Gigabase-scale deletion scanning of the human genome

Koeppel J, Keith A, Sgrizzi S, Chen P, Daza RM, Quaisar F, Anastasia E, Song Z, Shendure J, Pinglay S.

2026

doi:10.64898/2026.05.29.728882.

Chromothripsis and ecDNA initiated by N4BP2 nuclease fragmentation of cytoplasm-exposed chromosomes.

Krupina K, Goginashvili A, Baughn MW, Moore S, Steele CD, Nguyen AT, Zhang DL, Koeppel J, Trivedi P, Malhotra A, Jenkins D, Shiau AK, Miyake Y, Koga T, Miki S, Furnari FB, Campbell PJ, Alexandrov LB, Cleveland DW.

Science (New York, N.Y.), 2025

doi:10.1126/science.ado0977.

Randomizing the human genome by engineering recombination between repeat elements.

Koeppel J, Ferreira R, Vanderstichele T, Riedmayr LM, Peets EM, Girling G, Weller J, Murat P, Liberante FG, Ellis T, Church GM, Parts L.

Science (New York, N.Y.), 2025

doi:10.1126/science.ado3979.

Multiplex generation and single-cell analysis of structural variants in mammalian genomes.

Pinglay S, Lalanne JB, Daza RM, Kottapalli S, Quaisar F, Koeppel J, Garge RK, Li X, Lee DS, Shendure J.

Science (New York, N.Y.), 2025

doi:10.1126/science.ado5978.

Resolution of a human super-enhancer by targeted genome randomisation

Koeppel J, Murat P, Girling G, Peets EM, Gouley M, Rebernig V, Maheshwari A, Hepkema J, Weller J, Johnkingsly Jebaraj JH, Crawford R, Liberante FG, Parts L.

2025

doi:10.1101/2025.01.14.632548.

Engineering structural variants to interrogate genome function.

Koeppel J, Weller J, Vanderstichele T, Parts L.

Nature genetics, 2024

doi:10.1038/s41588-024-01981-7.

Base editing screens define the genetic landscape of cancer drug resistance mechanisms.

Coelho MA, Strauss ME, Watterson A, Cooper S, Bhosle S, Illuzzi G, Karakoc E, Dinçer C, Vieira SF, Sharma M, Moullet M, Conticelli D, Koeppel J, McCarten K, Cattaneo CM, Veninga V, Picco G, Parts L, Forment JV, Voest EE, Marioni JC, Bassett A, Garnett MJ.

Nature genetics, 2024

doi:10.1038/s41588-024-01948-8.

Randomizing the human genome by engineering recombination between repeat elements

Koeppel J, Ferreira R, Vanderstichele T, Riedmayr LM, Peets EM, Girling G, Weller J, Liberante FG, Ellis T, Church GM, Parts L.

2024

doi:10.1101/2024.01.22.576745.

Prediction of prime editing insertion efficiencies using sequence features and DNA repair determinants.

Koeppel J, Weller J, Peets EM, Pallaseni A, Kuzmin I, Raudvere U, Peterson H, Liberante FG, Parts L.

Nature biotechnology, 2023

doi:10.1038/s41587-023-01678-y.

BTB_BCL6 dimers as building blocks for reversible drug-induced protein oligomerization.

Nitsch L, Jensen P, Yoon H, Koeppel J, Burman SSR, Fischer ES, Scholl C, Fröhling S, Słabicki M.

Cell reports methods, 2022

doi:10.1016/j.crmeth.2022.100193.

Small-molecule-induced polymerization triggers degradation of BCL6.

Słabicki M, Yoon H, Koeppel J, Nitsch L, Roy Burman SS, Di Genua C, Donovan KA, Sperling AS, Hunkeler M, Tsai JM, Sharma R, Guirguis A, Zou C, Chudasama P, Gasser JA, Miller PG, Scholl C, Fröhling S, Nowak RP, Fischer ES, Ebert BL.

Nature, 2020

doi:10.1038/s41586-020-2925-1.

Selection of Oncogenic Mutant Clones in Normal Human Skin Varies with Body Site.

Fowler JC, King C, Bryant C, Hall MWJ, Sood R, Ong SH, Earp E, Fernandez-Antoran D, Koeppel J, Dentro SC, Shorthouse D, Durrani A, Fife K, Rytina E, Milne D, Roshan A, Mahububani K, Saeb-Parsy K, Hall BA, Gerstung M, Jones PH.

Cancer discovery, 2020

doi:10.1158/2159-8290.cd-20-1092.

The CDK inhibitor CR8 acts as a molecular glue degrader that depletes cyclin K.

Słabicki M, Kozicka Z, Petzold G, Li YD, Manojkumar M, Bunker RD, Donovan KA, Sievers QL, Koeppel J, Suchyta D, Sperling AS, Fink EC, Gasser JA, Wang LR, Corsello SM, Sellar RS, Jan M, Gillingham D, Scholl C, Fröhling S, Golub TR, Fischer ES, Thomä NH, Ebert BL.

Nature, 2020

doi:10.1038/s41586-020-2374-x.