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Ruy Miguel Ribeiro finished his undergraduate studies in Engenharia Física Tecnológica at Instituto Superior Técnico, LIsboa, in 1994, and completed the degree of Doctor of Philosophy in "Mathematical Biology" in 1999 at the Department of Zoology, University of Oxford, UK. He is a staff scientist at Los Alamos National Laboratory, NM, USA and Guest Associate Professor at Faculdade de Medicina da Universidade de Lisboa. He has published over 140 papers in the international peer-reviewed literature. He uses mathematical, statistical and computational models to study the immune system and the immune response against infectious agents. This work is done in close proximity with clinical and experimental investigators to develop appropriate models to analyze experimental data on HIV, hepatitis C, hepatitis B, influenza, SARS, and homeostasis and dynamics of T cells, in health and disease. The domains of study include infection dynamics, pharmacological interventions, evolution of resistance, vaccine development and pathogenesis, both at the within-host and epidemiological level. He works directly with experimental collaborators to tackle questions of clinical relevance to our understanding of viral infections. In his Ciência Vitae the most frequent terms to contextualize his scientific production are: data analysis; experimental design; data modeling; viral dynamics; immune system dynamics; pharmacokinetics; modeling biological systems; HIV; HCV; HBV; influenza; Zika.
Identificação

Identificação pessoal

Nome completo
Ruy Miguel Ribeiro

Nomes de citação

  • Ribeiro, Ruy M.

Identificadores de autor

Ciência ID
9A15-E40B-738F
ORCID iD
0000-0002-3988-8241

Domínios de atuação

  • Ciências Exatas - Matemática - Estatística e Probabilidades
  • Ciências Exatas - Matemática - Matemática Aplicada
  • Ciências Médicas e da Saúde - Ciências da Saúde - Epidemiologia
  • Ciências Médicas e da Saúde - Ciências da Saúde - Doenças Infeciosas

Idiomas

Idioma Conversação Leitura Escrita Compreensão Peer-review
Português (Idioma materno)
Inglês Utilizador proficiente (C2) Utilizador proficiente (C2) Utilizador proficiente (C2) Utilizador proficiente (C2) Utilizador proficiente (C2)
Espanhol; Castelhano Utilizador proficiente (C1) Utilizador proficiente (C1) Utilizador independente (B1) Utilizador proficiente (C1) Utilizador elementar (A2)
Francês Utilizador elementar (A1) Utilizador elementar (A1) Utilizador elementar (A1) Utilizador elementar (A1)
Alemão Utilizador elementar (A1) Utilizador elementar (A1) Utilizador elementar (A1) Utilizador elementar (A1)
Formação
Grau Classificação
1999
Concluído
Mathematical Biology (Doctor of Philosophy)
University of Oxford Department of Zoology, Reino Unido
"Models of Viral Diversity and Disease Development in HIV Infection" (TESE/DISSERTAÇÃO)
N/A
1994
Concluído
Engenharia Física Tecnológica (Licenciatura)
Universidade de Lisboa Instituto Superior Técnico, Portugal
"Pattern Formation in Reaction-Diffusion Equations" (TESE/DISSERTAÇÃO)
18
Percurso profissional

Ciência

Categoria Profissional
Instituição de acolhimento
Empregador
2015 - Atual Investigador (Investigação) Instituto de Medicina Molecular João Lobo Antunes, Portugal
2003 - Atual Investigador (Investigação) Los Alamos National Laboratory, Estados Unidos
Los Alamos National Laboratory Theoretical Biology and Biophysics Division, Estados Unidos
2015 - 2020/08 Investigador (Investigação) Universidade de Lisboa Instituto de Saúde Ambiental, Portugal
2012/03 - 2013/04 Investigador (Investigação) Instituto de Medicina Molecular João Lobo Antunes, Portugal

Docência no Ensino Superior

Categoria Profissional
Instituição de acolhimento
Empregador
2021/01/01 - Atual Professor Associado Convidado (Docente Universitário) Universidade de Lisboa Faculdade de Medicina, Portugal
2017/02/01 - 2020/08/01 Professor Associado (Docente Universitário) Universidade de Lisboa Faculdade de Medicina, Portugal
2012/02/01 - 2017/01/01 Professor Associado Convidado (Docente Universitário) Universidade de Lisboa Faculdade de Medicina, Portugal

Outros

Categoria Profissional
Instituição de acolhimento
Empregador
2006/06/01 - Atual Investigator / Adjunct Professor University of New Mexico, Estados Unidos
2003/02/01 - 2004/04/01 Marie Curie Postdoctoral Fellow University of Oxford, Reino Unido
2000/01/01 - 2003/01/01 Postdoctoral Research Associate Los Alamos National Laboratory, Estados Unidos
2000/05/01 - 2001/06/01 Volunteer tutor of “English as a Second Language”, Espanola, NM, USA Let's Read, Estados Unidos
1994/10/01 - 1996/05/01 Business Analyst McKinsey and Company Portugal, Portugal
Projetos

Bolsa

Designação Financiadores
2022/02/01 - 2027/01/31 Spatial Models of Intrahepatic Hepatitis Virus Propagation
R01 AI116868
Investigador responsável
Los Alamos National Laboratory, Estados Unidos
National Institutes of Health
Em curso
2018/08 - 2021/08 QuaSHLat - Quantitative Studies of HIV Latency
PTDC/MAT-APL/31602/2017
Fundação para a Ciência e a Tecnologia
2016/02 - 2021/01 Spatial Models of Intrahepatic Hepatitis C Virus Propagation in Humans National Institute of Allergy and Infectious Diseases
2013/08 - 2017/07 Quantifying Immune VS. Viral Killing of SIV Infected and Latently Infected Cells National Institute of Allergy and Infectious Diseases
2003/09 - 2014/05 COBRE Center for Evolutionary and Theoretical Immunology National Center for Advancing Translational Sciences
2009/01 - 2012/01 Helper T cells as regulators and targets of HIV infection National Health and Medical Research Council
2005/01 - 2007/01 Understanding how the immune system controls infection with HIV National Health and Medical Research Council

Projeto

Designação Financiadores
2021/01/01 - Atual iSTARS - Informatics and Statistical Tools for the Advancement of Research Success
Principal Investigator, before leaving FMUL
Universidade de Lisboa Faculdade de Medicina, Portugal
EU Framework Programme for Research and Innovation Excellent Science
Em curso
Produções

