Jose Ramos-Mendez, PhD

Title(s)Asst Professor in Residence, Radiation Oncology
SchoolSchool of Medicine
Address1635 Divisadero Street
San Francisco CA 94115
Phone--
ORCID ORCID Icon0000-0002-8106-5142 Additional info
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    Collapse Biography 
    Collapse Education and Training
    Benemérita Universidad Autónoma de Puebla, Puebla, MéxicoMSc06/2010Applied Physics
    Benemérita Universidad Autónoma de Puebla, Puebla, MéxicoPhD12/2013Applied Physics
    Benemérita Universidad Autónoma de Puebla, Puebla, MéxicoBSc01/2008Applied Physics
    University of California Los Angeles, Los Angeles, CA06/2021CAMPEP Certificate Program
    University of California San Francisco, San Francisco, CA06/2023Medical Physics Residency
    Collapse Awards and Honors
    Northern California of the American Association of Physicists in Medicine2022  - 20221st Price - The Young Investigation Symposium
    Northern California of the American Association of Physicists in Medicine2022  - 20223rd Place - SLAM talk contest
    Radiation Research Society2021  - 2021Annual Meeting’s Featured Lectures
    Radiation Research Society2021  - 2021Scholar-In-Training Feature of the Month
    National Cancer Institute / ITCR2020  - 20203rd Place – Video contest for imaging category NCI/ITCR 2020 Virtual Annual PI meeting
    Journal of Radiation Research2019  - 2019Editor pick and front cover. Vol. 191, No. 2
    Mexican Research National System (SNI)2018Level I
    International Journal of Medical Physics2017  - 2017Front cover. Vol. 44, No. 1
    Mexican Research National System (SNI)2016  - 2018Level C
    The Cultural Vistas2011Alumni
    CONACyT, Mexico2010  - 2014National Fellow
    CONACyT, Mexico2008  - 2010National Fellow

    Collapse Overview 

    Collapse ORNG Applications 
    Collapse Featured Publications
    Collapse Collaboration Interests
    Collapse Faculty Mentoring

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. An integrated Monte Carlo track-structure simulation framework for modeling inter and intra-track effects on homogenous chemistry. Phys Med Biol. 2023 May 18. D-Kondo JN, Garcia Garcia OR, LaVerne JA, Faddegon BA, Schuemann J, Shin WG, Ramos-Mendez J. PMID: 37201533.
      View in: PubMed   Mentions:
    2. TOPAS-imaging: Extensions to the TOPAS simulation toolkit for medical imaging systems. Phys Med Biol. 2023 Mar 17. Lee H, Cheon BW, Feld J, Grogg K, Perl J, Ramos-Mendez J, Faddegon BA, Min CH, Paganetti H, Schuemann J. PMID: 36930985.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    3. Prediction of DNA rejoining kinetics and cell survival after proton irradiation for V79 cells using Geant4-DNA. Phys Med. 2022 Dec 20; 105:102508. Sakata D, Hirayama R, Shin WG, Belli M, Tabocchini MA, Stewart RD, Belov O, Bernal MA, Bordage MC, Brown JMC, Dordevic M, Emfietzoglou D, Francis Z, Guatelli S, Inaniwa T, Ivanchenko V, Karamitros M, Kyriakou I, Lampe N, Li Z, Meylan S, Michelet C, Nieminen P, Perrot Y, Petrovic I, Ramos-Mendez J, Ristic-Fira A, Santin G, Schuemann J, Tran HN, Villagrasa C, Incerti S. PMID: 36549067.
      View in: PubMed   Mentions:    Fields:    
    4. Impact of DNA Geometry and Scoring on Monte Carlo Track-Structure Simulations of Initial Radiation-Induced Damage. Radiat Res. 2022 09 01; 198(3):207-220. Bertolet A, Ramos-Méndez J, McNamara A, Yoo D, Ingram S, Henthorn N, Warmenhoven JW, Faddegon B, Merchant M, McMahon SJ, Paganetti H, Schuemann J. PMID: 35767729; PMCID: PMC9458623.
      View in: PubMed   Mentions: 1     Fields:    
    5. TOPAS-nBio simulation of temperature-dependent indirect DNA strand break yields. Phys Med Biol. 2022 07 08; 67(14). Ramos-Méndez J, García-García O, Domínguez-Kondo J, LaVerne JA, Schuemann J, Moreno-Barbosa E, Faddegon B. PMID: 35714599; PMCID: PMC9512025.
