Peter Van Loo, Ph.D.

Peer-Reviewed Articles

1. Tang C, Sherry AD, Seo A, Hara K, Choi H, Liu S, Sun X, Montoya A, Ludmir EB, Shah AY, Jonasch E, Zurita AJ, Kovitz C, Alhalabi O, Goswami S, Hahn AW, Campbell MT, Hernandez A, Nead KT, Van Loo P, Su S, Battey CJ, LaBella ML, Ratzel S, Acevedo A, Genovese G, Sircar K, Karam JA, Tannir NM, Msaouel P. Metastasis-directed radiotherapy without systemic therapy for oligometastatic clear-cell renal-cell carcinoma: primary efficacy analysis of a single-arm, single-centre, phase 2 trial. Lancet Oncol, 2025. e-Pub 2025. PMID: 40915303.
2. Gimeno-Valiente F, Castignani C, Larose Cadieux E, Mensah NE, Liu X, Chen K, Chervova O, Karasaki T, Weeden CE, Richard C, Lai S, Martinez-Ruiz C, Lim EL, Frankell AM, Watkins TBK, Stavrou G, Usaite I, Lu WT, Marinelli D, Saghafinia S, Wilson GA, Dhami P, Vaikkinen H, Steif J, Veeriah S, Hynds RE, Hirst M, Hiley C, Feber A, Deniz O, Jamal-Hanjani M, McGranahan N, Beck S, Demeulemeester J, Tanic M, Swanton C, Van Loo P, Kanu N. DNA methylation cooperates with genomic alterations during non-small cell lung cancer evolution. Nat Genet 57(9):2226-2237, 2025. e-Pub 2025. PMID: 40931149.
3. Salcedo A, Tarabichi M, Buchanan A, Espiritu SMG, Zhang H, Zhu K, Ou Yang TH, Leshchiner I, Anastassiou D, Guan Y, Jang GH, Mootor MFE, Haase K, Deshwar AG, Zou W, Umar I, Dentro S, Wintersinger JA, Chiotti K, Demeulemeester J, Jolly C, Sycza L, Ko M, Wedge DC, Morris QD, Ellrott K, Van Loo P, Boutros PC. Crowd-sourced benchmarking of single-sample tumor subclonal reconstruction. Nat Biotechnol 43(4):581-592, 2025. e-Pub 2025. PMID: 38862616.
4. Bentham, R, Jones, TP, Black, JR, Martínez-Ruiz, C, Dietzen, M, Litovchenko, M, Thol, K, Watkins, TB, Bailey, C, Pich, O, Zhang, Z, Van Loo, P, Swanton, C, McGranahan, N. ImmuneLENS characterizes systemic immune dysregulation in aging and cancer. Nature Genetics 57(3):694-705, 2025. e-Pub 2025. PMID: 39966644.
5. Baker TM, Lai S, Lynch AR, Lesluyes T, Yan H, Ogilvie HA, Verfaillie A, Dentro S, Bowes AL, Pillay N, Flanagan AM, Swanton C, Spellman PT, Tarabichi M, Van Loo P. The History of Chromosomal Instability in Genome-Doubled Tumors. Cancer Discov 14(10):1810-1822, 2024. e-Pub 2024. PMID: 38943574.
6. Puttick C, Jones TP, Leung MM, Galvez-Cancino F, Liu J, Varas-Godoy M, Rowan A, Pich O, Martinez-Ruiz C, Bentham R, Dijkstra KK, Black JRM, Rosenthal R, Kanu N, Litchfield K, Salgado R, Moore DA, Van Loo P, Jamal-Hanjani M, Quezada SA, Swanton C, McGranahan N. MHC Hammer reveals genetic and non-genetic HLA disruption in cancer evolution. Nat Genet 56(10):2121-2131, 2024. e-Pub 2024. PMID: 39358601.
7. John E, Lesluyes T, Baker TM, Tarabichi M, Gillenwater A, Wang JR, Van Loo P, Zhao X. Reconstructing oral cavity tumor evolution through brush biopsy. Sci Rep 14(1):22591, 2024. e-Pub 2024. PMID: 39343812.
8. Rahman S, Bloye G, Farah N, Demeulemeester J, Costa JR, O'Connor D, Pocock R, Rapoz-D'Silva T, Turna A, Wang L, Lee SW, Fielding AK, Roels J, Jaksik R, Dawidowska M, Van Vlierberghe P, Hadjur S, Hughes JR, Davies J, Gutierrez A, Kelliher M, Van Loo P, Dawson MA, Mansour MR. Focal deletions of a promoter tether activate the IRX3 oncogene in T-cell acute lymphoblastic leukemia. Blood 144(22):2319-2326, 2024. e-Pub 2024. PMID: 39316719.
9. Pourebrahim R, Montoya RH, Akiyama H, Ostermann L, Khazaei S, Muftuoglu M, Baran N, Zhao R, Lesluyes T, Liu B, Khoury JD, Gagea M, Van Loo P, Andreeff M. Age-specific induction of mutant p53 drives clonal hematopoiesis and acute myeloid leukemia in adult mice. Cell Rep Med 5(5):101558, 2024. e-Pub 2024. PMID: 38733986.
10. Kuzmin E, Baker TM, Van Loo P, Glass L. Dynamics of karyotype evolution. Chaos 34(5), 2024. e-Pub 2024. PMID: 38717409.
