Publications and patents are also listed at Google Scholar

If you have difficulty obtaining any of the papers listed here, email Jake.


  1. Wadhwa RR, Dhawan A, Williamson DF and Scott JG. A flat persistence diagram for improved visualization of topological features in persistent homology
  2. Vander Velde R, Yoon N, Marusyk V, Dhawan A, Balynska O, Desai B, Peral D, Myroshnychenko D, Poleszhuk J, Liu K, Mian O, Abazeed M, Haura E, Scott JG and Marusyk A. Resistance to ALK targeting therapies as a gradual Darwinian adaptation to inhibitor specific selective pressures
  3. Gluzman M, Scott JG and Vladimirski A. Optimizing adaptive cancer therapy: dynamic programming and evolutionary game theory.
  4. Published, peer-reviewed articles


  5. Rockne R, Hawkins-Daarud A, Swanson KR, Sluka JP, Glazier JA, Macklin P, Hormuth D, Jarrett AM, Fonseca Lima EAB, Oden J, Birosa G, Yankeelov TE, Curtius K, Al Bakir I, Wodarz D, Komarova N, Aparicio L, Bordyuh M, Rabadan R, Finley S, Enderling H, Caudell JJ, Moros EG, Anderson ARA, Gatenby R, Kaznatcheev A, Jeavons P, Krishnan N, Pelesko J, Wadhwa R, Yoon N, Nichol D, Marusyk A, Hinczewski M and Scott JG,
    The 2019 Mathematical Oncology Roadmap.

    Physical Biology
  6. Dhawan A, Barberis A, Cheng WC, Domingo E, West C, Maughan T, Scott JG, Harris AL and Buffa FM,
    Guidelines for using sigQC for systematic evaluation of gene signatures.

    Nature Protocols
  7. Kaznatcheev A, Peacock J, Basanta D, Marusyk A and Scott JG., Fibroblasts and alectinib switch the evolutionary games that non-small cell lung cancer plays.
    Nature Ecology and Evolution
  8. Nichol D, Rutter J, Bryant C, Hujer AM, Lek S, Adams MD, Jeavons P, Anderson ARA, Bonomo RA and Scott JG. Antibiotic collateral sensitivity is contingent on the repeatability of evolution.
    Nature Communications
  9. Scott JG, Dhawan A, Hjelmeland A, Lathia J, Chumakova A, Hitomi M, Fletcher AG, Maini PK and Anderson ARA, Recasting the cancer stem cell hypothesis: unification using a continuum model of microenvironmental forces.
    Current Stem Cell Reports
  10. 2018

  11. Dhawan A, Scott JG, Harris AL and Buffa FM, Pan-cancer characterisation of microRNA with hallmarks of cancer reveals role of microRNA-mediated downregulation of tumour suppressor genes
  12. Dhawan A, Harris AL, Buffa FM and Scott JG. Endogenous miRNA sponges mediate the generation of oscillatory dynamics for a non-coding RNA network
  13. Wadhwa RR, Williamson DFK, Dhawan A and Scott JG. TDAstats: R pipeline for computing persistent homology in topological data analysis. Journal of Open Source Software
  14. Mirzaev I, Williamson DFK and Scott JG. egtplot: A python package for three strategy evolutionary games. Journal of Open Source Software
  15. Vargas R, Gopal C, Kuzmishin GB, DeBernardo R, Koyfman SA, Jha BK, Mian OY, Scott JG, Adams DJ, Peacock CD and Mohamed E Abazeed. Case study: patient-derived clear cell adenocarcinoma xenograft model longitudinally predicts treatment response. npj Precision Oncology
  16. Nichol D, Bonomo RA and Scott JG. It's too soon to pull the plug on antibiotic cycling. The Lancet Infectious Disease
  17. Curtis GL, Lawrenz JM, George J, Styron JF, Scott J, Shah C, Shepard DR, Rubin B, Nystrom LM and Mesko NW. Adult soft tissue sarcoma and time to treatment initiation: An analysis of the National Cancer Database. Journal of Surgical Oncology
  18. Kang J, Rancati T, Lee S, Oh JH, Kerns SL, Scott JG, Schwartz R, Kim S, Rosenstein BS. Machine Learning and Radiogenomics: Lessons Learned and Future Directions. Frontiers in Oncology
  19. Alfonso JCL, Parsai S, Joshi N, Godley A, Koyfman SA, Caudell JJ, Fuller CD, Enderling H and Scott JG. Temporally-Feathered Intensity Modulated Radiation Therapy: A technique to reduce normal tissue toxicity. Medical Physics
  20. Yoon N, Vander Velde R, Marusyk A and Scott JG. Optimal Therapy Scheduling Based on a Pair of Collaterally Sensitive Drugs, in press, Bulletin of Mathematical Biology
  21. Ahmed KA, Scott JG, Arrington JA, Naghavi AO, Grass GD, Perez BA, Caudell JJ, Berglund AE, Welsh EA, Eschrich SA, Dilling TJ and Torres-Roca JF. Radiosensitivity of Lung Metastases by Primary Histology and Implications for Stereotactic Body Radiation Therapy Using the Genomically Adjusted Radiation Dose. Journal of Thoracic Oncology
  22. 2017

