

Publications
2025
Jin W., Deng Y., La Marca J.E., Lelliott E.J., Diepstraten S. T., König C., Tai L., Snetkova V., Dorighi K. M., Hoberecht L., Hedditch M.G., Whelan L., Healey G., Fayle D., Lau K., Potts M.A., Chen M.Z., Johnston A.P.R., Liao Y., Shi W., Kueh A. J., Haley B., Fortin J.P., Herold M.J. (2025) Advancing the genetic engineering toolbox by combining AsCas12a knock-in mice with ultra-compact screening. ​Nature Communications 16, 974. doi.org/10.1038/s41467-025-56282-2. ​​​
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2024
Thrift WJ, Lounsbury NW, Broadwell Q., Heidersbach A., Freund E., Abdolazimi Y., Phung QT, Chen J., Capietto AH, Tong AJ, Rose CM, Blanchette C., Lill JR, Haley B. , Delamarre L., Bourgon R., Liu K., Jhunjhunwala S. (2024) Vers la conception de cibles améliorées d'immunothérapie contre le cancer avec un modèle de présentation peptide-MHC-I, HLApollo. Nature Communications 15, 10752. doi.org/10.1038/s41467-024-54887-7
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Snetkova V., Galan C., Lopez R., Rios AR, Kudo T., Dorighi K., Warming S., Haley BJ (2024) Cas12a modifié par Degron améliore le criblage CRISPR à cellule unique. bioRxiv 2024. 12.08.627374.
est ce que je.org/10.1101/2024.12.08.627374
Gurung HR, Heidersbach AJ, Darwish M., Fung Chan PP, Li J., Beresini M., Zill OA, Wallace A., Tong AJ, Hascall D., Torres E., Chang A., Lou HW, Abdolazimi Y., Hammer C., Xavier-Magalhães A., Marcu A., Vaidya S., Le DD, Akhmetzyanova I., Oh SA, Moore AJ, Uche UN, Laur MB, Notturno RJ, Ebert PJR, Blanchette C., Haley B ., Rose CM (2024) Découverte systématique de paires néoépitope–HLA pour les néoantigènes partagés entre les patients et les types de tumeurs. Nature Biotechnology 42, 1107–1117. doi.org/10.1038/s41587-023-01945-y
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Dorighi KM, Zhu A., Fortin JP, Hung-Hao Lo J., Sudhamsu J., Wendorff TJ, Durinck S., Callow M., Foster SA, Haley B. (2024) Découverte accélérée de variants résistants aux médicaments grâce à une plateforme d'édition de bases mutagènes améliorée et évolutive. Cell Reports 43(6) : 114313. doi.org/10.1016/j.celrep.2024.114313
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Srinivasan R., Sun T., Sandles A., Wu D., Wang L., Heidersbach A., Ho C., Xie S., Ng A., Haley B . (2024)
Circuits CRISPR/Cas9 chimiquement inductibles pour la perturbation génétique à plage dynamique ultra-élevée. bioRxiv 2024.12.27.630546. doi.org/10.1101/2024.12.27.630546
Malong L., Roskosch J., Hager C., Fortin JP, Schmucki R., Callow MG, Weile C., Romeo V., Patsch C., Martin S., Costa M., Modrusan Z., Villaseñor R., Koller E., Haley B ., Spang A., Roudnicky F. (2024) Un criblage CRISPR/Cas9 révèle des protéines à l'interface endosome-Golgi qui modulent l'activité ASO cellulaire. bioRxiv 2024.12.17.628665. doi.org/10.1101/2024.12.17.628665
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2023
Guidi R., Wedeles C., Xu D., Kolmus K., Headland S.E., Teng G., Guillory J., Zeng Y.J., Cheung T.K., Chaudhuri S., Modrusan Z., Liang Y., Horswell S., Haley B., Rutz S., Rose C., Franke Y., Kirkpatrick D.S., Hackney J.A., Wilson M.S. (2023) Argonaute3-SF3B3 complex controls pre-mRNA splicing to restrain type 2 immunity. Cell Reports 42(12):113515. doi.org/10.1016/j.celrep.2023.113515
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Tong A-J., Leylek R., Herzner A-M., Rigas D., Wichner S., Blanchette C., Tahtinen S., Kemball C.C., Mellman I., Haley B., Freund E.C., Delamarre L. (2023) Nucleotide modifications enable rational design of TLR7-selective ligands by blocking RNase cleavage. Journal of Experimental Medicine 221(2): e20230341. doi.org/10.1084/jem.20230341
