Publications

Publications and patents are also listed on Google Scholar

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

 

Preprints

  1. Lin-Rahardja K, Scarborough JA, Scott JG
    Personalizing chemotherapy drug selection using a novel transcriptomic chemogram
    Preprint: https://www.biorxiv.org/content/10.1101/2024.12.17.628754v1
  2. Barker-Clarke R, Gray JM, Tadele DS, Hinczewski M, Scott JG
    Maintaining, masking, and mimicking selection: the interplay of cell-intrinsic and cell-extrinsic effects upon eco-evolutionary dynamics
    Preprint: https://www.biorxiv.org/content/10.1101/2023.03.15.532871v2
  3. King ES, Stacy AE, Scott JG
    A low-footprint, fluorescence-based bacterial time-kill assay for estimating dose-dependent cell death dynamics
    Preprint: https://www.biorxiv.org/content/10.1101/2024.03.08.584154v3
  4. Card KJ, Crozier D, Durmaz A, Gray J, Creary J, Stocks A, Maltas J, Bonomo RA, Burke ZDC, Scott JG
    Evolution under vancomycin selection drives divergent collateral sensitivity patterns in Staphylococcus aureus
    Preprint: https://www.biorxiv.org/content/10.1101/2023.11.30.569373v3
  5. Ho E, Cecco Loris De, Cavalieri S, Sedor G,..., Torres-Roca JF, Scott JG
    A clinicogenomic model including GARD predicts outcome for radiation treated patients with HPV+ oropharyngeal squamous cell carcinoma
    Preprint: https://www.medrxiv.org/content/10.1101/2023.09.14.23295538v1
  6. Vargas R, Petty A, Durmaz A, Lin-Rahardja K, Reizes O, Debernardo R, Scott JG
    TP53 mutations in endometrial cancer contribute to clinically-relevant radiation resistance and highlight the potential for biomarker-driven radiosensitization strategies
    Preprint: https://www.biorxiv.org/content/10.1101/2022.09.06.505009v2
  7. Krishan N and Scott JG.
    Range expansion shifts clonal interference patterns in evolving populations
    Preprint: https://www.biorxiv.org/content/10.1101/794867v2

Published, peer-reviewed articles

    2025

  1. King ES, Pelesko J, Maltas J, Owen SJ, Dolson E, Scott JG
    Fitness seascapes are necessary for realistic modeling of the evolutionary response to drug therapy.
    Science Advances
    Preprint: https://www.biorxiv.org/content/10.1101/2022.06.10.495696.abstract

