Publications

[* joint first authors] [# corresponding author]

41. Accumulation of oncogenic mutations during progression from healthy tissue to cancer

R Zhang, I Bozic#.

bioRxiv 10.1101/2024.02.18.580841, 2024.

40. Early-stage cancer results in a multiplicative increase in cell-free DNA originating from healthy tissue

K Mamis, I Bozic#.

bioRxiv 10.1101/2024.01.26.577500, 2024.

39. Stochastic model for cell population dynamics quantifies homeostasis in colonic crypts and its disruption in early tumorigenesis

K Mamis, R Zhang, I Bozic#.

Proceedings of the Royal Society B 290: 20231020, 2023.

38. Ultra-deep mutational landscape in chronic lymphocytic leukemia uncovers dynamics of resistance to targeted therapies

D Woolston*, ND Lee*, M Shadman*, E Latorre-Esteves, XR Tee, J Fredrickson, BF Kohrn, O Sala-Torra, C Ujjani, A Eckel, B Till, M Fang, J Radich, I Bozic#, RA Risques#, CCS Yeung#

Haematologica 109, 835-845, 2023. [PDF]

37. Waiting times in a branching process model of colorectal cancer initiation

R Zhang, OA Ukogu, I Bozic#.

Theoretical Population Biology 151: 44-63, 2023. [PDF]

36. Clonal interactions in cancer: integrating quantitative models with experimental and clinical data.

ND Lee, K Kaveh, I Bozic#.

Seminars in Cancer Biology 92: 61-73, 2023.

35. In vivo modeling of CLL transformation to Richter’s syndrome reveals convergent evolutionary paths and therapeutic vulnerabilities

E ten Hacken, T Sewastianik, S Yin, G Brunsting Hoffmann, M Gruber, K Clement, L Penter, RA Redd, N Ruthen, S Hergalant, A Sholokhova, G Fell, EM Parry, J Broseus, R Guieze, F Lucas, M Hernandez-Sanchez, K Baranowski, J Southard, H Joyal, L Billington, FFD Regis, E Witten, M Uduman, BA Knisbacher, S Li, H Lyu, T Vaisitti, S Deaglio, G Inghirami, P Feugier, S Stilgenbauer, E Tausch, MS Davids, G Getz, KJ Livak, I Bozic, DS Neuberg, R Carrasco, CJ Wu.

Blood Cancer Discovery 4: 1-20, 2023.

34. Inferring parameters of cancer evolution in chronic lymphocytic leukemia

ND Lee, I Bozic#.

PLOS Computational Biology 18: e1010677, 2022. [PDF]

33. A mechanistic model of malignant transformation in vestibular schwannoma

CGB Paterson, I Bozic, MJ Smith, X Hoad, DGR Evans

British Journal of Cancer 127: 1843–1857, 2022. [PDF]

32. Estimating the transfer rates of bacterial plasmids with an adapted Luria–Delbrück fluctuation analysis

O Kosterlitz, A Muñiz Tirado, C Wate, C Elg, I Bozic, EM Top, B Kerr

PLOS Biology 20: e3001732, 2022. [PDF]

31. Quantification of the selective advantage of driver mutations is dependent on the underlying model and stage of tumor evolution

I Bozic#.

Cancer Research 82: 21-24, 2022. [PDF]

30. Modelling CAR T-cell therapy with patient preconditioning

KL Owens, I Bozic#.

Bulletin of Mathematical Biology 83: 42, 2021. [PDF]

29. Mathematical model of colorectal cancer initiation

C Paterson, H Clevers#, I Bozic#.

Proc Natl Acad Sci USA 117: 20681-20688, 2020. [PDF] [software]

28. Delineating the evolutionary dynamics of cancer from theory to reality

I Bozic#, CJ Wu.

Nature Cancer 1: 580-588, 2020. [PDF]

27. On measuring selection in cancer from subclonal mutation frequencies

I Bozic#, C Paterson, B Waclaw.