  23. Ottino-Loffler B, Scott JG, and Strogatz SH, Evolutionary dynamics of incubation periods. eLife 2017;6:e30212.
  24. Zhou M, Scott JG, Chaudhury B, Hall L, Goldgof D, Yeom KW, Iv M, Ou Y, Kalpathy-Cramer J, Napel S and Gillies R. Radiomics in Brain Tumor: Image Assessment, Quantitative Feature Descriptors, and Machine-Learning Approaches. American Journal of Neuroradiology (2017)
  25. Karthik N, Ward MC, Scott JG, Mesko N and Shah CS. Factors Associated With Acute and Chronic Wound Complications in Patients With Soft-Tissue Sarcoma With Long-Term Follow-Up. American Journal of Clinical Oncology
  26. Naghavi AO, Gonzalez RJ, Scott JG, Abuodeh YA, Echevarria M, Mullinax JE, Ahmed KA, Harrison LB and Fernandez DC., Staged Reconstruction Brachytherapy Has Lower Overall Cost in Recurrent Soft Tissue Sarcoma. Practical Radiation Oncology
  27. Naghavi AO, Fernandez DC, Mesko N, Juloori A, Martinez A, Scott JG, Shah C and Harrison LB. American Brachytherapy Society consensus statement for soft tissue sarcoma brachytherapy. Brachytherapy
  28. Ottino-Löffler B, Scott JG, and Strogatz SH. Takeover times for a simple model of network infection . Physical Review E
  29. Scott JG and Marusyk A, Somatic clonal evolution: A selection-centric perspective. Biochimica et Biophysica Acta (BBA)-Reviews on Cancer
  30. Kaznatcheev A, Vander Velde R, Scott JG and Basanta D., Cancer treatment scheduling and dynamic heterogeneity in social dilemmas of tumour acidity and vasculature. British Journal of Cancer
  31. Naghavi AO, Gonzalez RJ, Scott JG, Kim Y, Abuodeh YA, Strom TJ, Echevarria M, Mullinax JE, Ahmed KA, Harrison LB and Fernandez DC., Staged reconstruction brachytherapy has lower overall cost in recurrent soft-tissue sarcoma. Journal of contemporary brachytherapy
  32. McFarland CD, Yaglom JA, Wojtkowiak JW, Scott JG, Morse DL, Sherman MY and Mirny L., The damaging effect of passenger mutations on cancer progression. Cancer Research
  33. Grassberger C, Scott JG and Paganetti H., Biomathematical Optimization of Radiation Therapy in the Era of Targeted Agents. International Journal of Radiation Oncology
  34. Dhawan A, Nichol D, Kinose F, Abazeed ME, Marusyk A, Haura EB and Scott JG., Collateral sensitivity networks reveal evolutionary instability and novel treatment strategies in ALK mutated non-small cell lung cancer. Scientific Reports
  35. 2016