    2. 2024

  2. Nosrat, F., Dede, C., McCullum, L. B., Garcia, R., Mohamed, A. S. R., Scott, J. G., Bates, J. E., McDonald, B. A., Wahid, K. A., Naser, M. A., He, R., Karagoz, A., Moreno, A. C., van Dijk, L. V., Brock, K. K., Heukelom, J., Hosseinian, S., Hemmati, M., Schaefer, A. J., & Fuller, C. D.
    Optimal timing of organs-at-risk-sparing adaptive radiation therapy for head-and-neck cancer under re-planning resource constraints.
    Physics and Imaging in Radiation Oncology
  3. Scarborough, J., Weaver, D., & Scott, J. G.
    Gene signatures and oncology treatment implications.
    Hematology/Oncology Clinics
  4. Dinh, M. N., Hitomi, M., Al-Turaihi, Z. A., & Scott, J. G.
    Alamar Blue assay optimization to minimize drug interference and inter-assay viability.
    MethodsX
  5. Wei, R., Hitomi, M., Sadler, T., Yehia, L., Calvetti, D., Scott, J. G., & Eng, C.
    Quantitative evaluation of DNA damage repair dynamics to elucidate predictors of autism vs. cancer in individuals with germline PTEN variants.
    PLOS Computational Biology
  6. Chang, C. W., Hu, M., Ghavidel, B., Wynne, J. F., Qiu, R. L. J., Washington, M., Kayode, O., Chin, W. G., Yang, K., Scott, J. G., Patel, A. B., & Yang, X.
    An LLM-based framework for zero-shot de-identifying flexible text data in protected health information enabling potential risk-informed patient safety.
    International Journal of Radiation Oncology, Biology, Physics
  7. Amarell, K., Guo, B., Cho, Y. B., Ramalingam, A., Stephans, K. L., Suh, J. H., Scott, J. G., & Campbell, S. R.
    Spatially fractionated radiotherapy (SFRT) for large tumors: A single institutional experience of dosimetry and clinical outcomes.
    International Journal of Radiation Oncology, Biology, Physics
  8. Fan, C. A., Nystrom, L., Mesko, N., Mayo, Z. S., Burke, Z. D., Shah, C. S., Koyfman, S. A., Scott, J. G., & Campbell, S. R.
    Matched cohort analysis of ultra-hypofractionated preoperative radiation therapy vs. standard fractionation for soft tissue sarcoma.
    International Journal of Radiation Oncology, Biology, Physics
  9. Gopalakrishnan, V., Feng, B., Somasundaram, E., Pelesko, J., Stephans, K. L., Piper, J., Qiu, R. L. J., & Scott, J. G.
    Temporally corrected dose accumulation: Standardizing analysis and documentation of re-irradiation.
    International Journal of Radiation Oncology, Biology, Physics
  10. Kocsis, J., Dylong, M., Patsko, A., Reddy, C. A., Somasundaram, E., Smile, T., Scott, J. G., Shah, C. S., Angelov, L., Anderson, P., Zahler, S., Trucco, M., Thomas, S., Johnson, S., Qi, P., Magnelli, A., Campbell, S. R., & Murphy, E. S.
    Stereotactic body radiation therapy (SBRT) for metastatic osteosarcoma: Local control outcomes with local failure dosimetric analysis.
    International Journal of Radiation Oncology, Biology, Physics
  11. Mayo, Z. S., Fan, C., Jia, X., Parker, S. M., Kocsis, J., Shah, C. S., Scott, J. G., & Campbell, S. R.
    Meta-analysis of 5-fraction preoperative radiotherapy for soft tissue sarcoma.
    American Journal of Clinical Oncology
  12. Shultes, P. V., Weaver, D. T., Tadele, D. S., Barker-Clarke, R. J., & Scott, J. G.
    Cell-cell fusion in cancer: The next cancer hallmark?
    The International Journal of Biochemistry & Cell Biology
  13. 15. Wang, M., Scott, J. G., & Vladimirsky, A.
    Threshold-awareness in adaptive cancer therapy
    PLOS Computational Biology
  14. Naghavi, A. O., Bryant, J. M., Kim, Y., Weygand, J., Redler, G., Sim, A. J., Miller, J., Coucoules, K., Michael, L. T., Gloria, W. E., Yang, G., Rosenberg, S. A., Ahmed, K., Bui, M. M., Henderson-Jackson, E. B., Lee, A., Lee, C. D., Gonzalez, R. J., Feygelman, V., Eschrich, S. A., Scott, J. G., Torres-Roca, J., Latifi, K., Parikh, N., & Costello, J.
    Habitat escalated adaptive therapy (HEAT): A phase 2 trial utilizing radiomic habitat-directed and genomic-adjusted radiation dose (GARD) optimization for high-grade soft tissue sarcoma
    BMC Cancer
  15. Maltas J, Tadele DS, Durmaz A, McFarland CD, Hinczewski M, Scott JG
    Frequency-dependent ecological interactions increase the prevalence and shape the distribution of pre-existing drug resistance
    PRX Life
    Preprint: https://www.biorxiv.org/content/10.1101/2023.03.16.533001v1
  16. King ES, Tadele DS, Pierce B, Hinczewski M, Scott JG
    Diverse mutant selection windows shape spatial heterogeneity in evolving populations
    PLOS Computational Biology
    Preprint: https://www.biorxiv.org/content/10.1101/2023.03.09.531899v3
  17. Weaver DT, Maltas J, Scott JG
    Reinforcement Learning informs optimal treatment strategies to limit antibiotic resistance
    PNAS
    Preprint: https://www.biorxiv.org/content/10.1101/2023.01.12.523765v1

