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Manon Ragonnet-Cronin

Title(s)Postdoctoral Scholar, Medicine
SchoolHealth Sciences
Address200 W. Arbor Drive #8208
San Diego CA 92103
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    Collapse Biography 
    Collapse Education and Training
    University of California, San Diego, USAHIV transmission networks
    University of Edinburgh, UKPhD2015Evolutionary Biology
    University of Ottawa, CanadaMSc2011Bioinformatics
    University of Manchester, UKBSc (Hons)2008Genetics

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Sorting by race/ethnicity across HIV genetic transmission networks in three major metropolitan areas in the United States. AIDS Res Hum Retroviruses. 2020 Dec 21. Ragonnet-Cronin M, Benbow N, Hayford C, Poortinga K, Ma F, Forgione LA, Sheng Z, Hu Y, Torian L, Wertheim JO. PMID: 33349132.
      View in: PubMed   Mentions:    Fields:    
    2. Database of epidemic trends and control measures during the first wave of COVID-19 in mainland China. Int J Infect Dis. 2020 Oct 31; 102:463-471. Fu H, Wang H, Xi X, Boonyasiri A, Wang Y, Hinsley W, Fraser KJ, McCabe R, Olivera Mesa D, Skarp J, Ledda A, Dewé T, Dighe A, Winskill P, van Elsland SL, Ainslie KEC, Baguelin M, Bhatt S, Boyd O, Brazeau NF, Cattarino L, Charles G, Coupland H, Cucunuba ZM, Cuomo-Dannenburg G, Donnelly CA, Dorigatti I, Eales OD, FitzJohn RG, Flaxman S, Gaythorpe KAM, Ghani AC, Green WD, Hamlet A, Hauck K, Haw DJ, Jeffrey B, Laydon DJ, Lees JA, Mellan T, Mishra S, Nedjati-Gilani G, Nouvellet P, Okell L, Parag KV, Ragonnet-Cronin M, Riley S, Schmit N, Thompson HA, Unwin HJT, Verity R, Vollmer MAC, Volz E, Walker PGT, Walters CE, Watson OJ, Whittaker C, Whittles LK, Imai N, Bhatia S, Ferguson NM. PMID: 33130212.
      View in: PubMed   Mentions:    Fields:    
    3. Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City region. Genome Res. 2020 12; 30(12):1781-1788. Maurano MT, Ramaswami S, Zappile P, Dimartino D, Boytard L, Ribeiro-Dos-Santos AM, Vulpescu NA, Westby G, Shen G, Feng X, Hogan MS, Ragonnet-Cronin M, Geidelberg L, Marier C, Meyn P, Zhang Y, Cadley J, Ordoñez R, Luther R, Huang E, Guzman E, Arguelles-Grande C, Argyropoulos KV, Black M, Serrano A, Call ME, Kim MJ, Belovarac B, Gindin T, Lytle A, Pinnell J, Vougiouklakis T, Chen J, Lin LH, Rapkiewicz A, Raabe V, Samanovic MI, Jour G, Osman I, Aguero-Rosenfeld M, Mulligan MJ, Volz EM, Cotzia P, Snuderl M, Heguy A. PMID: 33093069.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansPHPublic HealthCTClinical Trials
    4. From Hospital to the Community: Redesigning the Human Immunodeficiency Virus (HIV) Clinical Service Model to Respond to an Outbreak of HIV Among People Who Inject Drugs. J Infect Dis. 2020 Sep 02; 222(Supplement_5):S410-S419. Metcalfe R, Ragonnet-Cronin M, Bradley-Stewart A, McAuley A, Stubbs H, Ritchie T, O'Hara R, Trayner K, Glover C, Laverty L, Sills L, Brown K, Gunson R, Campbell J, Milsoevic C, Anderson P, Peters SE. PMID: 32877546.
      View in: PubMed   Mentions:    Fields:    
    5. SARS-CoV-2 infection prevalence on repatriation flights from Wuhan City, China. J Travel Med. 2020 Aug 24. Thompson HA, Imai N, Dighe A, Ainslie KEC, Baguelin M, Bhatia S, Bhatt S, Boonyasiri A, Boyd O, Brazeau NF, Cattarino L, Cooper LV, Coupland H, Cucunuba Z, Cuomo-Dannenburg G, Djaafara B, Dorigatti I, Elsland S, FitzJohn R, Fu H, Gaythorpe KAM, Green W, Hallett T, Hamlet A, Haw D, Hayes S, Hinsley W, Jeffrey B, Knock E, Laydon DJ, Lees J, Mangal TD, Mellan T, Mishra S, Mousa A, Nedjati-Gilani G, Nouvellet P, Okell L, Parag KV, Ragonnet-Cronin M, Riley S, Unwin HJT, Verity R, Vollmer M, Volz E, Walker PGT, Walters C, Wang H, Wang Y, Watson OJ, Whittaker C, Whittles LK, Winskill P, Xi X, Donnelly CA, Ferguson NM. PMID: 32830853.
      View in: PubMed   Mentions:    Fields:    
    6. Sequencing identifies multiple, early introductions of SARS-CoV2 to New York City Region. medRxiv. 2020 Apr 21. Maurano MT, Ramaswami S, Zappile P, Dimartino D, Boytard L, Ribeiro-Dos-Santos AM, Vulpescu NA, Westby G, Shen G, Feng X, Hogan MS, Ragonnet-Cronin M, Geidelberg L, Marier C, Meyn P, Zhang Y, Cadley J, Ordoñez R, Luther R, Huang E, Guzman E, Arguelles-Grande C, Argyropoulos KV, Black M, Serrano A, Call ME, Kim MJ, Belovarac B, Gindin T, Lytle A, Pinnell J, Vougiouklakis T, Chen J, Lin LH, Rapkiewicz A, Raabe V, Samanovic MI, Jour G, Osman I, Aguero-Rosenfeld M, Mulligan MJ, Volz EM, Cotzia P, Snuderl M, Heguy A. PMID: 32511587.
      View in: PubMed   Mentions:
    7. Hepatitis C virus genotype 1 and 2 recombinant genomes and the phylogeographic history of the 2k/1b lineage. Virus Evol. 2019 Jul; 5(2):vez041. Hostager R, Ragonnet-Cronin M, Murrell B, Hedskog C, Osinusi A, Susser S, Sarrazin C, Svarovskaia E, Wertheim JO. PMID: 31616569.
      View in: PubMed   Mentions:
    8. HIV co-infection is associated with increased transmission risk in patients with chronic hepatitis C virus. J Viral Hepat. 2019 11; 26(11):1351-1354. Ragonnet-Cronin M, Hostager R, Hedskog C, Osinusi A, Svarovskaia E, Wertheim JO. PMID: 31194901.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    9. Consent and criminalisation concerns over phylogenetic analysis of surveillance data - Authors' reply. Lancet HIV. 2019 07; 6(7):e420-e421. Wertheim JO, Morris S, Ragonnet-Cronin M. PMID: 31272659.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    10. FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences. Bioinformatics. 2019 06 01; 35(11):1852-1861. Moshiri N, Ragonnet-Cronin M, Wertheim JO, Mirarab S. PMID: 30395173.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    11. Understanding disclosed and cryptic HIV transmission risk via genetic analysis: what are we missing and when does it matter? Curr Opin HIV AIDS. 2019 05; 14(3):205-212. Ragonnet-Cronin M, Hodcroft EB, Wertheim JO. PMID: 30946142.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    12. HIV transmission networks among transgender women in Los Angeles County, CA, USA: a phylogenetic analysis of surveillance data. Lancet HIV. 2019 03; 6(3):e164-e172. Ragonnet-Cronin M, Hu YW, Morris SR, Sheng Z, Poortinga K, Wertheim JO. PMID: 30765313.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    13. Non-disclosed men who have sex with men in UK HIV transmission networks: phylogenetic analysis of surveillance data. Lancet HIV. 2018 06; 5(6):e309-e316. Ragonnet-Cronin M, Hué S, Hodcroft EB, Tostevin A, Dunn D, Fawcett T, Pozniak A, Brown AE, Delpech V, Brown AJL. PMID: 29893244.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansPHPublic Health
    14. Recent and Rapid Transmission of HIV Among People Who Inject Drugs in Scotland Revealed Through Phylogenetic Analysis. J Infect Dis. 2018 05 25; 217(12):1875-1882. Ragonnet-Cronin M, Jackson C, Bradley-Stewart A, Aitken C, McAuley A, Palmateer N, Gunson R, Goldberg D, Milosevic C, Leigh Brown AJ. PMID: 29546333.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCellsPHPublic Health
    15. Intrapatient viral diversity and treatment outcome in patients with genotype 3a hepatitis C virus infection on sofosbuvir-containing regimens. J Viral Hepat. 2018 04; 25(4):344-353. Bhardwaj N, Ragonnet-Cronin M, Murrell B, Chodavarapu K, Martin R, Chang S, Miller MD, Feld JJ, Sulkowski M, Mangia A, Wertheim JO, Osinusi A, McNally J, Brainard D, Mo H, Svarovskaia ES. PMID: 29112331.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCellsCTClinical Trials