      View in: PubMed   Mentions: 1     Fields:    
    6. DNA damage modeled with Geant4-DNA: effects of plasmid DNA conformation and experimental conditions. Phys Med Biol. 2021 12 15; 66(24). D-Kondo N, Moreno-Barbosa E, Štephán V, Stefanová K, Perrot Y, Villagrasa C, Incerti S, De Celis Alonso B, Schuemann J, Faddegon B, Ramos-Méndez J. PMID: 34787099.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    7. TOPAS-nBio validation for simulating water radiolysis and DNA damage under low-LET irradiation. Phys Med Biol. 2021 09 03; 66(17). Ramos-Méndez J, LaVerne JA, Domínguez-Kondo N, Milligan J, Štepán V, Stefanová K, Perrot Y, Villagrasa C, Shin WG, Incerti S, McNamara A, Paganetti H, Perl J, Schuemann J, Faddegon B. PMID: 34412044; PMCID: PMC8639218.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    8. The relation between microdosimetry and induction of direct damage to DNA by alpha particles. Phys Med Biol. 2021 07 30; 66(15). Bertolet A, Ramos-Méndez J, Paganetti H, Schuemann J. PMID: 34280910; PMCID: PMC8483580.
      View in: PubMed   Mentions: 3     Fields:    
    9. Geant4-DNA simulation of the pre-chemical stage of water radiolysis and its impact on initial radiochemical yields. Phys Med. 2021 Aug; 88:86-90. Shin WG, Ramos-Mendez J, Tran NH, Okada S, Perrot Y, Villagrasa C, Incerti S. PMID: 34198026.
      View in: PubMed   Mentions: 6     Fields:    
    10. Publisher's Note: "Dispersion calibration for the National Ignition Facility electron-positron-proton spectrometers for intense laser matter interactions" [Rev. Sci. Instrum. 92, 033516 (2021)]. Rev Sci Instrum. 2021 May 01; 92(5):059902. von der Linden J, Ramos-Mendez J, Faddegon B, Massin D, Fiksel G, Holder JP, Willingale L, Peebles J, Edwards MR, Chen H. PMID: 34243233.
      View in: PubMed   Mentions:    Fields:    
    11. On the Equivalence of the Biological Effect Induced by Irradiation of Clusters of Heavy Atom Nanoparticles and Homogeneous Heavy Atom-Water Mixtures. Cancers (Basel). 2021 Apr 23; 13(9). Villagomez-Bernabe B, Ramos-Méndez J, Currell FJ. PMID: 33922478; PMCID: PMC8122863.
      View in: PubMed   Mentions: 1  
    12. Validation of the TOPAS Monte Carlo toolkit for HDR brachytherapy simulations. Brachytherapy. 2021 Jul-Aug; 20(4):911-921. Berumen F, Ma Y, Ramos-Méndez J, Perl J, Beaulieu L. PMID: 33896732.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    13. Boronated Condensed DNA as a Heterochromatic Radiation Target Model. Biomacromolecules. 2021 04 12; 22(4):1675-1684. Perry CC, Ramos-Méndez J, Milligan JR. PMID: 33750108.
      View in: PubMed   Mentions: 3     Fields:    
    14. Dispersion calibration for the National Ignition Facility electron-positron-proton spectrometers for intense laser matter interactions. Rev Sci Instrum. 2021 Mar 01; 92(3):033516. von der Linden J, Ramos-Méndez J, Faddegon B, Massin D, Fiksel G, Holder JP, Willingale L, Peebles J, Edwards MR, Chen H. PMID: 33820046.
      View in: PubMed   Mentions:    Fields:    
    15. Assessment of DNA damage with an adapted independent reaction time approach implemented in Geant4-DNA for the simulation of diffusion-controlled reactions between radio-induced reactive species and a chromatin fiber. Med Phys. 2021 Feb; 48(2):890-901. Tran HN, Ramos-Méndez J, Shin WG, Perrot Y, Faddegon B, Okada S, Karamitros M, Davídková M, Štepán V, Incerti S, Villagrasa C. PMID: 33232522; PMCID: PMC7986154.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    16. Report on G4-Med, a Geant4 benchmarking system for medical physics applications developed by the Geant4 Medical Simulation Benchmarking Group. Med Phys. 2021 Jan; 48(1):19-56. Arce P, Bolst D, Bordage MC, Brown JMC, Cirrone P, Cortés-Giraldo MA, Cutajar D, Cuttone G, Desorgher L, Dondero P, Dotti A, Faddegon B, Fedon C, Guatelli S, Incerti S, Ivanchenko V, Konstantinov D, Kyriakou I, Latyshev G, Le A, Mancini-Terracciano C, Maire M, Mantero A, Novak M, Omachi C, Pandola L, Perales A, Perrot Y, Petringa G, Quesada JM, Ramos-Méndez J, Romano F, Rosenfeld AB, Sarmiento LG, Sakata D, Sasaki T, Sechopoulos I, Simpson EC, Toshito T, Wright DH. PMID: 32392626; PMCID: PMC8054528.