Publicações

Artigo em conferência
  1. Portêlo, A.; Lemos, J.M.; Vinga, S.; Ribeiro, R.M.; Cruz, J.P.; Valadas, E.. "Parameter estimation and identifiability of a HIV-1 model". 2013.
    10.1109/MED.2013.6608798
Artigo em revista
  1. Dhaubhadel, Sayera; Ganguly, Kumkum; Ribeiro, Ruy M.; Cohn, Judith D.; Hyman, James M.; Hengartner, Nicolas W.; Kolade, Beauty; et al. "High dimensional predictions of suicide risk in 4.2 million US Veterans using ensemble transfer learning". Scientific Reports 14 1 (2024): http://dx.doi.org/10.1038/s41598-024-51762-9.
    10.1038/s41598-024-51762-9
  2. Bevelynn Williams; Jonathan Carruthers; Joseph J. Gillard; Grant Lythe; Alan S. Perelson; Ruy M. Ribeiro; Carmen Molina-París; Martín López-García. "The reproduction number and its probability distribution for stochastic viral dynamics". Journal of The Royal Society Interface (2024): https://doi.org/10.1098/rsif.2023.0400.
    10.1098/rsif.2023.0400
  3. Mithra R. Kumar; Emily J. Fray; Alexandra M. Bender; Carolin Zitzmann; Ruy M. Ribeiro; Alan S. Perelson; Dan H. Barouch; Janet D. Siliciano; Robert F. Siliciano. "Biphasic decay of intact SHIV genomes following initiation of antiretroviral therapy complicates analysis of interventions targeting the reservoir". Proceedings of the National Academy of Sciences (2023): https://doi.org/10.1073/pnas.2313209120.
    10.1073/pnas.2313209120
  4. Policicchio, Benjamin B.; Cardozo-Ojeda, Erwing Fabian; Xu, Cuiling; Ma, Dongzhu; He, Tianyu; Raehtz, Kevin D.; Sivanandham, Ranjit; et al. "CD8+ T cells control SIV infection using both cytolytic effects and non-cytolytic suppression of virus production". Nature Communications 14 1 (2023): http://dx.doi.org/10.1038/s41467-023-42435-8.
    10.1038/s41467-023-42435-8
  5. McMyn, Natalie F.; Varriale, Joseph; Fray, Emily J.; Zitzmann, Carolin; MacLeod, Hannah; Lai, Jun; Singhal, Anushka; et al. "The latent reservoir of inducible, infectious HIV-1 does not decrease despite decades of antiretroviral therapy". Journal of Clinical Investigation 133 17 (2023): http://dx.doi.org/10.1172/jci171554.
    10.1172/jci171554
  6. Phan, Tin; Brozak, Samantha; Pell, Bruce; Oghuan, Jeremiah; Gitter, Anna; Hu, Tao; Ribeiro, Ruy M.; et al. "Making waves: Integrating wastewater surveillance with dynamic modeling to track and predict viral outbreaks". Water Research 243 (2023): 120372. http://dx.doi.org/10.1016/j.watres.2023.120372.
    10.1016/j.watres.2023.120372
  7. Ribeiro, Ruy M; Choudhary, Manish C; Deo, Rinki; Giganti, Mark J; Moser, Carlee; Ritz, Justin; Greninger, Alexander L; et al. "Variant-Specific Viral Kinetics in Acute COVID-19". The Journal of Infectious Diseases 228 Supplement (2023): S136-S143. http://dx.doi.org/10.1093/infdis/jiad314.
    10.1093/infdis/jiad314
  8. Apetrei, Cristian; Gaufin, Thaidra; Brocca-Cofano, Egidio; Sivanandham, Ranjit; Sette, Paola; He, Tianyu; Sivanandham, Sindhuja; et al. "T cell activation is insufficient to drive SIV disease progression". JCI Insight 8 14 (2023): http://dx.doi.org/10.1172/jci.insight.161111.
    10.1172/jci.insight.161111
  9. Ana Rita Henriques; Marta Gromicho; Julian Grosskreutz; Magdalena Kuzma-Kozakiewicz; Susanne Petri; Hilmi Uysal; Susana Pinto; et al. "Association of the practice of contact sports with the development of amyotrophic lateral sclerosis". Amyotrophic Lateral Sclerosis and Frontotemporal Degeneration (2023): https://doi.org/10.1080/21678421.2023.2189911.
    10.1080/21678421.2023.2189911
  10. Luis Graca; Ana Caetano Faria; Ruy M. Ribeiro. "Illuminating a blind spot in SARS-CoV-2 immunity". Nature Immunology (2023): https://doi.org/10.1038/s41590-023-01518-w.
    10.1038/s41590-023-01518-w
  11. Silvério-António, Manuel; Rodrigues, Ana Maria; Teixeira, Filipa; Tavares-Costa, José; Bernardo, Alexandra; Pimenta, Sofia; Lagoas Gomes, João; et al. "Sex and body mass index impact on digit circumference for Leeds Dactylitis Index calculation". Clinical and Experimental Rheumatology 42 (2023): 174. http://dx.doi.org/10.55563/clinexprheumatol/v78pc5.
    10.55563/clinexprheumatol/v78pc5
  12. Thio, Chloe L; Taddese, Maraake; Saad, Yasmeen; Zambo, Kristina; Ribeiro, Ruy M; Grudda, Tanner; Sulkowski, Mark S; et al. "Hepatitis B e Antigen-Negative Single Hepatocyte Analysis Shows Transcriptional Silencing and Slow Decay of Infected Cells With Treatment". The Journal of Infectious Diseases 228 9 (2023): 1219-1226. http://dx.doi.org/10.1093/infdis/jiad124.
    10.1093/infdis/jiad124
  13. Nair, Manoj S.; Ribeiro, Ruy M.; Wang, Maple; Bowen, Anthony D.; Liu, Lihong; Guo, Yicheng; Chang, Jennifer Y.; et al. "Changes in serum-neutralizing antibody potency and breadth post-SARS-CoV-2 mRNA vaccine boost". iScience 26 4 (2023): 106345. http://dx.doi.org/10.1016/j.isci.2023.106345.
    10.1016/j.isci.2023.106345
  14. Fray, Emily J.; Wu, Fengting; Simonetti, Francesco R.; Zitzmann, Carolin; Sambaturu, Narmada; Molina-Paris, Carmen; Bender, Alexandra M.; et al. "Antiretroviral therapy reveals triphasic decay of intact SIV genomes and persistence of ancestral variants". Cell Host & Microbe 31 3 (2023): 356-372.e5. http://dx.doi.org/10.1016/j.chom.2023.01.016.
    10.1016/j.chom.2023.01.016
  15. Chora, Ângelo Ferreira; Marques, Sofia; Gonçalves, Joana Lisboa; Lima, Priscila; Gomes da Costa, Daniel; Fernandez-Ruiz, Daniel; Marreiros, Maria Inês; et al. "Interplay between liver and blood stages of Plasmodium infection dictates malaria severity via ¿d T cells and IL-17-promoted stress erythropoiesis". Immunity 56 3 (2023): 592-605.e8. http://dx.doi.org/10.1016/j.immuni.2023.01.031.
    10.1016/j.immuni.2023.01.031
  16. Sachithanandham, Jaiprasath; Balagopal, Ashwin; Leep-Lazar, Julia; Quinn, Jeffrey; Bowden, Kenneth; Ward, Kathleen; Ribeiro, Ruy M; Sulkowski, Mark S. "Second-Phase Hepatitis C Plasma Viral Kinetics Directly Reflects Reduced Intrahepatic Burden of Hepatitis C Virus". The Journal of Infectious Diseases 228 3 (2023): 311-320. http://dx.doi.org/10.1093/infdis/jiad025.
    10.1093/infdis/jiad025
  17. Malato, João; Ribeiro, Ruy M; Fernandes, Eugénia; Leite, Pedro Pinto; Casaca, Pedro; Antunes, Carlos; Fonseca, Válter R; Gomes, Manuel Carmo; Graca, Luis. "Stability of hybrid versus vaccine immunity against BA.5 infection over 8 months". The Lancet Infectious Diseases 23 2 (2023): 148-150. http://dx.doi.org/10.1016/s1473-3099(22)00833-7.
    10.1016/s1473-3099(22)00833-7
  18. Manish C. Choudhary; Kara W. Chew; Rinki Deo; James P. Flynn; James Regan; Charles R. Crain; Carlee Moser; et al. "Emergence of SARS-CoV-2 escape mutations during Bamlanivimab therapy in a phase II randomized clinical trial". Nature Microbiology (2022): https://doi.org/10.1038/s41564-022-01254-1.
    10.1038/s41564-022-01254-1
  19. Malato, João; Ribeiro, Ruy M.; Leite, Pedro P.; Casaca, Pedro; Fernandes, Eugénia; Antunes, Carlos; Fonseca, Válter R.; Gomes, Manuel C.; Graca, Luis. "Risk of BA.5 Infection among Persons Exposed to Previous SARS-CoV-2 Variants". New England Journal of Medicine 387 10 (2022): 953-954. http://dx.doi.org/10.1056/nejmc2209479.
    10.1056/nejmc2209479
  20. Chew, Kara W.; Moser, Carlee; Daar, Eric S.; Wohl, David A.; Li, Jonathan Z.; Coombs, Robert W.; Ritz, Justin; et al. "Antiviral and clinical activity of bamlanivimab in a randomized trial of non-hospitalized adults with COVID-19". Nature Communications 13 1 (2022): http://dx.doi.org/10.1038/s41467-022-32551-2.
    10.1038/s41467-022-32551-2
  21. Sanche, Steven; Cassidy, Tyler; Chu, Pinghan; Perelson, Alan S.; Ribeiro, Ruy M.; Ke, Ruian. "A simple model of COVID-19 explains disease severity and the effect of treatments". Scientific Reports 12 1 (2022): http://dx.doi.org/10.1038/s41598-022-18244-2.
    10.1038/s41598-022-18244-2
  22. Quinn JR; Goyal A; Ribeiro RM; Massaccesi G; Bailey JR; Thomas DL; Balagopal A. "Antiretroviral therapy for HIV and intrahepatic hepatitis C virus replication.". AIDS (London, England) (2022): http://europepmc.org/abstract/med/34690280.
    10.1097/qad.0000000000003116
  23. White JA; Simonetti FR; Beg S; McMyn NF; Dai W; Bachmann N; Lai J; et al. "Complex decay dynamics of HIV virions, intact and defective proviruses, and 2LTR circles following initiation of antiretroviral therapy.". Proceedings of the National Academy of Sciences of the United States of America (2022): http://europepmc.org/abstract/med/35110411.
    10.1073/pnas.2120326119