    16. Bayesian inference reveals ancient origin of simian foamy virus in orangutans. Infect Genet Evol. 2017 07; 51:54-66. Reid MJC, Switzer WM, Schillaci MA, Klegarth AR, Campbell E, Ragonnet-Cronin M, Joanisse I, Caminiti K, Lowenberger CA, Galdikas BMF, Hollocher H, Sandstrom PA, Brooks JI. PMID: 28274887.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    17. Using nearly full-genome HIV sequence data improves phylogeny reconstruction in a simulated epidemic. Sci Rep. 2016 12 23; 6:39489. Yebra G, Hodcroft EB, Ragonnet-Cronin ML, Pillay D, Brown AJ. PMID: 28008945.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCellsPHPublic Health
    18. Identifying Transmission Clusters with Cluster Picker and HIV-TRACE. AIDS Res Hum Retroviruses. 2017 03; 33(3):211-218. Rose R, Lamers SL, Dollar JJ, Grabowski MK, Hodcroft EB, Ragonnet-Cronin M, Wertheim JO, Redd AD, German D, Laeyendecker O. PMID: 27824249.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansCells
    19. A Direct Comparison of Two Densely Sampled HIV Epidemics: The UK and Switzerland. Sci Rep. 2016 09 19; 6:32251. Ragonnet-Cronin ML, Shilaih M, Günthard HF, Hodcroft EB, Böni J, Fearnhill E, Dunn D, Yerly S, Klimkait T, Aubert V, Yang WL, Brown AE, Lycett SJ, Kouyos R, Brown AJ. PMID: 27642070.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCellsPHPublic Health
    20. Detailed phylogenetic analysis of primate T-lymphotropic virus type 1 (PTLV-1) sequences from orangutans (Pongo pygmaeus) reveals new insights into the evolutionary history of PTLV-1 in Asia. Infect Genet Evol. 2016 09; 43:434-50. Reid MJ, Switzer WM, Schillaci MA, Ragonnet-Cronin M, Joanisse I, Caminiti K, Lowenberger CA, Galdikas BM, Sandstrom PA, Brooks JI. PMID: 27245152.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    21. Transmission of Non-B HIV Subtypes in the United Kingdom Is Increasingly Driven by Large Non-Heterosexual Transmission Clusters. J Infect Dis. 2016 May 01; 213(9):1410-8. Ragonnet-Cronin M, Lycett SJ, Hodcroft EB, Hué S, Fearnhill E, Brown AE, Delpech V, Dunn D, Leigh Brown AJ. PMID: 26704616.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansCells
    22. Lack of Effectiveness of Antiretroviral Therapy in Preventing HIV Infection in Serodiscordant Couples in Uganda: An Observational Study. PLoS One. 2015; 10(7):e0132182. Birungi J, Min JE, Muldoon KA, Kaleebu P, King R, Khanakwa S, Nyonyintono M, Chen Y, Mills EJ, Lyagoba F, Ragonnet-Cronin M, Wangisi J, Lourenco L, Moore DM. PMID: 26171777.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    23. Correction: Geographic and Temporal Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted HIV-1 Drug Resistance: An Individual-Patient- and Sequence-Level Meta-Analysis. PLoS Med. 2015 Jun; 12(6):e1001845. Rhee SY, Blanco JL, Jordan MR, Taylor J, Lemey P, Varghese V, Hamers RL, Bertagnolio S, de Wit TF, Aghokeng AF, Albert J, Avi R, Avila-Rios S, Bessong PO, Brooks JI, Boucher CA, Brumme ZL, Busch MP, Bussmann H, Chaix ML, Chin BS, D'Aquin TT, De Gascun CF, Derache A, Descamps D, Deshpande AK, Djoko CF, Eshleman SH, Fleury H, Frange P, Fujisaki S, Harrigan PR, Hattori J, Holguin A, Hunt GM, Ichimura H, Kaleebu P, Katzenstein D, Kiertiburanakul S, Kim JH, Kim SS, Li Y, Lutsar I, Morris L, Ndembi N, Kee PN, Paranjape RS, Peeters M, Poljak M, Price MA, Ragonnet-Cronin ML, Reyes-Terán G, Rolland M, Sirivichayakul S, Smith DM, Soares MA, Soriano VV, Ssemwanga D, Stanojevic M, Stefani MA, Sugiura W, Sungkanuparph S, Tanuri A, Tee KK, Truong HM, van de Vijver DA, Vidal N, Yang C, Yang R, Yebra G, Ioannidis JP, Vandamme AM, Shafer RW. PMID: 26030872.