    18. 2023

  18. Cho YB, Yoon N, Suh JH, Scott JG
    Radio-immune response modelling for spatially fractionated radiotherapy
    Physics in Medicine & Biology
  19. Torres-Roca JF, Grass D, Scott JG, Eschrich S
    Towards Data Driven RT Prescription: Integrating Genomics into RT Clinical Practice
    Seminars in Radiation Oncology
  20. Barker-Clarke R, Weaver DT, Scott JG
    Graph 'texture' features as novel metrics that can summarize complex biological graphs
    Physics in Medicine & Biology
    Preprint: https://www.biorxiv.org/content/10.1101/2022.11.21.517417v2
  21. Somasundaram E, Wadhwa RR, Litzler A, Barker-Clarke R, Qi P, Videtic G, Stephans K, Pennell NA, Raymond D, Yang K, Kattan MW, Scott JG
    Clinical Nomogram Using Novel Computed Tomography–Based Radiomics Predicts Survival in Patients With Non–Small-Cell Lung Cancer Treated With Stereotactic Body Radiation Therapy
    JCO Clinical Cancer Informatics
    Preprint: https://www.medrxiv.org/content/10.1101/2022.06.21.22276718v1
  22. Kewan T, Durmaz A, Bahaj W, Gurnari C, Terkawi L, Awada H, Ogbue OD, Ahmed R, Pagliuca S, Awada H, Kutoba Y. Minako M, Povilawan B, Al-Share B, Patel B, Carraway H, Scott JG, Balasubramanian S, Bat T, Madanat Y, Sekeres M, Haferlach T, Visconte V, Maciejewski J
    Molecular patterns identify distinct subclasses of myeloid neoplasia
    Nature Communications
  23. Scarborough JA, Eschrich SA, Torres-Roca J, Dhawan A, Scott JG
    Exploiting convergent evolution to derive a pan-cancer cisplatin sensitivity gene expression signature
    NPJ Precision Oncology
    Preprint: https://www.medrxiv.org/content/10.1101/2021.11.10.21265799v1
  24. Lin-Rahardja K, Weaver DT, Scarborough JA, Scott JG
    Evolution-Informed Strategies for Combating Drug Resistance in Cancer
    International Journal of Molecular Sciences

    25. 2022

  25. Huynh L, Scott JG, Thomas PJ
    Inferring Density-Dependent Population Dynamics Mechanisms through Rate Disambiguation for Logistic Birth-Death Processes
    Journal of Mathematical Biology
    Preprint: https://www.biorxiv.org/content/10.1101/2022.05.10.491405.abstract
  26. Gopalakrishnan V, Crozier D, Card KJ, Chick LD, Krishnan NP, McClure E, Pelesko J, Williamson DFK, Nichol D, Mandal S, Bonomo RA and Scott JG.
    A low-cost, open source, evolutionary bioreactor and its educational use
    eLife
    Preprint: https://www.biorxiv.org/content/10.1101/729434v5
  27. Durmaz A, Scott JG.
    Stability of scRNA-Seq Analysis Workflows is Susceptible to Preprocessing and is Mitigated by Regularized or Supervised Approaches
    Evolutionary Bioinformatics
    Preprint: https://www.biorxiv.org/content/10.1101/2021.02.15.431268v1
  28. Farrokhian N, Maltas J, Ellsworth P, Durmaz A, Dinh M, Hitomi M, Kaznatcheev A, Marusyk A, Scott JG.
    Measuring competitive exclusion in non–small cell lung cancer
    Science Advances
    Preprint: https://www.biorxiv.org/content/10.1101/2020.09.18.303966v5
  29. Yang K, Scott JG.
    A Phenome-Wide Association Study and the Discovery of a New Clinical Spectrum of Hereditary Cancer Genes
    Jama Oncology

