2021 – Research Director at French National Institute of Health (INSERM)

2012-2021 Researcher at INSERM

2009 – 2012 Postdoctoral research fellow
Supervision : Pr. Alan S. Perelson
Theoretical Biology & Biophysics, Los Alamos National Laboratory, NM, USA

2007 – 2009 Postdoctoral research fellow
Supervision : Pr. Avidan U. Neumann
Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University. Tel-Aviv, Israel

2003-2006 PhD in biostatistics
Supervision : Dr. Rodolphe Thiébaut & Pr. Daniel Commenges
Institut de Santé Publique, d’Epidémiologie et de Developpement (ISPED), Bordeaux, France.

Néant N, Lingas G, Le Hingrat Q, Ghosn J, Engelmann I, Lepiller Q, Gaymard A, Ferré V, Hartard C, Plantier JC, Thibault V, Marlet J, Montes B, Bouiller K, Lescure FX, Timsit JF, Faure E, Poissy J, Chidiac C, Raffi F, Kimmoun A, Etienne M, Richard JC, Tattevin P, Garot D, Le Moing V, Bachelet D, Tardivon C, Duval X, Yazdanpanah Y, Mentré F, Laouénan C, Visseaux B, Guedj J, French COVID Cohort Investigators and French Cohort Study groups
Modeling SARS-CoV-2 viral kinetics and association with mortality in hospitalized patients from the French COVID cohort.
Proceedings of the National Academy of Sciences of the United States of America 2021, 118,

Gonçalves A, Maisonnasse P, Donati F, Albert M, Behillil S, Contreras V, Naninck T, Marlin R, Solas C, Pizzorno A, Lemaitre J, Kahlaoui N, Terrier O, Ho Tsong Fang R, Enouf V, Dereuddre-Bosquet N, Brisebarre A, Touret F, Chapon C, Hoen B, Lina B, Rosa Calatrava M, de Lamballerie X, Mentré F, Le Grand R, van der Werf S, Guedj J
SARS-CoV-2 viral dynamics in non-human primates.
PLoS computational biology 2021, 17, e1008785.

Maisonnasse P, Guedj J, Contreras V, Behillil S, Solas C, Marlin R, Naninck T, Pizzorno A, Lemaitre J, Gonçalves A, Kahlaoui N, Terrier O, Fang RHT, Enouf V, Dereuddre-Bosquet N, Brisebarre A, Touret F, Chapon C, Hoen B, Lina B, Calatrava MR, van der Werf S, de Lamballerie X, Le Grand R
Hydroxychloroquine use against SARS-CoV-2 infection in non-human primates.
Nature 2020, 585, 584-587.

Madelain V, Baize S, Jacquot F, Reynard S, Fizet A, Barron S, Solas C, Lacarelle B, Carbonnelle C, Mentré F, Raoul H, de Lamballerie X, Guedj J
Ebola viral dynamics in nonhuman primates provides insights into virus immuno-pathogenesis and antiviral strategies.
Nature Communications 2018, 9, 4013.

Guedj J, Piorkowski G, Jacquot F, Madelain V, Nguyen THT, Rodallec A, Gunther S, Carbonnelle C, Mentre F, Raoul H, de Lamballerie X
Antiviral efficacy of favipiravir against Ebola virus: A translational study in cynomolgus macaques.
PLoS Med 2018, 15, e1002535.

Desmée S, Mentré F, Veyrat-Follet C, Sébastien B, Guedj J
Using the SAEM algorithm for mechanistic joint models characterizing the relationship between nonlinear PSA kinetics and survival in prostate cancer patients.
Biometrics 2017, 73, 305-312.

Guedj J, Dahari H, Rong L, Sansone ND, Nettles RE, Cotler SJ, Layden TJ, Uprichard SL, Perelson AS
Modeling shows that the NS5A inhibitor daclatasvir has two modes of action and yields a shorter estimate of the hepatitis C virus half-life.
Proceedings of the National Academy of Sciences of the United States of America 2013, 110, 3991–3996.

2024

Lingas G, Planas D, Péré H, Porrot F, Guivel-Benhassine F, Staropoli I, Duffy D, Chapuis N, Gobeaux C, Veyer D, Delaugerre C, Le Goff J, Getten P, Hadjadj J, Bellino A, Parfait B, Treluyer JM, Schwartz O, Guedj J, Kernéis S, Terrier B
Neutralizing Antibody Levels as a Correlate of Protection Against SARS-CoV-2 Infection: A Modeling Analysis.
Clinical Pharmacology and Therapeutics 2024, 115, 86-94.

Gonçalves A, Marchand M, Chan P, Jin JY, Guedj J, Bruno R
Comparison of two-stage and joint TGI-OS modeling using data from six atezolizumab clinical studies in patients with metastatic non-small cell lung cancer.
CPT: pharmacometrics & systems pharmacology 2024, 13, 68-78.

Hites M, Lapique EL, Massonnaud CR, Belhadi D, Jamard S, Goehringer F, Danion F, Reignier J, de Castro N, Garot D, Lacombe K, Tolsma V, Faure E, Malvy D, Staub T, Courjon J, Cazenave-Roblot F, Dyrhol Riise AM, Leturnier P, Martin-Blondel G, Roger C, Akinosoglou K, Moing VL, Piroth L, Sellier P, Lescure X, Trøseid M, Clevenbergh P, Dalgard O, Gallien S, Gousseff M, Loubet P, Vardon-Bounes F, Visée C, Belkhir L, Botelho-Nevers É, Cabié A, Kotanidou A, Lanternier F, Rouveix-Nordon E, Silva S, Thiery G, Poignard P, Carcelain G, Diallo A, Mercier N, Terzic V, Bouscambert-Duchamp M, Gaymard A, Trabaud MA, Destras G, Josset L, Billard N, Han THL, Guedj J, Couffin-Cadiergues S, Dechanet A, Delmas C, Esperou H, Fougerou-Leurent C, Mestre SL, Métois A, Noret M, Bally I, Dergan-Dylon S, Tubiana S, Kalif O, Bergaud N, Leveau B, Eustace J, Greil R, Hajdu E, Halanova M, Paiva JA, Piekarska A, Rodriguez Baño J, Tonby K, Trojánek M, Tsiodras S, Unal S, Burdet C, Costagliola D, Yazdanpanah Y, Peiffer-Smadja N, Mentré F, Ader F, DisCoVeRy study group
Tixagevimab-cilgavimab (AZD7442) for the treatment of patients hospitalized with COVID-19 (DisCoVeRy): A phase 3, randomized, double-blind, placebo-controlled trial.
The Journal of Infection 2024, 88, 106120.