11. Kuzmin E, Baker TM, Lesluyes T, Monlong J, Abe KT, Coelho PP, Schwartz M, Del Corpo J, Zou D, Morin G, Pacis A, Yang Y, Martinez C, Barber J, Kuasne H, Li R, Bourgey M, Fortier AM, Davison PG, Omeroglu A, Guiot MC, Morris Q, Kleinman CL, Huang S, Gingras AC, Ragoussis J, Bourque G, Van Loo P, Park M. Evolution of chromosome-arm aberrations in breast cancer through genetic network rewiring. Cell Rep 43(4):113988, 2024. e-Pub 2024. PMID: 38517886.
12. Woodcock DJ, Sahli A, Teslo R, Bhandari V, Gruber AJ, Ziubroniewicz A, Gundem G, Xu Y, Butler A, Anokian E, Pope BJ, Jung CH, Tarabichi M, Dentro SC, Farmery JHR, Prostate Group CI, Van Loo P, Warren AY, Gnanapragasam V, Hamdy FC, Bova GS, Foster CS, Neal DE, Lu YJ, Kote-Jarai Z, Fraser M, Bristow RG, Boutros PC, Costello AJ, Corcoran NM, Hovens CM, Massie CE, Lynch AG, Brewer DS, Eeles RA, Cooper CS, Wedge DC. Genomic evolution shapes prostate cancer disease type. Cell Genom 4(3):100511, 2024. e-Pub 2024. PMID: 38428419.
13. Heeke S, Gay CM, Estecio MR, Tran H, Morris BB, Zhang B, Tang X, Raso MG, Rocha P, Lai S, Arriola E, Hofman P, Hofman V, Kopparapu P, Lovly CM, Concannon K, De Sousa LG, Lewis WE, Kondo K, Hu X, Tanimoto A, Vokes NI, Nilsson MB, Stewart A, Jansen M, Horváth I, Gaga M, Panagoulias V, Raviv Y, Frumkin D, Wasserstrom A, Shuali A, Schnabel CA, Xi Y, Diao L, Wang Q, Zhang J, Van Loo P, Wang J, Wistuba II, Byers LA, Heymach JV. Tumor- and circulating-free DNA methylation identifies clinically relevant small cell lung cancer subtypes. Cancer Cell 42(2):225-237.e5, 2024. e-Pub 2024. PMID: 38278149.
14. Huang KK, Ma H, Chong RHH, Uchihara T, Lian BSX, Zhu F, Sheng T, Srivastava S, Tay ST, Sundar R, Tan ALK, Ong X, Lee M, Ho SWT, Lesluyes T, Ashktorab H, Smoot D, Van Loo P, Chua JS, Ramnarayanan K, Lau LHS, Gotoda T, Kim HS, Ang TL, Khor C, Lee JWJ, Tsao SKK, Yang WL, Teh M, Chung H, So JBY, Yeoh KG, Tan P, Singapore Gastric Cancer Consortium. Spatiotemporal genomic profiling of intestinal metaplasia reveals clonal dynamics of gastric cancer progression. Cancer Cell 41(12):2019-2037.e8, 2023. e-Pub 2023. PMID: 37890493.
15. Hasan, AM, Cremaschi, P, Wetterskog, D, Jayaram, A, Wong, SQ, Williams, S, Pasam, A, Trigos, A, Trujillo, B, Grist, E, Friedrich, S, Vainauskas, O, Parry, M, Ismail, M, Devlies, W, Wingate, A, Linch, M, Naceur-Lombardelli, C, Zaccaria, S, Hessey, S, Shiu, KK, Bridgewater, J, Hochhauser, D, Forster, M, Lee, SM, Ahmad, T, Papadatos-Pastos, D, Janes, SM, Van Loo, P, Enfield, K, Mcgranahan, N, Huebner, A, Quezada, SA, Beck, S, Parker, PJ, Enver, T, Hynds, RE, Pearce, DR, Falzon, M, Proctor, I, Sinclair, R, Lok, Cw, Rhodes, Z, Moore, DA, Marafioti, T, Mitchison, M, Ellery, P, Sivakumar, M, Linch, M, Brandner, S, Rowan, AJ, Hiley, CT, Veeriah, S, Shaw, H, Naceur-Lombardelli, C, Toncheva, A, Prymas, P, Watkins, TB, Bailey, C, Martínez-Ruiz, C, Litchfield, K, Al-Bakir, M, Kanu, N, Ward, S, Lim, E, Reading, JL, Chain, B, Watkins, TB, Akay, M, Flanagan, AM, Biswas, D, Pich, O, Dietzen, M, Puttick, C, Colliver, E, Magness, A, Angelova, M, Black, JR, Lucas, O, Hill, W, Liu, WK, Frankell, AM, Magno, N, Athanasopoulou, F, Salgado, R, Lee, C, Grigoriadis, K, Al-Sawaf, O, Karasaki, T, Bunkum, A, Noorani, I, Benafif, S, Barbe, V, Bola, SK, Leone, G, Alifrangis, C, McGovern, U, Thol, K, Gamble, S, Ung, SK, Sahwangarrom, T, Marin, CP, Wong, S, Pawlik, P, Lam, JM, Richard, C, Vendramin, R, Dijkstra, K, Rane, J, Nicod, J, Dwornik, A, Bowles, K, Zaidi, R, Gishen, F, Stone, P, Stirling, C, Turajlic, S, Larkin, J, Pickering, L, Furness, AJ, Young, K, Drake, WM, Edmonds, K, Hunter, N, Mangwende, M, Pearce, K, Grostate, L, Au, L, Spain, L, Shepherd, ST, Yan, H, Shum, B, Tippu, Z, Hanley, B, Spencer, C, Emmerich, M, Gerard, CL, Schmitt, AM, Del