    30. 2021

  30. Scarborough JA and Scott JG.
    Translation of Precision Medicine Research Into Biomarker-Informed Care in Radiation Oncology
    Seminars in Radiation Oncology
  31. Weaver DT, Pishas KI, Williamson D, Scarborough JA, Lessnick SL, Dhawan A and Scott JG.
    Network potential identifies therapeutic miRNA cocktails in Ewings Sarcoma
    Plos Computational Biology
    Preprint: https://www.biorxiv.org/content/10.1101/854695v1
  32. Yoon N, Krishnan N, Scott JG.
    Modeling of collaterally sensitive drug cycles, and optimization of the drug effect in the spirit of adaptive therapy
    Journal of Mathematical Biology
    Preprint: https://www.biorxiv.org/content/10.1101/2020.07.02.184952v1
  33. Somasundaram E, Litzler A, Wadhwa RR, Scott JG.
    Persistent Homology of Tumor CT Scans Predicts Survival In Lung Cancer
    Medical Physics
    Preprint: https://www.medrxiv.org/content/10.1101/2020.12.06.20244863v1
  34. Scott JG, Sedor G, Ellsworth P, Scarborough JA, Ahmed K, Oliver DE, Eschrich SA, Kattan MW, Torres-Roca JF.
    GARD is a pan-cancer predictor of clinical outcome in radiation treated patients
    Lancet Oncology
    Preprint: https://www.medrxiv.org/content/10.1101/2020.12.19.20248484v1
  35. Scarborough JA, Tom MC, Kattan MW, Scott JG.
    Revisiting a null hypothesis: Exploring the parameters of oligometastasis treatment
    International Journal of Radiation Oncology*Biology*Physics
    Preprint: https://www.medrxiv.org/content/10.1101/2020.08.10.20172098v1
  36. Parsai S, Qiu RLJ, Qi P, Sedor G, Fuller CD, Murray E, Majkszak D, Dorio N, Koyfman S, Woody N, Joshi N, Scott JG.
    In vivo assessment of the safety of standard fractionation temporally feathered radiation therapy (TFRT) for head and neck squamous cell carcinoma: An R-IDEAL stage I/2a first-in-humans/feasibility demonstration of new technology implementation
    Radiotherapy and Oncology
    Preprint: https://www.medrxiv.org/content/10.1101/2021.01.05.21249232v1
  37. Weaver DT, McElvany BD, Gopalakrishnan V, Card KJ, Crozier D, Dhawan A, Dinh MN, Dolson E, Farrokhian N, Hitomi M, Ho E, Jagdish T, King ES, Cadnum JL, Donskey CJ, Krishnan N, Kuzmin G, Li J, Maltas J, Mo J, Pelesko J, Scarborough JA, Sedor G, Tian E, An GC, Diehl SA, Scott JG.
    UV decontamination of personal protective equipment with idle laboratory biosafety cabinets during the COVID-19 pandemic
    Plos One
    Preprint: https://www.medrxiv.org/content/10.1101/2020.03.25.20043489v2
  38. Kayani BJ, Weaver DT, Gopalakrishnan V, King ES, Dolson E, Krishnan N, Pelesko J, Scott MJ, Hitomi M, Cadnum JL, Li DF, Donskey CJ, Scott JG, Charnas I.
    UV-C Tower for point-of-care decontamination of filtering facepiece respirators
    American Journal of Infection Control
    Preprint: https://www.medrxiv.org/content/10.1101/2020.03.25.20043489v2
  39. Somasundaram EV, Brown SE, Litzler A, Scott JG, Wadhwa RR
    Benchmarking R packages for Calculation of Persistent Homology
    The R journal
  40. Awada H, Durmaz A, Gurnari C, Kishtagari A, Meggendorfer M, Kerr CM, Kuzmanovic T, Durrani J, Shreve J, Nagata Y, Radivoyevitch T, Advani AS, Ravandi F, Carraway HE, Nazha A, Haferlach C, Saunthararajah Y, Scott JG, Visconte V, Kantarjian H, Kadia T, Sekeres MA, Haferlach T, Maciejewski JP,
    Machine Learning Integrates Genomic Signatures for Subclassification beyond Primary and Secondary Acute Myeloid Leukemia
    Blood