  24. Ruian Ke; Carolin Zitzmann; David D. Ho; Ruy M. Ribeiro; Alan S. Perelson. "In vivo kinetics of SARS-CoV-2 infection and its relationship with a person’s infectiousness". Proceedings of the National Academy of Sciences (2021): https://doi.org/10.1073/pnas.2111477118.
    10.1073/pnas.2111477118
  25. Catarina De Sousa; Ruy M. Ribeiro; Fausto J. Pinto. "Infective Endocarditis as the Cause of Death: A Population based Study in Portugal, from 2002 to 2018". Acta Médica Portuguesa 34 12 (2021): 833-833. https://doi.org/10.20344/amp.14609.
    10.20344/amp.14609
  26. Garrido MM; Marta JC; Ribeiro RM; Pinheiro LC; Holdenrieder S; Guimarães JT. "Comparison of Three Assays for Total and Free PSA Using Hybritech and WHO Calibrations.". In vivo (Athens, Greece) (2021): http://europepmc.org/abstract/med/34697179.
    10.21873/invivo.12643
  27. Canto E Castro L; Gomes A; Serrano M; Pereira AHG; Ribeiro R; Napoleão P; Domingues I; et al. "Longitudinal SARS-CoV-2 seroprevalence in Portugal and antibody maintenance 12 months after infection.". European journal of immunology (2021): http://europepmc.org/abstract/med/34695227.
    10.1002/eji.202149619
  28. Canto E Castro L; Pereira AHG; Ribeiro R; Alves C; Veloso L; Vicente V; Alves D; et al. "Prevalence of SARS-CoV-2 Antibodies after First 6 Months of COVID-19 Pandemic, Portugal.". Emerging infectious diseases (2021): http://europepmc.org/abstract/med/34437830.
    10.3201/eid2711.210636
  29. Santos CD; Santos AF; das Neves RC; Ribeiro RM; Rodrigues F; Caneiras C; Spruit MA; Bárbara C. "Telemonitoring of daily activities compared to the six-minute walk test further completes the puzzle of oximetry-guided interventions.". Scientific reports (2021): http://europepmc.org/abstract/med/34400715.
    10.1038/s41598-021-96060-w
  30. Garrido MM; Ribeiro RM; Krüger K; Pinheiro LC; Guimarães JT; Holdenrieder S. "Relevance of Circulating Nucleosomes, HMGB1 and sRAGE for Prostate Cancer Diagnosis.". In vivo (Athens, Greece) (2021): http://europepmc.org/abstract/med/34182498.
    10.21873/invivo.12492
  31. Garrido MM; Ribeiro RM; Krüger K; Pinheiro LC; Guimarães JT; Holdenrieder S. "Are Proinflammatory Cytokines Relevant for the Diagnosis of Prostate Cancer?". Anticancer research (2021): http://europepmc.org/abstract/med/34083299.
    10.21873/anticanres.15090
  32. Garrido MM; Ribeiro RM; Pinheiro LC; Holdenrieder S; Guimarães JT. "The prostate health index (PHI) density: Are there advantages over PHI or over the prostate-specific antigen density?". Clinica chimica acta; international journal of clinical chemistry (2021): http://europepmc.org/abstract/med/34097882.
    10.1016/j.cca.2021.06.006
  33. Regan J; Flynn JP; Rosenthal A; Jordan H; Li Y; Chishti R; Giguel F; et al. "Viral Load Kinetics of Severe Acute Respiratory Syndrome Coronavirus 2 in Hospitalized Individuals With Coronavirus Disease 2019.". Open forum infectious diseases (2021): http://europepmc.org/abstract/med/34430669.
    10.1093/ofid/ofab153
  34. Garrido MM; Marta JC; Ribeiro RM; Pinheiro LC; Guimarães JT. "Serum lipids and prostate cancer.". Journal of clinical laboratory analysis (2021): http://europepmc.org/abstract/med/33724557.
    10.1002/jcla.23705
  35. Ashish Goyal; Alan S. Perelson; Abraham J. Kandathil; Jeffrey Quinn; Ashwin Balagopal; Ruy M. Ribeiro. "HIV influences clustering and intracellular replication of hepatitis C virus". Journal of Viral Hepatitis (2021): https://doi.org/10.1111/jvh.13429.
    10.1111/jvh.13429
  36. de Sousa C; Ribeiro RM; Pinto FJ. "The burden of infective endocarditis in Portugal in the last 30 years - a systematic review of observational studies.". Revista portuguesa de cardiologia : orgao oficial da Sociedade Portuguesa de Cardiologia = Portuguese journal of cardiology : an official journal of the Portuguese Society of Cardiology (2021): http://europepmc.org/abstract/med/33648807.
    10.1016/j.repc.2020.07.014
  37. Katharine Best; Rustom Antia; Dan H. Barouch; Jeremie Guedj; Ruy M. Ribeiro; Alan S. Perelson. "Zika virus dynamics: Effects of inoculum dose, the innate immune response and viral interference". PLOS Computational Biology (2021): https://doi.org/10.1371/journal.pcbi.1008564.
    10.1371/journal.pcbi.1008564
  38. Balagopal A; Grudda T; Ribeiro RM; Saad YS; Hwang HS; Quinn J; Murphy M; et al. "Single hepatocytes show persistence and transcriptional inactivity of hepatitis B.". JCI insight (2020): http://europepmc.org/abstract/med/33004689.
    10.1172/jci.insight.140584
  39. Gil Marques F; Poli E; Malaquias J; Carvalho T; Portêlo A; Ramires A; Aldeia F; et al. "Low doses of ionizing radiation activate endothelial cells and induce angiogenesis in peritumoral tissues.". Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology (2020): http://europepmc.org/abstract/med/33004178.
    10.1016/j.radonc.2020.06.038
  40. Santos CD; das Neves RC; Ribeiro RM; Caneiras C; Rodrigues F; Spruit MA; Bárbara C. "Novel Input for Designing Patient-Tailored Pulmonary Rehabilitation: Telemonitoring Physical Activity as a Vital Sign-SMARTREAB Study.". Journal of clinical medicine (2020): http://europepmc.org/abstract/med/32751825.
    10.3390/jcm9082450
  41. Nogueira PJ; de Araújo Nobre M; Costa A; Ribeiro RM; Furtado C; Bacelar Nicolau L; Camarinha C; et al. "The Role of Health Preconditions on COVID-19 Deaths in Portugal: Evidence from Surveillance Data of the First 20293 Infection Cases.". Journal of clinical medicine (2020): http://europepmc.org/abstract/med/32722159.
    10.3390/jcm9082368
  42. Ruy M Ribeiro; Luis Graca. "Untangling the immune basis of disease susceptibility". eLife (2020): https://doi.org/10.7554/eLife.56886.
    10.7554/eLife.56886
  43. da Costa PM; Lages P; Onofre S; Ribeiro RM. "The impact of negative lymph nodes in the survival outcomes of pN+ patients following radical gastrectomy: the inverse lymph node ratio as a better score to study negative lymph nodes.". Updates in surgery (2020): http://europepmc.org/abstract/med/32388806.
    10.1007/s13304-020-00757-y
  44. Isabel De Santiago; Ruy Ribeiro; Leonor Bacelar Nicolau; Rui Tato Marinho; José Pereira-Miguel. "Consumption of Alcohol and Drugs in the School Population of Sao Tome and Principe". Acta Médica Portuguesa (2020): https://doi.org/10.20344/amp.11876.
    10.20344/amp.11876
  45. Vieira-Sousa E; Alves P; Rodrigues AM; Teixeira F; Tavares-Costa J; Bernardo A; Pimenta S; et al. "GO-DACT: a phase 3b randomised, double-blind, placebo-controlled trial of GOlimumab plus methotrexate (MTX) versus placebo plus MTX in improving DACTylitis in MTX-naive patients with psoriatic arthritis.". Annals of the rheumatic diseases (2020): http://europepmc.org/abstract/med/32193187.
    10.1136/annrheumdis-2019-216500
  46. He T; Xu C; Krampe N; Dillon SM; Sette P; Falwell E; Haret-Richter GS; et al. "High-fat diet exacerbates SIV pathogenesis and accelerates disease progression.". The Journal of clinical investigation (2019): http://europepmc.org/abstract/med/31710311.
    10.1172/JCI121208
  47. Cardozo EF; Ji D; Lau G; Schinazi RF; Chen GF; Ribeiro RM; Perelson AS. "Disentangling the lifespans of hepatitis C virus-infected cells and intracellular vRNA replication-complexes during direct-acting anti-viral therapy.". Journal of Viral Hepatitis (2019): http://europepmc.org/abstract/med/31670859.
    10.1111/jvh.13229
  48. Soares MV; Azevedo RI; Ferreira IA; Bucar S; Ribeiro AC; Vieira A; Pereira PNG; et al. "Naive and Stem Cell Memory T Cell Subset Recovery Reveals Opposing Reconstitution Patterns in CD4 and CD8 T Cells in Chronic Graft vs. Host Disease.". Frontiers in immunology (2019): http://europepmc.org/abstract/med/30894856.
    10.3389/fimmu.2019.00334
  49. Youfang Cao; Xue Lei; Ruy M. Ribeiro; Alan S. Perelson; Jie Liang. "Probabilistic control of HIV latency and transactivation by the Tat gene circuit". Proceedings of the National Academy of Sciences 115 49 (2018): 12453-12458. https://doi.org/10.1073/pnas.1811195115.
    10.1073/pnas.1811195115
  50. Conway JM; Ribeiro RM. "Modeling the immune response to HIV infection.". Current opinion in systems biology (2018): http://europepmc.org/abstract/med/31463420.
    10.1016/j.coisb.2018.10.006
  51. Minskaia E; Saraiva BC; Soares MMV; Azevedo RI; Ribeiro RM; Kumar SD; Vieira AIS; Lacerda JF. "Molecular Markers Distinguishing T Cell Subtypes With TSDR Strand-Bias Methylation.". Frontiers in immunology (2018): http://europepmc.org/abstract/med/30455694.
