ABC)
• Intra-Genomic Replicates (IGR)