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Gurung H., Heidersbach A., Darwish M., Chan P., Li J., Beresini M., Zill O., Wallace A., Tong A-J., Hascall D., Torres E., Chang A., Lou K., Abdolazimi Y., Moore A., Uche U., Laur M., Notturno R., Ebert P.J.R., Blanchette C., Haley B., Rose C.M. (2023) Discovery of prevalent, clinically actionable tumor neoepitopes via integrated biochemical and cell-based platforms. Nature Biotechnology. Epub ahead of print. doi.org/10.1101/2022.10.27.513529
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Ortiz-Muñoz G., Brown M., Carbone C.B., Pechuan-Jorge X., Rouilly V., Lindberg H., Ritter A.T., Raghupathi G., Sun Q., Nicotra T., Mantri S.R., Yang A., Doerr J., Nagarkar D., Darmanis S., Haley B., Mariathasan S., Wang Y., Gomez-Roca C., de Andrea C.E., Spigel D., Wu T., Delamarre L., Schöneberg J., Modrusan Z., Price R., Turley S.J., Mellman I., Moussion C. (2023) In situ tumour arrays reveal early environmental control of cancer immunity. Nature 618:827-833. doi.org/10.1038/s41586-023-06132-2
Heidersbach A.J., Dorighi K.M., Gomez J.A., Jacobi A.M., Haley B. (2023) A versatile, high-efficiency platform for CRISPR-based gene activation.Nature Communications
14(1):902.doi:https://doi.org/10.1038/s41467-023-36452-w
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Freund E.C., Haag S.M., Haley B., Murthy A. Optimized Nonviral Gene Disruption in Primary Murine and Human Myeloid Cells. (2023) Methods in Molecular Biology 2618:201-217. doi: 10.1007/978-1-0716-2938-3_15
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Calses P.C., Pham V.C., Guarnaccia A.D., Choi M., Verschueren E., Bakker S.T., Pham T.H., Hinkle T., Liu C., Chang M.T., Kljavin N., Bakalarski C., Haley B., Zou J., Yan C., Song X., Lin X., Rowntree R., Ashworth A., Dey A., Lill J.R. (2023) TEAD proteins associate with DNA repair proteins to facilitate cellular recovery from DNA damage. Molecular & Cellular Proteomics 22(2):100496. doi.org/10.1016/j.mcpro.2023.100496
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2022
Chen H., Durinck S., Patel H., Foreman O., Mesh K., Eastham J., Caothien R., Newman R.J., Roose-Girma M., Darmanis S., Warming S., Lattanzi A., Liang Y., Haley B. (2022) Population-wide gene disruption in the murine lung epithelium via AAV-mediated delivery of CRISPR-Cas9 components. Molecular Therapy - Methods & Clinical Development. 27:431-449. doi.org/10.1016/j.omtm.2022.10.016
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Pribluda A., Daemen A., Lima A.N., Wang X., Hafner M., Poon C., Modrusan Z., Katakam A.K., Foreman O., Eastham J., Hung J., Haley B., Garcia J.T., Jackson E.L., Junttila M.R. (2022) EHMT2 methyltransferase governs cell identity in the lung and is required for KRASG12D tumor development and propagation. Elife (11):e57648. doi.org/10.7554/eLife.57648
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Deng Y., Diepstraten S.T., Potts M.A., Giner G., Trezise S., Ng A.P., Healey G., Kane S.R., Cooray A., Behrens K., Heidersbach A., Kueh A.J., Pal M., Wilcox S., Tai L., Alexander W.S., Visvader J.E., Nutt S.L., Strasser A., Haley B., Zhao Q., Kelly G.L., Herold M.J. (2022) Generation of a CRISPR activation mouse that enables modeling of aggressive lymphoma and interrogation of venetoclax resistance. Nature Communications 13(1):4739. doi.org/10.1038/s41467-022-32485-9
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Oh S.A., Senger K., Madireddi S., Shaw D., Akhmetzyanova I., Ishizuka I.E., Tarighat S., Lo J.H., Shaw D., Haley B., Rutz S. (2022) High efficiency, multiplexed non-viral engineering of human T cells using plasmid donor DNA. Journal of Experimental Medicine. 219(5):e20211530.