Passaes C, Desjardins D, Chapel A, Monceaux V, Lemaitre J, Mélard A, Perdomo-Celis F, Planchais C, Gourvès M, Dimant N, David A, Dereuddre-Bosquet N, Barrail-Tran A, Gouget H, Guillaume C, Relouzat F, Lambotte O, Guedj J, Müller-Trutwin M, Mouquet H, Rouzioux C, Avettand-Fenoël V, Le Grand R, Sáez-Cirión A
Early antiretroviral therapy favors post-treatment SIV control associated with the expansion of enhanced memory CD8+ T-cells.
Nature Communications 2024, 15, 178.

2023

El Messaoudi S, Lemenuel-Diot A, Gonçalves A, Guedj J
A Semi-mechanistic Model to Characterize the Long-Term Dynamics of Hepatitis B Virus Markers During Treatment With Lamivudine and Pegylated Interferon.
Clinical Pharmacology and Therapeutics 2023, 113, 390-400.

Chenane HR, Lingas G, Menidjel R, Laouenan C, Tubiana S, Descamps D, Le Hingrat Q, Abel L, Guedj J, Malhotra S, Kumar-Singh S, Visseaux B, Ghosn J, Charpentier C, Lebourgeois S, French COVID Cohort Study Group
High sera levels of SARS-CoV-2 N antigen are associated with death in hospitalized COVID-19 patients.
Journal of Medical Virology 2023, 95, e29247.

Néant N, Lingas G, Gaymard A, Belhadi D, Hites M, Staub T, Greil R, Paiva JA, Poissy J, Peiffer-Smadja N, Costagliola D, Yazdanpanah Y, Bouscambert-Duchamp M, Gagneux-Brunon A, Ader F, Mentré F, Wallet F, Burdet C, Guedj J, DisCoVeRy study group
Association between SARS-CoV-2 viral kinetics and clinical score evolution in hospitalized patients.
CPT: pharmacometrics & systems pharmacology 2023, 12, 2027-2037.

Suñer C, Ubals M, Tarín-Vicente EJ, Mendoza A, Alemany A, Hernández-Rodríguez Á, Casañ C, Descalzo V, Ouchi D, Marc A, Rivero À, Coll P, Oller X, Miguel Cabrera J, Vall-Mayans M, Dolores Folgueira M, Ángeles Melendez M, Agud-Dios M, Gil-Cruz E, Paris de Leon A, Ramírez Marinero A, Buhiichyk V, Galván-Casas C, Paredes R, Prat N, Sala Farre MR, Bonet-Simó JM, Farré M, Ortiz-Romero PL, Clotet B, García-Patos V, Casabona J, Guedj J, Cardona PJ, Blanco I, Movie Group, Marks M, Mitjà O
Viral dynamics in patients with monkeypox infection: a prospective cohort study in Spain.
The Lancet. Infectious Diseases 2023, 23, 445-453.

Bruno R, Chanu P, Kågedal M, Mercier F, Yoshida K, Guedj J, Li C, Beyer U, Jin JY
Support to early clinical decisions in drug development and personalised medicine with checkpoint inhibitors using dynamic biomarker-overall survival models.
British Journal of Cancer 2023

Kerioui M, Beaulieu M, Desmée S, Bertrand J, Mercier F, Jin JY, Bruno R, Guedj J
Nonlinear multilevel joint model for individual lesion kinetics and survival to characterize intra-individual heterogeneity in patients with advanced cancer.
Biometrics 2023

Kerioui M, Bertrand J, Desmée S, Le Tourneau C, Mercier F, Bruno R, Guedj J
Assessing the Increased Variability in Individual Lesion Kinetics During Immunotherapy: Does It Exist, and Does It Matter?.
JCO precision oncology 2023, 7, e2200368.

Nguyen BT, Marc A, Suñer C, Marks M, Ubals M, Hernández-Rodríguez Á, Melendez MÁ, Movie Group, Hruby DE, Russo AT, Mentré F, Mitjà O, Grosenbach DW, Guedj J
Early administration of tecovirimat shortens the time to mpox clearance in a model of human infection.
PLoS biology 2023, 21, e3002249.

Marc A, Marlin R, Donati F, Prague M, Kerioui M, Hérate C, Alexandre M, Dereuddre-Bosquet N, Bertrand J, Contreras V, Behillil S, Maisonnasse P, Van Der Werf S, Le Grand R, Guedj J
Impact of variants of concern on SARS-CoV-2 viral dynamics in non-human primates.
PLoS computational biology 2023, 19, e1010721.

Clairon Q, Prague M, Planas D, Bruel T, Hocqueloux L, Prazuck T, Schwartz O, Thiébaut R, Guedj J
Modeling the kinetics of the neutralizing antibody response against SARS-CoV-2 variants after several administrations of Bnt162b2.
PLoS computational biology 2023, 19, e1011282.

2022

Elie B, Roquebert B, Sofonea MT, Trombert-Paolantoni S, Foulongne V, Guedj J, Haim-Boukobza S, Alizon S
Variant-specific SARS-CoV-2 within-host kinetics.
Journal of Medical Virology 2022, 94, 3625-3633.

Guk J, Bridier-Nahmias A, Magnan M, Grall N, Duval X, Clermont O, Ruppé E, d'Humières C, Tenaillon O, Denamur E, Mentré F, Guedj J, Burdet C, CEREMI study group
Modeling the bacterial dynamics in the gut microbiota following an antibiotic-induced perturbation.
CPT: pharmacometrics & systems pharmacology 2022, 11, 906-918.

Prague M, Alexandre M, Thiébaut R, Guedj J
Within-host models of SARS-CoV-2: What can it teach us on the biological factors driving virus pathogenesis and transmission?.
Anaesthesia, Critical Care & Pain Medicine 2022, 41, 101055.

