Ruy M. Ribeiro - Publications

Affiliations: 
Theoretical Division Los Alamos National Laboratory, Los Alamos, NM, United States 

169 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Ke R, Zitzmann C, Ho DD, Ribeiro RM, Perelson AS. In vivo kinetics of SARS-CoV-2 infection and its relationship with a person's infectiousness. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34857628 DOI: 10.1073/pnas.2111477118  1
2021 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). 35: 3431-3439. PMID 34697179 DOI: 10.21873/invivo.12643  1
2021 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). PMID 34690280 DOI: 10.1097/QAD.0000000000003116  1
2021 Choudhary MC, Chew KW, Deo R, Flynn JP, Regan J, Crain CR, Moser C, Hughes M, Ritz J, Ribeiro RM, Ke R, Dragavon JA, Javan AC, Nirula A, Klekotka P, et al. Emergence of SARS-CoV-2 Resistance with Monoclonal Antibody Therapy. Medrxiv : the Preprint Server For Health Sciences. PMID 34545376 DOI: 10.1101/2021.09.03.21263105  1
2021 Regan J, Flynn JP, Rosenthal A, Jordan H, Li Y, Chishti R, Giguel F, Corry H, Coxen K, Fajnzylber J, Gillespie E, Kuritzkes DR, Hacohen N, Goldberg MB, Filbin MR, ... Ribeiro RM, et al. Viral Load Kinetics of Severe Acute Respiratory Syndrome Coronavirus 2 in Hospitalized Individuals With Coronavirus Disease 2019. Open Forum Infectious Diseases. 8: ofab153. PMID 34430669 DOI: 10.1093/ofid/ofab153  1
2021 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. 11: 16600. PMID 34400715 DOI: 10.1038/s41598-021-96060-w  1
2021 Ke R, Zitzmann C, Ho DD, Ribeiro RM, Perelson AS. In vivo kinetics of SARS-CoV-2 infection and its relationship with a person's infectiousness. Medrxiv : the Preprint Server For Health Sciences. PMID 34230935 DOI: 10.1101/2021.06.26.21259581  1
2021 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). 35: 2207-2212. PMID 34182498 DOI: 10.21873/invivo.12492  1
2021 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. 520: 133-138. PMID 34097882 DOI: 10.1016/j.cca.2021.06.006  1
2021 Garrido MM, Ribeiro RM, Krüger K, Pinheiro LC, Guimarães JT, Holdenrieder S. Are Proinflammatory Cytokines Relevant for the Diagnosis of Prostate Cancer? Anticancer Research. 41: 3067-3073. PMID 34083299 DOI: 10.21873/anticanres.15090  1
2021 Garrido MM, Marta JC, Ribeiro RM, Pinheiro LC, Guimarães JT. Serum lipids and prostate cancer. Journal of Clinical Laboratory Analysis. e23705. PMID 33724557 DOI: 10.1002/jcla.23705  1
2021 De Sousa C, Ribeiro RM, Pinto FJ. Infective Endocarditis as the Cause of Death: A Populationbased Study in Portugal, from 2002 to 2018. Acta Medica Portuguesa. PMID 33687320 DOI: 10.20344/amp.14609  1
2021 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. PMID 33648807 DOI: 10.1016/j.repc.2020.07.014  1
2021 Best K, Barouch DH, Guedj J, Ribeiro RM, Perelson AS. Zika virus dynamics: Effects of inoculum dose, the innate immune response and viral interference. Plos Computational Biology. 17: e1008564. PMID 33471814 DOI: 10.1371/journal.pcbi.1008564  1
2020 Goyal A, Perelson AS, Kandathil AJ, Quinn J, Balagopal A, Ribeiro RM. HIV influences clustering and intracellular replication of hepatitis C virus. Journal of Viral Hepatitis. PMID 33128322 DOI: 10.1111/jvh.13429  1
2020 Nogueira PJ, de Araújo Nobre M, Costa A, Ribeiro RM, Furtado C, Bacelar Nicolau L, Camarinha C, Luís M, Abrantes R, Carneiro AV. Reply to Comment on Nogueira, P.J., et al. "The Role of Health Preconditions on COVID-19 Deaths in Portugal: Evidence from Surveillance Data of the First 20293 Infection Cases". 2020, , 2368. Journal of Clinical Medicine. 9. PMID 33121184 DOI: 10.3390/jcm9113449  1
2020 Balagopal A, Grudda T, Ribeiro RM, Saad YS, Hwang HS, Quinn J, Murphy M, Ward K, Sterling RK, Zhang Y, Perelson AS, Sulkowski MS, Osburn WO, Thio CL. Single hepatocytes show persistence and transcriptional inactivity of hepatitis B. Jci Insight. 5. PMID 33004689 DOI: 10.1172/jci.insight.140584  0.01
2020 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. 9. PMID 32751825 DOI: 10.3390/Jcm9082450  0.01
2020 Nogueira PJ, de Araújo Nobre M, Costa A, Ribeiro RM, Furtado C, Bacelar Nicolau L, Camarinha C, Luís M, Abrantes R, Vaz Carneiro A. 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. 9. PMID 32722159 DOI: 10.3390/Jcm9082368  1
2020 Ribeiro RM, Graca L. Untangling the immune basis of disease susceptibility. Elife. 9. PMID 32406819 DOI: 10.7554/Elife.56886  1
2020 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. PMID 32388806 DOI: 10.1007/s13304-020-00757-y  0.01
2020 De Santiago I, Ribeiro R, Nicolau LB, Marinho RT, Pereira-Miguel J. Consumption of Alcohol and Drugs in the School Population of Sao Tome and Principe. Acta Medica Portuguesa. 33: 237-245. PMID 32238237 DOI: 10.20344/Amp.11876  0.01
2020 Vieira-Sousa E, Alves P, Rodrigues AM, Teixeira F, Tavares-Costa J, Bernardo A, Pimenta S, Pimentel-Santos FM, Gomes JL, Aguiar R, Pinto P, Videira T, Catita C, Santos H, Borges J, ... Ribeiro RM, 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. 79: 490-498. PMID 32193187 DOI: 10.1136/Annrheumdis-2019-216500  1
2019 He T, Xu C, Krampe N, Dillon SM, Sette P, Falwell E, Haret-Richter GS, Butterfield T, Dunsmore TL, Jr WMM, Martin KJ, Policicchio BB, Raehtz KD, Penn EP, Tracy RP, Ribeiro RM, et al. High-fat diet exacerbates SIV pathogenesis and accelerates disease progression. The Journal of Clinical Investigation. PMID 31710311 DOI: 10.1172/Jci121208  1