  36. Perni S, Mohamed AS, Scott JG, Enderling H, Garden AS, Gunn GB, Rosenthal DI and Fuller CD, CT-based volumetric tumor growth velocity: A novel imaging prognostic indicator in oropharyngeal cancer patients receiving radiotherapy. Oral oncology
  37. Farhidzadeh H, Goldgof DB, Hall LO, Scott JG, Gatenby RA, Gillies RJ and Raghavan M., A quantitative histogram-based approach to predict treatment outcome for Soft Tissue Sarcomas using pre-and post-treatment MRIs. 2016 IEEE International Conference on Systems, Man, and Cybernetics (SMC) (2016)
  38. Rietman, EA, Scott JG, Tuszynski JA and Klement GL., Personalized anticancer therapy selection using molecular landscape topology and thermodynamics. Oncotarget
  39. Naghavi AO, Gonzalez RJ, Scott JG, Mullinax JE, Abuodeh YA, Kim Y, Binitie O, Ahmed KA, Bui MM, Saini AS, and Zager JS and Fernandez DC., Implications of staged reconstruction and adjuvant brachytherapy in the treatment of recurrent soft tissue sarcoma. Brachytherapy
  40. Werner B, Scott JG, Sottoriva A, Anderson ARA, Traulsen A and Altrock PM., The cancer stem cell fraction in hierarchically organized tumors can be estimated using mathematical modeling and patient-specific treatment trajectories. Cancer research
  41. Farhidzadeh H, Kim JY, Scott JG, Goldgof DB, Hall LO and Harrison LB., Classification of progression free survival with nasopharyngeal carcinoma tumors . Proc. SPIE, Medical Imaging
  42. Farhidzadeh H, Chaudhury B, Scott JG, Goldgof DB, Hall LO, Gatenby RA, Gillies RJ and Raghavan M., Signal intensity analysis of ecological defined habitat in soft tissue sarcomas to predict metastasis development. , Proc. SPIE, Medical Imaging
  43. Scott JG, Fletcher AG, Anderson ARA and Maini PK., Spatial metrics of tumour vascular organisation predict radiation efficacy in a computational model. , PLoS Computational Biology
  44. Scott JG, Berglund A, Schell MJ, Mihaylov I, Fulp WJ, Yue B, Welsh E, Caudell JJ, Ahmed K, Strom TS and Mellon E and Torres-Roca JT. A genome-based model for adjusting radiotherapy dose (GARD): a retrospective, cohort-based study. The Lancet Oncology
  45. 2015

  46. Nichol D, Jeavons P, Fletcher AG, Bonomo RA, Maini PK, Paul JL, Gatenby RA, Anderson ARA and Scott, JG. Steering evolution with sequential therapy to prevent the emergence of bacterial antibiotic resistance. PLoS Computational Biology
  47. Kaznatcheev A, Scott JG and Basanta D. Edge effects in game-theoretic dynamics of spatially structured tumours. Proceedings of the Royal Society: Interface
  48. Arora D, Frakes J, Scott JG, Opp D, Johnson C, Song J and Harris E. Incidental radiation to uninvolved internal mammary lymph nodes in breast cancer. Breast cancer research and treatment
  49. 2014

  50. Gallaher J, Cook LM, Gupta S, Araujo A, Dhillon J, Park JY, Scott JG, Pow-Sang J, Basanta D and Lynch CC. Improving treatment strategies for patients with metastatic castrate resistant prostate cancer through personalized computational modeling. Clinical and experimental metastasis
  51. Scott JG, Fletcher AG, Maini PK, Anderson ARA and Gerlee P. A filter-flow perspective of haematogenous metastasis offers a non-genetic paradigm for personalised cancer therapy. European journal of cancer
  52. Baldock AL, Yagle K, Born DE, Ahn S, Trister AD, Neal M, Johnston SK, Bridge CA, Basanta D, Scott JG, Malone H and Swanson KR. Invasion and proliferation kinetics in enhancing gliomas predict IDH1 mutation status. Neuro Oncology
  53. Scott JG, Hjelmeland AB, Chinnaiyan P, Anderson ARA, Basanta D. Microenvironmental variables must influence intrinsic phenotypic parameters of cancer stem cells to affect tumourigenicity. PLoS Computational Biology
  54. 2013