Rosario, L, Carlyle, E, Lewis, C, Holt, L, Lucanas, A, O’Flaherty, M, Hazell, S, Mudhar, H, Messiou, C, Latifoltojar, A, Fendler, A, Byrne, F, Pallikonda, H, Lobon, I, Coulton, A, Cattin, AL, Deng, D, Feng, H, Rowan, A, Yousaf, N, Popat, S, Curtis, O, Milner-Watts, C, Stamp, G, Nye, E, Murra, A, Korteweg, J, Kelly, D, Terry, L, Biano, J, Peat, K, Kelly, K, Grieco, C, Le, ML, D’Arienzo, PD, Turay, E, Hill, P, Josephs, D, Irshad, S, Spicer, J, Mahadeva, U, Green, A, Stewart, R, Wright, N, Pulman, G, Mitu, R, Phillips-Boyd, S, Enting, D, Rudman, S, Ghosh, S, Karapanagiotou, E, Pintus, E, Tutt, A, Howlett, S, Brenton, JD, Caldas, C, Fitzgerald, RC, Jimenez-Linan, M, Provenzano, E, Cluroe, A, Paterson, A, Aitken, S, Allinson, K, Stewart, GD, McDermott, U, Beddowes, E, Maughan, TS, Ansorge, O, Campbell, PJ, Roxburgh, P, Fraser, S, Blyth, KG, Le Quesne, J, Krebs, M, Blackhall, FH, Summers, Y, Oliveira, P, Ortega-Franco, A, Dive, C, Gomes, F, Carter, M, Dransfield, J, Thomas, AL, Fennell, D, Shaw, J, Wilson, C, Marrone, D, Naidu, B, Baijal, S, Tanchel, B, Langman, G, Robinson, A, Collard, M, Cockcroft, P, Ferris, C, Bancroft, H, Kerr, A, Middleton, G, Webb, J, Kadiri, S, Colloby, P, Olisemeke, B, Wilson, R, Shackleford, H, Osman, A, Tomlinson, I, Jogai, S, Holden, S, Fernandes, T, McNeish, IA, Hampton, B, McKenzie, M, Hackshaw, A, Sharp, A, Chan, K, Farrelly, L, Bridger, H, Leslie, R, Tookman, A, Swanton, C, Jamal-Hanjani, M, Lise, S, Sandhu, S, Attard, G. Copy number architectures define treatment-mediated selection of lethal prostate cancer clones. Nature communications 14(1), 2023. e-Pub 2023. PMID: 37563129.
16. Nurminen A, Jaatinen S, Taavitsainen S, Högnäs G, Lesluyes T, Ansari-Pour N, Tolonen T, Haase K, Koskenalho A, Kankainen M, Jasu J, Rauhala H, Kesäniemi J, Nikupaavola T, Kujala P, Rinta-Kiikka I, Riikonen J, Kaipia A, Murtola T, Tammela TL, Visakorpi T, Nykter M, Wedge DC, Van Loo P, Bova GS. Cancer origin tracing and timing in two high-risk prostate cancers using multisample whole genome analysis: prospects for personalized medicine. Genome Med 15(1):82, 2023. e-Pub 2023. PMID: 37828555.
17. Watkins TBK, Colliver EC, Huska MR, Kaufmann TL, Lim EL, Duncan CB, Haase K, Van Loo P, Swanton C, McGranahan N, Schwarz RF. Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity. PLoS Comput Biol 19(10):e1011379, 2023. e-Pub 2023. PMID: 37871126.
18. O'Connor D, Demeulemeester J, Conde L, Kirkwood A, Fung K, Papaleonidopoulou F, Bloye G, Farah N, Rahman S, Hancock J, Bateman C, Inglott S, Mee J, Herrero J, Van Loo P, Moorman AV, Vora A, Mansour MR. The Clinicogenomic Landscape of Induction Failure in Childhood and Young Adult T-Cell Acute Lymphoblastic Leukemia. J Clin Oncol 41(19):3545-3556, 2023. e-Pub 2023. PMID: 37098241.
19. Abbosh, C, Frankell, AM, Harrison, T, Kisistok, J, Garnett, A, Johnson, L, Veeriah, S, Moreau, M, Chesh, A, Chaunzwa, TL, Weiss, J, Schroeder, MR, Ward, S, Grigoriadis, K, Shahpurwalla, A, Litchfield, K, Puttick, C, Biswas, D, Karasaki, T, Black, JR, Martínez-Ruiz, C, Bakir, MA, Pich, O, Watkins, TB, Lim, E, Huebner, A, Moore, DA, Godin-Heymann, N, L’Hernault, A, Bye, H, Odell, A, Roberts, P, Gomes, F, Patel, AJ, Manzano, E, Hiley, CT, Carey, N, Riley, J, Cook, DE, Hodgson, D, Stetson, D, Barrett, JC, Kortlever, RM, Evan, GI, Hackshaw, A, Daber, RD, Shaw, J, Van Loo, P, Pan, X, Yuan, Y. Tracking early lung cancer metastatic dissemination in TRACERx using ctDNA. Nature 616(7957):553-562, 2023. e-Pub 2023. PMID: 37055640.