Delattre R, Seurat J, Haddad F, Nguyen TT, Gaborieau B, Kane R, Dufour N, Ricard JD, Guedj J, Debarbieux L
Combination of in vivo phage therapy data with in silico model highlights key parameters for pneumonia treatment efficacy.
Cell Reports 2022, 39, 110825.

Kerioui M, Desmée S, Mercier F, Lin A, Wu B, Jin JY, Shen X, Le Tourneau C, Bruno R, Guedj J
Assessing the impact of organ-specific lesion dynamics on survival in patients with recurrent urothelial carcinoma treated with atezolizumab or chemotherapy.
ESMO open 2022, 7, 100346.

Cosentino G, Bernard M, Ambroise J, Giannoli JM, Guedj J, Débarre F, Blanquart F
SARS-CoV-2 viral dynamics in infections with Alpha and Beta variants of concern in the French community.
The Journal of Infection 2022, 84, 94-118.

Ader F, Bouscambert-Duchamp M, Hites M, Peiffer-Smadja N, Poissy J, Belhadi D, Diallo A, Lê MP, Peytavin G, Staub T, Greil R, Guedj J, Paiva JA, Costagliola D, Yazdanpanah Y, Burdet C, Mentré F, DisCoVeRy Study Group
Remdesivir plus standard of care versus standard of care alone for the treatment of patients admitted to hospital with COVID-19 (DisCoVeRy): a phase 3, randomised, controlled, open-label trial.
The Lancet. Infectious Diseases 2022, 22, 209-221.

Thielebein A, Ighodalo Y, Taju A, Olokor T, Omiunu R, Esumeh R, Ebhodaghe P, Ekanem A, Igenegbale G, Giwa R, Renevey A, Hinzmann J, Müller J, Pallasch E, Pahlmann M, Guedj J, Nwatuzor J, Femi Babatunde O, Adomeh DI, Asogun D, Akpede N, Okogbenin S, Günther S, Oestereich L, Duraffour S, Ogbaini-Emovon E
Virus persistence after recovery from acute Lassa fever in Nigeria: a 2-year interim analysis of a prospective longitudinal cohort study.
The Lancet. Microbe 2022, 3, e32-e40.

Marlin R, Desjardins D, Contreras V, Lingas G, Solas C, Roques P, Naninck T, Pascal Q, Behillil S, Maisonnasse P, Lemaitre J, Kahlaoui N, Delache B, Pizzorno A, Nougairede A, Ludot C, Terrier O, Dereuddre-Bosquet N, Relouzat F, Chapon C, Ho Tsong Fang R, van der Werf S, Rosa Calatrava M, Malvy D, de Lamballerie X, Guedj J, Le Grand R
Antiviral efficacy of favipiravir against Zika and SARS-CoV-2 viruses in non-human primates.
Nature Communications 2022, 13, 5108.

Lingas G, Néant N, Gaymard A, Belhadi D, Peytavin G, Hites M, Staub T, Greil R, Paiva JA, Poissy J, Peiffer-Smadja N, Costagliola D, Yazdanpanah Y, Wallet F, Gagneux-Brunon A, Mentré F, Ader F, Burdet C, Guedj J, Bouscambert-Duchamp M
Effect of remdesivir on viral dynamics in COVID-19 hospitalized patients: a modelling analysis of the randomized, controlled, open-label DisCoVeRy trial.
The Journal of Antimicrobial Chemotherapy 2022, 77, 1404-1412.

Kerioui M, Bertrand J, Bruno R, Mercier F, Guedj J, Desmée S
Modelling the association between biomarkers and clinical outcome: An introduction to nonlinear joint models.
British Journal of Clinical Pharmacology 2022, 88, 1452-1463.

El Messaoudi S, Lemenuel-Diot A, Gonçalves A, Guedj J
A semi-mechanistic model to characterize the long-term dynamic of HBV markers during treatment with lamivudine and Peg-IFN.
Clinical Pharmacology & Therapeutics 2022

2021

Guk J, Guedj J, Burdet C, Andremont A, de Gunzburg J, Ducher A, Mentré F
Modeling the Effect of DAV132, a Novel Colon-Targeted Adsorbent, on Fecal Concentrations of Moxifloxacin and Gut Microbiota Diversity in Healthy Volunteers.
Clinical Pharmacology and Therapeutics 2021, 109, 1045-1054.

Eloy P, Le Grand R, Malvy D, Guedj J
Combined treatment of molnupiravir and favipiravir against SARS-CoV-2 infection: One + zero equals two?.
EBioMedicine 2021, 74, 103663.

Tubiana S, Burdet C, Houhou N, Thy M, Manchon P, Blanquart F, Charpentier C, Guedj J, Alavoine L, Behillil S, Leclercq A, Lucet JC, Yazdanpanah Y, Attia M, Demeret C, Rose T, Bielicki JA, Bruijning-Verhagen P, Goossens H, Descamps D, van der Werf S, Lina B, Duval X, CoVCONTACT study group, Principal investigator, Sponsor: Inserm
High-risk exposure without personal protective equipment and infection with SARS-CoV-2 in-hospital workers - The CoV-CONTACT cohort.
The Journal of Infection 2021, 82, 186-230.

Driouich JS, Cochin M, Lingas G, Moureau G, Touret F, Petit PR, Piorkowski G, Barthélémy K, Laprie C, Coutard B, Guedj J, de Lamballerie X, Solas C, Nougairède A
Favipiravir antiviral efficacy against SARS-CoV-2 in a hamster model.
Nature Communications 2021, 12, 1735.

Maisonnasse P, Aldon Y, Marc A, Marlin R, Dereuddre-Bosquet N, Kuzmina NA, Freyn AW, Snitselaar JL, Gonçalves A, Caniels TG, Burger JA, Poniman M, Bontjer I, Chesnais V, Diry S, Iershov A, Ronk AJ, Jangra S, Rathnasinghe R, Brouwer PJM, Bijl TPL, van Schooten J, Brinkkemper M, Liu H, Yuan M, Mire CE, van Breemen MJ, Contreras V, Naninck T, Lemaître J, Kahlaoui N, Relouzat F, Chapon C, Ho Tsong Fang R, McDanal C, Osei-Twum M, St-Amant N, Gagnon L, Montefiori DC, Wilson IA, Ginoux E, de Bree GJ, García-Sastre A, Schotsaert M, Coughlan L, Bukreyev A, van der Werf S, Guedj J, Sanders RW, van Gils MJ, Le Grand R
COVA1-18 neutralizing antibody protects against SARS-CoV-2 in three preclinical models.
Nature Communications 2021, 12, 6097.