    10.3389/fimmu.2018.02540
  52. Sivanandham R; Brocca-Cofano E; Krampe N; Falwell E; Venkatraman SMK; Ribeiro RM; Apetrei C; Pandrea I. "Neutrophil extracellular trap production contributes to pathogenesis in SIV-infected nonhuman primates.". The Journal of clinical investigation (2018): http://europepmc.org/abstract/med/30204591.
    10.1172/JCI99420
  53. Alan S. Perelson; Ruy M. Ribeiro. "Introduction to modeling viral infections and immunity". Immunological Reviews 285 1 (2018): 5-8. https://doi.org/10.1111/imr.12700.
    10.1111/imr.12700
  54. Erwing Fabian Cardozo; Cristian Apetrei; Ivona Pandrea; Ruy M. Ribeiro. "The dynamics of simian immunodeficiency virus after depletion of CD8+ cells". Immunological Reviews 285 1 (2018): 26-37. https://doi.org/10.1111/imr.12691.
    10.1111/imr.12691
  55. Ruian Ke; Hui Li; Shuyi Wang; Wenge Ding; Ruy M. Ribeiro; Elena E. Giorgi; Tanmoy Bhattacharya; et al. "Superinfection and cure of infected cells as mechanisms for hepatitis C virus adaptation and persistence". Proceedings of the National Academy of Sciences 115 30 (2018): E7139-E7148. https://doi.org/10.1073/pnas.1805267115.
    10.1073/pnas.1805267115
  56. Romero-Severson EO; Ribeiro RM; Castro M. "Noise Is Not Error: Detecting Parametric Heterogeneity Between Epidemiologic Time Series.". Frontiers in microbiology (2018): http://europepmc.org/abstract/med/30050514.
    10.3389/fmicb.2018.01529
  57. Policicchio BB; Cardozo EF; Sette P; Xu C; Haret-Richter G; Dunsmore T; Apetrei C; Pandrea I; Ribeiro RM. "Dynamics of Simian Immunodeficiency Virus Two-Long-Terminal-Repeat Circles in the Presence and Absence of CD8+ Cells.". Journal of virology (2018): http://europepmc.org/abstract/med/29643246.
    10.1128/JVI.02100-17
  58. Murray JM; Ribeiro RM. "Special Issue "Mathematical Modeling of Viral Infections".". Viruses (2018): http://europepmc.org/abstract/med/29866993.
    10.3390/v10060303
  59. Vaidya NK; Ribeiro RM; Liu P; Haynes BF; Tomaras GD; Perelson AS. "Correlation Between Anti-gp41 Antibodies and Virus Infectivity Decay During Primary HIV-1 Infection.". Frontiers in microbiology (2018): http://europepmc.org/abstract/med/29973924.
    10.3389/fmicb.2018.01326
  60. Vieira-Sousa E; Canhão H; Alves P; Rodrigues AM; Teixeira F; Tavares-Costa J; Bernardo A; et al. "The GO-DACT protocol: a multicentre, randomized, double-blind, parallel-group study to compare the efficacy of golimumab in combination with methotrexate (MTX) versus MTX monotherapy.". Acta reumatologica portuguesa (2018): http://europepmc.org/abstract/med/30091952.
  61. Policicchio BB; Sette P; Xu C; Haret-Richter G; Dunsmore T; Pandrea I; Ribeiro RM; Apetrei C. "Emergence of resistance mutations in simian immunodeficiency virus (SIV)-infected rhesus macaques receiving non-suppressive antiretroviral therapy (ART).". PloS one (2018): http://europepmc.org/abstract/med/29466356.
    10.1371/journal.pone.0190908
  62. Kaderali L; Theis F; Ganusov VV; Ciupe SM; Mehr R; Ribeiro RM; Hernandez-Vargas EA. "Editorial: Integrative Computational Systems Biology Approaches in Immunology and Medicine.". Frontiers in microbiology (2018): http://europepmc.org/abstract/med/30728819.
    10.3389/fmicb.2018.03338
  63. Goyal A; Ribeiro RM; Perelson AS. "The Role of Infected Cell Proliferation in the Clearance of Acute HBV Infection in Humans.". Viruses (2017): http://europepmc.org/abstract/med/29156567.
    10.3390/v9110350
  64. Schechter ME; Andrade BB; He T; Richter GH; Tosh KW; Policicchio BB; Singh A; et al. "Inflammatory monocytes expressing tissue factor drive SIV and HIV coagulopathy.". Science translational medicine (2017): http://europepmc.org/abstract/med/28855397.
    10.1126/scitranslmed.aam5441
  65. E. Fabian Cardozo; Daniel C. Douek; Adriana Andrade; John W. Mellors; Daniel R. Kuritzkes; Alan S. Perelson; Ruy M. Ribeiro. "Treatment with integrase inhibitor suggests a new interpretation of HIV RNA decay curves that reveals a subset of cells with slow integration". PLOS Pathogens 13 7 (2017): e1006478-e1006478. https://doi.org/10.1371%2Fjournal.ppat.1006478.
    10.1371/journal.ppat.1006478
  66. Ribeiro, Ruy M.. "The maths of memory.". eLife (2017): http://europepmc.org/abstract/med/28453436.
    10.7554/elife.26754
  67. Honeycutt, J.B.; Thayer, W.O.; Baker, C.E.; Ribeiro, R.M.; Lada, S.M.; Cao, Y.; Cleary, R.A.; et al. "HIV persistence in tissue macrophages of humanized myeloid-only mice during antiretroviral therapy". Nature Medicine (2017): http://www.scopus.com/inward/record.url?eid=2-s2.0-85017503329&partnerID=MN8TOARS.
    10.1038/nm.4319
  68. Ribeiro, Ruy M.. "Single-Genome Sequencing of Hepatitis C Virus in Donor-Recipient Pairs Distinguishes Modes and Models of Virus Transmission and Early Diversification". JOURNAL OF VIROLOGY (2016): www.orcid.org.
    10.1128/JVI.02156-15
  69. Ribeiro, Ruy M.. "Estimating biologically relevant parameters under uncertainty for experimental within-host murine West Nile virus infection". JOURNAL OF THE ROYAL SOCIETY INTERFACE (2016): www.orcid.org.
    10.1098/rsif.2016.0130
  70. Ribeiro, Ruy M.. "Trypanosoma brucei Parasites Occupy and Functionally Adapt to the Adipose Tissue in Mice". CELL HOST & MICROBE (2016): www.orcid.org.
    10.1016/j.chom.2016.05.002
  71. Ribeiro, Ruy M.. "Mathematics in modern immunology". INTERFACE FOCUS (2016): www.orcid.org.
    10.1098/rsfs.2015.0093
  72. Ribeiro, Ruy M.. "Antibiotic and Antiinflammatory Therapy Transiently Reduces Inflammation and Hypercoagulation in Acutely SIV-Infected Pigtailed Macaques". PLOS PATHOGENS (2016): www.orcid.org.
    10.1371/journal.ppat.1005384
  73. Ribeiro, Ruy M.. "Modeling the Effects of Morphine on Simian Immunodeficiency Virus Dynamics". PLoS Computational Biology (2016): www.orcid.org.
    10.1371/journal.pcbi.1005127
  74. Ribeiro, Ruy M.. "Multi-dose Romidepsin Reactivates Replication Competent SIV in Post-antiretroviral Rhesus Macaque Controllers". PLoS Pathogens (2016): www.orcid.org.
    10.1371/journal.ppat.1005879
  75. Ribeiro, Ruy M.. "Early HIV RNA decay during raltegravir-containing regimens exhibits two distinct subphases (1a and 1b)". AIDS (2015): www.orcid.org.
    10.1097/QAD.0000000000000843
  76. Ribeiro, Ruy M.. "Transmitted Virus Fitness and Host T Cell Responses Collectively Define Divergent Infection Outcomes in Two HIV-1 Recipients". PLOS PATHOGENS (2015): www.orcid.org.
    10.1371/journal.ppat.1004565
  77. Ribeiro, Ruy M.. "Early microbial translocation blockade reduces SIV-mediated inflammation and viral replication". JOURNAL OF CLINICAL INVESTIGATION (2014): www.orcid.org.
    10.1172/JCI75090
  78. Ribeiro, Ruy M.. "Antibody Responses during Hepatitis B Viral Infection". PLOS COMPUTATIONAL BIOLOGY (2014): www.orcid.org.
    10.1371/journal.pcbi.1003730
  79. Ribeiro, Ruy M.. "Inferring Viral Dynamics in Chronically HCV Infected Patients from the Spatial Distribution of Infected Hepatocytes". PLOS COMPUTATIONAL BIOLOGY (2014): www.orcid.org.
    10.1371/journal.pcbi.1003934
  80. Ribeiro, Ruy M.. "Human systems immunology Hypothesis-based modeling and unbiased data-driven approaches". SEMINARS IN IMMUNOLOGY (2013): www.orcid.org.
    10.1016/j.smim.2012.11.003
  81. Ribeiro, Ruy M.. "Modeling the within-host dynamics of HIV infection". BMC BIOLOGY (2013): www.orcid.org.
    10.1186/1741-7007-11-96
  82. Ribeiro, Ruy M.. "Kinetics of Coinfection with Influenza A Virus and Streptococcus pneumoniae". PLOS PATHOGENS (2013): www.orcid.org.
    10.1371/journal.ppat.1003238
  83. Ribeiro, Ruy M.. "Kinetics of Myeloid Dendritic Cell Trafficking and Activation Impact on Progressive, Nonprogressive and Controlled SIV Infections". PLOS PATHOGENS (2013): www.orcid.org.
    10.1371/journal.ppat.1003600
  84. Ribeiro, Ruy M.. "Use of Laser Capture Microdissection to Map Hepatitis C Virus-Positive Hepatocytes in Human Liver". GASTROENTEROLOGY (2013): www.orcid.org.
    10.1053/j.gastro.2013.08.034
  85. Ribeiro, Ruy M.. "The fate of CD4(+) T cells under tolerance-inducing stimulation a modeling perspective". IMMUNOLOGY AND CELL BIOLOGY (2013): www.orcid.org.
    10.1038/icb.2013.63
  86. Caridade, M.; Graca, L.; Ribeiro, R.M.. "Mechanisms underlying CD4+ Treg immune regulation in the adult: From experiments to models". Frontiers in Immunology 4 NOV (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84890360171&partnerID=MN8TOARS.