20. Ng, KW, Boumelha, J, Enfield, K, Almagro, J, Cha, H, Pich, O, Karasaki, T, Moore, DA, Salgado, R, Sivakumar, M, Young, GR, Molina-Arcas, M, de Carné Trécesson, S, Anastasiou, P, Fendler, A, Au, L, Shepherd, ST, Martínez-Ruiz, C, Puttick, C, Black, JR, Watkins, TB, Kim, H, Shim, S, Faulkner, N, Attig, J, Veeriah, S, Magno, N, Ward, S, Frankell, AM, Al-Bakir, M, Lim, E, Hill, MS, Wilson, GA, Cook, DE, Birkbak, NJ, Behrens, A, Yousaf, N, Popat, S, Hackshaw, A, Rowan, AJ, Huebner, A, Campbell, BB, Bailey, C, Lee, C, Biswas, D, Colliver, E, Athanasopoulou, F, Van Loo, P, Pan, X, Yuan, Y. Antibodies against endogenous retroviruses promote lung cancer immunotherapy. Nature 616(7957):563-573, 2023. e-Pub 2023. PMID: 37046094.
21. Hill, W, Lim, E, Weeden, CE, Lee, C, Augustine, M, Chen, K, Kuan, FC, Marongiu, F, Evans, EJ, Moore, DA, Rodrigues, FS, Pich, O, Bakker, B, Cha, H, Myers, R, van Maldegem, F, Boumelha, J, Veeriah, S, Rowan, AJ, Naceur-Lombardelli, C, Karasaki, T, Sivakumar, M, De, S, Caswell, DR, Nagano, A, Black, JR, Martínez-Ruiz, C, Ryu, MH, Huff, RD, Li, S, Favé, MJ, Magness, A, Suárez-Bonnet, A, Priestnall, SL, Lüchtenborg, M, Lavelle, K, Pethick, J, Hardy, S, McRonald, FE, Lin, MH, Troccoli, CI, Ghosh, M, Miller, YE, Merrick, DT, Keith, RL, Al-Bakir, M, Bailey, C, Van Loo, P, Pan, X, Yuan, Y. Lung adenocarcinoma promotion by air pollutants. Nature 616(7955):159-167, 2023. e-Pub 2023. PMID: 37020004.
22. Al-Sawaf, O, Weiss, J, Skrzypski, M, Lam, JM, Karasaki, T, Zambrana, F, Kidd, AC, Frankell, AM, Watkins, TB, Martínez-Ruiz, C, Puttick, C, Black, JR, Huebner, A, Bakir, MA, Sokac, M, Collins, S, Veeriah, S, Magno, N, Naceur-Lombardelli, C, Prymas, P, Toncheva, A, Ward, S, Jayanth, N, Salgado, R, Bridge, CP, Christiani, DC, Mak, RH, Bay, C, Rosenthal, MH, Sattar, N, Welsh, P, Liu, Y, Perrimon, N, Popuri, K, Beg, MF, Mcgranahan, N, Hackshaw, A, Breen, DM, O'Rahilly, S, Birkbak, NJ, Aerts, HJ, Watkins, TB, Aerts, HJ, Lester, JF, Bajaj, A, Nakas, A, Sodha-Ramdeen, A, Van Loo, P, Pan, X, Yuan, Y. Body composition and lung cancer-associated cachexia in TRACERx. Nature medicine 29(4):846-858, 2023. e-Pub 2023. PMID: 37045997.
23. Martínez-Ruiz C, Black JRM, Puttick C, Hill MS, Demeulemeester J, Larose Cadieux E, Thol K, Jones TP, Veeriah S, Naceur-Lombardelli C, Toncheva A, Prymas P, Rowan A, Ward S, Cubitt L, Athanasopoulou F, Pich O, Karasaki T, Moore DA, Salgado R, Colliver E, Castignani C, Dietzen M, Huebner A, Al Bakir M, Tanic M, Watkins TBK, Lim EL, Al-Rashed AM, Lang D, Clements J, Cook DE, Rosenthal R, Wilson GA, Frankell AM, de Carné Trécesson S, East P, Kanu N, Litchfield K, Birkbak NJ, Hackshaw A, Beck S, Van Loo P, Jamal-Hanjani M, TRACERx Consortium, Swanton C, McGranahan N. Genomic-transcriptomic evolution in lung cancer and metastasis. Nature 616(7957):543-552, 2023. e-Pub 2023. PMID: 37046093.
24. Karasaki T, Moore DA, Veeriah S, Naceur-Lombardelli C, Toncheva A, Magno N, Ward S, Bakir MA, Watkins TBK, Grigoriadis K, Huebner A, Hill MS, Frankell AM, Abbosh C, Puttick C, Zhai H, Gimeno-Valiente F, Saghafinia S, Kanu N, Dietzen M, Pich O, Lim EL, Martínez-Ruiz C, Black JRM, Biswas D, Campbell BB, Lee C, Colliver E, Enfield KSS, Hessey S, Hiley CT, Zaccaria S, Litchfield K, Birkbak NJ, Cadieux EL, Demeulemeester J, Van Loo P, Adusumilli PS, Tan KS, Cheema W, Sanchez-Vega F, Jones DR, Rekhtman N, Travis WD, Hackshaw A, Marafioti T, Salgado R, Le Quesne J, Nicholson AG, TRACERx Consortium, McGranahan N, Swanton C, Jamal-Hanjani M. Evolutionary characterization of lung adenocarcinoma morphology in TRACERx. Nat Med 29(4):833-845, 2023. e-Pub 2023. PMID: 37045996.