Néant N, Lingas G, Le Hingrat Q, Ghosn J, Engelmann I, Lepiller Q, Gaymard A, Ferré V, Hartard C, Plantier JC, Thibault V, Marlet J, Montes B, Bouiller K, Lescure FX, Timsit JF, Faure E, Poissy J, Chidiac C, Raffi F, Kimmoun A, Etienne M, Richard JC, Tattevin P, Garot D, Le Moing V, Bachelet D, Tardivon C, Duval X, Yazdanpanah Y, Mentré F, Laouénan C, Visseaux B, Guedj J, French COVID Cohort Investigators and French Cohort Study groups
Modeling SARS-CoV-2 viral kinetics and association with mortality in hospitalized patients from the French COVID cohort.
Proceedings of the National Academy of Sciences of the United States of America 2021, 118,

Lê MP, Peiffer-Smadja N, Guedj J, Neant N, Mentré F, Ader F, Yazdanpanah Y, Peytavin G, C21DFSC
Rationale of a loading dose initiation for hydroxychloroquine treatment in COVID-19 infection in the DisCoVeRy trial-authors' response.
The Journal of Antimicrobial Chemotherapy 2021, 76, 277-279.

Gonçalves A, Lemenuel-Diot A, Cosson V, Jin Y, Feng S, Bo Q, Guedj J
What drives the dynamics of HBV RNA during treatment?.
Journal of Viral Hepatitis 2021, 28, 383-392.

Lingas G, Rosenke K, Safronetz D, Guedj J
Lassa viral dynamics in non-human primates treated with favipiravir or ribavirin.
PLoS computational biology 2021, 17, e1008535.

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 2021, 17, e1008564.

Czuppon P, Débarre F, Gonçalves A, Tenaillon O, Perelson AS, Guedj J, Blanquart F
Success of prophylactic antiviral therapy for SARS-CoV-2: Predicted critical efficacies and impact of different drug-specific mechanisms of action.
PLoS computational biology 2021, 17, e1008752.

Gonçalves A, Maisonnasse P, Donati F, Albert M, Behillil S, Contreras V, Naninck T, Marlin R, Solas C, Pizzorno A, Lemaitre J, Kahlaoui N, Terrier O, Ho Tsong Fang R, Enouf V, Dereuddre-Bosquet N, Brisebarre A, Touret F, Chapon C, Hoen B, Lina B, Rosa Calatrava M, de Lamballerie X, Mentré F, Le Grand R, van der Werf S, Guedj J
SARS-CoV-2 viral dynamics in non-human primates.
PLoS computational biology 2021, 17, e1008785.

Reynard S, Gloaguen E, Baillet N, Madelain V, Guedj J, Raoul H, de Lamballerie X, Mullaert J, Baize S
Early control of viral load by favipiravir promotes survival to Ebola virus challenge and prevents cytokine storm in non-human primates.
PLoS neglected tropical diseases 2021, 15, e0009300.

Bonil L, Lingas G, Coupeau D, Lucet JC, Guedj J, Visseaux B, Muylkens B
Survival of SARS-CoV-2 on Non-Porous Materials in an Experimental Setting Representative of Fomites.
Coatings 2021, 11, 371.

Marc A, Kerioui M, Blanquart F, Bertrand J, Mitjà O, Corbacho-Monné M, Marks M, Guedj J
Quantifying the relationship between SARS-CoV-2 viral load and infectiousness.
eLife 2021, 10, e69302.

2020

Eloy P, Solas C, Touret F, Mentré F, Malvy D, de Lamballerie X, Guedj J
Dose rationale for favipiravir use in patients infected with SARS-CoV-2.
Clinical Pharmacology and Therapeutics 2020

Madelain V, Mentré F, Baize S, Anglaret X, Laouénan C, Oestereich L, Nguyen THT, Malvy D, Piorkowski G, Graw F, Günther S, Raoul H, de Lamballerie X, Guedj J
Modeling Favipiravir Antiviral Efficacy Against Emerging Viruses: From Animal Studies to Clinical Trials.
CPT: pharmacometrics & systems pharmacology 2020, 9, 258-271.

Gonçalves A, Bertrand J, Ke R, Comets E, de Lamballerie X, Malvy D, Pizzorno A, Terrier O, Rosa Calatrava M, Mentré F, Smith P, Perelson AS, Guedj J
Timing of Antiviral Treatment Initiation is Critical to Reduce SARS-CoV-2 Viral Load.
CPT: pharmacometrics & systems pharmacology 2020, 9, 509-514.

Kerioui M, Mercier F, Bertrand J, Tardivon C, Bruno R, Guedj J, Desmée S
Bayesian inference using Hamiltonian Monte-Carlo algorithm for nonlinear joint modeling in the context of cancer immunotherapy.
Statistics in Medicine 2020, 39, 4853-4868.

Mercier F, Kerioui M, Desmée S, Guedj J, Krieter O, Bruno R
Longitudinal analysis of organ-specific tumor lesion sizes in metastatic colorectal cancer patients receiving first line standard chemotherapy in combination with anti-angiogenic treatment.
Journal of Pharmacokinetics and Pharmacodynamics 2020, 47, 613-625.

Madelain V, Duthey A, Mentré F, Jacquot F, Solas C, Lacarelle B, Vallvé A, Barron S, Barrot L, Mundweiler S, Thomas D, Carbonnelle C, Raoul H, de Lamballerie X, Guedj J
Ribavirin does not potentiate favipiravir antiviral activity against Ebola virus in non-human primates.
Antiviral Research 2020, 177, 104758.

Passaes C, Millet A, Madelain V, Monceaux V, David A, Versmisse P, Sylla N, Gostick E, Llewellyn-Lacey S, Price DA, Blancher A, Dereuddre-Bosquet N, Desjardins D, Pancino G, Le Grand R, Lambotte O, Müller-Trutwin M, Rouzioux C, Guedj J, Avettand-Fenoel V, Vaslin B, Sáez-Cirión A
Optimal Maturation of the SIV-Specific CD8+ T Cell Response after Primary Infection Is Associated with Natural Control of SIV: ANRS SIC Study.
Cell Reports 2020, 32, 108174.

Friberg LE, Guedj J
Acute bacterial or viral infection-What's the difference? A perspective from PKPD modellers.
Clinical Microbiology and Infection: The Official Publication of the European Society of Clinical Microbiology and Infectious Diseases 2020, 26, 1133-1136.

Maisonnasse P, Guedj J, Contreras V, Behillil S, Solas C, Marlin R, Naninck T, Pizzorno A, Lemaitre J, Gonçalves A, Kahlaoui N, Terrier O, Fang RHT, Enouf V, Dereuddre-Bosquet N, Brisebarre A, Touret F, Chapon C, Hoen B, Lina B, Calatrava MR, van der Werf S, de Lamballerie X, Le Grand R
Hydroxychloroquine use against SARS-CoV-2 infection in non-human primates.
Nature 2020, 585, 584-587.

Lê MP, Peiffer-Smadja N, Guedj J, Néant N, Mentré F, Ader F, Yazdanpanah Y, Peytavin G
Rationale of a loading dose initiation for hydroxychloroquine treatment in COVID-19 infection in the DisCoVeRy trial.
The Journal of Antimicrobial Chemotherapy 2020, 75, 2376-2380.

Bruno R, Bottino D, de Alwis DP, Fojo AT, Guedj J, Liu C, Swanson KR, Zheng J, Zheng Y, Jin JY
Progress and Opportunities to Advance Clinical Cancer Therapeutics Using Tumor Dynamic Models.
Clinical Cancer Research: An Official Journal of the American Association for Cancer Research 2020, 26, 1787-1795.

Gonçalves A, Mentré F, Lemenuel-Diot A, Guedj J
Model Averaging in Viral Dynamic Models.
The AAPS journal 2020, 22, 48.

2019

Tardivon C, Desmée S, Kerioui M, Bruno R, Wu B, Mentré F, Mercier F, Guedj J
Association Between Tumor Size Kinetics and Survival in Patients With Urothelial Carcinoma Treated With Atezolizumab: Implication for Patient Follow-Up.
Clinical Pharmacology and Therapeutics 2019, 106, 810-820.

Burdet C, Nguyen TT, Duval X, Ferreira S, Andremont A, Guedj J, Mentré F, DAV132-CL-1002 Study Group
Impact of Antibiotic Gut Exposure on the Temporal Changes in Microbiome Diversity.
Antimicrobial Agents and Chemotherapy 2019, 63, e00820-19.

2018

Madelain V, Baize S, Jacquot F, Reynard S, Fizet A, Barron S, Solas C, Lacarelle B, Carbonnelle C, Mentré F, Raoul H, de Lamballerie X, Guedj J
Ebola viral dynamics in nonhuman primates provides insights into virus immuno-pathogenesis and antiviral strategies.
Nature Communications 2018, 9, 4013.

Rhodes SJ, Guedj J, Fletcher HA, Lindenstrøm T, Scriba TJ, Evans TG, Knight GM, White RG
Using vaccine Immunostimulation/Immunodynamic modelling methods to inform vaccine dose decision-making.
NPJ vaccines 2018, 3, 36.

Fourati S, Guedj J, Chevaliez S, Nguyen THT, Roudot-Thoraval F, Ruiz I, Soulier A, Scoazec G, Varaut A, Poiteau L, Francois M, Mallat A, Hézode C, Pawlotsky JM
Viral kinetics analysis and virological characterization of treatment failures in patients with chronic hepatitis C treated with sofosbuvir and an NS5A inhibitor.
Alimentary Pharmacology & Therapeutics 2018, 47, 665-673.

Petit C, Samson A, Morita S, Ursino M, Guedj J, Jullien V, Comets E, Zohar S
Unified approach for extrapolation and bridging of adult information in early-phase dose-finding paediatric studies.
Statistical Methods in Medical Research 2018, 27, 1860-1877.

Guedj J, Piorkowski G, Jacquot F, Madelain V, Nguyen THT, Rodallec A, Gunther S, Carbonnelle C, Mentre F, Raoul H, de Lamballerie X
Antiviral efficacy of favipiravir against Ebola virus: A translational study in cynomolgus macaques.
PLoS Med 2018, 15, e1002535.

Quintela BdM, Conway JM, Hyman JM, Guedj J, Dos Santos RW, Lobosco M, Perelson AS
A New Age-Structured Multiscale Model of the Hepatitis C Virus Life-Cycle During Infection and Therapy With Direct-Acting Antiviral Agents.
Frontiers in Microbiology 2018, 9, 601.

2017

Sissoko D, Duraffour S, Kerber R, Kolie JS, Beavogui AH, Camara AM, Colin G, Rieger T, Oestereich L, Pályi B, Wurr S, Guedj J, Nguyen THT, Eggo RM, Watson CH, Edmunds WJ, Bore JA, Koundouno FR, Cabeza-Cabrerizo M, Carter LL, Kafetzopoulou LE, Kuisma E, Michel J, Patrono LV, Rickett NY, Singethan K, Rudolf M, Lander A, Pallasch E, Bockholt S, Rodríguez E, Di Caro A, Wölfel R, Gabriel M, Gurry C, Formenty P, Keïta S, Malvy D, Carroll MW, Anglaret X, Günther S
Persistence and clearance of Ebola virus RNA from seminal fluid of Ebola virus disease survivors: a longitudinal analysis and modelling study.
The Lancet. Global Health 2017, 5, e80-e88.

Nguyen THT, Guedj J, Uprichard SL, Kohli A, Kottilil S, Perelson AS
The paradox of highly effective sofosbuvir-based combination therapy despite slow viral decline: can we still rely on viral kinetics?.
Scientific Reports 2017, 7, 10233.

Carrillo-Bustamante P, Nguyen THT, Oestereich L, Günther S, Guedj J, Graw F
Determining Ribavirin's mechanism of action against Lassa virus infection.
Scientific Reports 2017, 7, 11693.

Best K, Guedj J, Madelain V, de Lamballerie X, Lim SY, Osuna CE, Whitney JB, Perelson AS
Zika plasma viral dynamics in nonhuman primates provides insights into early infection and antiviral strategies.
Proceedings of the National Academy of Sciences of the United States of America 2017, 114, 8847-8852.

