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Jose Ramos Mendez, PhD

Title(s)Assistant Researcher, Radiation Oncology
SchoolSchool of Medicine
Address1600 Divisadero
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
    Collapse Awards and Honors
    CONACyT, Mexico2008  - 2010National Fellow
    CONACyT, Mexico2010  - 2014National Fellow

    Collapse Overview 

    Collapse ORNG Applications 
    Collapse Featured Publications
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    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. Independent Reaction Times method in Geant4-DNA: implementation and performance. Med Phys. 2020 Sep 24. 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.
      View in: PubMed   Mentions:
    2. LET-Dependent Intertrack Yields in Proton Irradiation at Ultra-High Dose Rates Relevant for FLASH Therapy. Radiat Res. 2020 Aug 28. Ramos-Méndez J, Domínguez-Kondo N, Schuemann J, McNamara A, Moreno-Barbosa E, Faddegon B. PMID: 32857855.
      View in: PubMed   Mentions:    Fields:    
    3. 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.
      View in: PubMed   Mentions:    Fields:    
    4. Cellular Response to Proton Irradiation: A Simulation Study with TOPAS-nBio. Radiat Res. 2020 Jul 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.
      View in: PubMed   Mentions:    Fields:    
    5. 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.
    6. 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.
      View in: PubMed   Mentions:    Fields:    
    7. 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.
      View in: PubMed   Mentions:    Fields:    
    8. 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.
      View in: PubMed   Mentions:
    9. 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.
    10. 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: 1     Fields:    
    11. 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.
    12. 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.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    13. 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.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    14. 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.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    15. 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.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    16. 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.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    17. 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.
      View in: PubMed   Mentions:    Fields:    
    18. 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.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    19. 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.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    20. The effect of beam purity and scanner complexity on proton CT accuracy. 2017; 44(1):284-298. Piersimoni P, Ramos-Méndez J, Geoghegan T, Bashkirov VA, Schulte RW, Faddegon BA.
    21. 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.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    22. Dose assessment for the fetus considering scattered and secondary radiation from photon and proton therapy when treating a brain tumor of the mother. 2016; 61(2):683-95. Geng C, Moteabbed M, Seco J, Gao Y, Xu XG, Ramos-Méndez J, Faddegon B, Paganetti H.
    23. Experimental depth dose curves of a 67.5 MeV proton beam for benchmarking and validation of Monte Carlo simulation. 2015; 42(7):4199-4210. Faddegon BA, Shin J, Castenada CM, Ramos-Méndez J, Daftari IK.
    24. 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.
      View in: PubMed   Mentions:    Fields:    Translation:PHPublic Health
    25. 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.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansAnimalsCells
    26. 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.
      View in: PubMed   Mentions:    Fields:    
    27. 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.
    28. 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.
      View in: PubMed   Mentions: 8     Fields:    Translation:Humans
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