    10.3389/fimmu.2013.00378
  87. Ribeiro, Ruy M.. "Modeling Quasispecies and Drug Resistance in Hepatitis C Patients Treated with a Protease Inhibitor". BULLETIN OF MATHEMATICAL BIOLOGY (2012): www.orcid.org.
    10.1007/s11538-012-9736-y
  88. Ribeiro, Ruy M.. "Agent-based and phylogenetic analyses reveal how HIV-1 moves between risk groups Injecting drug users sustain the heterosexual epidemic in Latvia". EPIDEMICS (2012): www.orcid.org.
    10.1016/j.epidem.2012.04.002
  89. Ribeiro, Ruy M.. "Quantifying the activity of anti-HIV treatment in silico". NATURE MEDICINE (2012): www.orcid.org.
    10.1038/nm.2698
  90. Ribeiro, Ruy M.. "Coagulation biomarkers predict disease progression in SIV-infected nonhuman primates". BLOOD (2012): www.orcid.org.
    10.1182/blood-2012-03-414706
  91. Ribeiro, Ruy M.. "Quantifying the Diversification of Hepatitis C Virus (HCV) during Primary Infection Estimates of the In Vivo Mutation Rate". PLOS PATHOGENS (2012): www.orcid.org.
    10.1371/journal.ppat.1002881
  92. Ribeiro, Ruy M.. "Elucidation of Hepatitis C Virus Transmission and Early Diversification by Single Genome Sequencing". PLOS PATHOGENS (2012): www.orcid.org.
    10.1371/journal.ppat.1002880
  93. Ribeiro, Ruy M.. "Modelling deuterium labelling of lymphocytes with temporal and/or kinetic heterogeneity". JOURNAL OF THE ROYAL SOCIETY INTERFACE (2012): www.orcid.org.
    10.1098/rsif.2012.0149
  94. Ribeiro, Ruy M.. "Effect of 1918 PB1-F2 Expression on Influenza A Virus Infection Kinetics". PLOS COMPUTATIONAL BIOLOGY (2011): www.orcid.org.
    10.1371/journal.pcbi.1001081
  95. Ribeiro, Ruy M.. "Immunovirological Analyses of Chronically Simian Immunodeficiency Virus SIVmnd-1-and SIVmnd-2-Infected Mandrills (Mandrillus sphinx)". JOURNAL OF VIROLOGY (2011): www.orcid.org.
    10.1128/JVI.05693-11
  96. Ribeiro, Ruy M.. "Functional Cure of SIVagm Infection in Rhesus Macaques Results in Complete Recovery of CD4(+) T Cells and Is Reverted by CD8(+) Cell Depletion". PLOS PATHOGENS (2011): www.orcid.org.
    10.1371/journal.ppat.1002170
  97. Ribeiro, Ruy M.. "Evolution of Drug-Resistant Viral Populations during Interruption of Antiretroviral Therapy". JOURNAL OF VIROLOGY (2011): www.orcid.org.
    10.1128/JVI.02389-10
  98. Ribeiro, Ruy M.. "CD8+Lymphocytes Control Viral Replication in SIVmac239-Infected Rhesus Macaques without Decreasing the Lifespan of Productively Infected Cells". PLOS PATHOGENS (2010): www.orcid.org.
    10.1371/journal.ppat.1000747
  99. Ribeiro, Ruy M.. "Response network analysis of differential gene expression in human epithelial lung cells during avian influenza infections". BMC BIOINFORMATICS (2010): www.orcid.org.
    10.1186/1471-2105-11-170
  100. Ribeiro, Ruy M.. "Estimation of the Initial Viral Growth Rate and Basic Reproductive Number during Acute HIV-1 Infection". JOURNAL OF VIROLOGY (2010): www.orcid.org.
    10.1128/JVI.00127-10
  101. Ribeiro, Ruy M.. "Rapid Emergence of Protease Inhibitor Resistance in Hepatitis C Virus". SCIENCE TRANSLATIONAL MEDICINE (2010): www.orcid.org.
    10.1126/scitranslmed.3000544
  102. Ribeiro, Ruy M.. "Viral Dynamics during Primary Simian Immunodeficiency Virus Infection Effect of Time-Dependent Virus Infectivity". JOURNAL OF VIROLOGY (2010): www.orcid.org.
    10.1128/JVI.02284-09
  103. Ribeiro, Ruy M.. "Current Estimates for HIV-1 Production Imply Rapid Viral Clearance in Lymphoid Tissues". PLOS COMPUTATIONAL BIOLOGY (2010): www.orcid.org.
    10.1371/journal.pcbi.1000906
  104. Ribeiro, Ruy M.. "Hepatitis B Virus Kinetics under Antiviral Therapy Sheds Light on Differences in Hepatitis B e Antigen Positive and Negative Infections". JOURNAL OF INFECTIOUS DISEASES (2010): www.orcid.org.
    10.1086/656528
  105. Ribeiro, Ruy M.. "Experimental depletion of CD8(+) cells in acutely SIVagm-Infected African Green Monkeys results in increased viral replication". RETROVIROLOGY (2010): www.orcid.org.
    10.1186/1742-4690-7-42
  106. Smith, A.M.; Ribeiro, R.M.; Ribeiro, Ruy M.. "Modeling the viral dynamics of influenza a virus infection". Critical Reviews in Immunology 30 3 (2010): 291-298. http://www.scopus.com/inward/record.url?eid=2-s2.0-77951003840&partnerID=MN8TOARS.
    10.1615/CritRevImmunol.v30.i3.60
  107. Lewin SR; Ribeiro RM; Avihingsanon A; Bowden S; Matthews G; Marks P; Locarnini SA; et al. "Viral dynamics of hepatitis B virus DNA in human immunodeficiency virus-1-hepatitis B virus coinfected individuals: similar effectiveness of lamivudine, tenofovir, or combination therapy.". Hepatology (Baltimore, Md.) (2009): http://europepmc.org/abstract/med/19115219.
    10.1002/hep.22754
  108. Dahari H; Shudo E; Ribeiro RM; Perelson AS; Dahari, H.; Shudo, E.; Ribeiro, R.M.; Perelson, A.S.. "Mathematical modeling of HCV infection and treatment.". Methods in molecular biology (Clifton, N.J.) 510 (2009): 439-453. http://europepmc.org/abstract/med/19009281.
    10.1007/978-1-59745-394-3_33
  109. Ribeiro, Ruy M.; Lay, M.D.H.; Zhang, L.; Ribeiro, R.M.; Mueller, S.N.; Belz, G.T.; Davenport, M.P.. "Kinetics of Major Histocompatibility Class I Antigen Presentation in Acute Infection". JOURNAL OF IMMUNOLOGY 182 2 (2009): 902-911. www.orcid.org.
    10.4049/jimmunol.182.2.902
  110. Ribeiro, Ruy M.. "Modeling Complex Decay Profiles of Hepatitis B Virus During Antiviral Therapy". HEPATOLOGY (2009): www.orcid.org.
    10.1002/hep.22586
  111. Ribeiro, Ruy M.. "Limited ability of humoral immune responses in control of viremia during infection with SIVsmmD215 strain". BLOOD (2009): www.orcid.org.
    10.1182/blood-2008-09-177741
  112. Ribeiro, Ruy M.. "Modeling HCV kinetics under therapy using PK and PD information". EXPERT OPINION ON DRUG METABOLISM & TOXICOLOGY (2009): www.orcid.org.
    10.1517/17425250902787616
  113. Ribeiro, Ruy M.. "The race between infection and immunity how do pathogens set the pace?". TRENDS IN IMMUNOLOGY (2009): www.orcid.org.
    10.1016/j.it.2008.11.001
  114. Ribeiro, Ruy M.. "Division-linked differentiation can account for CD8(+) T-cell phenotype in vivo". EUROPEAN JOURNAL OF IMMUNOLOGY (2009): www.orcid.org.
    10.1002/eji.200838554
  115. Ribeiro, Ruy M.. "The level of monocyte turnover predicts disease progression in the macaque model of AIDS". BLOOD (2009): www.orcid.org.
    10.1182/blood-2009-02-204263
  116. Ribeiro, Ruy M.. "Effect of B-Cell Depletion on Viral Replication and Clinical Outcome of Simian Immunodeficiency Virus Infection in a Natural Host". JOURNAL OF VIROLOGY (2009): www.orcid.org.
    10.1128/JVI.00880-09
  117. Ribeiro, Ruy M.. "The evolutionary rate dynamically tracks changes in HIV-1 epidemics Application of a simple method for optimizing the evolutionary rate in phylogenetic trees with longitudinal data". Epidemics (2009): www.orcid.org.
    10.1016/j.epidem.2009.10.003
  118. Weinberger, A.D.; Perelson, A.S.; Ribeiro, R.M.; Weinberger, L.S.. "Accelerated Immunodeficiency by Anti-CCR5 Treatment in HIV Infection". PLoS Computational Biology 5 8 (2009): http://www.scopus.com/inward/record.url?eid=2-s2.0-70449713920&partnerID=MN8TOARS.
    10.1371/journal.pcbi.1000467
  119. Ribeiro, Ruy M.. "A Mathematical Model of Hepatitis C Virus Dynamics in Patients With High Baseline Viral Loads or Advanced Liver Disease". GASTROENTEROLOGY (2009): www.orcid.org.
    10.1053/j.gastro.2008.12.060
  120. Shudo E; Ribeiro RM; Talal AH; Perelson AS; Shudo, E.; Ribeiro, R.M.; Talal, A.H.; Perelson, A.S.. "A hepatitis C viral kinetic model that allows for time-varying drug effectiveness.". Antiviral therapy 13 7 (2008): 919-926. http://europepmc.org/abstract/med/19043926.
  121. Ribeiro, Ruy M.. "The effect of early versus delayed challenge after vaccination in controlling SHIV 89.6P infection". VIROLOGY (2008): www.orcid.org.
    10.1016/j.virol.2008.07.042
  122. Ribeiro, Ruy M.. "Estimating the Impact of Vaccination on Acute Simian-Human Immunodeficiency Virus/Simian Immunodeficiency Virus Infections". JOURNAL OF VIROLOGY (2008): www.orcid.org.
    10.1128/JVI.01596-08
  123. Ribeiro, Ruy M.. "Estimating drug efficacy and viral dynamic parameters HIV and HCV". STATISTICS IN MEDICINE (2008): www.orcid.org.
    10.1002/sim.3116
  124. Ribeiro, Ruy M.. "Modeling amantadine treatment of influenza A virus in vitro". JOURNAL OF THEORETICAL BIOLOGY (2008): www.orcid.org.
    10.1016/j.jtbi.2008.05.031
  125. Ribeiro, Ruy M.. "Real Time Bayesian Estimation of the Epidemic Potential of Emerging Infectious Diseases". PLoS One (2008): www.orcid.org.
    10.1371/journal.pone.0002185
  126. Pandrea, I.; Gaufin, T.; Brenchley, J.M.; Gautam, R.; Monjure, C.; Gautam, A.; Coleman, C.; et al. "Cutting edge: Experimentally induced immune activation in natural hosts of simian immunodeficiency virus induces significant increases in viral replication and CD4+ T cell depletion". Journal of Immunology 181 10 (2008): 6687-6691. http://www.scopus.com/inward/record.url?eid=2-s2.0-58149177783&partnerID=MN8TOARS.
    10.4049/jimmunol.181.10.6687
  127. Ribeiro, Ruy M.. "Simian immunodeficiency virus SIVagm dynamics in African green monkeys". JOURNAL OF VIROLOGY (2008): www.orcid.org.
    10.1128/JVI.02402-07
  128. Ribeiro, Ruy M.. "Dynamics of T- and B-lymphocyte turnover in a natural host of simian immunodeficiency virus". JOURNAL OF VIROLOGY (2008): www.orcid.org.
    10.1128/JVI.02197-07
  129. Ribeiro, Ruy M.. "The contribution of the thymus to the recovery of peripheral naive T-cell numbers during antiretroviral treatment for HIV infection". JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES (2008): www.orcid.org.
    10.1097/QAI.0b013e318184fb28
  130. Ribeiro, Ruy M.. "Modelling the kinetics of hepatitis C virus RNA decline over 4 weeks of treatment with pegylated interferon alpha-2b". JOURNAL OF VIRAL HEPATITIS (2008): www.orcid.org.
    10.1111/j.1365-2893.2008.00977.x
  131. Ribeiro, Ruy M.. "Modelling hepatitis C virus kinetics during treatment with pegylated interferon alpha-2b errors in the estimation of viral kinetic parameters". JOURNAL OF VIRAL HEPATITIS (2008): www.orcid.org.
    10.1111/j.1365-2893.2007.00954.x
  132. Ribeiro, Ruy M.; Pandrea, I.V.; Gautam, R.; Ribeiro, R.M.; Brenchley, J.M.; Butler, I.F.; Pattison, M.; et al. "Acute loss of intestinal CD4+ T cells is not predictive of simian immunodeficiency virus virulence.". Journal of immunology (Baltimore, Md. : 1950) 179 5 (2007): 3035-3046. http://europepmc.org/abstract/med/17709518.
    10.4049/jimmunol.179.5.3035
  133. Bettencourt LMA; Ribeiro RM; Chowell G; Lant T; Castillo-Chavez C; Bettencourt, L.M.A.; Ribeiro, R.M.; et al. "Towards Real Time Epidemiology: Data Assimilation, Modeling and Anomaly Detection of Health Surveillance Data Streams.". Intelligence and Security Informatics: Biosurveillance 4506 LNCS (2007): http://europepmc.org/abstract/PMC/PMC7122958.
    10.1007/978-3-540-72608-1_8
  134. Ribeiro, Ruy M.. "The role of cells refractory to productive infection in acute hepatitis B viral dynamics". PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007): www.orcid.org.
    10.1073/pnas.0603626104
  135. Lau, G.K.K.; Cooksley, H.; Ribeiro, R.M.; Powers, K.A.; Shudo, E.; Bowden, S.; Hui, C.-K.; et al. "Impact of early viral kinetics on T-cell reactivity during antiviral therapy in chronic hepatitis B". Antiviral Therapy 12 5 (2007): 705-718. http://www.scopus.com/inward/record.url?eid=2-s2.0-34547768137&partnerID=MN8TOARS.
  136. Ribeiro, Ruy M.. "Dynamics of CD4(+) T cells in HIV-1 infection". IMMUNOLOGY AND CELL BIOLOGY (2007): www.orcid.org.
    10.1038/sj.icb.7100056
  137. Ribeiro, Ruy M.. "Understanding the mechanisms and limitations of immune control of HIV". IMMUNOLOGICAL REVIEWS (2007): www.orcid.org.
    10.1111/j.1600-065X.2006.00485.x
  138. Ribeiro, Ruy M.. "Determining thymic output quantitatively using models to interpret experimental T-cell receptor excision circle (TREC) data". IMMUNOLOGICAL REVIEWS (2007): www.orcid.org.
    10.1111/j.1600-065X.2006.00493.x
  139. Ribeiro, Ruy M.. "Mathematical modeling of subgenomic hepatitis C virus replication in Huh-7 cells". JOURNAL OF VIROLOGY (2007): www.orcid.org.
    10.1128/JVI.01304-06
  140. Ribeiro, Ruy M.. "Early ribavirin pharmacokinetics, HCV RNA and alanine aminotransferase kinetics in HIV/HCV co-infected patients during treatment with pegylated interferon and ribavirin". JOURNAL OF HEPATOLOGY (2007): www.orcid.org.
    10.1016/j.jhep.2007.01.027
  141. Ribeiro, Ruy M.. "Triphasic decline of hepatitis C virus RNA during antiviral therapy". HEPATOLOGY (2007): www.orcid.org.
    10.1002/hep.21657
  142. Ribeiro, Ruy M.. "Modeling hepatitis C virus dynamics Liver regeneration and critical drug efficacy". JOURNAL OF THEORETICAL BIOLOGY (2007): www.orcid.org.
    10.1016/j.jtbi.2007.03.006
  143. Ribeiro, Ruy M.. "Modeling the mechanisms of acute hepatitis B virus infection". JOURNAL OF THEORETICAL BIOLOGY (2007): www.orcid.org.
    10.1016/j.jtbi.2007.02.017
  144. Ribeiro, Ruy M.. "Unequal evolutionary rates in the human immunodeficiency virus type I (HIV-1) pandemic The evolutionary rate of HIV-1 slows down when the epidemic rate increases". JOURNAL OF VIROLOGY (2007): www.orcid.org.
    10.1128/JVI.00985-07
  145. Ribeiro, Ruy M.. "Influence of peak viral load on the extent of CD4(+) T-cell depletion in simian HIV infection". JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES (2006): www.orcid.org.
    10.1097/01.qai.0000199232.31340.d3
  146. Ribeiro, Ruy M.. "Kinetics of hepatitis C virus reinfection after liver transplantation". LIVER TRANSPLANTATION (2006): www.orcid.org.
    10.1002/lt.20572
  147. Ribeiro, Ruy M.. "Naive and memory cell turnover as drivers of CCR5-to-CXCR4 tropism switch in human immunodeficiency virus type 1 Implications for therapy". JOURNAL OF VIROLOGY (2006): www.orcid.org.
    10.1128/JVI.80.2.802-809.2006
  148. Ribeiro, Ruy M.. "Pharmacodynamics of PEG-IFN alpha differentiate HIV/HCV coinfected sustained virological responders from nonresponders". HEPATOLOGY (2006): www.orcid.org.
    10.1002/hep.21136
  149. Ribeiro, Ruy M.. "Th-1-type cytotoxic CD8(+) T-lymphocyte responses to simian immunodeficiency virus (SIV) are a consistent feature of natural SIV infection in sooty mangabeys". JOURNAL OF VIROLOGY (2006): www.orcid.org.
    10.1128/JVI.80.6.2771-2783.2006
  150. Layden-Almer, J.E.; Kuiken, C.; Ribeiro, R.M.; Kunstman, K.J.; Perelson, A.S.; Layden, T.J.; Wolinsky, S.M.. "Hepatitis C virus genotype 1a NS5A pretreatment sequence variation and viral kinetics in African American and white patients". Journal of Infectious Diseases 192 6 (2005): 1078-1087. http://www.scopus.com/inward/record.url?eid=2-s2.0-24644442144&partnerID=MN8TOARS.
    10.1086/432760
  151. Perelson, A.S.; Ribeiro, R.M.. "Mutagenic effects of ribavirin in vivo". Journal of Hepatology 43 4 (2005): 553-555. http://www.scopus.com/inward/record.url?eid=2-s2.0-24344463108&partnerID=MN8TOARS.
    10.1016/j.jhep.2005.07.003
  152. Davenport, M.P.; Zhang, L.; Bagchi, A.; Fridman, A.; Fu, T.-M.; Schleif, W.; Shiver, J.W.; Ribeiro, R.M.; Perelson, A.S.. "High-potency human immunodeficiency virus vaccination leads to delayed and reduced CD8+ T-cell expansion but improved virus control". Journal of Virology 79 15 (2005): 10059-10062. http://www.scopus.com/inward/record.url?eid=2-s2.0-22544453325&partnerID=MN8TOARS.
    10.1128/JVI.79.15.10059-10062.2005
  153. Arron, S.T.; Ribeiro, R.M.; Gettie, A.; Bohm, R.; Blanchard, J.; Yu, J.; Perelson, A.S.; Ho, D.D.; Zhang, L.. "Impact of thymectomy on the peripheral T cell pool in rhesus macaques before and after infection with simian immunodeficiency virus". European Journal of Immunology 35 1 (2005): 46-55. http://www.scopus.com/inward/record.url?eid=2-s2.0-12344285945&partnerID=MN8TOARS.
    10.1002/eji.200424996
  154. Elson, K.; Ribeiro, R.M.; Perelson, A.S.; Simmons, A.; Speck, P.. "The life span of ganglionic glia in murine sensory ganglia estimated by uptake of bromodeoxyuridine". Experimental Neurology 186 1 (2004): 99-103. http://www.scopus.com/inward/record.url?eid=2-s2.0-1242293838&partnerID=MN8TOARS.
    10.1016/j.expneurol.2003.10.017
  155. Davenport, M.P.; Ribeiro, R.M.; Chao, D.L.; Perelson, A.S.. "Predicting the impact of a nonsterilizing vaccine against human immunodeficiency virus". Journal of Virology 78 20 (2004): 11340-11351. http://www.scopus.com/inward/record.url?eid=2-s2.0-4644249733&partnerID=MN8TOARS.
    10.1128/JVI.78.20.11340-11351.2004
  156. Talal, A.H.; Shata, M.T.; Markatou, M.; Dorante, G.; Chadburn, A.; Koch, R.; Neumann, A.U.; Ribeiro, R.M.; Perelson, A.S.. "Virus Dynamics and Immune Responses during Treatment in Patients Coinfected with Hepatitis C and HIV". Journal of Acquired Immune Deficiency Syndromes 35 2 (2004): 103-113. http://www.scopus.com/inward/record.url?eid=2-s2.0-1642499256&partnerID=MN8TOARS.