Ragonnet R, Deuffic-Burban S, Boesecke C, Guiguet M, Lacombe K, Guedj J, Rockstroh JK, Yazdanpanah Y
Estimating the Time to Diagnosis and the Chance of Spontaneous Clearance During Acute Hepatitis C in Human Immunodeficiency Virus-Infected Individuals.
Open Forum Infectious Diseases 2017, 4, ofw235.

Desmée S, Mentré F, Veyrat-Follet C, Sébastien B, Guedj J
Using the SAEM algorithm for mechanistic joint models characterizing the relationship between nonlinear PSA kinetics and survival in prostate cancer patients.
Biometrics 2017, 73, 305-312.

Madelain V, Guedj J, Mentré F, Nguyen THT, Jacquot F, Oestereich L, Kadota T, Yamada K, Taburet AM, de Lamballerie X, Raoul H
Favipiravir Pharmacokinetics in Nonhuman Primates and Insights for Future Efficacy Studies of Hemorrhagic Fever Viruses.
Antimicrobial Agents and Chemotherapy 2017, 61, e01305-16.

Vernet MA, Reynard S, Fizet A, Schaeffer J, Pannetier D, Guedj J, Rives M, Georges N, Garcia-Bonnet N, Sylla AI, Grovogui P, Kerherve JY, Savio C, Savio-Coste S, de Séverac ML, Zloczewski P, Linares S, Harouna S, Abdoul BM, Petitjean F, Samake N, Shepherd S, Kinda M, Koundouno FR, Joxe L, Mateo M, Lecine P, Page A, Tchamdja TM, Schoenhals M, Barbe S, Simon B, Tran-Minh T, Longuet C, L'Hériteau F, Baize S
Clinical, virological, and biological parameters associated with outcomes of Ebola virus infection in Macenta, Guinea.
JCI insight 2017, 2, e88864.

Desmee S, Mentre F, Veyrat-Follet C, Sebastien B, Guedj J
Nonlinear joint models for individual dynamic prediction of risk of death using Hamiltonian Monte Carlo: application to metastatic prostate cancer.
BMC Med Res Methodol 2017, 17, 105.

Nguyen TH, Guedj J, Anglaret X, Laouenan C, Madelain V, Taburet AM, Baize S, Sissoko D, Pastorino B, Rodallec A, Piorkowski G, Carazo S, Conde MN, Gala JL, Bore JA, Carbonnelle C, Jacquot F, Raoul H, Malvy D, de Lamballerie X, Mentre F
Favipiravir pharmacokinetics in Ebola-Infected patients of the JIKI trial reveals concentrations lower than targeted.
PLoS Negl Trop Dis 2017, 11, e0005389.

Cento V, Nguyen THT, Di Carlo D, Biliotti E, Gianserra L, Lenci I, Di Paolo D, Calvaruso V, Teti E, Cerrone M, Romagnoli D, Melis M, Danieli E, Menzaghi B, Polilli E, Siciliano M, Nicolini LA, Di Biagio A, Magni CF, Bolis M, Antonucci FP, Di Maio VC, Alfieri R, Sarmati L, Casalino P, Bernardini S, Micheli V, Rizzardini G, Parruti G, Quirino T, Puoti M, Babudieri S, D'Arminio Monforte A, Andreoni M, Craxì A, Angelico M, Pasquazzi C, Taliani G, Guedj J, Perno CF, Ceccherini-Silberstein F
Improvement of ALT decay kinetics by all-oral HCV treatment: Role of NS5A inhibitors and differences with IFN-based regimens.
PloS One 2017, 12, e0177352.

2016

Madelain V, Nguyen TH, Olivo A, de Lamballerie X, Guedj J, Taburet AM, Mentre F
Ebola Virus Infection: Review of the Pharmacokinetic and Pharmacodynamic Properties of Drugs Considered for Testing in Human Efficacy Trials.
Clin Pharmacokinet 2016, 55, 907-23.

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 2016, 13,

Sissoko D, Laouenan C, Folkesson E, M'Lebing AB, Beavogui AH, Baize S, Camara AM, Maes P, Shepherd S, Danel C, Carazo S, Conde MN, Gala JL, Colin G, Savini H, Bore JA, Le Marcis F, Koundouno FR, Petitjean F, Lamah MC, Diederich S, Tounkara A, Poelart G, Berbain E, Dindart JM, Duraffour S, Lefevre A, Leno T, Peyrouset O, Irenge L, Bangoura N, Palich R, Hinzmann J, Kraus A, Barry TS, Berette S, Bongono A, Camara MS, Chanfreau Munoz V, Doumbouya L, Souley Harouna n, Kighoma PM, Koundouno FR, Réné Lolamou n, Loua CM, Massala V, Moumouni K, Provost C, Samake N, Sekou C, Soumah A, Arnould I, Komano MS, Gustin L, Berutto C, Camara D, Camara FS, Colpaert J, Delamou L, Jansson L, Kourouma E, Loua M, Malme K, Manfrin E, Maomou A, Milinouno A, Ombelet S, Sidiboun AY, Verreckt I, Yombouno P, Bocquin A, Carbonnelle C, Carmoi T, Frange P, Mely S, Nguyen VK, Pannetier D, Taburet AM, Treluyer JM, Kolie J, Moh R, Gonzalez MC, Kuisma E, Liedigk B, Ngabo D, Rudolf M, Thom R, Kerber R, Gabriel M, Di Caro A, Wölfel R, Badir J, Bentahir M, Deccache Y, Dumont C, Durant JF, El Bakkouri K, Gasasira Uwamahoro M, Smits B, Toufik N, Van Cauwenberghe S, Ezzedine K, D'Ortenzio E, Dortenzio E, Pizarro L, Etienne A, Guedj J, Fizet A, Barte de Sainte Fare E, Murgue B, Tran-Minh T, Rapp C, Piguet P, Poncin M, Draguez B, Allaford Duverger T, Barbe S, Baret G, Defourny I, Carroll M, Raoul H, Augier A, Eholie SP, Yazdanpanah Y, Levy-Marchal C, Antierrens A, Van Herp M, Günther S, de Lamballerie X, Keïta S, Mentre F, Anglaret X, Malvy D, JIKI Study Group
Experimental Treatment with Favipiravir for Ebola Virus Disease (the JIKI Trial): A Historically Controlled, Single-Arm Proof-of-Concept Trial in Guinea.
PLoS medicine 2016, 13, e1001967.