      View in: PubMed   Mentions: 14     Fields:    
    17. Independent reaction times method in Geant4-DNA: Implementation and performance. Med Phys. 2020 Nov; 47(11):5919-5930. Ramos-Méndez J, Shin WG, Karamitros M, Domínguez-Kondo J, Tran NH, Incerti S, Villagrasa C, Perrot Y, Štepán V, Okada S, Moreno-Barbosa E, Faddegon B. PMID: 32970844; PMCID: PMC7891885.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    18. Monte Carlo simulation of the effect of magnetic fields on brachytherapy dose distributions in lung tissue material. PLoS One. 2020; 15(10):e0238704. Moreno-Barbosa F, de Celis-Alonso B, Moreno-Barbosa E, Hernández-López JM, Geoghegan T, Ramos-Méndez J. PMID: 33035214; PMCID: PMC7546478.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    19. LET-Dependent Intertrack Yields in Proton Irradiation at Ultra-High Dose Rates Relevant for FLASH Therapy. Radiat Res. 2020 10 02; 194(4):351-362. Ramos-Méndez J, Domínguez-Kondo N, Schuemann J, McNamara A, Moreno-Barbosa E, Faddegon B. PMID: 32857855; PMCID: PMC7644138.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    20. Monte Carlo track-structure for the radionuclide Copper-64: characterization of S-values, nanodosimetry and quantification of direct damage to DNA. Phys Med Biol. 2020 07 27; 65(15):155005. Carrasco-Hernández J, Ramos-Méndez J, Faddegon B, Jalilian AR, Moranchel M, Ávila-Rodríguez MA. PMID: 32303013; PMCID: PMC7757752.
      View in: PubMed   Mentions: 2     Fields:    
    21. Cellular Response to Proton Irradiation: A Simulation Study with TOPAS-nBio. Radiat Res. 2020 07 08; 194(1):9-21. Zhu H, McNamara AL, McMahon SJ, Ramos-Mendez J, Henthorn NT, Faddegon B, Held KD, Perl J, Li J, Paganetti H, Schuemann J. PMID: 32401689; PMCID: PMC7484135.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    22. Report on G4‐Med, a Geant4 benchmarking system for medical physics applications developed by the Geant4 Medical Simulation Benchmarking Group. Medical Physics. 2020. Arce, P. Bolst, D. Cutajar, D. Guatelli, S. Le, A. Rosenfeld, A.B. Sakata, D. Bordage, M-C. Brown, J.M.C. Cirrone, P. Cuttone, G. Pandola, L. Petringa, G. Cort?s-Giraldo, M.A. Quesada, J.M. Desorgher, L. Dondero, P. Mantero, A. Dotti, A. Wright, D.H. Faddegon, B. Ramos-M?ndez, J. Fedon, C. Incerti, S. Ivanchenko, V. Konstantinov, D. Latyshev, G. Kyriakou, I. Mancini-Terracciano, C. Maire, M. Novak, M. Omachi, C. Toshito, T. Perales, A. Perrot, Y. Romano, F. Sarmiento, L.G. Sasaki, T. Sechopoulos, I. Simpson, E.C. View Publication.
    23. A parameter sensitivity study for simulating DNA damage after proton irradiation using TOPAS-nBio. Phys Med Biol. 2020 04 23; 65(8):085015. Zhu H, McNamara AL, Ramos-Mendez J, McMahon SJ, Henthorn NT, Faddegon B, Held KD, Perl J, Li J, Paganetti H, Schuemann J. PMID: 32101803; PMCID: PMC7748977.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    24. The TOPAS tool for particle simulation, a Monte Carlo simulation tool for physics, biology and clinical research. Phys Med. 2020 Apr; 72:114-121. Faddegon B, Ramos-Méndez J, Schuemann J, McNamara A, Shin J, Perl J, Paganetti H. PMID: 32247964; PMCID: PMC7192305.
