• 2025
  Zhukova A, Gascuel O, Accounting for contact tracing in epidemiological birth-death models., PLoS Comput Biol 2025 May; 21(5): e1012461.
• 2024
  Hawkey J, Frézal L, Tran Dien A, Zhukova A, Brown D, Chattaway MA, Simon S, Izumiya H, Fields PI, De Lappe N, Kaftyreva L, Xu X, Isobe J, Clermont D, Njamkepo E, Akeda Y, Issenhuth-Jeanjean S, Makarova M, Wang Y, Hunt M, Jenkins BM, Ravel M, Guibert V, Serre E, Matveeva Z, Fabre L, Cormican M, Yue M, Zhu B, Morita M, Iqbal Z, Silva Nodari C, Pardos de la Gandara M, Weill FX, Genomic perspective on the bacillus causing paratyphoid B fever., Nat Commun 2024 Dec; 15(1): 10143.
• 2024
  Xie R, Adam DC, Hu S, Cowling BJ, Gascuel O, Zhukova A, Dhanasekaran V, Integrating contact tracing data to enhance outbreak phylodynamic inference: a deep learning approach., Mol Biol Evol 2024 Nov; (): .
• 2024
  Maestri R, Perez-Lamarque B, Zhukova A, Morlon H, Recent evolutionary origin and localized diversity hotspots of mammalian coronaviruses., Elife 2024 Aug; 13(): .
• 2024
  Morel M, Zhukova A, Lemoine F, Gascuel O, Accurate Detection of Convergent Mutations in Large Protein Alignments with ConDor., Genome Biol Evol 2024 Mar; (): .
• 2024
  Anjou C, Lotoux A, Zhukova A, Royer M, Caulat LC, Capuzzo E, Morvan C, Martin-Verstraete I, The multiplicity of thioredoxin systems meets the specific lifestyles of Clostridia., PLoS Pathog 2024 Feb; 20(2): e1012001.
• 2023
  Zhukova A, Hecht F, Maday Y, Gascuel O, Fast and Accurate Maximum-Likelihood Estimation of Multi-Type Birth-Death Epidemiological Models from Phylogenetic Trees., Syst Biol 2023 Sep; (): .
• 2023
  Holtz A, Baele G, Bourhy H, Zhukova A, Integrating full and partial genome sequences to decipher the global spread of canine rabies virus., Nat Commun 2023 Jul; 14(1): 4247.
• 2023
  Zhukova A, Dunn D, Gascuel O, Modeling Drug Resistance Emergence and Transmission in HIV-1 in the UK., Viruses 2023 May; 15(6): .
• 2022
  Voznica J, Zhukova A, Boskova V, Saulnier E, Lemoine F, Moslonka-Lefebvre M, Gascuel O, , Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks., Nat Commun 2022 Jul; 13(1): 3896.
• 2022
  Shaikh B, Smith LP, Vasilescu D, Marupilla G, Wilson M, Agmon E, Agnew H, Andrews SS, Anwar A, Beber ME, Bergmann FT, Brooks D, Brusch L, Calzone L, Choi K, Cooper J, Detloff J, Drawert B, Dumontier M, Ermentrout GB, Faeder JR, Freiburger AP, Fröhlich F, Funahashi A, Garny A, Gennari JH, Gleeson P, Goelzer A, Haiman Z, Hasenauer J, Hellerstein JL, Hermjakob H, Hoops S, Ison JC, Jahn D, Jakubowski HV, Jordan R, Kalaš M, König M, Liebermeister W, Sheriff RSM, Mandal S, McDougal R, Medley JK, Mendes P, Müller R, Myers CJ, Naldi A, Nguyen TVN, Nickerson DP, Olivier BG, Patoliya D, Paulevé L, Petzold LR, Priya A, Rampadarath AK, Rohwer JM, Saglam AS, Singh D, Sinha A, Snoep J, Sorby H, Spangler R, Starruß J, Thomas PJ, van Niekerk D, Weindl D, Zhang F, Zhukova A, Goldberg AP, Schaff JC, Blinov ML, Sauro HM, Moraru II, Karr JR, , BioSimulators: a central registry of simulation engines and services for recommending specific tools., Nucleic Acids Res 2022 May; (): .
• 2022
  Fillâtre P, Dufour MJ, Behillil S, Vatan R, Reusse P, Gabellec A, Velmans N, Montagne C, Geffroy Du Coudret S, Droumaguet E, Merour V, Enouf V, Buzelé R, Valence M, Guillotel E, Gagnière B, Baidaliuk A, Zhukova A, Tourdjman M, Thibault V, Grolhier C, Pronier C, Lescure FX, Simon-Loriere E, Costagliola D, Van Der Werf S, Tattevin P, Massart N, A new SARS-CoV-2 variant with high lethality poorly detected by RT-PCR on nasopharyngeal samples: an observational study., Clin Microbiol Infect 2022 Feb; 28(2): 298.e9-298.e15.
• 2022
  Seabra SG, Libin PJK, Theys K, Zhukova A, Potter BI, Nebenzahl-Guimaraes H, Gorbalenya AE, Sidorov IA, Pimentel V, Pingarilho M, de Vasconcelos ATR, Dellicour S, Khouri R, Gascuel O, Vandamme AM, Baele G, Cuypers L, Abecasis AB, , Genome-wide diversity of Zika virus: Exploring spatio-temporal dynamics to guide a new nomenclature proposal., Virus Evol 2022 ; 8(1): veac029.