PLOS Computational Biology 15: e1007368, 2019. [PDF]

26. Growth dynamics in naturally progressing chronic lymphocytic leukaemia

M Gruber*, I Bozic*, I Leshchiner*, D Livitz*, K Stevenson, L Rassenti, D Rosebrock, A Taylor-Weiner, O Olive, R Goyetche, SM Fernandes, J Sun, C Stewart, A Wong, C Cibulskis, W Zhang, JG Reiter, JM Gerold, JG Gribben, KR Rai, MJ Keating, JR Brown, D Neuberg, TJ Kipps, MA Nowak, G Getz, CJ Wu.

Nature 570: 474–479, 2019. [PDF] [software]

25. Comprehensive analysis of tumour initiation, spatial and temporal progression under multiple lines of treatment

I Leshchiner, D Livitz, JF Gainor, D Rosebrock, O Spiro, A Martinez, E Mroz, JJ Lin, C Stewart, J Kim, L Elagina, I Bozic, M Mino-Kenudson, M Rooney, SH Ignatius Ou, CJ Wu, JW Rocco, JA Engelman, AT Shaw, G Getz.

bioRxiv 2019 [pdf]

24. Dormant tumour cells, their niches and the influence of immunity

ET Goddard, I Bozic, SR Riddell, CM Ghajar.

Nature Cell Biology 20: 1240-1249, 2018. [PDF]

23. The evolutionary landscape of chronic lymphocytic leukemia treated with ibrutinib targeted therapy

DA Landau, C Sun, D Rosebrock, SEM Herman, J Fein, M Sivina, C Underbayev, D Liu, J Hoellenriegel, S Ravichandran, MZH Farooqui, W Zhang, C Cibulskis, A Zviran, DS Neuberg, D Livitz, I Bozic, I Leshchiner, G Getz, JA Burger, A Wiestner, CJ Wu.

Nature Communications 8: 2185, 2017. [PDF]

22. Resisting resistance

I Bozic#, MA Nowak#.

Annual Review of Cancer Biology 1: 203-221, 2017. [PDF]

21. Reconstructing metastatic seeding patterns of human cancers

JG Reiter, AP Makohon-Moore, JM Gerold, I Bozic, K Chatterjee, CA Iacobuzio-Donahue, B Vogelstein, MA Nowak.

Nature Communications 8: 14114, 2017. [PDF]

20. Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer

AP Makohon-Moore, M Zhang, JG Reiter, I Bozic, B Allen, D Kundu, K Chatterjee, F Wong, Y Jiao, LD Wood, RH Hruban, MA Nowak, N Papadopoulos, KW Kinzler, B Vogelstein, CA Iacobuzio-Donahue.

Nature Genetics 49: 358-366, 2017. [PDF]

19. Tumor and immune cell dynamics explain the PSA bounce after prostate cancer brachytherapy

Y Yamamoto, CP Offord, G Kimura, S Kuribayashi, H Takeda, S Tsuchiya, H Shimojo, H Kanno, I Bozic, MA Nowak, Ž Bajzer, D Dingli. British Journal of Cancer 115: 195-202, 2016. [PDF]

18. Clonal evolution in patients with chronic lymphocytic leukemia developing resistance to BTK inhibition

JA Burger*, DA Landau*, AN Taylor-Weiner*, I Bozic*, H Zhang*, K Sarosiek, L Wang, C Stewart, J Fan, J Hoellenriegel, M Sivina, AM Dubuc, C Fraser, Y Han, S Li, KJ Livak, L Zou, YWan, S Konoplev, C Sougnez, LV Abruzzo, SL Carter, MJ Keating, MS Davids, WG Wierda, K Cibulskis, T Zenz, L Werner, P Dal Cin, P Kharchencko, D Neuberg, H Kantarjian, E Lander, S Gabriel, S O’Brien, A Letai, DA Weitz, MA Nowak, G Getz, CJ Wu.

Nature Communications 7: 11589, 2016. [PDF]

17. Quantifying clonal and subclonal passenger mutations in cancer evolution

I Bozic#, JM Gerold, MA Nowak#.