      View in: PubMed   Mentions: 26     Fields:    Translation:Humans
    25. DNA Condensation with a Boron-Containing Cationic Peptide for Modeling Boron Neutron Capture Therapy. Radiat Phys Chem Oxf Engl 1993. 2020 Jan; 166. Perry CC, Ramos-Méndez J, Milligan JR. PMID: 32454570; PMCID: PMC7243597.
      View in: PubMed   Mentions: 2  
    26. Evaluation of the influence of physical and chemical parameters on water radiolysis simulations under MeV electron irradiation using Geant4-DNA. Journal of Applied Physics. 2019; 126(11):114301-13pp. W.-G. Shin, J. Ramos-Méndez, B. Faddegon, H. N. Tran, C. Villagrasa, Y. Perrot, S. Okada, M. Karamitros, D. Emfietzoglou, I. Kyriaku, M. C. Bordage, D. Sakata, S. Guatelli, H. J. Choi, C. H. Min, S. B. Lee and S. Incerti. View Publication.
    27. Radio-enhancement by gold nanoparticles and their impact on water radiolysis for x-ray, proton and carbon-ion beams. Phys Med Biol. 2019 08 28; 64(17):175005. Rudek B, McNamara A, Ramos-Méndez J, Byrne H, Kuncic Z, Schuemann J. PMID: 31295730.
      View in: PubMed   Mentions: 11     Fields:    
    28. Monte Carlo geometry modeling for particle transport using conformal geometric algebra. Advances in Applied Clifford Algebras. 2019; 29(2):26-16pp. E. Ulises Moya-Sánchez, A. Moisés Maciel-Hernández, Adrian S. Niebla, José Ramos-Méndez and Oscar Carbajal-Espinosa. View Publication.
    29. TOPAS-nBio: An Extension to the TOPAS Simulation Toolkit for Cellular and Sub-cellular Radiobiology. Radiat Res. 2019 02; 191(2):125-138. Schuemann J, McNamara AL, Ramos-Méndez J, Perl J, Held KD, Paganetti H, Incerti S, Faddegon B. PMID: 30609382; PMCID: PMC6377808.
      View in: PubMed   Mentions: 45     Fields:    Translation:HumansCells
    30. Simultaneous optimization of RBE-weighted dose and nanometric ionization distributions in treatment planning with carbon ions. Phys Med Biol. 2019 01 04; 64(1):015015. Burigo LN, Ramos-Méndez J, Bangert M, Schulte RW, Faddegon B. PMID: 30523890; PMCID: PMC7164666.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    31. Fast calculation of nanodosimetric quantities in treatment planning of proton and ion therapy. Phys Med Biol. 2018 Nov 28; 63(23):235015. Ramos-Méndez J, Burigo LN, Schulte R, Chuang C, Faddegon B. PMID: 30484432; PMCID: PMC8691449.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    32. A New Standard DNA Damage (SDD) Data Format. Radiat Res. 2019 01; 191(1):76-92. Schuemann J, McNamara AL, Warmenhoven JW, Henthorn NT, Kirkby KJ, Merchant MJ, Ingram S, Paganetti H, Held KD, Ramos-Mendez J, Faddegon B, Perl J, Goodhead DT, Plante I, Rabus H, Nettelbeck H, Friedland W, Kundrát P, Ottolenghi A, Baiocco G, Barbieri S, Dingfelder M, Incerti S, Villagrasa C, Bueno M, Bernal MA, Guatelli S, Sakata D, Brown JMC, Francis Z, Kyriakou I, Lampe N, Ballarini F, Carante MP, Davídková M, Štepán V, Jia X, Cucinotta FA, Schulte R, Stewart RD, Carlson DJ, Galer S, Kuncic Z, Lacombe S, Milligan J, Cho SH, Sawakuchi G, Inaniwa T, Sato T, Li W, Solov'yov AV, Surdutovich E, Durante M, Prise KM, McMahon SJ. PMID: 30407901; PMCID: PMC6407706.
      View in: PubMed   Mentions: 22     Fields:    Translation:Cells
    33. Geometrical structures for radiation biology research as implemented in the TOPAS-nBio toolkit. Phys Med Biol. 2018 09 06; 63(17):175018. McNamara AL, Ramos-Méndez J, Perl J, Held K, Dominguez N, Moreno E, Henthorn NT, Kirkby KJ, Meylan S, Villagrasa C, Incerti S, Faddegon B, Paganetti H, Schuemann J. PMID: 30088810; PMCID: PMC6176684.