25. Frankell AM, Dietzen M, Al Bakir M, Lim EL, Karasaki T, Ward S, Veeriah S, Colliver E, Huebner A, Bunkum A, Hill MS, Grigoriadis K, Moore DA, Black JRM, Liu WK, Thol K, Pich O, Watkins TBK, Naceur-Lombardelli C, Cook DE, Salgado R, Wilson GA, Bailey C, Angelova M, Bentham R, Martínez-Ruiz C, Abbosh C, Nicholson AG, Le Quesne J, Biswas D, Rosenthal R, Puttick C, Hessey S, Lee C, Prymas P, Toncheva A, Smith J, Xing W, Nicod J, Price G, Kerr KM, Naidu B, Middleton G, Blyth KG, Fennell DA, Forster MD, Lee SM, Falzon M, Hewish M, Shackcloth MJ, Lim E, Benafif S, Russell P, Boleti E, Krebs MG, Lester JF, Papadatos-Pastos D, Ahmad T, Thakrar RM, Lawrence D, Navani N, Janes SM, Dive C, Blackhall FH, Summers Y, Cave J, Marafioti T, Herrero J, Quezada SA, Peggs KS, Schwarz RF, Van Loo P, Miedema DM, Birkbak NJ, Hiley CT, Hackshaw A, Zaccaria S, TRACERx Consortium, Jamal-Hanjani M, McGranahan N, Swanton C. The evolution of lung cancer and impact of subclonal selection in TRACERx. Nature 616(7957):525-533, 2023. e-Pub 2023. PMID: 37046096.
26. Al Bakir M, Huebner A, Martínez-Ruiz C, Grigoriadis K, Watkins TBK, Pich O, Moore DA, Veeriah S, Ward S, Laycock J, Johnson D, Rowan A, Razaq M, Akther M, Naceur-Lombardelli C, Prymas P, Toncheva A, Hessey S, Dietzen M, Colliver E, Frankell AM, Bunkum A, Lim EL, Karasaki T, Abbosh C, Hiley CT, Hill MS, Cook DE, Wilson GA, Salgado R, Nye E, Stone RK, Fennell DA, Price G, Kerr KM, Naidu B, Middleton G, Summers Y, Lindsay CR, Blackhall FH, Cave J, Blyth KG, Nair A, Ahmed A, Taylor MN, Procter AJ, Falzon M, Lawrence D, Navani N, Thakrar RM, Janes SM, Papadatos-Pastos D, Forster MD, Lee SM, Ahmad T, Quezada SA, Peggs KS, Van Loo P, Dive C, Hackshaw A, Birkbak NJ, Zaccaria S, TRACERx Consortium, Jamal-Hanjani M, McGranahan N, Swanton C. The evolution of non-small cell lung cancer metastases in TRACERx. Nature 616(7957):534-542, 2023. e-Pub 2023. PMID: 37046095.
27. Birkeälv S, Harland M, Matsuyama LSAS, Rashid M, Mehta I, Laye JP, Haase K, Mell T, Iyer V, Robles-Espinoza CD, McDermott U, van Loo P, Kuijjer ML, Possik PA, Maria Engler SS, Bishop DT, Newton-Bishop J, Adams DJ. Mutually exclusive genetic interactions and gene essentiality shape the genomic landscape of primary melanoma. J Pathol 259(1):56-68, 2023. e-Pub 2023. PMID: 36219477.
28. Buhigas, C, Warren, AY, Leung, WK, Whitaker, H, Luxton, HJ, Hawkins, S, Kay, J, Butler, A, Xu, Y, Woodcock, DJ, Merson, S, Frame, FM, Sahli, A, Abascal, F, Gihawi, A, Lambert, A, Thompson, A, Futreal, A, Menzies, A, Baddage, A, Ng, A, Sahil, A, Kremeyer, B, Al-Lazikani, B, Massie, C, Greenman, CD, Ogden, C, Verrill, C, Fisher, C, Berney, D, Burns, D, Leongamornlert, DA, Jones, D, Nicol, D, Wedge, D, Cahill, D, Easton, DF, Rowe, E, Riabchenko, E, Bancroft, EK, Mayer, E, Anokian, E, Hamdy, FC, Park, G, Pelvender, G, Leeman, G, Gundem, G, Zhang, H, Mills, IG, Van Loo, P. The architecture of clonal expansions in morphologically normal tissue from cancerous and non-cancerous prostates. Molecular cancer 21(1), 2022. e-Pub 2022. PMID: 36131292.
29. Kaufmann TL, Petkovic M, Watkins TBK, Colliver EC, Laskina S, Thapa N, Minussi DC, Navin N, Swanton C, Van Loo P, Haase K, Tarabichi M, Schwarz RF. MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution. Genome Biol 23(1):241, 2022. e-Pub 2022. PMID: 36376909.
30. Cao S, Wang JR, Ji S, Yang P, Dai Y, Guo S, Montierth MD, Shen JP, Zhao X, Chen J, Lee JJ, Guerrero PA, Spetsieris N, Engedal N, Taavitsainen S, Yu K, Livingstone J, Bhandari V, Hubert SM, Daw NC, Futreal PA, Efstathiou E, Lim B, Viale A, Zhang J, Nykter M, Czerniak BA, Brown PH, Swanton C, Msaouel P, Maitra A, Kopetz S, Campbell P, Speed TP, Boutros PC, Zhu H, Urbanucci A, Demeulemeester J, Van Loo P, Wang W. Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression. Nat Biotechnol 40(11):1624-1633, 2022. e-Pub 2022. PMID: 35697807.
31. Cross W, Lyskjær I, Lesluyes T, Hargreaves S, Strobl AC, Davies C, Waise S, Hames-Fathi S, Oukrif D, Ye H, Amary F, Tirabosco R, Gerrand C, Baker T, Barnes D, Steele C, Alexandrov L, Bond G, Genomics England Research Consortium, Cool P, Pillay N, Van Loo P, Flanagan AM. A genetic model for central chondrosarcoma evolution correlates with patient outcome. Genome Med 14(1):99, 2022. e-Pub 2022. PMID: 36042521.
32. Wu, Y, Biswas, D, Usaite, I, Angelova, M, Boeing, S, Karasaki, T, Veeriah, S, Czyzewska-Khan, J, Morton, C, Joseph, M, Hessey, S, Reading, JL, Georgiou, A, Al-Bakir, M, Birkbak, NJ, Price, G, Khalil, M, Kerr, K, Richardson, S, Cheyne, H, Cruickshank, T, Wilson, GA, Rosenthal, R, Aerts, HJ, Hewish, M, Anand, G, Khan, SA, Lau, K, Sheaff, M, Schmid, P, Lim, L, Conibear, J, Schwarz, R, Kaufmann, TL, Huska, M, Shaw, J, Riley, J, Primrose, L, Fennell, D, Hackshaw, A, Ngai, Y, Sharp, A, Pressey, O, Smith, S, Gower, N, Dhanda, H, Chan, K, Chakraborty, S, Litchfield, K, Van Loo, P. A local human Vδ1 T cell population is associated with survival in nonsmall-cell lung cancer. Nature Cancer 3(6):696-709, 2022. e-Pub 2022. PMID: 35637401.
33. Drews RM, Hernando B, Tarabichi M, Haase K, Lesluyes T, Smith PS, Morrill Gavarró L, Couturier DL, Liu L, Schneider M, Brenton JD, Van Loo P, Macintyre G, Markowetz F. A pan-cancer compendium of chromosomal instability. Nature 606(7916):976-983, 2022. e-Pub 2022. PMID: 35705807.
34. Steele CD, Abbasi A, Islam SMA, Bowes AL, Khandekar A, Haase K, Hames-Fathi S, Ajayi D, Verfaillie A, Dhami P, McLatchie A, Lechner M, Light N, Shlien A, Malkin D, Feber A, Proszek P, Lesluyes T, Mertens F, Flanagan AM, Tarabichi M, Van Loo P, Alexandrov LB, Pillay N. Signatures of copy number alterations in human cancer. Nature 606(7916):984-991, 2022. e-Pub 2022. PMID: 35705804.
35. Demeulemeester J, Dentro SC, Gerstung M, Van Loo P. Biallelic mutations in cancer genomes reveal local mutational determinants. Nat Genet 54(2):128-133, 2022. e-Pub 2022. PMID: 35145300.
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117. Wibom C, Ghasimi S, Van Loo P, Brännström T, Trygg J, Lau C, Henriksson R, Bergenheim T, Andersson U, Rydén P, Melin B. EGFR gene variants are associated with specific somatic aberrations in glioma. PLoS One 7(12):e47929, 2012. e-Pub 2012. PMID: 23236348.
118. Reumers J, De Rijk P, Zhao H, Liekens A, Smeets D, Cleary J, Van Loo P, Van Den Bossche M, Catthoor K, Sabbe B, Despierre E, Vergote I, Hilbush B, Lambrechts D, Del-Favero J. Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing. Nat Biotechnol 30(1):61-8, 2011. e-Pub 2011. PMID: 22178994.
119. Rosebeck S, Madden L, Jin X, Gu S, Apel IJ, Appert A, Hamoudi RA, Noels H, Sagaert X, Van Loo P, Baens M, Du MQ, Lucas PC, McAllister-Lucas LM. Cleavage of NIK by the API2-MALT1 fusion oncoprotein leads to noncanonical NF-kappaB activation. Science 331(6016):468-72, 2011. e-Pub 2011. PMID: 21273489.
120. Van Loo P, Nordgard SH, Lingjærde OC, Russnes HG, Rye IH, Sun W, Weigman VJ, Marynen P, Zetterberg A, Naume B, Perou CM, Børresen-Dale AL, Kristensen VN. Allele-specific copy number analysis of tumors. Proc Natl Acad Sci U S A 107(39):16910-5, 2010. e-Pub 2010. PMID: 20837533.
121. Thienpont B, Zhang L, Postma AV, Breckpot J, Tranchevent LC, Van Loo P, Møllgård K, Tommerup N, Bache I, Tümer Z, van Engelen K, Menten B, Mortier G, Waggoner D, Gewillig M, Moreau Y, Devriendt K, Larsen LA. Haploinsufficiency of TAB2 causes congenital heart defects in humans. Am J Hum Genet 86(6):839-49, 2010. e-Pub 2010. PMID: 20493459.
122. Barriot R, Breckpot J, Thienpont B, Brohée S, Van Vooren S, Coessens B, Tranchevent LC, Van Loo P, Gewillig M, Devriendt K, Moreau Y. Collaboratively charting the gene-to-phenotype network of human congenital heart defects. Genome Med 2(3):16, 2010. e-Pub 2010. PMID: 20193066.