PLOS Computational Biology 12: e1004731, 2016. [PDF]

16. Mutations driving CLL and their evolution in progression and relapse

DA Landau, E Tausch, AN Taylor-Weiner, C Stewart, JG Reiter, J Bahlo, S Kluth, I Bozic, M Lawrence, S Bottcher, SL Carter, K Cibulskis, D Mertens, C Sougnez, M Rosenberg, JM Hess, J Edelmann, S Kless, M Kneba, M Ritgen, A Fink, K Fischer, S Gabriel, E Lander, MA Nowak, H Dohner, M Hallek, D Neuberg, G Getz, S Stilgenbauer, CJ Wu.

Nature 526: 525-530, 2015. [PDF]

15. Vertical suppression of the EGFR pathway prevents onset of resistance in colorectal cancers

S Misale*, I Bozic*, JS Tong, A Peraza-Penton, A Lallo, F Baldi, K Lin, M Truini, L Trusolino, A Bertotti, F Di Nicolantonio, MA Nowak, L Zhang, K Wood, A Bardelli.

Nature Communications 6: 8305, 2015. [PDF]

14. A spatial model predicts that dispersal and cell turnover limit intratumour heterogeneity

B Waclaw, I Bozic, ME Pittman, RH Hruban, B Vogelstein, MA Nowak.

Nature 525: 261-264, 2015. [PDF]

13. The (not so) immortal strand hypothesis

C Tomasetti, I Bozic.

Stem Cell Research 14: 238-241, 2015. [PDF]

12. Timing and heterogeneity of mutations associated with drug resistance in metastatic cancers

I Bozic#, MA Nowak#.

Proc Natl Acad Sci USA 111: 15964-15968, 2014. [PDF] [Supplement]

11. Unwanted evolution

I Bozic, MA Nowak.

Science 342: 938-939, 2013.

10. Evolutionary dynamics of cancer in response to targeted combination therapy

I Bozic*, JG Reiter*, B Allen*, T Antal, K Chatterjee, P Shah, YS Moon, A Yaqubie, N Kelly, DT Le, EJ Lipson, PB Chapman, LA Diaz Jr, B Vogelstein, MA Nowak.

eLife 2: e00747, 2013. [PDF] [Supplement]

9. TTP: Tool for tumor progression

JG Reiter, I Bozic, K Chatterjee, MA Nowak.

In Proceedings of 25th International Conference on Computer Aided Verification, Lecture Notes in Computer Science 8044: 101-106, 2013. [PDF]

8. The effect of one additional driver mutation on tumor progression

JG Reiter*, I Bozic*, B Allen, K Chatterjee, MA Nowak.

Evolutionary Applications 6: 34-45, 2013. [PDF]

7. The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers

LA Diaz Jr, R Williams, J Wu, J R Hecht, J Berlin, B Allen, I Bozic, JG Reiter, MA Nowak, KW Kinzler, KS Oliner, B Vogelstein.

Nature 486: 537-540, 2012. [PDF]

6. Dynamics of targeted cancer therapy

I Bozic, B Allen, MA Nowak.

Trends in Molecular Medicine 18: 311-316, 2012.

5. Distant metastasis occurs late during the genetic evolution of pancreatic cancer

S Yachida, S Jones, I Bozic, T Antal, R Leary, B Fu, M Kamiyama, RH Hruban, JR Eshleman, MA Nowak, VE Velculescu, KW Kinzler, B Vogelstein, CA Iacobuzio-Donahue.

Nature 467: 1114-1117, 2010. [PDF]

4. Accumulation of driver and passenger mutations during tumor progression

I Bozic, T Antal, H Ohtsuki, H Carter, D Kim, S Chen, R Karchin, KW Kinzler, B Vogelstein, MA Nowak.

Proc Natl Acad Sci USA 107: 18545-18550, 2010. [PDF]

3. Zero-divisor graphs of matrices over commutative rings

I Bozic, Z Petrovic.

Communications in Algebra 37: 1186-1192, 2009.

2. Prediction of supertype-specific HLA class I binding peptides using support vector machines

GL Zhang, I Bozic, CK Kwoh, JT August, V Brusic. .

Journal of Immunological Methods 320: 143-154, 2007.

1. Predictive vaccinology: optimization of predictions using support vector machine classifiers

I Bozic, GL Zhang, V Brusic.

In Proceedings of the 6th International Conference on Intelligent Data Engineering and Automated Learning, Lecture Notes in Computer Science 3578: 375-381, 2005.