  55. Belmonte-Beitia SJ, Woolley TE, Scott JG, Maini PK and Gaffney EA. Modelling biological invasions: individual to population scales at interfaces. Journal of Theoretical Biology
  56. Scott JG, Basanta D, Anderson ARA and Gerlee P. A mathematical model of tumour self-seeding reveals secondary metastatic deposits as drivers of primary tumour growth. Journal of Theoretical Biology
  57. McTyre E, Scott JG and Chinnaiyan P. Whole brain radiotherapy for brain metastasis. Surgical Neurology International
  58. 2012

  59. Scott JG, Kuhn P and Anderson ARA. Unifying metastasis—integrating intravasation, circulation and end-organ colonization. Nature Reviews Cancer
  60. Scott JG, Bauchet L, Fraum TJ, Nayak L, Cooper AR, Chao ST, Suh JH, Vogelbaum MA, Peereboom DM, Zouaoui S, Mathieu‐Daudé H and Iwamoto F. Recursive partitioning analysis of prognostic factors for glioblastoma patients aged 70 years or older. Cancer
  61. Finkelstein SE, Rodriguez F, Dunn M, Farmello M-J, Smilee R, Janssen W, Kang L, Chuang T, Seigne J, Pow-Sang J, Torres-Roca JF, Heysek R, Biagoli M, Shankar R, Scott JG, Antonia S, Gabrilovich D, Fishman M. Serial assessment of lymphocytes and apoptosis in the prostate during coordinated intraprostatic dendritic cell injection and radiotherapy. Immunotherapy
  62. Scott JG. Phase i trialist. The Lancet Oncology
  63. Basanta D, Scott JG, Fishman MN, Ayala G, Hayward SW and Anderson ARA. Investigating prostate cancer tumour–stroma interactions: clinical and biological insights from an evolutionary game. British Journal of Cancer
  64. Scott JG, Tsai YY, Chinnaiyan P and Yu HHM. Effectiveness of radiotherapy for elderly patients with glioblastoma. International Journal of Radiation Oncology*Biology*Physics
  65. Scott JG, Suh JH, Elson P, Barnett GH, Vogelbaum MA, Peereboom DM, Stevens GHJ, Elinzano H, Chao ST. Aggressive treatment is appropriate for glioblastoma multiforme patients 70 years old or older: a retrospective review of 206 cases. Neuro Oncology
  66. 2011

  67. Basanta D, Scott JG, Rockne R, Swanson KR and Anderson ARA. The role of IDH1 mutated tumour cells in secondary glioblastomas: an evolutionary game theoretical view. Physical Biology
  68. 2010

  69. Packer CD, Carnell RC, Tomcho PM and Scott JG. Development of a four-day service-learning rotation for third-year medical students. Teaching and Learning in Medicine
  70. 2009

  71. Oh S, Scott JG, Shin DH, Suh TS and Kim S. Measurements of dose discrepancies due to inhomogeneities and radiographic contrast in balloon catheter brachytherapy. Medical Physics
  72. Elias HG, Scott JG, Metheny L, Quereshy FA. Multiple myeloma presenting as mandibular ill-defined radiolucent lesion with numb chin syndrome: a case report. Journal of Oral and Maxillofacial Surgery
  73. 2008

  74. Fening SD, Kovacic J, Kambic H, McLean S, Scott JG and Miniaci A., The Effects of Modified Posterior Tibial Slope on Anterior Cruciate Ligament Strain and Knee Kinematics–A Human Cadaveric Study. Journal of knee surgery
  75. 2007

  76. Scott JG, Lee H, Barsoum W and Van Den Bogert AJ., The effect of tibiofemoral loading on proximal tibiofibular joint motion. Journal of anatomy