2019 Cardozo EF, Ji D, Lau G, Schinazi RF, Chen GF, Ribeiro RM, Perelson AS. Disentangling the life-spans of hepatitis C virus infected cells and intracellular vRNA replication-complexes during direct acting antiviral therapy. Journal of Viral Hepatitis. PMID 31670859 DOI: 10.1111/Jvh.13229  1
2019 Bretaña NA, Gray RT, Cunningham EB, Betz-Stablein B, Ribeiro R, Graw F, Luciani F, Lloyd AR. Combined treatment and prevention strategies for hepatitis C virus elimination in the prisons in New South Wales: a modelling study. Addiction (Abingdon, England). PMID 31633853 DOI: 10.1111/Add.14830  1
2019 Gil Marques F, Poli E, Malaquias J, Carvalho T, Portêlo A, Ramires A, Aldeia F, Ribeiro RM, Vitorino E, Diegues I, Costa L, Coutinho J, Pina F, Mareel M, Constantino Rosa Santos S. 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. PMID 31376927 DOI: 10.1016/J.Radonc.2019.06.035  0.01
2019 Soares MV, Azevedo RI, Ferreira IA, Bucar S, Ribeiro AC, Vieira A, Pereira PNG, Ribeiro RM, Ligeiro D, Alho AC, Soares AS, Camacho N, Martins C, Lourenço F, Moreno R, 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. 10: 334. PMID 30894856 DOI: 10.3389/Fimmu.2019.00334  1
2019 Boer RJd, Ribeiro R, Borghans J. Decision letter: Differential impact of self and environmental antigens on the ontogeny and maintenance of CD4+ T cell memory Elife. DOI: 10.7554/Elife.48901.Sa1  1
2019 Vieira-Sousa E, Alves P, Rodrigues AM, Teixeira F, Tavares-Costa J, Bernardo A, Pimenta S, Santos FPD, Gomes JL, Aguiar R, Videira T, Pinto P, Catita C, Santos H, Borges J, ... ... Ribeiro RM, et al. SAT0368 GO-DACT: A RANDOMIZED DOUBLE-BLIND PLACEBO-CONTROLED PROOF-OF-CONCEPT TRIAL OF GOLIMUMAB PLUS METHOTREXATE (MTX) VERSUS MTX MONOTHERAPY, IN IMPROVING DACTYLITIS, IN MTX NAïVE PSORIATIC ARTHRITIS PATIENTS Annals of the Rheumatic Diseases. 78: 1266-1266. DOI: 10.1136/Annrheumdis-2019-Eular.5164  1
2018 Conway JM, Ribeiro RM. Modeling the immune response to HIV infection. Current Opinion in Systems Biology. 12: 61-69. PMID 31463420 DOI: 10.1016/J.Coisb.2018.10.006  0.01
2018 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. 9: 3338. PMID 30728819 DOI: 10.3389/Fmicb.2018.03338  1
2018 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. 9: 2540. PMID 30455694 DOI: 10.3389/Fimmu.2018.02540  1
2018 Cao Y, Lei X, Ribeiro RM, Perelson AS, Liang J. Probabilistic control of HIV latency and transactivation by the Tat gene circuit. Proceedings of the National Academy of Sciences of the United States of America. PMID 30455316 DOI: 10.1073/Pnas.1811195115  1
2018 Sivanandham R, Brocca-Cofano E, Krampe N, Falwell E, Kilapandal Venkatraman SM, Ribeiro RM, Apetrei C, Pandrea I. Neutrophil extracellular trap production contributes to pathogenesis in SIV-infected nonhuman primates. The Journal of Clinical Investigation. PMID 30204591 DOI: 10.1172/Jci99420  1
2018 Cardozo EF, Apetrei C, Pandrea I, Ribeiro RM. The dynamics of simian immunodeficiency virus after depletion of CD8+ cells. Immunological Reviews. 285: 26-37. PMID 30129200 DOI: 10.1111/Imr.12691  1
2018 Perelson AS, Ribeiro RM. Introduction to modeling viral infections and immunity. Immunological Reviews. 285: 5-8. PMID 30129196 DOI: 10.1111/Imr.12700  1
2018 Vieira-Sousa E, Canhão H, Alves P, Rodrigues AM, Teixeira F, Tavares-Costa J, Bernardo A, Pimenta S, Pimentel-Santos F, Gomes JL, Aguiar R, Videira T, Pinto P, Catita C, Santos H, ... ... Ribeiro RM, 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. 43: 80-92. PMID 30091952  1
2018 Romero-Severson EO, Ribeiro RM, Castro M. Noise Is Not Error: Detecting Parametric Heterogeneity Between Epidemiologic Time Series. Frontiers in Microbiology. 9: 1529. PMID 30050514 DOI: 10.3389/Fmicb.2018.01529  1
2018 Ke R, Li H, Wang S, Ding W, Ribeiro RM, Giorgi EE, Bhattacharya T, Barnard RJO, Hahn BH, Shaw GM, Perelson AS. Superinfection and cure of infected cells as mechanisms for hepatitis C virus adaptation and persistence. Proceedings of the National Academy of Sciences of the United States of America. PMID 29987026 DOI: 10.1073/Pnas.1805267115  1
2018 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. 9: 1326. PMID 29973924 DOI: 10.3389/Fmicb.2018.01326  1
2018 Murray JM, Ribeiro RM. Special Issue "Mathematical Modeling of Viral Infections". Viruses. 10. PMID 29866993 DOI: 10.3390/V10060303  0.01
2018 Policicchio BB, Cardozo EF, Sette P, Xu C, Haret-Richter G, Dunsmore T, Apetrei C, Pandrea I, Ribeiro RM. The dynamics of SIV 2-LTR Circles in the Presence and Absence of CD8 Cells. Journal of Virology. PMID 29643246 DOI: 10.1128/Jvi.02100-17  1
2018 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. 13: e0190908. PMID 29466356 DOI: 10.1371/Journal.Pone.0190908  1
2017 Goyal A, Ribeiro RM, Perelson AS. The Role of Infected Cell Proliferation in the Clearance of Acute HBV Infection in Humans. Viruses. 9. PMID 29156567 DOI: 10.3390/V9110350  1
2017 Schechter ME, Andrade BB, He T, Richter GH, Tosh KW, Policicchio BB, Singh A, Raehtz KD, Sheikh V, Ma D, Brocca-Cofano E, Apetrei C, Tracy R, Ribeiro RM, Sher A, et al. Inflammatory monocytes expressing tissue factor drive SIV and HIV coagulopathy. Science Translational Medicine. 9. PMID 28855397 DOI: 10.1126/Scitranslmed.Aam5441  1