      View in: PubMed   Mentions: 18     Fields:    Translation:Humans
    34. Helium CT: Monte Carlo simulation results for an ideal source and detector with comparison to proton CT. Med Phys. 2018 Jul; 45(7):3264-3274. Piersimoni P, Faddegon BA, Méndez JR, Schulte RW, Volz L, Seco J. PMID: 29727481; PMCID: PMC8145780.
      View in: PubMed   Mentions: 6     Fields:    
    35. Monte Carlo simulation of chemistry following radiolysis with TOPAS-nBio. Phys Med Biol. 2018 05 17; 63(10):105014. Ramos-Méndez J, Perl J, Schuemann J, McNamara A, Paganetti H, Faddegon B. PMID: 29697057; PMCID: PMC6027650.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansCells
    36. Flagged uniform particle splitting for variance reduction in proton and carbon ion track-structure simulations. Phys Med Biol. 2017 Jul 06; 62(15):5908-5925. Ramos-Méndez J, Schuemann J, Incerti S, Paganetti H, Schulte R, Faddegon B. PMID: 28594336; PMCID: PMC5785278.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    37. The effect of beam purity and scanner complexity on proton CT accuracy. Med Phys. 2017 Jan; 44(1):284-298. Piersimoni P, Ramos-Méndez J, Geoghegan T, Bashkirov VA, Schulte RW, Faddegon BA. PMID: 28066887; PMCID: PMC5362942.
      View in: PubMed   Mentions: 10     Fields:    
    38. Validation of the radiobiology toolkit TOPAS-nBio in simple DNA geometries. Phys Med. 2017 Jan; 33:207-215. McNamara A, Geng C, Turner R, Mendez JR, Perl J, Held K, Faddegon B, Paganetti H, Schuemann J. PMID: 28017738; PMCID: PMC5292291.
      View in: PubMed   Mentions: 25     Fields:    Translation:Cells
    39. Dose assessment for the fetus considering scattered and secondary radiation from photon and proton therapy when treating a brain tumor of the mother. Phys Med Biol. 2016 Jan 21; 61(2):683-95. Geng C, Moteabbed M, Seco J, Gao Y, Xu XG, Ramos-Méndez J, Faddegon B, Paganetti H. PMID: 26716718.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    40. Experimental depth dose curves of a 67.5 MeV proton beam for benchmarking and validation of Monte Carlo simulation. Med Phys. 2015 Jul; 42(7):4199-210. Faddegon BA, Shin J, Castenada CM, Ramos-Méndez J, Daftari IK. PMID: 26133619; PMCID: PMC4474955.
      View in: PubMed   Mentions: 4     Fields:    Translation:PHPublic Health
    41. Extension of TOPAS for the simulation of proton radiation effects considering molecular and cellular endpoints. Phys Med Biol. 2015 Jul 07; 60(13):5053-70. Polster L, Schuemann J, Rinaldi I, Burigo L, McNamara AL, Stewart RD, Attili A, Carlson DJ, Sato T, Ramos Méndez J, Faddegon B, Perl J, Paganetti H. PMID: 26061666; PMCID: PMC4511084.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansAnimalsCells
    42. A framework for implementation of organ effect models in TOPAS with benchmarks extended to proton therapy. Phys Med Biol. 2015 Jul 07; 60(13):5037-52. Ramos-Méndez J, Perl J, Schümann J, Shin J, Paganetti H, Faddegon B. PMID: 26061583; PMCID: PMC4498397.
      View in: PubMed   Mentions: 2     Fields:    
    43. Improved efficiency in Monte Carlo simulation for passive-scattering proton therapy. Improved efficiency in Monte Carlo simulation for passive-scattering proton therapy. 2015; 60(13):5019-5035. J Ramos Méndez, J Perl, J Schümann, J Shin, H Paganetti, B Faddegon. View Publication.
    44. Geometrical splitting technique to improve the computational efficiency in Monte Carlo calculations for proton therapy. Med Phys. 2013 Apr; 40(4):041718. Ramos-Méndez J, Perl J, Faddegon B, Schümann J, Paganetti H. PMID: 23556888; PMCID: PMC3618101.
      View in: PubMed   Mentions: 13     Fields:    Translation:Humans
    45. SU-E-T-478: Geometrical Splitting Technique to Improve the Computational Efficiency in Monte Carlo Calculations for Proton Therapy. Med Phys. 2012 Jun; 39(6Part17):3815. Ramos-Mendez J, Perl J, Faddegon B, Paganetti H. PMID: 28517444.
      View in: PubMed   Mentions:    Fields:    
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