Canini L, Guedj J, Chatterjee A, Lemenuel-Diot A, Smith PF, Perelson AS
Modelling the interaction between danoprevir and mericitabine in the treatment of chronic HCV infection.
Antiviral Therapy 2016, 21, 297-306.

2015

Nguyen T, Guedj J
HCV Kinetic Models and Their Implications in Drug Development.
CPT: pharmacometrics & systems pharmacology 2015, 4, 231–242.

Laouenan C, Guedj J, Peytavin G, Nguyen TT, Lapalus M, Khelifa-Mouri F, Boyer N, Zoulim F, Serfaty L, Bronowicki JP, Martinot-Peignoux M, Lada O, Asselah T, Dorival C, Hezode C, Carrat F, Nicot F, Marcellin P, Mentre F
A Model-Based Illustrative Exploratory Approach to Optimize the Dosing of Peg-IFN/RBV in Cirrhotic Hepatitis C Patients Treated With Triple Therapy.
CPT Pharmacometrics Syst Pharmacol 2015, 4, e00008.

Madelain V, Oestereich L, Graw F, Nguyen THT, de Lamballerie X, Mentré F, Günther S, Guedj J
Ebola virus dynamics in mice treated with favipiravir.
Antiviral Research 2015, 123, 70–77.

K-Kutala B, Bedossa P, Guedj J, Asselah T, Martinot-Peignoux M, Duval X, Marcellin P
Patients with chronic hepatitis C without advanced fibrosis and hepatocellular carcinoma: a retrospective clinical-pathological study.
Digestive and Liver Disease: Official Journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver 2015, 47, 296–302.

Bouazza N, Treluyer JM, Foissac F, Mentré F, Taburet AM, Guedj J, Anglaret X, de Lamballerie X, Keïta S, Malvy D, Frange P
Favipiravir for children with Ebola.
Lancet (London, England) 2015, 385, 603–604.

Mentré F, Taburet AM, Guedj J, Anglaret X, Keïta S, de Lamballerie X, Malvy D
Dose regimen of favipiravir for Ebola virus disease.
The Lancet. Infectious Diseases 2015, 15, 150–151.

Perelson AS, Guedj J
Modelling hepatitis C therapy-predicting effects of treatment.
Nature Reviews. Gastroenterology & Hepatology 2015, 12, 437–445.

Andrade A, Guedj J, Rosenkranz SL, Lu D, Mellors J, Kuritzkes DR, Perelson AS, Ribeiro RM, ACTG A5249s protocol team
Early HIV RNA decay during raltegravir-containing regimens exhibits two distinct subphases (1a and 1b).
AIDS (London, England) 2015, 29, 2419–2426.

Guedj J, Nguyen THT
Can we use viral kinetic models to individualize treatment?.
Liver International: Official Journal of the International Association for the Study of the Liver 2015, 35, 297–298.

Petit C, Jullien V, Samson A, Guedj J, Kiechel JR, Zohar S, Comets E
Designing a Pediatric Study for an Antimalarial Drug by Using Information from Adults.
Antimicrobial Agents and Chemotherapy 2015, 60, 1481-1491.

Kutala BK, Guedj J, Asselah T, Boyer N, Mouri F, Martinot-Peignoux M, Valla D, Marcellin P, Duval X
Impact of treatment against hepatitis C virus on overall survival of naive patients with advanced liver disease.
Antimicrobial Agents and Chemotherapy 2015, 59, 803–810.

Desmée S, Mentré F, Veyrat-Follet C, Guedj J
Nonlinear Mixed-effect Models for Prostate-specific Antigen Kinetics and Link with Survival in the Context of Metastatic Prostate Cancer: A Comparison by Simulation of Two-stage and Joint Approaches.
The AAPS journal 2015, 17, 691–699.

Canini L, Chatterjee A, Guedj J, Lemenuel-Diot A, Brennan B, Smith PF, Perelson AS
A pharmacokinetic/viral kinetic model to evaluate the treatment effectiveness of danoprevir against chronic HCV.
Antiviral Therapy 2015, 20, 469–477.

2014

Guedj J, Yu J, Levi M, Li B, Kern S, Naoumov NV, Perelson AS
Modeling viral kinetics and treatment outcome during alisporivir interferon-free treatment in hepatitis C virus genotype 2 and 3 patients.
Hepatology (Baltimore, Md.) 2014, 59, 1706–1714.

Guedj J, Rotman Y, Cotler SJ, Koh C, Schmid P, Albrecht J, Haynes-Williams V, Liang TJ, Hoofnagle JH, Heller T, Dahari H
Understanding early serum hepatitis D virus and hepatitis B surface antigen kinetics during pegylated interferon-alpha therapy via mathematical modeling.
Hepatology (Baltimore, Md.) 2014, 60, 1902–1910.

Nguyen THT, Mentré F, Levi M, Yu J, Guedj J
A pharmacokinetic-viral kinetic model describes the effect of alisporivir as monotherapy or in combination with peg-IFN on hepatitis C virologic response.
Clinical Pharmacology and Therapeutics 2014, 96, 599–608.

Sherman KE, Guedj J, Shata MT, Blackard JT, Rouster SD, Castro M, Feinberg J, Sterling RK, Goodman Z, Aronow BJ, Perelson AS
Modulation of HCV replication after combination antiretroviral therapy in HCV/HIV co-infected patients.
Science Translational Medicine 2014, 6, 246ra98.

Laouénan C, Marcellin P, Lapalus M, Khelifa-Mouri F, Boyer N, Zoulim F, Serfaty L, Bronowicki JP, Martinot-Peignoux M, Lada O, Asselah T, Dorival C, Hézode C, Carrat F, Nicot F, Peytavin G, Mentré F, Guedj J
Using pharmacokinetic and viral kinetic modeling to estimate the antiviral effectiveness of telaprevir, boceprevir, and pegylated interferon during triple therapy in treatment-experienced hepatitis C virus-infected cirrhotic patients.
Antimicrobial Agents and Chemotherapy 2014, 58, 5332-5341.

