Publications

Global genetic interaction network of a human cell maps conserved principles and informs functional interpretation of gene co-essentiality profiles.

Billmann M, Costanzo M, Zhang X, Hassan AZ, Rahman M, Brown KR, Chan KS, Tong AHY, Pons C, Ward HN, Ross C, van Leeuwen J, Aregger M, Lawson KA, Mair B, Roth AF, Sen NE, Forster DT, Tan G, Mero P, Masud SN, Lee Y, Aguilera-Uribe M, Ušaj M, Almeida SMT, Aulakh K, Bhojoo U, Birkadze S, Budijono N, Cai X, Caumanns JJ, Chalmers JJ, Chandrashekhar M, Chang D, Climie R, Dasgupta K, Drazic A, Echenique JIR, Gacesa R, Farias AG, Habsid A, Horecka I, Kantautas K, Ji F, Kim DK, Lee SY, Liang W, Lim HJ, Lin K, Lu X, Maier M, Nami B, Nixon A, Mikolajewicz N, Mokhtaridoost M, Nedyalkova L, Rohde T, Rodrigues MS, Soste M, Schultz E, Wang W, Seetharaman A, Shuteriqi E, Sizova O, Taylor DT, Tereshchenko M, Tieu D, Turowec J, Ubhi T, Varland S, Wang KE, Wang ZY, Wei J, Xiao YX, Maass PG, Reversade B, Brown GW, Cravatt BF, Dixon SJ, Wyatt HDM, Röst HL, Roth FP, Xia T, Bader GD, Loewith R, Davis NG, Andrews B, Myers CL, Moffat J, Boone C.  Cell. 2026 Jun 11;189(12):3736-3759.e58. 

Generation of Allogeneic CAR-T Circumvents Functional Deficits in Patient-Derived Autologous Product for Glioblastoma.

Salim SK, Shaikh MV, Wei J, Maich WT, Anand A, Tang OY, Subapanditha MK, Alizada Z, Suk Y, Singh M, Zhai K, Khanna A, Brakel B, Dimitrov V, Tabunshchyk Z, Chan K, Brown KR, Vora P, O’Rourke DM, Binder ZA, Venugopal C, Moffat J, Singh SK. Generation of Allogeneic CAR-T Circumvents Functional Deficits in Patient-Derived Autologous Product for Glioblastoma. Int J Cancer. 2026 Apr 24. 

Reactive oligodendrocytes promote glioblastoma progression through CCL5/CCR5-mediated glioma stem cell maintenance.

Genetic suppression features ABHD18 as a Barth syndrome therapeutic target.

Masud SN, Srivastava A, Mero P, Echezarreta VS, Anderson E, van Buren L, Wei J, Taylor DT, Farias AG, Mikolajewicz N, Shaw A, Murareanu BM, Lohbihler M, Carney OS, van Heeringen S, Clijsters L, Sizova O, van Ameijde J, Nye F, Habsid A, Nedyalkova L, McDonald L, Simpson C, Wybenga-Groot L, Brown KR, Nho N, Suciu RM, Chan K, Tong AHY, Vaz FM, Evers B, Lesurf R, Papaz T, Nutter LMJ, Protze S, Billmann M, Costanzo M, Andrews BJ, Myers CL, Mital S, Vernon H, Brummelkamp TR, Boone C, Scott IC, Niphakis MJ, Strathdee D, Nijman SMB, Blomen VA, Moffat J.  Nature. 2025 Sep;645(8082):1029-1038.  

Phenotypic screens for SIRPA expression reveal RAB21 as a general regulator of macrophage surface identity.

Granda Farias A, Feng B, Khan S, Ngo W, Wu JLY, Aguilera-Uribe M, Grewal S, Mero P, Singh SK, Kislinger T, Chan WCW, Moffat J.  Cell Rep. 2025 Jul 22;44(7):115921. 

Protocol for CRISPR-based endogenous protein tagging in mammalian cells.

Xiao YX, Wei J, Philip R, Sharma A, Pelletier L, Moffat J.  STAR Protoc. 2025 Mar 21;6(1):103571. 

Functional profiling of murine glioma models highlights targetable immune evasion phenotypes.

Mikolajewicz N, Tatari N, Wei J, Savage N, Granda Farias A, Dimitrov V, Chen D, Zador Z, Dasgupta K, Aguilera-Uribe M, Xiao YX, Lee SY, Mero P, McKenna D, Venugopal C, Brown KR, Han H, Singh S, Moffat J.  Acta Neuropathol. 2024 Nov 27;148(1):74.

Targeting axonal guidance dependencies in glioblastoma with ROBO1 CAR T cells.