2017 Cardozo EF, Andrade A, Mellors JW, Kuritzkes DR, Perelson AS, Ribeiro RM. 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: e1006478. PMID 28678879 DOI: 10.1371/Journal.Ppat.1006478  1
2017 Borghans J, Ribeiro RM. The maths of memory. Elife. 6. PMID 28453436 DOI: 10.7554/Elife.26754  1
2017 Honeycutt JB, Thayer WO, Baker CE, Ribeiro RM, Lada SM, Cao Y, Cleary RA, Hudgens MG, Richman DD, Garcia JV. HIV persistence in tissue macrophages of humanized myeloid-only mice during antiretroviral therapy. Nature Medicine. PMID 28414330 DOI: 10.1038/Nm.4319  1
2016 Vaidya NK, Ribeiro RM, Perelson AS, Kumar A. Modeling the Effects of Morphine on Simian Immunodeficiency Virus Dynamics. Plos Computational Biology. 12: e1005127. PMID 27668463 DOI: 10.1371/Journal.Pcbi.1005127  0.01
2016 Policicchio BB, Xu C, Brocca-Cofano E, Raehtz KD, He T, Ma D, Li H, Sivanandham R, Haret-Richter GS, Dunsmore T, Trichel A, Mellors JW, Hahn BH, Shaw GM, Ribeiro RM, et al. Multi-dose Romidepsin Reactivates Replication Competent SIV in Post-antiretroviral Rhesus Macaque Controllers. Plos Pathogens. 12: e1005879. PMID 27632364 DOI: 10.1371/Journal.Ppat.1005879  1
2016 Trindade S, Rijo-Ferreira F, Carvalho T, Pinto-Neves D, Guegan F, Aresta-Branco F, Bento F, Young SA, Pinto A, Van Den Abbeele J, Ribeiro RM, Dias S, Smith TK, Figueiredo LM. Trypanosoma brucei Parasites Occupy and Functionally Adapt to the Adipose Tissue in Mice. Cell Host & Microbe. PMID 27237364 DOI: 10.1016/J.Chom.2016.05.002  1
2016 Banerjee S, Guedj J, Ribeiro RM, Moses M, Perelson AS. Estimating biologically relevant parameters under uncertainty for experimental within-host murine West Nile virus infection. Journal of the Royal Society, Interface / the Royal Society. 13. PMID 27075003 DOI: 10.1098/Rsif.2016.0130  1
2016 Castro M, Lythe G, Molina-París C, Ribeiro RM. Mathematics in modern immunology. Interface Focus. 6: 20150093. PMID 27051512 DOI: 10.1098/Rsfs.2015.0093  1
2016 Pandrea I, Xu C, Stock JL, Frank DN, Ma D, Policicchio BB, He T, Kristoff J, Cornell E, Haret-Richter GS, Trichel A, Ribeiro RM, Tracy R, Wilson C, Landay AL, et al. Antibiotic and Antiinflammatory Therapy Transiently Reduces Inflammation and Hypercoagulation in Acutely SIV-Infected Pigtailed Macaques. Plos Pathogens. 12: e1005384. PMID 26764484 DOI: 10.1371/Journal.Ppat.1005384  1
2015 Andrade A, Guedj J, Rosenkranz SL, Lu D, Mellors J, Kuritzkes DR, Perelson AS, Ribeiro RM. Early HIV RNA decay during raltegravir-containing regimens exhibits two distinct subphases (1a and 1b). Aids (London, England). 29: 2419-26. PMID 26558541 DOI: 10.1097/Qad.0000000000000843  1
2015 Li H, Stoddard M, Wang S, Giorgi EE, Blair L, Learn G, Hahn B, Alter H, Busch M, Fierer D, Ribeiro RM, Perelson AS, Bhattacharya T, Shaw GM. Single Genome Sequencing of Hepatitis C Virus in Donor-Recipient Pairs Distinguishes Modes and Models of Virus Transmission and Early Diversification. Journal of Virology. PMID 26468546 DOI: 10.1128/Jvi.02156-15  1
2015 Yue L, Pfafferott KJ, Baalwa J, Conrod K, Dong CC, Chui C, Rong R, Claiborne DT, Prince JL, Tang J, Ribeiro RM, Cormier E, Hahn BH, Perelson AS, Shaw GM, et al. Transmitted virus fitness and host T cell responses collectively define divergent infection outcomes in two HIV-1 recipients. Plos Pathogens. 11: e1004565. PMID 25569444 DOI: 10.1371/Journal.Ppat.1004565  1
2014 Graw F, Balagopal A, Kandathil AJ, Ray SC, Thomas DL, Ribeiro RM, Perelson AS. Inferring viral dynamics in chronically HCV infected patients from the spatial distribution of infected hepatocytes. Plos Computational Biology. 10: e1003934. PMID 25393308 DOI: 10.1371/Journal.Pcbi.1003934  1
2014 Ciupe SM, Ribeiro RM, Perelson AS. Antibody responses during hepatitis B viral infection. Plos Computational Biology. 10: e1003730. PMID 25078553 DOI: 10.1371/Journal.Pcbi.1003730  1
2014 Kristoff J, Haret-Richter G, Ma D, Ribeiro RM, Xu C, Cornell E, Stock JL, He T, Mobley AD, Ross S, Trichel A, Wilson C, Tracy R, Landay A, Apetrei C, et al. Early microbial translocation blockade reduces SIV-mediated inflammation and viral replication. The Journal of Clinical Investigation. 124: 2802-6. PMID 24837437 DOI: 10.1172/Jci75090  1
2013 Caridade M, Graca L, Ribeiro RM. Mechanisms Underlying CD4+ Treg Immune Regulation in the Adult: From Experiments to Models. Frontiers in Immunology. 4: 378. PMID 24302924 DOI: 10.3389/Fimmu.2013.00378  1
2013 Caridade M, Oliveira VG, Agua-Doce A, Graca L, Ribeiro RM. The fate of CD4+ T cells under tolerance-inducing stimulation: a modeling perspective. Immunology and Cell Biology. 91: 652-60. PMID 24145855 DOI: 10.1038/Icb.2013.63  1
2013 Wijewardana V, Kristoff J, Xu C, Ma D, Haret-Richter G, Stock JL, Policicchio BB, Mobley AD, Nusbaum R, Aamer H, Trichel A, Ribeiro RM, Apetrei C, Pandrea I. Kinetics of myeloid dendritic cell trafficking and activation: impact on progressive, nonprogressive and controlled SIV infections. Plos Pathogens. 9: e1003600. PMID 24098110 DOI: 10.1371/Journal.Ppat.1003600  1
2013 Perelson AS, Ribeiro RM. Modeling the within-host dynamics of HIV infection. Bmc Biology. 11: 96. PMID 24020860 DOI: 10.1186/1741-7007-11-96  1