• 2021
  Blassel* L, Zhukova* A, Villabona-Arenas CJ, Atkins KE, Hué S, Gascuel O, , Drug resistance mutations in HIV: new bioinformatics approaches and challenges., Curr Opin Virol 2021 Sep; 51(): 56-64.
• 2021
  Zhukova A, Voznica J, Dávila Felipe M, To TH, Pérez L, Martínez Y, Pintos Y, Méndez M, Gascuel O, Kouri V, Cuban history of CRF19 recombinant subtype of HIV-1., PLoS Pathog 2021 Aug; 17(8): e1009786.
• 2021
  Bennedbæk M, Zhukova A, Tang M-HE, Bennet J, Munderi P, Ruxrungtham K, Gisslen M, Worobey M, Lundgren JD, Marvig RL, for the INSIGHT START study group, Phylogenetic analysis of HIV-1 shows frequent cross-country transmission and local population expansions, Virus Evolution, 2021, veab055.
• 2021
  Grant R, Nguyen TTT, Dao MH, Pham HTT, Piorkowski G, Pham TDT, Cao TM, Huynh LTK, Nguyen QH, Vien LDK, Lemoine F, Zhukova A, Hoang DTN, Nguyen HT, Nguyen NT, Le LB, Ngo MNQ, Tran TC, Le NNT, Nguyen MN, Pham HT, Hoang TTD, Dang TV, Vu AT, Nguyen QNT, de Lamballerie X, Pham QD, Luong QC, Fontanet A, , Maternal and neonatal outcomes related to Zika virus in pregnant women in Southern Vietnam: An epidemiological and virological prospective analysis., Lancet Reg Health West Pac 2021 Jun; 11(): 100163.
• 2020
  Zhukova A, Blassel L, Lemoine F, Morel M, Voznica J, Gascuel O, Origin, evolution and global spread of SARS-CoV-2, Comptes Rendus Biologies 2020; 20 p.
• 2020
  Oprea* M, Njamkepo* E, Cristea* D, Zhukova* A, Clark CG, Kravetz AN, Monakhova E, Ciontea AS, Cojocaru R, Rauzier J, Damian M, Gascuel O, Quilici ML, Weill FX, , The seventh pandemic of cholera in Europe revisited by microbial genomics., Nat Commun 2020 10; 11(1): 5347.
• 2020
  Keating SM, Waltemath D, König M, Zhang F, Dräger A, Chaouiya C, Bergmann FT, Finney A, Gillespie CS, Helikar T, Hoops S, Malik-Sheriff RS, Moodie SL, Moraru II, Myers CJ, Naldi A, Olivier BG, Sahle S, Schaff JC, Smith LP, Swat MJ, Thieffry D, Watanabe L, Wilkinson DJ, Blinov ML, Begley K, Faeder JR, Gómez HF, Hamm TM, Inagaki Y, Liebermeister W, Lister AL, Lucio D, Mjolsness E, Proctor CJ, Raman K, Rodriguez N, Shaffer CA, Shapiro BE, Stelling J, Swainston N, Tanimura N, Wagner J, Meier-Schellersheim M, Sauro HM, Palsson B, Bolouri H, Kitano H, Funahashi A, Hermjakob H, Doyle JC, Hucka M, SBML Level 3 Community members , SBML Level 3: an extensible format for the exchange and reuse of biological models., Mol. Syst. Biol. 2020 Aug; 16(8): e9110.
• 2020
  Zhukova A, Gascuel O, Duchene S, Ayres D, Lemey P & Baele G, Efficiently Analysing Large Viral Data Sets in Computational Phylogenomics, In Phylogenetics in the Genomic Era, Scornavacca C Delsuc F & Galtier N (eds). 2020; 5.3:1--5.3:43.
• 2019
  Ishikawa* SA, Zhukova* A, Iwasaki W, Gascuel O, A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios, Mol. Biol. Evol. 2019 Sep;36(9):2069-2085.
• 2017
  Zhukova A, Cutino-Moguel T, Gascuel O, Pillay D, The Role of Phylogenetics as a Tool to Predict the Spread of Resistance, J. Infect. Dis. 2017 12;216(suppl_9):S820-S823.
• 2017
  Zhukova A, Fernandes LG, Hugon P, Pappas CJ, Sismeiro O, Coppée JY, Becavin C, Malabat C, Eshghi A, Zhang JJ, Yang FX, Picardeau M, Genome-Wide Transcriptional Start Site Mapping and sRNA Identification in the Pathogen Leptospira interrogans, Front Cell Infect Microbiol 2017;7:10.
• 2016
  Waltemath D, Karr J, Bergmann F, Chelliah V, Hucka M, Krantz M, Liebermeister W, Mendes P, Myers C, Pir P, Alaybeyoglu B, Aranganathan N, Baghalian K, Bittig A, Burke P, Cantarelli M, Chew Y, Costa R, Cursons J, Czauderna T, Goldberg A, Gomez H, Hahn J, Hameri T, Gardiol D, Kazakiewicz D, Kiselev I, Knight-Schrijver V, Knupfer C, Konig M, Lee D, Lloret-Villas A, Mandrik N, Medley J, Moreau B, Naderi-Meshkin H, Palaniappan S, Priego-Espinosa D, Scharm M, Sharma M, Smallbone K, Stanford N, Song JH, Theile T, Tokic M, Tomar N, Toure V, Uhlendorf J, Varusai T, Watanabe L, Wendland F, Wolfien M, Yurkovich J, Zhu Y, Zardilis A, Zhukova A, Schreiber F, Toward community standards and software for whole-cell modeling, IEEE Trans Biomed Eng 2016 Jun;.
• 2015
  Zhukova A, Sherman DJ, