1. C. Wu, E. Gunnarsson, E.M. Myklebust, A. Kohn-Luque, D.S. Tadele, J.M. Enserink, A. Frigessi, J. Foo, K. Leder. Using birth-death processes to infer tumor subpopulation structure from live-cell imaging drug screening data, submitted.

  2. E. Gunnarsson, J. Foo. Mathematical models of resistance evolution under continuous and pulsed anti-cancer therapies, (invited book chapter) accepted.

  3. A. Li, D. Kibby, J. Foo. A Comparison of Mutation and Amplification-Driven Resistance Mechanisms and Their Impacts on Tumor Recurrence, Journal of Mathematical Biology, 87, 59 (2023). https://doi.org/10.1007/s00285-023-01992-8 Link

  4. A. Kohn-Luque, E. M. Myklebust, D. S. Tadele, M. Gilberto, J. Noory, E. Harivel, P. Arsenteva, S. Mumenthaler, F. Schjesvold, K. Tasken, J. Enserink, K. Leder, A. Frigessi, J. Foo. Phenotypic deconvolution in heterogeneous cell populations using drug screening data, Cell Reports Methods, 2023. Link

  5. E. Gunnarsson, J. Foo, K. Leder. Statistical inference of the rates of cell proliferation and phenotypic switching in cancer. J. Theoretical Biology, 2023. Link

  6. J. Foo, E. Gunnarsson, K. Leder, D. Sivakoff. Dynamics of advantageous mutant spread in spatial death-birth and birth-death Moran models, Comm. Appl. Math. Comput. 2023. Link

  7. Foo, J., Gunnarsson, E., Leder, K, and Storey, K. Spread of premalignant mutant clones and cancer initiation in multilayered tissue, Annals of Applied Probability, 2023. Link

  8. Foo, J., Rockne, R., Basanta, D. et. al. Roadmap on plasticity and epigenetics in cancer, Physical Biology, Vol 19 (3) 2022. Link

  9. Foo, J. Cancer Evolution in Spatially Structured Tissue. Notices of the AMS, 2021. Link

  10. Gunnarsson, E., Leder, K, and Foo. J. Exact site frequency spectra of neutrally evolving tumors, transition between power laws and signatures of cell viability. Theoretical Population Biology, Volume 142, December 2021, Pages 67-90, 2021. Link *Hon. Mention Feldman Prize

  11. Foo, J., Leder, K., and Schweinsberg, J. Mutation timing in a spatial model of evolution. Stochastic Processes and their Applications, Volume 130, Issue 10, Pages 6388-6413, October 2020. Link

  12. Kim, S., Choung, S., Sun, R., Ung, N., Hashemi, N., Lau, R., Spiller, E., Gasho, J., Foo, J., Mumenthaler, S. Comparison of cell and organoid-level analysis of patient-derived 3D organoids to evaluate tumor cell growth dynamics and drug response. SLAS Discovery, Volume: 25 issue: 7, page(s): 744-754, April 2020. Link

  13. Gunnarsson, E., De, S., Leder, K., and Foo, J. Understanding the role of phenotypic switching in cancer drug resistance. Journal of Theoretical Biology, Volume 490, 7 April 2020, 110162. Link

  14. Goldberg EE and Foo, J. Memory in trait macroevolution. American Naturalist, 2020. doi: 10.1086/705992 Link

  15. Storey K, Leder K, Hawkins-Daarud A, Swanson K, Ahmed A, Rockne R, Foo J. Glioblastoma recurrence and the role of MGMT methylation. JCO Clinical Cancer Informatics. 2019 (3)p. 1-12. Link

  16. Kaveh K, Takahashi Y, Farrar MA, Storme G, Guido M, Piepenburg J, Penning J, Foo J, Leder KZ, Hui SK. Combination therapeutics of Nilotinib and radiation in acute lymphoblastic leukemia as an effective method against drug-resistance. PLoS Computational Biology. 2017 Jul 6;13(7):e1005482. Link

  17. Storey K, Ryser MD, Leder K, Foo J. Spatial measures of genetic heterogeneity during carcinogenesis. Bulletin of Mathematical Biology. 2017 Feb 1;79(2):237-76. PDF

  18. Lindsay, D., Garvey, C., Mumenthaler, S., Foo, J. An evolutionary perspective on cancer treatment response. In: Ujvari B, Roche B, Thomas F, editors. Ecology and Evolution of Cancer. Academic Press; 2017 Feb 8.