2013 Kandathil AJ, Graw F, Quinn J, Hwang HS, Torbenson M, Perelson AS, Ray SC, Thomas DL, Ribeiro RM, Balagopal A. Use of laser capture microdissection to map hepatitis C virus-positive hepatocytes in human liver. Gastroenterology. 145: 1404-13.e1-10. PMID 23973767 DOI: 10.1053/J.Gastro.2013.08.034  1
2013 Smith AM, Adler FR, Ribeiro RM, Gutenkunst RN, McAuley JL, McCullers JA, Perelson AS. Kinetics of coinfection with influenza A virus and Streptococcus pneumoniae. Plos Pathogens. 9: e1003238. PMID 23555251 DOI: 10.1371/Journal.Ppat.1003238  1
2013 Arazi A, Pendergraft WF, Ribeiro RM, Perelson AS, Hacohen N. Human systems immunology: hypothesis-based modeling and unbiased data-driven approaches. Seminars in Immunology. 25: 193-200. PMID 23375135 DOI: 10.1016/J.Smim.2012.11.003  1
2013 Portêlo A, Lemos JM, Vinga S, Ribeiro RM, Cruz JP, Valadas E. Parameter estimation and identifiability of a HIV-1 model 2013 21st Mediterranean Conference On Control and Automation, Med 2013 - Conference Proceedings. 691-696. DOI: 10.1109/MED.2013.6608798  1
2012 Ribeiro RM, Li H, Wang S, Stoddard MB, Learn GH, Korber BT, Bhattacharya T, Guedj J, Parrish EH, Hahn BH, Shaw GM, Perelson AS. Quantifying the diversification of hepatitis C virus (HCV) during primary infection: estimates of the in vivo mutation rate. Plos Pathogens. 8: e1002881. PMID 22927817 DOI: 10.1371/Journal.Ppat.1002881  1
2012 Li H, Stoddard MB, Wang S, Blair LM, Giorgi EE, Parrish EH, Learn GH, Hraber P, Goepfert PA, Saag MS, Denny TN, Haynes BF, Hahn BH, Ribeiro RM, Perelson AS, et al. Elucidation of hepatitis C virus transmission and early diversification by single genome sequencing. Plos Pathogens. 8: e1002880. PMID 22927816 DOI: 10.1371/Journal.Ppat.1002880  1
2012 Graw F, Leitner T, Ribeiro RM. Agent-based and phylogenetic analyses reveal how HIV-1 moves between risk groups: injecting drug users sustain the heterosexual epidemic in Latvia. Epidemics. 4: 104-16. PMID 22664069 DOI: 10.1016/J.Epidem.2012.04.002  1
2012 Pandrea I, Cornell E, Wilson C, Ribeiro RM, Ma D, Kristoff J, Xu C, Haret-Richter GS, Trichel A, Apetrei C, Landay A, Tracy R. Coagulation biomarkers predict disease progression in SIV-infected nonhuman primates Blood. 120: 1357-1366. PMID 22653975 DOI: 10.1182/Blood-2012-03-414706  1
2012 Rong L, Ribeiro RM, Perelson AS. Modeling quasispecies and drug resistance in hepatitis C patients treated with a protease inhibitor. Bulletin of Mathematical Biology. 74: 1789-817. PMID 22639338 DOI: 10.1007/S11538-012-9736-Y  1
2012 De Boer RJ, Perelson AS, Ribeiro RM. Modelling deuterium labelling of lymphocytes with temporal and/or kinetic heterogeneity. Journal of the Royal Society, Interface / the Royal Society. 9: 2191-200. PMID 22513720 DOI: 10.1098/Rsif.2012.0149  1
2012 Ribeiro RM. Quantifying the activity of anti-HIV treatment in silico. Nature Medicine. 18: 355-6. PMID 22395700 DOI: 10.1038/Nm.2698  1
2012 Apetrei C, Sumpter B, Souquiere S, Chahroudi A, Makuwa M, Reed P, Ribeiro RM, Pandrea I, Roques P, Silvestri G. Immunovirological analyses of chronically simian immunodeficiency virus: SIVmnd-1- and SIVmnd-2-infected mandrills (Mandrillus sphinx) Journal of Virology. 86: 1900. DOI: 10.1128/JVI.07026-11  1
2011 Apetrei C, Sumpter B, Souquiere S, Chahroudi A, Makuwa M, Reed P, Ribeiro RM, Pandrea I, Roques P, Silvestri G. Immunovirological analyses of chronically simian immunodeficiency virus SIVmnd-1- and SIVmnd-2-infected mandrills (Mandrillus sphinx). Journal of Virology. 85: 13077-87. PMID 21957286 DOI: 10.1128/Jvi.05693-11  1
2011 Pandrea I, Gaufin T, Gautam R, Kristoff J, Mandell D, Montefiori D, Keele BF, Ribeiro RM, Veazey RS, Apetrei C. 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. 7: e1002170. PMID 21829366 DOI: 10.1371/Journal.Ppat.1002170  1
2011 Wang D, Hicks CB, Goswami ND, Tafoya E, Ribeiro RM, Cai F, Perelson AS, Gao F. Evolution of drug-resistant viral populations during interruption of antiretroviral therapy. Journal of Virology. 85: 6403-15. PMID 21490094 DOI: 10.1128/Jvi.02389-10  1
2011 Smith AM, Adler FR, McAuley JL, Gutenkunst RN, Ribeiro RM, McCullers JA, Perelson AS. Effect of 1918 PB1-F2 expression on influenza A virus infection kinetics. Plos Computational Biology. 7: e1001081. PMID 21379324 DOI: 10.1371/Journal.Pcbi.1001081  1
2010 Ribeiro RM, Germanidis G, Powers KA, Pellegrin B, Nikolaidis P, Perelson AS, Pawlotsky JM. Hepatitis B virus kinetics under antiviral therapy sheds light on differences in hepatitis B e antigen positive and negative infections. The Journal of Infectious Diseases. 202: 1309-18. PMID 20874517 DOI: 10.1086/656528  1
2010 De Boer RJ, Ribeiro RM, Perelson AS. Current estimates for HIV-1 production imply rapid viral clearance in lymphoid tissues. Plos Computational Biology. 6: e1000906. PMID 20824126 DOI: 10.1371/Journal.Pcbi.1000906  1
2010 Gaufin T, Ribeiro RM, Gautam R, Dufour J, Mandell D, Apetrei C, Pandrea I. Experimental depletion of CD8+ cells in acutely SIVagm-infected African Green Monkeys results in increased viral replication. Retrovirology. 7: 42. PMID 20459829 DOI: 10.1186/1742-4690-7-42  1
2010 Rong L, Dahari H, Ribeiro RM, Perelson AS. Rapid emergence of protease inhibitor resistance in hepatitis C virus. Science Translational Medicine. 2: 30ra32. PMID 20445200 DOI: 10.1126/Scitranslmed.3000544  1
2010 Tatebe K, Zeytun A, Ribeiro RM, Hoffmann R, Harrod KS, Forst CV. Response network analysis of differential gene expression in human epithelial lung cells during avian influenza infections. Bmc Bioinformatics. 11: 170. PMID 20370926 DOI: 10.1186/1471-2105-11-170  0.01
2010 Smith AM, Ribeiro RM. Modeling the viral dynamics of influenza A virus infection. Critical Reviews in Immunology. 30: 291-8. PMID 20370636 DOI: 10.1615/Critrevimmunol.V30.I3.60  1
2010 Ribeiro RM, Qin L, Chavez LL, Li D, Self SG, Perelson AS. Estimation of the initial viral growth rate and basic reproductive number during acute HIV-1 infection. Journal of Virology. 84: 6096-102. PMID 20357090 DOI: 10.1128/Jvi.00127-10  1
2010 Vaidya NK, Ribeiro RM, Miller CJ, Perelson AS. Viral dynamics during primary simian immunodeficiency virus infection: effect of time-dependent virus infectivity. Journal of Virology. 84: 4302-10. PMID 20147390 DOI: 10.1128/Jvi.02284-09  1
2010 Klatt NR, Shudo E, Ortiz AM, Engram JC, Paiardini M, Lawson B, Miller MD, Else J, Pandrea I, Estes JD, Apetrei C, Schmitz JE, Ribeiro RM, Perelson AS, Silvestri G. CD8+ lymphocytes control viral replication in SIVmac239-infected rhesus macaques without decreasing the lifespan of productively infected cells. Plos Pathogens. 6: e1000747. PMID 20126441 DOI: 10.1371/Journal.Ppat.1000747  1
2009 Maljkovic Berry I, Athreya G, Kothari M, Daniels M, Bruno WJ, Korber B, Kuiken C, Ribeiro RM, Leitner T. 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. 1: 230-9. PMID 21352769 DOI: 10.1016/J.Epidem.2009.10.003  1
2009 Weinberger AD, Perelson AS, Ribeiro RM, Weinberger LS. Accelerated immunodeficiency by anti-CCR5 treatment in HIV infection. Plos Computational Biology. 5: e1000467. PMID 19680436 DOI: 10.1371/Journal.Pcbi.1000467  1
2009 Gaufin T, Pattison M, Gautam R, Stoulig C, Dufour J, MacFarland J, Mandell D, Tatum C, Marx MH, Ribeiro RM, Montefiori D, Apetrei C, Pandrea I. Effect of B-cell depletion on viral replication and clinical outcome of simian immunodeficiency virus infection in a natural host. Journal of Virology. 83: 10347-57. PMID 19656874 DOI: 10.1128/Jvi.00880-09  1
2009 Hasegawa A, Liu H, Ling B, Borda JT, Alvarez X, Sugimoto C, Vinet-Oliphant H, Kim WK, Williams KC, Ribeiro RM, Lackner AA, Veazey RS, Kuroda MJ. The level of monocyte turnover predicts disease progression in the macaque model of AIDS. Blood. 114: 2917-25. PMID 19383966 DOI: 10.1182/Blood-2009-02-204263  1
2009 Shudo E, Ribeiro RM, Perelson AS. Modeling HCV kinetics under therapy using PK and PD information. Expert Opinion On Drug Metabolism & Toxicology. 5: 321-32. PMID 19331594 DOI: 10.1517/17425250902787616  1
2009 Dahari H, Layden-Almer JE, Kallwitz E, Ribeiro RM, Cotler SJ, Layden TJ, Perelson AS. A mathematical model of hepatitis C virus dynamics in patients with high baseline viral loads or advanced liver disease. Gastroenterology. 136: 1402-9. PMID 19208338 DOI: 10.1053/J.Gastro.2008.12.060  1
2009 Gaufin T, Gautam R, Kasheta M, Ribeiro R, Ribka E, Barnes M, Pattison M, Tatum C, MacFarland J, Montefiori D, Kaur A, Pandrea I, Apetrei C. Limited ability of humoral immune responses in control of viremia during infection with SIVsmmD215 strain. Blood. 113: 4250-61. PMID 19168789 DOI: 10.1182/Blood-2008-09-177741  1
2009 Davenport MP, Belz GT, Ribeiro RM. The race between infection and immunity: how do pathogens set the pace? Trends in Immunology. 30: 61-6. PMID 19138564 DOI: 10.1016/J.It.2008.11.001  1
2009 Schlub TE, Venturi V, Kedzierska K, Wellard C, Doherty PC, Turner SJ, Ribeiro RM, Hodgkin PD, Davenport MP. Division-linked differentiation can account for CD8+ T-cell phenotype in vivo. European Journal of Immunology. 39: 67-77. PMID 19130548 DOI: 10.1002/Eji.200838554  1
2009 Lay MD, Zhang L, Ribeiro RM, Mueller SN, Belz GT, Davenport MP. Kinetics of major histocompatibility class I antigen presentation in acute infection. Journal of Immunology (Baltimore, Md. : 1950). 182: 902-11. PMID 19124733 DOI: 10.4049/Jimmunol.182.2.902  1
2009 Lewin SR, Ribeiro RM, Avihingsanon A, Bowden S, Matthews G, Marks P, Locarnini SA, Ruxrungtham K, Perelson AS, Dore GJ. 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.). 49: 1113-21. PMID 19115219 DOI: 10.1002/Hep.22754  0.04
2009 Dahari H, Shudo E, Ribeiro RM, Perelson AS. Modeling complex decay profiles of hepatitis B virus during antiviral therapy. Hepatology (Baltimore, Md.). 49: 32-8. PMID 19065674 DOI: 10.1002/Hep.22586  1
2009 Dahari H, Shudo E, Ribeiro RM, Perelson AS. Mathematical modeling of HCV infection and treatment. Methods in Molecular Biology (Clifton, N.J.). 510: 439-53. PMID 19009281 DOI: 10.1007/978-1-59745-394-3_33  1
2008 Shudo E, Ribeiro RM, Talal AH, Perelson AS. A hepatitis C viral kinetic model that allows for time-varying drug effectiveness. Antiviral Therapy. 13: 919-26. PMID 19043926  1
2008 Pandrea I, Gaufin T, Brenchley JM, Gautam R, Monjure C, Gautam A, Coleman C, Lackner AA, Ribeiro RM, Douek DC, Apetrei C. 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 (Baltimore, Md. : 1950). 181: 6687-91. PMID 18981083 DOI: 10.4049/Jimmunol.181.10.6687  1
2008 Petravic J, Ribeiro RM, Casimiro DR, Mattapallil JJ, Roederer M, Shiver JW, Davenport MP. Estimating the impact of vaccination on acute simian-human immunodeficiency virus/simian immunodeficiency virus infections. Journal of Virology. 82: 11589-98. PMID 18799584 DOI: 10.1128/Jvi.01596-08  1
2008 Chavez LL, Davenport MP, Shiver JW, Tussey LG, Cox KS, Bachinsky M, Wang F, Huang L, Schleif WA, Davies ME, Tang A, Casimiro DR, Perelson AS, Ribeiro RM. The effect of early versus delayed challenge after vaccination in controlling SHIV 89.6P infection. Virology. 381: 75-80. PMID 18793788 DOI: 10.1016/J.Virol.2008.07.042  1
2008 Ribeiro RM, de Boer RJ. The contribution of the thymus to the recovery of peripheral naive T-cell numbers during antiretroviral treatment for HIV infection. Journal of Acquired Immune Deficiency Syndromes (1999). 49: 1-8. PMID 18667918 DOI: 10.1097/Qai.0B013E318184Fb28  1
2008 Beauchemin CA, McSharry JJ, Drusano GL, Nguyen JT, Went GT, Ribeiro RM, Perelson AS. Modeling amantadine treatment of influenza A virus in vitro. Journal of Theoretical Biology. 254: 439-51. PMID 18653201 DOI: 10.1016/J.Jtbi.2008.05.031  1
2008 Bettencourt LM, Ribeiro RM. Real time bayesian estimation of the epidemic potential of emerging infectious diseases. Plos One. 3: e2185. PMID 18478118 DOI: 10.1371/Journal.Pone.0002185  1
2008 Shudo E, Ribeiro RM, Perelson AS. Modelling hepatitis C virus kinetics during treatment with pegylated interferon α-2b: Errors in the estimation of viral kinetic parameters Journal of Viral Hepatitis. 15: 357-362. PMID 18380660 DOI: 10.1111/J.1365-2893.2007.00954.X  1
2008 Shudo E, Ribeiro RM, Perelson AS. Modelling the kinetics of hepatitis C virus RNA decline over 4 weeks of treatment with pegylated interferon α-2b Journal of Viral Hepatitis. 15: 379-382. PMID 18266841 DOI: 10.1111/J.1365-2893.2008.00977.X  1
2008 Pandrea I, Ribeiro RM, Gautam R, Gaufin T, Pattison M, Barnes M, Monjure C, Stoulig C, Dufour J, Cyprian W, Silvestri G, Miller MD, Perelson AS, Apetrei C. Simian immunodeficiency virus SIVagm dynamics in African green monkeys. Journal of Virology. 82: 3713-24. PMID 18216122 DOI: 10.1128/Jvi.02402-07  1
2008 Kaur A, Di Mascio M, Barabasz A, Rosenzweig M, McClure HM, Perelson AS, Ribeiro RM, Johnson RP. Dynamics of T- and B-lymphocyte turnover in a natural host of simian immunodeficiency virus. Journal of Virology. 82: 1084-93. PMID 18032490 DOI: 10.1128/Jvi.02197-07  1
2008 Perelson AS, Ribeiro RM. Estimating drug efficacy and viral dynamic parameters: HIV and HCV. Statistics in Medicine. 27: 4647-57. PMID 17960579 DOI: 10.1002/Sim.3116  1
2007 Lau GK, Cooksley H, Ribeiro RM, Powers KA, Shudo E, Bowden S, Hui CK, Anderson J, Sorbel J, Mondou E, Rousseau F, Lewin S, Perelson AS, Locornini S, Naoumov NV. Impact of early viral kinetics on T-cell reactivity during antiviral therapy in chronic hepatitis B. Antiviral Therapy. 12: 705-18. PMID 17713154  1
2007 Pandrea IV, Gautam R, Ribeiro RM, Brenchley JM, Butler IF, Pattison M, Rasmussen T, Marx PA, Silvestri G, Lackner AA, Perelson AS, Douek DC, Veazey RS, Apetrei C. Acute loss of intestinal CD4+ T cells is not predictive of simian immunodeficiency virus virulence. Journal of Immunology (Baltimore, Md. : 1950). 179: 3035-46. PMID 17709518 DOI: 10.4049/Jimmunol.179.5.3035  1
2007 Maljkovic Berry I, Ribeiro R, Kothari M, Athreya G, Daniels M, Lee HY, Bruno W, Leitner T. Unequal evolutionary rates in the human immunodeficiency virus type 1 (HIV-1) pandemic: the evolutionary rate of HIV-1 slows down when the epidemic rate increases. Journal of Virology. 81: 10625-35. PMID 17634235 DOI: 10.1128/Jvi.00985-07  1
2007 Dahari H, Ribeiro RM, Perelson AS. Triphasic decline of hepatitis C virus RNA during antiviral therapy. Hepatology (Baltimore, Md.). 46: 16-21. PMID 17596864 DOI: 10.1002/Hep.21657  1
2007 Dahari H, Lo A, Ribeiro RM, Perelson AS. Modeling hepatitis C virus dynamics: liver regeneration and critical drug efficacy. Journal of Theoretical Biology. 247: 371-81. PMID 17451750 DOI: 10.1016/J.Jtbi.2007.03.006  1
2007 Ciupe SM, Ribeiro RM, Nelson PW, Perelson AS. Modeling the mechanisms of acute hepatitis B virus infection. Journal of Theoretical Biology. 247: 23-35. PMID 17428501 DOI: 10.1016/J.Jtbi.2007.02.017  1
2007 Dahari H, Markatou M, Zeremski M, Haller I, Ribeiro RM, Licholai T, Perelson AS, Talal AH. 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. 47: 23-30. PMID 17412448 DOI: 10.1016/J.Jhep.2007.01.027  1
2007 Ribeiro RM. Dynamics of CD4+ T cells in HIV-1 infection. Immunology and Cell Biology. 85: 287-94. PMID 17389869 DOI: 10.1038/Sj.Icb.7100056  1
2007 Davenport MP, Ribeiro RM, Zhang L, Wilson DP, Perelson AS. Understanding the mechanisms and limitations of immune control of HIV. Immunological Reviews. 216: 164-75. PMID 17367342 DOI: 10.1111/J.1600-065X.2006.00485.X  1
2007 Ribeiro RM, Perelson AS. Determining thymic output quantitatively: using models to interpret experimental T-cell receptor excision circle (TREC) data. Immunological Reviews. 216: 21-34. PMID 17367332 DOI: 10.1111/J.1600-065X.2006.00493.X  1
2007 Ciupe SM, Ribeiro RM, Nelson PW, Dusheiko G, Perelson AS. 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. 104: 5050-5. PMID 17360406 DOI: 10.1073/Pnas.0603626104  1