    41. 2020

  41. Parsai S, Qui RLJ, Qi P, Alfonso JCL, Donaghue J, Murray E, Majkszak D, Dorio N, Fuller CD, Brock K, Koyfman S, Woody N, Joshi N, Scott JG.
    Technical Note: A step-by-step guide to temporally feathered radiation therapy planning for head and neck cancer
    Journal of Applied Clinical Medical Physics
    		42.
  42. Scott JG, Sedor G, Kattan MW, Peacock J, Grass GD, Mellon EA, Thapa R, Schell M, Waller A, Poppen S, Andl G, Eschrich SA, Dilling TJ, Dalton WS, Harrison LB, Fox T Torres-Roca JF.
    Personalizing Radiotherapy Prescription Dose Using Genomic Markers of Radiosensitivity and Normal Tissue Toxicity in Non-Small Cell Lung Cancer
    Journal of Thoracic Oncology
    Preprint: https://www.medrxiv.org/content/10.1101/2020.01.09.20017046v2
  43. Nagata Y, Zhao R, Awada H, Kerr CM, Mirzaev I, Kongkiatkamon S, Nazha A, Makishima H, Radivoyevitch T, Scott JG, Sekeres MA, Hobbs BP, Maciejewski JP.
    Machine learning demonstrates that somatic mutations imprint invariant morphologic features in myelodysplastic features
    Blood
  44. Grimes DR, Jansen M, Macauley RJ, Scott JG, Basanta D.
    Evidence for hypoxia increasing the tempo of evolution in glioblastoma
    British Journal of Cancer
    Preprint: https://www.biorxiv.org/content/10.1101/293712
  45. Iram S, Dolson E, Chiel J, Pelesko J, Krishnan N, Gungor O, Kuznets-Speck B, Defner S, Ilker E, Scott JG and Hinczewski M.
    Controlling the speed and trajectory of evolution with counterdiabatic driving
    Nature Physics
    Preprint: https://www.biorxiv.org/content/10.1101/867143v1
  46. Scarborough JA, McClure E, Anderson P, Dhawan A, Durmaz A, Lessnick SL, Hitomi M and Scott JG.
    Identifying states of collateral sensitivity during the evolution of therapeutic resistance in Ewing’s sarcoma
    iScience
    Preprint: https://www.biorxiv.org/content/10.1101/2020.02.11.943936v2
  47. Parsai S, Lawrenz J, Kilpatrick S, Rubin B, Hymes C, Gray M, Mesko N, Shah C, Nystrom L and Scott JG.
    Early Outcomes of Preoperative 5-fraction Radiation Therapy for Soft Tissue Sarcoma Followed by Immediate Surgical Resection
    Advances in Radiation Oncology
    Preprint: https://www.medrxiv.org/content/10.1101/2020.03.20.20038885v1.full
  48. 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.
    Nature Communications
    Preprint: https://www.biorxiv.org/content/10.1101/504837v2
  49. Gluzman M, Scott JG and Vladimirski A.
    Optimizing adaptive cancer therapy: dynamic programming and evolutionary game theory.
    Proceedings of the Royal Society, B
    Preprint: https://www.biorxiv.org/content/10.1101/491829v1.full

    50. 2019

  50. Scott JG, Maini PK, Anderson ARA and Fletcher AG.
    Inferring Tumour Proliferative Organisation from Phylogenetic Tree Measures in a Computational Model.
    Systematic Biology
    Preprint: https://www.biorxiv.org/content/10.1101/334946v2
  51. Ahmed KA, Liveringhouse CL, Mills MN, Figura NB, Grass GD, Washington IR, Harris EE, Czerniecki BJ, Blumencranz PW, Eschrich SA, Scott JG, Diaza R, Torres-Roca JF.
    Utilizing the genomically adjusted radiation dose (GARD) to personalize adjuvant radiotherapy in triple negative breast cancer management.
    EBioMedicine
    Preprint: https://www.biorxiv.org/content/10.1101/334946v2
  52. 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
  53. 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
  54. 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
    Preprint: https://www.biorxiv.org/content/early/2018/08/07/179259
  55. 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
    Preprint: https://www.biorxiv.org/content/10.1101/185892v4
  56. 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
    Preprint: https://www.biorxiv.org/content/10.1101/169615v2