Rotman Y, Noureddin M, Feld JJ, Guedj J, Witthaus M, Han H, Park YJ, Park SH, Heller T, Ghany MG, Doo E, Koh C, Abdalla A, Gara N, Sarkar S, Thomas E, Ahlenstiel G, Edlich B, Titerence R, Hogdal L, Rehermann B, Dahari H, Perelson AS, Hoofnagle JH, Liang TJ
Effect of ribavirin on viral kinetics and liver gene expression in chronic hepatitis C.
Gut 2014, 63, 161–169.

Nguyen TT, Guedj J, Chachaty E, de Gunzburg J, Andremont A, Mentré F
Mathematical modeling of bacterial kinetics to predict the impact of antibiotic colonic exposure and treatment duration on the amount of resistant enterobacteria excreted.
PLoS computational biology 2014, 10, e1003840.

Rong L, Guedj J, Dahari H, Perelson AS
Treatment of hepatitis C with an interferon-based lead-in phase: a perspective from mathematical modelling.
Antiviral Therapy 2014, 19, 469–477.

Guedj J, Pang PS, Denning J, Rodriguez-Torres M, Lawitz E, Symonds W, Perelson AS
Analysis of hepatitis C viral kinetics during administration of two nucleotide analogues: sofosbuvir (GS-7977) and GS-0938.
Antiviral Therapy 2014, 19, 211–220.

2013

Prague M, Commenges D, Guedj J, Drylewicz J, Thiébaut R
NIMROD: a program for inference via a normal approximation of the posterior in models with random effects based on ordinary differential equations.
Computer Methods and Programs in Biomedicine 2013, 111, 447–458.

Nguyen THT, Guedj J, Yu J, Levi M, Mentré F
Influence of a priori Information, Designs, and Undetectable Data on Individual Parameters Estimation and Prediction of Hepatitis C Treatment Outcome.
CPT: pharmacometrics & systems pharmacology 2013, 2, e56.

Guedj J, Dahari H, Rong L, Sansone ND, Nettles RE, Cotler SJ, Layden TJ, Uprichard SL, Perelson AS
Modeling shows that the NS5A inhibitor daclatasvir has two modes of action and yields a shorter estimate of the hepatitis C virus half-life.
Proceedings of the National Academy of Sciences of the United States of America 2013, 110, 3991–3996.

Cohen J, Guedj J, Fries N
Umbilical artery Doppler assessment: a clear disparity in ultrasound practice in a national survey.
Acta Obstetricia Et Gynecologica Scandinavica 2013, 92, 1115–1116.

Laouénan C, Guedj J, Mentré F
Clinical trial simulation to evaluate power to compare the antiviral effectiveness of two hepatitis C protease inhibitors using nonlinear mixed effect models: a viral kinetic approach.
BMC medical research methodology 2013, 13, 60.

Rong L, Guedj J, Dahari H, Coffield DJ, Levi M, Smith P, Perelson AS
Analysis of hepatitis C virus decline during treatment with the protease inhibitor danoprevir using a multiscale model.
PLoS computational biology 2013, 9, e1002959.

Guedj J, Dahari H, Uprichard SL, Perelson AS
The hepatitis C virus NS5A inhibitor daclatasvir has a dual mode of action and leads to a new virus half-life estimate.
Expert Review of Gastroenterology & Hepatology 2013, 7, 397–399.

2012

Guedj J, Dahari H, Shudo E, Smith P, Perelson AS
Hepatitis C viral kinetics with the nucleoside polymerase inhibitor mericitabine (RG7128).
Hepatology (Baltimore, Md.) 2012, 55, 1030–1037.

Guedj J, Dahari H, Pohl RT, Ferenci P, Perelson AS
Understanding silibinin's modes of action against HCV using viral kinetic modeling.
Journal of Hepatology 2012, 56, 1019–1024.

Zhou Y, Callendret B, Xu D, Brasky KM, Feng Z, Hensley LL, Guedj J, Perelson AS, Lemon SM, Lanford RE, Walker CM
Dominance of the CD4(+) T helper cell response during acute resolving hepatitis A virus infection.
The Journal of Experimental Medicine 2012, 209, 1481–1492.

Guedj H, Guedj J, Negro F, Lagging M, Westin J, Bochud PY, Bibert S, Neumann AU, DITTO-HCV study group
The impact of fibrosis and steatosis on early viral kinetics in HCV genotype 1-infected patients treated with Peg-IFN-alfa-2a and ribavirin.
Journal of Viral Hepatitis 2012, 19, 488–496.

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 2012, 8, e1002881.

Chatterjee A, Guedj J, Perelson AS
Mathematical modelling of HCV infection: what can it teach us in the era of direct-acting antiviral agents?.
Antiviral therapy 2012, 17, 1171–1182.

2011

Guedj J, Perelson AS
Second-phase hepatitis C virus RNA decline during telaprevir-based therapy increases with drug effectiveness: implications for treatment duration.
Hepatology (Baltimore, Md.) 2011, 53, 1801-1808.

Guedj J, Bazzoli C, Neumann AU, Mentré F
Design evaluation and optimization for models of hepatitis C viral dynamics.
Statistics in Medicine 2011, 30, 1045-1056.

Dahari H, Guedj J, Perelson AS, Layden TJ
Hepatitis C Viral Kinetics in the Era of Direct Acting Antiviral Agents and IL28B.
Current Hepatitis Reports 2011, 10, 214-227.

Guedj J, Thiébaut R, Commenges D
Joint modeling of the clinical progression and of the biomarkers' dynamics using a mechanistic model.
Biometrics 2011, 67, 59-66.

2010

Guedj J, Neumann AU
Understanding hepatitis C viral dynamics with direct-acting antiviral agents due to the interplay between intracellular replication and cellular infection dynamics.
Journal of Theoretical Biology 2010, 267, 330-340.

Guedj J, Rong L, Dahari H, Perelson AS
A perspective on modelling hepatitis C virus infection.
Journal of Viral Hepatitis 2010, 17, 825-833.

2007

Guedj J, Thiébaut R, Commenges D
Practical identifiability of HIV dynamics models.
Bulletin of Mathematical Biology 2007, 69, 2493-2513.

Guedj J, Thiébaut R, Commenges D
Maximum likelihood estimation in dynamical models of HIV.
Biometrics 2007, 63, 1198-1206.