  19. Lindsay, D., Foo, J. `Impact of tumor oxygenation on drug resistance evolution under hypoxia-activated prodrug therapy,' Proceedings of 5th International Conference on Biomedical Engineering, 2017.

  20. He, Q., Zhu, J., Dingli, D., Foo, J., Leder, K. `Optimized treatment schedules for Chronic Myeloid Leukemia,' PLoS Computational Biology (2016) Oct 20;12(10):e1005129. Link

  21. Ryser, M., Lee, W., Ready, N., Leder, K., Foo, J. `Quantifying the Dynamics of Field Cancerization in HPV-Ne gative Head and Neck Cancer: A Multiscale Modeling Approach,' Cancer Research (2016) doi: 10.1158/0008- 5472.CAN-16-1054. Link

  22. Lindsay, D., Garvey, C., Mumenthaler, S., Foo, J. `Leveraging hypoxia-activated prodrugs to prevent drug resistance in solid tumors.' PLoS Computational Biology (2016) Aug 25;12(8):e1005077. Link

  23. Garvey, C., Spiller, E., Lindsay, D., Chiang, C., Choi, N., Agus, D., Mallick, P., Foo, J., Mumenthaler, S.; `An image-based quantitative method for studying tumor cell dynamics driven by evolutionary selective pressures.' Scientific Reports 6 :29752 (2016). Link

  24. Durrett, R., Foo, J., Leder, K.; ‘Cancer initiation in spatially structured tissue,’ Journal of Mathematical Biology, (2016); Vol 72(5): pages 1369-400. PDF

  25. Foo, J., Liu, L., Leder, K., Riester, M., Iwasa, Y., Lengauer, C., Michor, F.; ‘An Evolutionary Approach for Identifying Driver Mutations in Colorectal Cancer,’ PLoS Computational Biology (2015) 11(9): e1004350. Link

  26. Mumenthaler, S., Foo, J., et. al. `The Impact of Microenvironmental Heterogeneity on the Evolution of Drug Resistance in Cancer Cells,' Cancer Informatics (2015) 4 (Suppl 4): 19–31. PDF

  27. Foo, J., Haskell, C., Komarova, N., Segal, R., Wood, K. `Modeling sympatric speciation in quasiperiodic environments,' IMA Volumes in Mathematics and its Applications: Applications of Dynamical Systems in Biology and Medicine, Volume 158, p. 149-174 (2015). PDF

  28. Foo, J., Leder, K., and Zhu, J. `Escape times for branching processes with random mutational fitness effects,' Stochastic Processes and their Applications (2014) Volume 124, Issue 11, p. 3661–3697. PDF

  29. Foo, J., Leder, K., and Ryser, M. `Multifocality and recurrence risk: A quantitative model of field cancerization,' Journal of Theoretical Biology (2014) Vol 355. PDF

  30. Aghili, L., Foo, J., De Gregori, J., and De, S. `The landscape of detectable somatically acquired amplifications and deletions in apparently normal human tissues of cancer patients,' Cell Repts (2014) Vol 7 Issue 4. PDF

  31. Foo, J. and Michor, F. `Evolution of acquired resistance to anti-cancer therapy,' Journal of Theoretical Biology (2014) Vol 355. link

  32. Foo, J. and Leder, K. `Dynamics of cancer recurrence,' Annals of Applied Probability (2013) Vol 23 (4), 1437-1468. PDF

  33. The Physical Sciences-Oncology Center Network (2013) A physical sciences network characterization of nonmalignant and metastatic cells. Scientific Reports 3, 1-12. Link

  34. Foo, J, Leder, K. and Mumenthaler, S. `Cancer as a moving target: Understanding the composition and rebound growth kinetics of recurrent tumors,' Evolutionary Applications (2013) Vol 6(1). Link

  35. Shu, J., Zhilian, X., Liang, E., Slipek, N,. Shen, D., Foo, J., Subramanian, S., Steer, C. `Dose-dependent differential mRNA target selection and regulation by let-7a-7f and miR-17-92 cluster microRNAs,' RNA Biology (2012) Vol 9 (10). Link

  36. Foo, J., Chmielecki, J., Pao, W., Michor, F. `Effects of pharmacokinetic processes and varied dosing schedules on the dynamics of acquired resistance to erlotinib in EGFR-mutant lung cancer,' Journal of Thoracic Oncology (2012) Vol 7 (10). PDF

  37. Tang, M., Foo, J., Gonen, M., Guilhot, J., Mahon, F., Michor, F. `Selection pressure exerted by imatinib therapy leads to disparate outcomes of imatinib discontinuation trals,' Haematalogica (2012) 2012 Vol 97(10). PDF

  38. Foo, J., Leder, K. `Rare events in cacner recurrence timing,'Proceediings of the 2012 Winter Simulation Conference IEEE.' (2012) 1-10.