    10.1097/00126334-200402010-00001
  157. Zhang, L.; Ribeiro, R.M.; Mascola, J.R.; Lewis, M.G.; Stiegler, G.; Katinger, H.; Perelson, A.S.; Davenport, M.P.. "Effects of Antibody on Viral Kinetics in Simian/Human Immunodeficiency Virus Infection: Implications for Vaccination". Journal of Virology 78 10 (2004): 5520-5522. http://www.scopus.com/inward/record.url?eid=2-s2.0-2342627375&partnerID=MN8TOARS.
    10.1128/JVI.78.10.5520-5522.2004
  158. Di Mascio, M.; Ribeiro, R.M.; Markowitz, M.; Ho, D.D.; Perelson, A.S.. "Modeling the long-term control of viremia in HIV-1 infected patients treated with antiretroviral therapy". Mathematical Biosciences 188 1-2 (2004): 47-62. http://www.scopus.com/inward/record.url?eid=2-s2.0-0842346379&partnerID=MN8TOARS.
    10.1016/j.mbs.2003.08.003
  159. Perelson, A.S.; Ribeiro, R.M.. "Hepatitis B virus kinetics and mathematical modeling". Seminars in Liver Disease 24 SUPPL. 1 (2004): 11-16. http://www.scopus.com/inward/record.url?eid=2-s2.0-2942590744&partnerID=MN8TOARS.
    10.1055/s-2004-828673
  160. Davenport, M.P.; Ribeiro, R.M.; Perelson, A.S.. "Kinetics of virus-specific CD8+ T cells and the control of human immunodeficiency virus infection". Journal of Virology 78 18 (2004): 10096-10103. http://www.scopus.com/inward/record.url?eid=2-s2.0-4444341172&partnerID=MN8TOARS.
    10.1128/JVI.78.18.10096-10103.2004
  161. Ramratnam, B.; Ribeiro, R.; He, T.; Chung, C.; Simon, V.; Vanderhoeven, J.; Hurley, A.; et al. "Intensification of Antiretroviral Therapy Accelerates the Decay of the HIV-1 Latent Reservoir and Decreases, but Does Not Eliminate, Ongoing Virus Replication". Journal of Acquired Immune Deficiency Syndromes 35 1 (2004): 33-37. http://www.scopus.com/inward/record.url?eid=2-s2.0-9144265028&partnerID=MN8TOARS.
    10.1097/00126334-200401010-00004
  162. Layden-Almer, J.E.; Ribeiro, R.M.; Wiley, T.; Perelson, A.S.; Layden, T.J.. "Viral dynamics and response differences in HCV-infected African American and white patients treated with IFN and ribavirin". Hepatology 37 6 (2003): 1343-1350. http://www.scopus.com/inward/record.url?eid=2-s2.0-0038820380&partnerID=MN8TOARS.
    10.1053/jhep.2003.50217
  163. Layden, T.J.; Layden, J.E.; Ribeiro, R.M.; Perelson, A.S.. "Mathematical modeling of viral kinetics: A tool to understand and optimize therapy". Clinics in Liver Disease 7 1 (2003): 163-178. http://www.scopus.com/inward/record.url?eid=2-s2.0-0037299166&partnerID=MN8TOARS.
    10.1016/S1089-3261(02)00063-6
  164. Torriani, F.J.; Ribeiro, R.M.; Gilbert, T.L.; Schrenk, U.M.; Clauson, M.; Pacheco, D.M.; Perelson, A.S.. "Hepatitis C Virus (HCV) and Human Immunodeficiency Virus (HIV) Dynamics during HCV Treatment in HCV/HIV Coinfection". Journal of Infectious Diseases 188 10 (2003): 1498-1507. http://www.scopus.com/inward/record.url?eid=2-s2.0-0346874143&partnerID=MN8TOARS.
    10.1086/379255
  165. Korthals Altes, H.; Ribeiro, R.M.; De Boer, R.J.. "The race between initial T-helper expansion and virus growth upon HIV infection influences polyclonality of the response and viral set-point". Proceedings of the Royal Society B: Biological Sciences 270 1522 (2003): 1349-1358. http://www.scopus.com/inward/record.url?eid=2-s2.0-0037963626&partnerID=MN8TOARS.
    10.1098/rspb.2003.2377
  166. Ribeiro, R.M.; Layden-Almer, J.; Powers, K.A.; Layden, T.J.; Perelson, A.S.. "Dynamics of alanine aminotransferase during hepatitis C virus treatment". Hepatology 38 2 (2003): 509-517. http://www.scopus.com/inward/record.url?eid=2-s2.0-0041764925&partnerID=MN8TOARS.
    10.1053/jhep.2003.50344
  167. Powers, K.A.; Dixit, N.M.; Ribeiro, R.M.; Golia, P.; Talal, A.H.; Perelson, A.S.; Powers KA; et al. "Modeling viral and drug kinetics: Hepatitis C virus treatment with pegylated interferon alfa-2b". Seminars in Liver Disease 23 SUPPL. 1 (2003): 13-18. http://www.scopus.com/inward/record.url?eid=2-s2.0-0041317673&partnerID=MN8TOARS.
    10.1055/s-2003-41630
  168. Lewin SR; Ribeiro RM; Kaufmann GR; Smith D; Zaunders J; Law M; Solomon A; et al. "Dynamics of T cells and TCR excision circles differ after treatment of acute and chronic HIV infection.". Journal of immunology (Baltimore, Md. : 1950) 169 8 (2002): 4657-4666. http://europepmc.org/abstract/med/12370406.
    10.4049/jimmunol.169.8.4657
  169. Ribeiro, R.M.; Perelson, A.S.. "Hepatitis B virus viral dynamics: Effects of drug dose and baseline alanine aminotransferase". Journal of Hepatology 37 2 (2002): 277-279. http://www.scopus.com/inward/record.url?eid=2-s2.0-0036022884&partnerID=MN8TOARS.
    10.1016/S0168-8278(02)00210-6
  170. Ribeiro, R.M.; Mohri, H.; Ho, D.D.; Perelson, A.S.. "In vivo dynamics of t cell activation, proliferation, and death in HIV-1 infection: Why are CD4+ but not CD8+ T cells depleted?". Proceedings of the National Academy of Sciences of the United States of America 99 24 (2002): 15572-15577. http://www.scopus.com/inward/record.url?eid=2-s2.0-0037180499&partnerID=MN8TOARS.
    10.1073/pnas.242358099
  171. Rosen, H.R.; Ribeiro, R.R.; Weinberger, L.; Wolf, S.; Chung, M.; Gretch, D.R.; Perelson, A.S.. "Early hepatitis C viral kinetics correlate with long-term outcome in patients receiving high dose induction followed by combination interferon and ribavirin therapy". Journal of Hepatology 37 1 (2002): 124-130. http://www.scopus.com/inward/record.url?eid=2-s2.0-0035991450&partnerID=MN8TOARS.
    10.1016/S0168-8278(02)00114-9
  172. Ribeiro, R.M.; Lo, A.; Perelson, A.S.. "Dynamics of hepatitis B virus infection". Microbes and Infection 4 8 (2002): 829-835. http://www.scopus.com/inward/record.url?eid=2-s2.0-0036629793&partnerID=MN8TOARS.
    10.1016/S1286-4579(02)01603-9
  173. Ribeiro, R.M.; Mohri, H.; Ho, D.D.; Perelson, A.S.. "Modeling deuterated glucose labeling of T-lymphocytes". Bulletin of Mathematical Biology 64 2 (2002): 385-405. http://www.scopus.com/inward/record.url?eid=2-s2.0-0036489838&partnerID=MN8TOARS.
    10.1006/bulm.2001.0282
  174. Lewin, S.R.; Ribeiro, R.M.; Walters, T.; Lau, G.K.; Bowden, S.; Locarnini, S.; Perelson, A.S.. "Analysis of hepatitis B viral load decline under potent therapy: Complex decay profiles observed". Hepatology 34 5 (2001): 1012-1020. http://www.scopus.com/inward/record.url?eid=2-s2.0-0034756599&partnerID=MN8TOARS.
    10.1053/jhep.2001.28509
  175. Mohri, H.; Perelson, A.S.; Tung, K.; Ribeiro, R.M.; Ramratnam, B.; Markowitz, M.; Kost, R.; et al. "Increased turnover of T lymphocytes in HIV-1 infection and its reduction by antiretroviral therapy". Journal of Experimental Medicine 194 9 (2001): 1277-1287. http://www.scopus.com/inward/record.url?eid=2-s2.0-0035169609&partnerID=MN8TOARS.
    10.1084/jem.194.9.1277
  176. Roberts, D.E.; Ribeiro, R.M.. "Comparison of different treatment regimens for the emergence of new resistance under therapy". Journal of Acquired Immune Deficiency Syndromes 27 4 (2001): 331-335. http://www.scopus.com/inward/record.url?eid=2-s2.0-0035424617&partnerID=MN8TOARS.
  177. Ribeiro, R.M.; Bonhoeffer, S.. "Production of resistant HIV mutants during antiretroviral therapy". Proceedings of the National Academy of Sciences of the United States of America 97 14 (2000): 7681-7686. http://www.scopus.com/inward/record.url?eid=2-s2.0-0034608864&partnerID=MN8TOARS.
    10.1073/pnas.97.14.7681
  178. Callaway DS; Ribeiro RM; Nowak MA; Callaway, D.S.; Ribeiro, R.M.; Nowak, M.A.. "Virus phenotype switching and disease progression in HIV-1 infection.". Proceedings. Biological sciences 266 1437 (1999): 2523-2530. http://europepmc.org/abstract/med/10693824.
    10.1098/rspb.1999.0955
  179. Ribeiro, R.M.; Bonhoeffer, S.. "A stochastic model for primary HIV infection: Optimal timing of therapy". AIDS 13 3 (1999): 351-357. http://www.scopus.com/inward/record.url?eid=2-s2.0-0032968677&partnerID=MN8TOARS.
    10.1097/00002030-199902250-00007
  180. Ribeiro, R.M.; Bonhoeffer, S.; Nowak, M.A.. "The frequency of resistant mutant virus before antiviral therapy". AIDS 12 5 (1998): 461-465. http://www.scopus.com/inward/record.url?eid=2-s2.0-0032568196&partnerID=MN8TOARS.
    10.1097/00002030-199805000-00006
Livro
  1. Ribeiro, R.M.; Dixit, N.M.; Perelson, A.S.. 13 Modelling the in vivo growth rate of HIV: implications for vaccination. 2005.
    10.1016/S1571-0831(06)80017-1
  2. Ribeiro, R.M.; Perelson, A.S.. The Analysis of HIV Dynamics Using Mathematical Models. 2004.
    10.1016/B978-012764051-8/50037-8
Atividades