Chokshi CR, Shaikh MV, Brakel B, Rossotti MA, Tieu D, Maich W, Anand A, Chafe SC, Zhai K, Suk Y, Kieliszek AM, Miletic P, Mikolajewicz N, Chen D, McNicol JD, Chan K, Tong AHY, Kuhlmann L, Liu L, Alizada Z, Mobilio D, Tatari N, Savage N, Aghaei N, Grewal S, Puri A, Subapanditha M, McKenna D, Ignatchenko V, Salamoun JM, Kwiecien JM, Wipf P, Sharlow ER, Provias JP, Lu JQ, Lazo JS, Kislinger T, Lu Y, Brown KR, Venugopal C, Henry KA, Moffat J, Singh SK.  Nat Med. 2024 Oct;30(10):2936-2946.

The TSC22D, WNK, and NRBP gene families exhibit functional buffering and evolved with Metazoa for cell volume regulation.

Xiao YX, Lee SY, Aguilera-Uribe M, Samson R, Au A, Khanna Y, Liu Z, Cheng R, Aulakh K, Wei J, Farias AG, Reilly T, Birkadze S, Habsid A, Brown KR, Chan K, Mero P, Huang JQ, Billmann M, Rahman M, Myers C, Andrews BJ, Youn JY, Yip CM, Rotin D, Derry WB, Forman-Kay JD, Moses AM, Pritišanac I, Gingras AC, Moffat J.  Cell Rep. 2024 Jul 23;43(7):114417.

Survival-based CRISPR genetic screens across a panel of permissive cell lines identify common and cell-specific SARS-CoV-2 host factors.

Chan K, Farias AG, Lee H, Guvenc F, Mero P, Brown KR, Ward H, Billmann M, Aulakh K, Astori A, Haider S, Marcon E, Braunschweig U, Pu S, Habsid A, Yan Tong AH, Christie-Holmes N, Budylowski P, Ghalami A, Mubareka S, Maguire F, Banerjee A, Mossman KL, Greenblatt J, Gray-Owen SD, Raught B, Blencowe BJ, Taipale M, Myers C, Moffat J.  Heliyon. 2023 Jan;9(1):e12744.

Chemical genomics with pyrvinium identifies C1orf115 as a regulator of drug efflux.

Masud SN, Chandrashekhar M, Aregger M, Tan G, Zhang X, Mero P, Pirman DA, Zaslaver O, Smolen GA, Lin ZY, Wong CJ, Boone C, Gingras AC, Montenegro-Burke JR, Moffat J.  Nat Chem Biol. 2022 Dec;18(12):1370-1379. 

Method to Map Gene Essentiality of Human Pluripotent Stem Cells by Genome-Scale CRISPR Screens with Inducible Cas9.

Mair B, Aregger M, Tong AHY, Chan KSK, Moffat J. A  Methods Mol Biol. 2022;2377:1-27.

Systematic mapping of genetic interactions for de novo fatty acid synthesis identifies C12orf49 as a regulator of lipid metabolism.

Aregger M, Lawson KA, Billmann M, Costanzo M, Tong AHY, Chan K, Rahman M, Brown KR, Ross C, Usaj M, Nedyalkova L, Sizova O, Habsid A, Pawling J, Lin ZY, Abdouni H, Wong CJ, Weiss A, Mero P, Dennis JW, Gingras AC, Myers CL, Andrews BJ, Boone C, Moffat J. Nat Metab. 2020 Jun;2(6):499-513.

Genetic interaction mapping and exon-resolution functional genomics with a hybrid Cas9-Cas12a platform.

Gonatopoulos-Pournatzis T, Aregger M, Brown KR, Farhangmehr S, Braunschweig U, Ward HN, Ha KCH, Weiss A, Billmann M, Durbic T, Myers CL, Blencowe BJ, Moffat J. Nat Biotechnol. 2020 May;38(5):638-648.

Pooled CRISPR-Based Genetic Screens in Mammalian Cells.

Chan K, Tong AHY, Brown KR, Mero P, Moffat J.  J Vis Exp. 2019 Sep 4;(151). 

CRISPR screens are feasible in TP53 wild-type cells.

Brown KR, Mair B, Soste M, Moffat J.  Mol Syst Biol. 2019 Aug;15(8):e8679. 

Essential Gene Profiles for Human Pluripotent Stem Cells Identify Uncharacterized Genes and Substrate Dependencies.

Mair B, Tomic J, Masud SN, Tonge P, Weiss A, Usaj M, Tong AHY, Kwan JJ, Brown KR, Titus E, Atkins M, Chan KSK, Munsie L, Habsid A, Han H, Kennedy M, Cohen B, Keller G, Moffat J. . Cell Rep. 2019 Apr 9;27(2):599-615.e12. 