  39. Mumenthaler S, Foo J, Leder K, et al. `Evolutionary modeling of combination strategies to overcome resistance to tyrosine kinase inhibitors in non-small cell lung cancer,' Mol. Pharm (2011) 8(6). Link

  40. Chmielecki J, Foo J, et al. `Optimization of dosing for EGFR-mutant non-small cell lung cancer with evolutionary cancer modeling,' Science Translational Medicine (2011) Vol 3, Issue 90: 90ra59. Link

  41. Leder, K., Foo, J., Skaggs, B., Gorre, M., Sawyers, C., Michor, F. `Diversity in pre-existing resistance to BCR-ABL inhibitors in Chronic Myeloid Leukemia,' PLoS ONE (2011)e27682. doi:10.1371/journal.pone.0027682. PDF SI

  42. Durrett, R., Foo, J. Leder, K., Mayberry, J., Michor, F. `Intra-tumor heterogeneity in evolutionary models of tumor progression' Genetics (2011) Vol 188 (2): 461-477. PDF

  43. Foo, J., Leder, K., and Michor, F. `Stochastic dynamics of cancer initiation,' Physical Biology (2011) Vol 8: 015002. PDF

  44. Foo, J. and Karniadakis, G. `Multi-Element Probabilistic Collocation in High Dimensions,' Journal of Computational Physics (2010) Vol 229(5): p.1536-1557. PDF

  45. Durrett, R., Foo, J. Leder, K., Mayberry, J., Michor, F. `Evolutionary dynamics of tumor progression with random fitness values' Theoretical Population Biology (2010) Vol 78: p.54-66. PDF

  46. Foo, J. and Michor, F. `Evolution of resistance to targeted anti-cancer therapies during general dosing schedules,' Journal of Theoretical Biology (2010) Vol 263 p. 179-188. PDF

  47. Foo, J. and Michor, F. `Evolution of resistance to targeted anti-cancer therapies during continuous and pulsed administration strategies,' PLoS Computational Biology (2009) 5, e1000557. Link

  48. Foo, J., Drummond, M., Clarkson, B., Holyoake, T., and Michor, F. `Eradication of Chronic Myeloid Leukemia Stem Cells: A Novel Mathematical Model Predicts No Therapeutic Benefit of Adding G-CSF to Imatinib,' PLoS Computational Biology (2009) 5, e10000503. PDF

  49. Foo, J., Sindi, S., and Karniadakis, G. `Using the Multi-Element Probabilistic Collocation Method for Sensitivity Analysis in Cellular Signaling Networks.' Systems Biology (2009) Vol 3(4):239-254. PDF

  50. Foo, J., Wan, X., Karniadakis, G. `A Multi-Element Probabilistic Collocation Method for PDEs with Parametric Uncertainty: Error Analysis and Applications' Journal of Computational Physics (2008) Vol 227: 9572-9595. PDF

  51. Prempraneerach, P., Foo, J., Triantafyllou, M., Chryssostomidis, C., Karniadakis, G. `Gradient-free Stochastic Sensitivity Analysis of the Ship-board Power System' International Simulation Multi-Conference (2008) Edinburgh, Scotland.

  52. Foo, J., Yosibash, Z., Karniadakis, G. `Stochastic Simulation of Riser-Sections with Uncertain Measured Pressure Loads and/or Uncertain Material Properties.' Computer Methods in Applied Mechanics and Engineering (2007) Vol 196: 4250-4271. PDF

  53. Bell, J., Foo, J., and Garcia, A. `Algorithm Refinement for the Stochastic Burgers Equation.' Journal of Computational Physics (2007) Vol 223 : 451-468. PDF

  54. Lucor, D., Foo, J., and Karniadakis, G. `Vortex mode selection of a rigid cylinder subject to VIV at low mass-damping.' Journal of Fluids and Structures (2005) Vol 20: 485-503. PDF

  55. Lucor, D., Foo, J., and Karniadakis, G. `Correlation Length and Force Phasing of a Rigid Cylinder Subject to VIV of Fully Coupled Fluid Structure Interactions.' in Fluid Mechanics and its Applications (2004) Vol 75 : 187-199.