doi.org/10.1084%2Fjem.20211530
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Zimmerman-Savill K.M., Lee B.B., Oeh J., Lin J., Lin E., Chung W-J., Young A., Chen W., Mis M., Mesh K., Eastham J., Gnad F., Jiang Z., Stawiski E.W., Haley B., Daemen A., Want X., Koeppen H., Modrusan Z., Martin S.E., Sampath D., Lin K. (2022) Distinct resistance mechanisms arise to allosteric vs. ATP-competitive AKT inhibitors. Nature Communications 13(1):2057. doi.org/10.1038/s41467-022-29655-0
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Tahtinen S., Tong A-J., Himmels P., Oh J., Paler-Martinez A., Kim L., Wichner S., Oei Y., McCarron M.J., Freund E.C., Amir Z.A., de la Cruz C.C., Haley B., Blanchette C., Schartner J.M., Ye W., Yadav M., Sahin U., Delamarre L., Mellman I. (2022) IL-1 and IL-1ra are key regulators of the inflammatory response to RNA vaccines. Nature Immunology 23:532–542. doi.org/10.1038/s41590-022-01160-y
Venkatanarayan A., Liang J., Yen I., Shanahan F., Haley B., Phu L., Verschueren E., Hinkle T.B., Kan D., Segal E., Long J.E., Lima T., Liau N.P.D., Sudhamsu J., Li J., Klijn C., Piskol R., Junttila M.R., Shaw A.S., Merchant M., Chang M.T., Kirkpatrick D.S., Malek S. (2022) CRAF dimerization with ARAF regulates KRAS-driven tumor growth. Cell Reports 38(6):110351. doi.org/10.1016/j.celrep.2022.110351
Carver J., Kern M., Ko P., Greenwood-Goodwin M., Yu X.C., Duan D., Tang D., Misaghi S., Auslaender S., Haley B., Yuk I.H., Shen A. (2022) A ribonucleoprotein-based decaplex CRISPR/Cas9 knockout strategy for CHO host engineering. Biotechnology Progress 38(1):e3212. doi.org/10.1002/btpr.3212
Chang M.T., Shanahan F., Nguyen T.T.T., Staben S.T., Gazzard L., Yamazoe S., Wertz I.E., Piskol R., Yang Y.A., Modrusan Z., Haley B., Evangelista M., Malek S., Foster S.A., Ye X. (2022) Identifying transcriptional programs underlying cancer drug response with TraCe-seq. Nature Biotechnology 40(1):86-93. doi.org/10.1038/s41587-021-01005-3
Senger, K., Akhmetzyanova I., Haley B., Rutz, S., Oh, S. (2022) Plasmid-based donor templates for non-viral CRISPR/Cas9-mediated gene knock-in in human T cells. Current Protocols 2022 2(9):e538. doi.org/10.1002/cpz1.538
Senger K. and Haley B. (2022) Non-viral alternatives to delivery of CRISPR-Cas gene editing components.CRISPR-Cas9 Based Genome Editing for Treating Genetic Disorders and Diseases. CRC Press.183-223. eBook:9781003088516
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Département d'ophtalmologie, Université de Montréal Centre de recherche de l'Hôpital Maisonneuve-Rosemont
Pavillon Claudine D'Amours
5415 Boul. de l'Assomption
Montréal (Québec) H1T 2M4 Canada