    57. 2018

  57. 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.
    Nature Communications
    Preprint: https://www.biorxiv.org/content/10.1101/238675v2
  58. Dhawan A, Harris AL, Buffa FM and Scott JG. Endogenous miRNA sponges mediate the generation of oscillatory dynamics for a non-coding RNA network.
    Journal of Theoretical Biology
    Preprint: https://www.biorxiv.org/content/early/2018/03/31/292029
  59. 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
  60. Mirzaev I, Williamson DFK and Scott JG. egtplot: A python package for three strategy evolutionary games.
    Journal of Open Source Software
    Preprint: https://www.biorxiv.org/content/10.1101/300004v2
  61. Vargas R, Gopal C, Kuzmishin GB, DeBernardo R, Koyfman SA, Jha BK, Mian OY, Scott JG, Adams DJ, Peacock CD and Abazeed ME. Case study: patient-derived clear cell adenocarcinoma xenograft model longitudinally predicts treatment response.
    npj Precision Oncology
  62. Nichol D, Bonomo RA and Scott JG. It's too soon to pull the plug on antibiotic cycling.
    The Lancet Infectious Disease
  63. 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
  64. 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
  65. 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
    Preprint: https://www.biorxiv.org/content/early/2017/09/03/184044
  66. Yoon N, Vander Velde R, Marusyk A and Scott JG. Optimal Therapy Scheduling Based on a Pair of Collaterally Sensitive Drugs.
    Bulletin of Mathematical Biology
    Preprint: https://www.biorxiv.org/content/early/2017/10/13/196824
  67. 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

    68. 2017

  68. Ottino-Loffler B, Scott JG, and Strogatz SH. Evolutionary dynamics of incubation periods.
    eLife
    Preprint: https://www.biorxiv.org/content/10.1101/144139v1
  69. 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
  70. 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
  71. 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
  72. 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
  73. Ottino-Löffler B, Scott JG, and Strogatz SH. Takeover times for a simple model of network infection.
    Physical Review E
  74. Scott JG and Marusyk A. Somatic clonal evolution: A selection-centric perspective.
    Biochimica et Biophysica Acta (BBA)-Reviews on Cancer
  75. 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
    Preprint: https://www.biorxiv.org/content/10.1101/067488v1
  76. 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
  77. 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
  78. Grassberger C, Scott JG and Paganetti H. Biomathematical Optimization of Radiation Therapy in the Era of Targeted Agents.
    International Journal of Radiation Oncology*Biology*Physics
  79. 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

    80. 2016

  80. 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
  81. 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
  82. Rietman, EA, Scott JG, Tuszynski JA and Klement GL. Personalized anticancer therapy selection using molecular landscape topology and thermodynamics.
    Oncotarget
  83. 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
  84. 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
  85. Farhidzadeh H, Kim JY, Scott JG, Goldgof DB, Hall LO and Harrison LB. Classification of progression free survival with nasopharyngeal carcinoma tumors.
    Proceedings of the SPIE, Medical Imaging
  86. 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.
    Proceedings of the SPIE, Medical Imaging
  87. 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
  88. 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

    89. 2015

  89. 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
  90. Kaznatcheev A, Scott JG and Basanta D. Edge effects in game-theoretic dynamics of spatially structured tumours.
    Proceedings of the Royal Society: Interface
  91. 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

    92. 2014

  92. 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
  93. 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
  94. 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
  95. 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

    96. 2013

  96. 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
  97. 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.
    Proceedings of the Royal Society: Interface
  98. McTyre E, Scott JG and Chinnaiyan P. Whole brain radiotherapy for brain metastasis.
    Surgical Neurology International

    99. 2012

  99. Scott JG, Kuhn P and Anderson ARA. Unifying metastasis—integrating intravasation, circulation and end-organ colonization.
    Nature Reviews Cancer
  100. 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
  101. 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
  102. Scott JG. Phase i trialist.
    The Lancet Oncology
  103. 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
  104. Scott JG, Tsai YY, Chinnaiyan P and Yu HHM. Effectiveness of radiotherapy for elderly patients with glioblastoma.
    International Journal of Radiation Oncology*Biology*Physics
  105. 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

    106. 2011

  106. 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

    107. 2010

  107. 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

    108. 2009

  108. 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
  109. 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

    110. 2008

  110. 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

    111. 2007

  111. Scott JG, Lee H, Barsoum W and Van Den Bogert AJ., The effect of tibiofemoral loading on proximal tibiofibular joint motion.
    Journal of anatomy (2007)