123. Sagaert X, Tousseyn T, Vanhentenrijk V, Van Loo P, Baens M, Marynen P, De Hertogh G, Geboes K, De Wolf-Peeters C. Comparative expressed sequence hybridization studies of t(11;18)(q21;q21)-positive and -negative gastric MALT lymphomas reveal both unique and overlapping gene programs. Mod Pathol 23(3):458-69, 2010. e-Pub 2010. PMID: 20081812.
124. Van Loo P, Tousseyn T, Vanhentenrijk V, Dierickx D, Malecka A, Vanden Bempt I, Verhoef G, Delabie J, Marynen P, Matthys P, De Wolf-Peeters C. T-cell/histiocyte-rich large B-cell lymphoma shows transcriptional features suggestive of a tolerogenic host immune response. Haematologica 95(3):440-8, 2010. e-Pub 2010. PMID: 19797726.
125. Sun W, Wright FA, Tang Z, Nordgard SH, Van Loo P, Yu T, Kristensen VN, Perou CM. Integrated study of copy number states and genotype calls using high-density SNP arrays. Nucleic Acids Res 37(16):5365-77, 2009. e-Pub 2009. PMID: 19581427.
126. Lehnert S, Van Loo P, Thilakarathne PJ, Marynen P, Verbeke G, Schuit FC. Evidence for co-evolution between human microRNAs and Alu-repeats. PLoS One 4(2):e4456, 2009. e-Pub 2009. PMID: 19209240.
127. Vanden Bempt I, Van Loo P, Drijkoningen M, Neven P, Smeets A, Christiaens MR, Paridaens R, De Wolf-Peeters C. Polysomy 17 in breast cancer: clinicopathologic significance and impact on HER-2 testing. J Clin Oncol 26(30):4869-74, 2008. e-Pub 2008. PMID: 18794552.
128. Tranchevent LC, Barriot R, Yu S, Van Vooren S, Van Loo P, Coessens B, De Moor B, Aerts S, Moreau Y. ENDEAVOUR update: a web resource for gene prioritization in multiple species. Nucleic Acids Res 36(Web Server issue):W377-84, 2008. e-Pub 2008. PMID: 18508807.
129. Van Loo P, Aerts S, Thienpont B, De Moor B, Moreau Y, Marynen P. ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues?. Genome Biol 9(4):R66, 2008. e-Pub 2008. PMID: 18394174.
130. Griffith OL, Montgomery SB, Bernier B, Chu B, Kasaian K, Aerts S, Mahony S, Sleumer MC, Bilenky M, Haeussler M, Griffith M, Gallo SM, Giardine B, Hooghe B, Van Loo P, Blanco E, Ticoll A, Lithwick S, Portales-Casamar E, Donaldson IJ, Robertson G, Wadelius C, De Bleser P, Vlieghe D, Halfon MS, Wasserman W, Hardison R, Bergman CM, Jones SJ, The Open Regulatory Annotation Consortium. ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res 36(Database issue):D107-13, 2008. e-Pub 2008. PMID: 18006570.
131. Pospisilova H, Baens M, Michaux L, Stul M, Van Hummelen P, Van Loo P, Vermeesch J, Jarosova M, Zemanova Z, Michalova K, Van den Berghe I, Alexander HD, Hagemeijer A, Vandenberghe P, Cools J, De Wolf-Peeters C, Marynen P, Wlodarska I. Interstitial del(14)(q) involving IGH: a novel recurrent aberration in B-NHL. Leukemia 21(9):2079-83, 2007. e-Pub 2007. PMID: 17525729.
132. Aerts S, Lambrechts D, Maity S, Van Loo P, Coessens B, De Smet F, Tranchevent LC, De Moor B, Marynen P, Hassan B, Carmeliet P, Moreau Y. Gene prioritization through genomic data fusion. Nat Biotechnol 24(5):537-44, 2006. e-Pub 2006. PMID: 16680138.
133. Aerts S, Van Loo P, Thijs G, Mayer H, de Martin R, Moreau Y, De Moor B. TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis. Nucleic Acids Res 33(Web Server issue):W393-6, 2005. e-Pub 2005. PMID: 15980497.
134. Aerts S, Van Loo P, Moreau Y, De Moor B. A genetic algorithm for the detection of new cis-regulatory modules in sets of coregulated genes. Bioinformatics 20(12):1974-6, 2004. e-Pub 2004. PMID: 15044242.
135. Aerts S, Van Loo P, Thijs G, Moreau Y, De Moor B. Computational detection of cis-regulatory modules. Bioinformatics 19 Suppl 2:ii5-14, 2003. e-Pub 2003. PMID: 14534164.

Invited Articles

1. Yan H, Tarabichi M, McGranahan N, Van Loo P. DeCiFering the subclonal composition of tumors. Cell Syst 12(10):955-957, 2021. e-Pub 2021. PMID: 34672959.
2. Voet T, Van Loo P. SNES makes sense? Single-cell exome sequencing evolves. Genome Biol 16:86, 2015. e-Pub 2015. PMID: 25926122.
3. Van Loo P, Campbell PJ. ABSOLUTE cancer genomics. Nat Biotechnol 30(7):620-1, 2012. e-Pub 2012. PMID: 22781683.

Review Articles

1. Baker TM, Waise S, Tarabichi M, Van Loo P. Aneuploidy and complex genomic rearrangements in cancer evolution. Nat Cancer 5(2):228-239, 2024. e-Pub 2024. PMID: 38286829.