      View in: PubMed   Mentions: 5     Fields:    
    24. Geographic and temporal trends in the molecular epidemiology and genetic mechanisms of transmitted HIV-1 drug resistance: an individual-patient- and sequence-level meta-analysis. PLoS Med. 2015 Apr; 12(4):e1001810. Rhee SY, Blanco JL, Jordan MR, Taylor J, Lemey P, Varghese V, Hamers RL, Bertagnolio S, Rinke de Wit TF, Aghokeng AF, Albert J, Avi R, Avila-Rios S, Bessong PO, Brooks JI, Boucher CA, Brumme ZL, Busch MP, Bussmann H, Chaix ML, Chin BS, D'Aquin TT, De Gascun CF, Derache A, Descamps D, Deshpande AK, Djoko CF, Eshleman SH, Fleury H, Frange P, Fujisaki S, Harrigan PR, Hattori J, Holguin A, Hunt GM, Ichimura H, Kaleebu P, Katzenstein D, Kiertiburanakul S, Kim JH, Kim SS, Li Y, Lutsar I, Morris L, Ndembi N, Ng KP, Paranjape RS, Peeters M, Poljak M, Price MA, Ragonnet-Cronin ML, Reyes-Terán G, Rolland M, Sirivichayakul S, Smith DM, Soares MA, Soriano VV, Ssemwanga D, Stanojevic M, Stefani MA, Sugiura W, Sungkanuparph S, Tanuri A, Tee KK, Truong HM, van de Vijver DA, Vidal N, Yang C, Yang R, Yebra G, Ioannidis JP, Vandamme AM, Shafer RW. PMID: 25849352.
      View in: PubMed   Mentions: 83     Fields:    Translation:HumansCells
    25. Analysis of the history and spread of HIV-1 in Uganda using phylodynamics. J Gen Virol. 2015 Jul; 96(Pt 7):1890-8. Yebra G, Ragonnet-Cronin M, Ssemwanga D, Parry CM, Logue CH, Cane PA, Kaleebu P, Brown AJ. PMID: 25724670.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    26. Phylogenetic analyses reveal HIV-1 infections between men misclassified as heterosexual transmissions. AIDS. 2014 Aug 24; 28(13):1967-75. Hué S, Brown AE, Ragonnet-Cronin M, Lycett SJ, Dunn DT, Fearnhill E, Dolling DI, Pozniak A, Pillay D, Delpech VC, Leigh Brown AJ. PMID: 24991999.
      View in: PubMed   Mentions: 28     Fields:    Translation:HumansCells
    27. Baseline clinical HIV genotypes are a valid measure of transmitted drug resistance within the treatment-naive population. . 2013 Dec 15; 64(5):443-7. Ragonnet-Cronin M, Lee BE, Plitt SS, Zahariadis G, Merks H, Sandstrom PA, Brooks JI. PMID: 24231785.
      View in: PubMed   Mentions:
    28. Automated analysis of phylogenetic clusters. BMC Bioinformatics. 2013 Nov 06; 14:317. Ragonnet-Cronin M, Hodcroft E, Hué S, Fearnhill E, Delpech V, Brown AJ, Lycett S. PMID: 24191891.
      View in: PubMed   Mentions: 103     Fields:    Translation:HumansCells
    29. Genetic diversity as a marker for timing infection in HIV-infected patients: evaluation of a 6-month window and comparison with BED. J Infect Dis. 2012 Sep 01; 206(5):756-64. Ragonnet-Cronin M, Aris-Brosou S, Joanisse I, Merks H, Vallée D, Caminiti K, Rekart M, Krajden M, Cook D, Kim J, Malloch L, Sandstrom P, Brooks J. PMID: 22826337.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansCells
    30. Adaptive evolution of HIV at HLA epitopes is associated with ethnicity in Canada. PLoS One. 2012; 7(5):e36933. Ragonnet-Cronin M, Aris-Brosou S, Joanisse I, Merks H, Vallee D, Caminiti K, Sandstrom P, Brooks J. PMID: 22693560.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    31. HIV-1 modulates the tRNA pool to improve translation efficiency. Mol Biol Evol. 2011 Jun; 28(6):1827-34. van Weringh A, Ragonnet-Cronin M, Pranckeviciene E, Pavon-Eternod M, Kleiman L, Xia X. PMID: 21216840.
      View in: PubMed   Mentions: 30     Fields:    Translation:HumansCells
    32. Longitudinal phylogenetic surveillance identifies distinct patterns of cluster dynamics. . 2010 Sep; 55(1):102-8. Ragonnet-Cronin M, Ofner-Agostini M, Merks H, Pilon R, Rekart M, Archibald CP, Sandstrom PA, Brooks JI. PMID: 20622676.
      View in: PubMed   Mentions:
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