2007 Dahari H, Ribeiro RM, Rice CM, Perelson AS. Mathematical modeling of subgenomic hepatitis C virus replication in Huh-7 cells. Journal of Virology. 81: 750-60. PMID 17035310 DOI: 10.1128/Jvi.01304-06  1
2007 Bettencourt LMA, Ribeiro RM, Chowell G, Lant T, Castillo-Chavez C. Towards real time epidemiology: Data assimilation, modeling and anomaly detection of health surveillance data streams Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4506: 79-90.  1
2006 Talal AH, Ribeiro RM, Powers KA, Grace M, Cullen C, Hussain M, Markatou M, Perelson AS. Pharmacodynamics of PEG-IFN alpha differentiate HIV/HCV coinfected sustained virological responders from nonresponders. Hepatology (Baltimore, Md.). 43: 943-53. PMID 16761329 DOI: 10.1002/Hep.21136  1
2006 Davenport MP, Zhang L, Shiver JW, Casmiro DR, Ribeiro RM, Perelson AS. Influence of peak viral load on the extent of CD4+ T-cell depletion in simian HIV infection. Journal of Acquired Immune Deficiency Syndromes (1999). 41: 259-65. PMID 16540926 DOI: 10.1097/01.Qai.0000199232.31340.D3  1
2006 Wang Z, Metcalf B, Ribeiro RM, McClure H, Kaur A. 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. 80: 2771-83. PMID 16501086 DOI: 10.1128/Jvi.80.6.2771-2783.2006  1
2006 Powers KA, Ribeiro RM, Patel K, Pianko S, Nyberg L, Pockros P, Conrad AJ, McHutchison J, Perelson AS. Kinetics of hepatitis C virus reinfection after liver transplantation. Liver Transplantation : Official Publication of the American Association For the Study of Liver Diseases and the International Liver Transplantation Society. 12: 207-16. PMID 16447184 DOI: 10.1002/Lt.20572  1
2006 Ribeiro RM, Hazenberg MD, Perelson AS, Davenport MP. Naïve and memory cell turnover as drivers of CCR5-to-CXCR4 tropism switch in human immunodeficiency virus type 1: implications for therapy. Journal of Virology. 80: 802-9. PMID 16378982 DOI: 10.1128/Jvi.80.2.802-809.2006  1
2006 Dahari H, Ribeiro RM, Rice CM, Perelson AS. 739 Mathematical modeling of subgenomic hepatitis C viral replication in HUH-7 cells Journal of Hepatology. 44. DOI: 10.1016/S0168-8278(06)80740-3  1
2005 Layden-Almer JE, Kuiken C, Ribeiro RM, Kunstman KJ, Perelson AS, Layden TJ, Wolinsky SM. Hepatitis C virus genotype 1a NS5A pretreatment sequence variation and viral kinetics in African American and white patients. The Journal of Infectious Diseases. 192: 1078-87. PMID 16107963 DOI: 10.1086/432760  1
2005 Perelson AS, Ribeiro RM. Mutagenic effects of ribavirin in vivo. Journal of Hepatology. 43: 553-5. PMID 16099528 DOI: 10.1016/J.Jhep.2005.07.003  1
2005 Davenport MP, Zhang L, Bagchi A, Fridman A, Fu TM, Schleif W, Shiver JW, Ribeiro RM, Perelson AS. High-potency human immunodeficiency virus vaccination leads to delayed and reduced CD8+ T-cell expansion but improved virus control. Journal of Virology. 79: 10059-62. PMID 16014966 DOI: 10.1128/Jvi.79.15.10059-10062.2005  1
2005 Arron ST, Ribeiro RM, Gettie A, Bohm R, Blanchard J, Yu J, Perelson AS, Ho DD, 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: 46-55. PMID 15593297 DOI: 10.1002/Eji.200424996  1
2005 Ribeiro RM, Dixit NM, Perelson AS. 13 Modelling the in vivo growth rate of HIV: implications for vaccination Studies in Multidisciplinarity. 3: 231-246. DOI: 10.1016/S1571-0831(06)80017-1  1
2004 Davenport MP, Ribeiro RM, Chao DL, Perelson AS. Predicting the impact of a nonsterilizing vaccine against human immunodeficiency virus. Journal of Virology. 78: 11340-51. PMID 15452255 DOI: 10.1128/Jvi.78.20.11340-11351.2004  1
2004 Davenport MP, Ribeiro RM, Perelson AS. Kinetics of virus-specific CD8+ T cells and the control of human immunodeficiency virus infection. Journal of Virology. 78: 10096-103. PMID 15331742 DOI: 10.1128/Jvi.78.18.10096-10103.2004  1
2004 Perelson AS, Ribeiro RM. Hepatitis B virus kinetics and mathematical modeling. Seminars in Liver Disease. 24: 11-6. PMID 15192796 DOI: 10.1055/S-2004-828673  1
2004 Zhang L, Ribeiro RM, Mascola JR, Lewis MG, Stiegler G, Katinger H, Perelson AS, Davenport MP. Effects of antibody on viral kinetics in simian/human immunodeficiency virus infection: implications for vaccination. Journal of Virology. 78: 5520-2. PMID 15113932 DOI: 10.1128/Jvi.78.10.5520-5522.2004  1
2004 Elson K, Ribeiro RM, Perelson AS, Simmons A, Speck P. The life span of ganglionic glia in murine sensory ganglia estimated by uptake of bromodeoxyuridine. Experimental Neurology. 186: 99-103. PMID 14980814 DOI: 10.1016/J.Expneurol.2003.10.017  1
2004 Di Mascio M, Ribeiro RM, Markowitz M, Ho DD, Perelson AS. Modeling the long-term control of viremia in HIV-1 infected patients treated with antiretroviral therapy. Mathematical Biosciences. 188: 47-62. PMID 14766093 DOI: 10.1016/J.Mbs.2003.08.003  1
2004 Talal AH, Shata MT, Markatou M, Dorante G, Chadburn A, Koch R, Neumann AU, Ribeiro RM, Perelson AS. Virus dynamics and immune responses during treatment in patients coinfected with hepatitis C and HIV. Journal of Acquired Immune Deficiency Syndromes (1999). 35: 103-13. PMID 14722440 DOI: 10.1097/00126334-200402010-00001  1
2004 Ramratnam B, Ribeiro R, He T, Chung C, Simon V, Vanderhoeven J, Hurley A, Zhang L, Perelson AS, Ho DD, Markowitz M. 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: 33-37. PMID 14707789 DOI: 10.1097/00126334-200401010-00004  1