Apresentação oral de trabalho

Título da apresentação Nome do evento
Anfitrião (Local do evento)
2000 Since 2000, I have over 70 invited lectures at international venues, including international meetings and institutions. I have also presented to the general public and high schools on topics of scientific interest.

Arbitragem científica em revista

Nome da revista (ISSN) Editora
2000 - Atual I have reviewed more than one hundred papers for international journals

Comissão de avaliação

Descrição da atividade
Tipo de assessoria
Instituição / Organização Entidade financiadora
2017 - Atual I have reviewed more than one hundred and twenty scientific projects for multiple international funding agencies (including from Australia, Switzerland, UK, USA, Netherlands, South Africa, European Union). In particular, I was a standing panel member of the Modeling and Analyses of Biological Systems study section of the National Institutes of Health, USA, from Oct 2017 to Jun 2021.

Tutoria

Tópico Nome do aluno
2008 - Atual I have mentored 15 postdoctoral researchers since 2008
Distinções

Outra distinção

2017 The Scretary's Appreciation Award
US Department of Energy, Estados Unidos
2004 Postdoctoral Publication Prize in Theoretical Physics (Honourable Mention)
Los Alamos National Laboratory, Estados Unidos
2003 Marie Curie Fellowship
European Union, Bélgica
1998 Mary Lunt Graduate Scholar
University of Oxford Saint Hugh's College, Reino Unido
1993 Be Brilliant - Futurist Competition Europe
Honeywell Corporation, Portugal