A rapid in vitro methodology for simultaneous target discovery and antibody generation against functional cell subpopulations.

Nixon AML, Duque A, Yelle N, McLaughlin M, Davoudi S, Pedley NM, Haynes J, Brown KR, Pan J, Hart T, Gilbert PM, Singh SK, O'Brien CA, Sidhu SS, Moffat J. Sci Rep. 2019 Jan 29;9(1):842.

Pooled Lentiviral CRISPR-Cas9 Screens for Functional Genomics in Mammalian Cells.

Aregger M, Chandrashekhar M, Tong AHY, Chan K, Moffat J.  Methods Mol Biol. 2019;1869:169-188.

Evaluation and Design of Genome-Wide CRISPR/SpCas9 Knockout Screens.

Hart T, Tong AHY, Chan K, Van Leeuwen J, Seetharaman A, Aregger M, Chandrashekhar M, Hustedt N, Seth S, Noonan A, Habsid A, Sizova O, Nedyalkova L, Climie R, Tworzyanski L, Lawson K, Sartori MA, Alibeh S, Tieu D, Masud S, Mero P, Weiss A, Brown KR, Usaj M, Billmann M, Rahman M, Constanzo M, Myers CL, Andrews BJ, Boone C, Durocher D, Moffat J. G3 (Bethesda). 2017 Aug 7;7(8):2719-2727. 

BAGEL: a computational framework for identifying essential genes from pooled library screens.

Hart T, Moffat J.  BMC Bioinformatics. 2016 Apr 16;17:164. 

High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities.

Genetic interaction mapping and exon-resolution functional genomics with a hybrid Cas9-Cas12a platform.

Gonatopoulos-Pournatzis T, Aregger M, Brown KR, Farhangmehr S, Braunschweig U, Ward HN, Ha KCH, Weiss A, Billman M, Durbic T, Myers CL, Blencowe BJ, Moffat J. Nature Biotechnology. 2020 May;38(5):638-648.

Systematic mapping of genetic interactions for de novo fatty acid synthesis identifies C12orf49 as a regulator of lipid metabolism.

Aregger M, Lawson KA, Billmann M, Costanzo M, Tong AHY, Chan K, Rahman M, Brown KR, Ross C, Usaj M, Nedyalkova L, Sizova O, Habsid A, Pawling J, Lin ZY, Abdouni H, Wong CJ, Weiss A, Mero P, Dennis JW, Gingras AC, Myers CL, Andrews BJ, Boone C, Moffat J. Nat Metabolism. 2020 Jun; 2(6):499-513.

Functional genomic landscape of cancer-intrinsic evasion of killing by T cells.

Lawson KA, Sousa CM, Zhang X, Kim E, Akthar R, Caumanns JJ, Yao Y, Mikolajewicz N, Abou Zid A, Fan ZP, Hui S, Krall JA, Simons DM, Slater CJ, De Jesus V, Tang L, Singh R, Goldford JE, Martin S, Huang Q, Francis EA, Habsid A, Climie R, Tieu D, Wei J, Li R, Tong AHY, Aregger M, Chan KS, Han H, Wang X, Mero P, Brumell JH, Finelli A, Ailles L, Bader G, Smolen GA, Kingsbury GA, Hart T, Kung C, Moffat J. Nature, 2020 Oct; 586(7827):120-126.

Chemical genomics with pyrvinium identifies C1orf115 as a regulator of drug efflux

Masud, S. N., Chandrashekhar, M., Aregger, M., Tan, G., Zhang, X., Mero, P., Pirman, D. A., Zaslaver, O., Smolen, G. A., Lin, Z.-Y., Wong, C. J., Boone, C., Gingras, A.-C., Montenegro-Burke, J. R., & Moffat, J. Nature Chemical Biology, 2022 Dec; 18(12): 1370–1379.

Essential gene profiles in breast, pancreatic, and ovarian cancer cells.

Marcotte R, Brown KR, Suarez F, Sayad A, Karamboulas K, Krzyzanowski PM, Sircoulomb F, Medrano M, Fedyshyn Y, Koh JLY, van Dyk D, Fedyshyn B, Luhova M, Brito GC, Vizeacoumar FJ, Vizeacoumar FS, Datti A, Kasimer D, Buzina A, Mero P, Misquitta C, Normand J, Haider M, Ketela T, Wrana JL, Rottapel R, Neel BG, Moffat J. Cancer Discovery. 2012 Feb;2(2):172-189.