2004 Ribeiro RM, Perelson AS. The Analysis of HIV Dynamics Using Mathematical Models Aids and Other Manifestations of Hiv Infection. 905-912. DOI: 10.1016/B978-012764051-8/50037-8  1
2003 Torriani FJ, Ribeiro RM, Gilbert TL, Schrenk UM, Clauson M, Pacheco DM, Perelson AS. Hepatitis C virus (HCV) and human immunodeficiency virus (HIV) dynamics during HCV treatment in HCV/HIV coinfection. The Journal of Infectious Diseases. 188: 1498-507. PMID 14624375 DOI: 10.1086/379255  1
2003 Korthals Altes H, Ribeiro RM, De Boer RJ. 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: 1349-1358. PMID 12965025 DOI: 10.1098/Rspb.2003.2377  1
2003 Powers KA, Dixit NM, Ribeiro RM, Golia P, Talal AH, Perelson AS. Modeling viral and drug kinetics: hepatitis C virus treatment with pegylated interferon alfa-2b. Seminars in Liver Disease. 23: 13-8. PMID 12934163 DOI: 10.1055/S-2003-41630  1
2003 Ribeiro RM, Layden-Almer J, Powers KA, Layden TJ, Perelson AS. Dynamics of alanine aminotransferase during hepatitis C virus treatment. Hepatology (Baltimore, Md.). 38: 509-17. PMID 12883496 DOI: 10.1053/Jhep.2003.50344  1
2003 Layden-Almer JE, Ribeiro RM, Wiley T, Perelson AS, Layden TJ. Viral dynamics and response differences in HCV-infected African American and white patients treated with IFN and ribavirin. Hepatology (Baltimore, Md.). 37: 1343-50. PMID 12774013 DOI: 10.1053/Jhep.2003.50217  1
2003 Layden TJ, Layden JE, Ribeiro RM, Perelson AS. Mathematical modeling of viral kinetics: a tool to understand and optimize therapy. Clinics in Liver Disease. 7: 163-78. PMID 12691465 DOI: 10.1016/S1089-3261(02)00063-6  1
2003 Lau G, Cooksley H, Mondou E, Brosgart C, Lewin S, Perelson A, Bowden S, Powers K, Ribeiro R, Locarnini S. 1160 Analysis of early viral kinetics and T-cell reactivity in relation to HBEAG seroconversion during the first 12 weeks of antiviral therapy for chronic hepatitis B Hepatology. 38: 715-715. DOI: 10.1016/S0270-9139(03)81198-9  1
2003 Golia P, Powers K, Dorante G, Cunningham-Rundles S, Ribeiro R, Shata MT, Perelson AS, Talal AH. 385 Pharmacodynamics and pharmacokinetics of hepatitis C virus (HCV) and pegylated interferon-alfa2B in human immunodeficiency virus (HIV)/HCV co-infected patients Hepatology. 38: 345-345. DOI: 10.1016/S0270-9139(03)80428-7  1
2002 Ribeiro RM, Mohri H, Ho DD, Perelson AS. 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: 15572-7. PMID 12434018 DOI: 10.1073/Pnas.242358099  1
2002 Lewin SR, Ribeiro RM, Kaufmann GR, Smith D, Zaunders J, Law M, Solomon A, Cameron PU, Cooper D, Perelson AS. Dynamics of T cells and TCR excision circles differ after treatment of acute and chronic HIV infection. Journal of Immunology (Baltimore, Md. : 1950). 169: 4657-66. PMID 12370406 DOI: 10.4049/Jimmunol.169.8.4657  1
2002 Ribeiro RM, Lo A, Perelson AS. Dynamics of hepatitis B virus infection. Microbes and Infection / Institut Pasteur. 4: 829-35. PMID 12270730 DOI: 10.1016/S1286-4579(02)01603-9  1
2002 Ribeiro RM, Perelson AS. Hepatitis B virus viral dynamics: effects of drug dose and baseline alanine aminotransferase. Journal of Hepatology. 37: 277-9. PMID 12127436 DOI: 10.1016/S0168-8278(02)00210-6  1
2002 Ribeiro RM, Mohri H, Ho DD, Perelson AS. Modeling deuterated glucose labeling of T-lymphocytes. Bulletin of Mathematical Biology. 64: 385-405. PMID 11926122 DOI: 10.1006/Bulm.2001.0282  1
2001 Mohri H, Perelson AS, Tung K, Ribeiro RM, Ramratnam B, Markowitz M, Kost R, Hurley A, Weinberger L, Cesar D, Hellerstein MK, Ho DD. Increased turnover of T lymphocytes in HIV-1 infection and its reduction by antiretroviral therapy Journal of Experimental Medicine. 194: 1277-1287. PMID 11696593 DOI: 10.1084/Jem.194.9.1277  1
2001 Lewin SR, Ribeiro RM, Walters T, Lau GK, Bowden S, Locarnini S, Perelson AS. Analysis of hepatitis B viral load decline under potent therapy: Complex decay profiles observed Hepatology. 34: 1012-1020. PMID 11679973 DOI: 10.1053/Jhep.2001.28509  1
2001 Roberts DE, Ribeiro RM. Comparison of different treatment regimens for the emergence of new resistance under therapy. Journal of Acquired Immune Deficiency Syndromes (1999). 27: 331-5. PMID 11468420 DOI: 10.1097/00126334-200108010-00002  1
2001 Locarnini S, Walters T, Lewin SR, Bowden S, Lau G, Ribeiro R, Perelson A. Hepatitis B virion (HBV) clearance is extremely rapid in a sub-set of chronically infected individuals Journal of Hepatology. 34: 124. DOI: 10.1016/S0168-8278(01)81323-4  1
2000 Ribeiro RM, Bonhoeffer S. Production of resistant HIV mutants during antiretroviral therapy Proceedings of the National Academy of Sciences of the United States of America. 97: 7681-7686. PMID 10884399 DOI: 10.1073/Pnas.97.14.7681  1
1999 Callaway DS, Ribeiro RM, Nowak MA. Virus phenotype switching and disease progression in HIV-1 infection. Proceedings. Biological Sciences / the Royal Society. 266: 2523-30. PMID 10693824 DOI: 10.1098/Rspb.1999.0955  1
1999 Ribeiro RM, Bonhoeffer S. A stochastic model for primary HIV infection: Optimal timing of therapy Aids. 13: 351-357. PMID 10199225 DOI: 10.1097/00002030-199902250-00007  1
1998 Ribeiro RM, Bonhoeffer S, Nowak MA. The frequency of resistant mutant virus before antiviral therapy Aids. 12: 461-465. PMID 9543443 DOI: 10.1097/00002030-199805000-00006  1
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