2. Bowes AL, Tarabichi M, Pillay N, Van Loo P. Leveraging single-cell sequencing to unravel intratumour heterogeneity and tumour evolution in human cancers. J Pathol 257(4):466-478, 2022. e-Pub 2022. PMID: 35438189.
3. Morotti M, Albukhari A, Alsaadi A, Artibani M, Brenton JD, Curbishley SM, Dong T, Dustin ML, Hu Z, McGranahan N, Miller ML, Santana-Gonzalez L, Seymour LW, Shi T, Van Loo P, Yau C, White H, Wietek N, Church DN, Wedge DC, Ahmed AA. Promises and challenges of adoptive T-cell therapies for solid tumours. Br J Cancer 124(11):1759-1776, 2021. e-Pub 2021. PMID: 33782566.
4. Tarabichi M, Salcedo A, Deshwar AG, Ni Leathlobhair M, Wintersinger J, Wedge DC, Van Loo P, Morris QD, Boutros PC. A practical guide to cancer subclonal reconstruction from DNA sequencing. Nat Methods 18(2):144-155, 2021. e-Pub 2021. PMID: 33398189.
5. Fittall MW, Van Loo P. Translating insights into tumor evolution to clinical practice: promises and challenges. Genome Med 11(1):20, 2019. e-Pub 2019. PMID: 30925887.
6. Jolly C, Van Loo P. Timing somatic events in the evolution of cancer. Genome Biol 19(1):95, 2018. e-Pub 2018. PMID: 30041675.
7. Macintyre G, Van Loo P, Corcoran NM, Wedge DC, Markowetz F, Hovens CM. How Subclonal Modeling Is Changing the Metastatic Paradigm. Clin Cancer Res 23(3):630-635, 2017. e-Pub 2017. PMID: 27864419.
8. Van Loo P, Voet T. Single cell analysis of cancer genomes. Curr Opin Genet Dev 24:82-91, 2014. e-Pub 2014. PMID: 24531336.
9. Van Loo P, Marynen P. Computational methods for the detection of cis-regulatory modules. Brief Bioinform 10(5):509-24, 2009. e-Pub 2009. PMID: 19498042.

Other Articles

1. Frankell, AM, Dietzen, M, Al-Bakir, M, Lim, E, Karasaki, T, Ward, S, Veeriah, S, Colliver, E, Huebner, A, Bunkum, A, Hill, MS, Grigoriadis, K, Moore, DA, Black, JR, Liu, WK, Thol, K, Pich, O, Watkins, TB, Naceur-Lombardelli, C, Cook, DE, Salgado, R, Wilson, GA, Bailey, C, Angelova, M, Bentham, R, Martínez-Ruiz, C, Abbosh, C, Nicholson, A, Le Quesne, J, Biswas, D, Rosenthal, R, Puttick, C, Hessey, S, Lee, C, Prymas, P, Toncheva, A, Smith, JC, Xing, W, Nicod, J, Price, G, Kerr, K, Naidu, B, Middleton, G, Blyth, KG, Fennell, D, Forster, M, Lee, SM, Van Loo, P, Pan, X, Yuan, Y Author Correction. Nature 631(8022):E15, 2024. PMID: 38965439.
2. Yakneen, S, Waszak, SM, Yakneen, S, Aminou, B, Bartolome, J, Boroevich, KA, Boyce, R, Brooks, AN, Buchanan, A, Buchhalter, I, Butler, A, Byrne, NJ, Cafferkey, A, Campbell, PJ, Chen, Z, Cho, S, Choi, W, Clapham, P, Davis-Dusenbery, BN, De La Vega, FM, Demeulemeester, J, Dow, MT, Dursi, LJ, Eils, J, Eils, R, Ellrott, K, Farcas, C, Favero, F, Fayzullaev, N, Ferretti, V, Flicek, P, Fonseca, NA, Gelpi, JL, Getz, G, Gibson, B, Grossman, RL, Harismendy, O, Heath, AP, Heinold, M, Hess, J, Hofmann, O, Hong, JH, Hudson, TJ, Hutter, B, Hutter, CM, Hübschmann, D, Imoto, S, Ivkovic, S, Jeon, SH, Van Loo, P Publisher Correction. Nature biotechnology 41(4):578, 2023. PMID: 32051562.

Book Chapters

1. Dentro SC, Wedge DC, Van Loo P. Principles of Reconstructing the Subclonal Architecture of Cancers. In: Cancer Evolution. 8. Cold Spring Harbor Laboratory Press, 2017.
2. Van Loo P, Nilsen G, Nordgard SH, Vollan HK, Børresen-Dale AL, Kristensen VN, Lingjærde OC. Analyzing cancer samples with SNP arrays. In: Microarray Bioinformatics, 57-72, 2012.

Letters to the Editor

1. Megyesfalvi Z, Heeke S, Drapkin BJ, Solta A, Kovacs I, Boettiger K, Horvath L, Ernhofer B, Fillinger J, Renyi-Vamos F, Aigner C, Schelch K, Lang C, Marko-Varga G, Gay CM, Byers LA, Morris BB, Heymach JV, Van Loo P, Hirsch FR, Dome B. Unfolding the secrets of small cell lung cancer progression: Novel approaches and insights through rapid autopsies. Cancer Cell 41: 1535-1540, 2023.
2. Tarabichi M, Martincorena I, Gerstung M, Leroi AM, Markowetz F, Evolution P, Group HW, Spellman PT, Morris QD, Lingjærde OC, Wedge DC, Van Loo P. Neutral tumor evolution?. Nat Genet 50: 1630-1633, 2018.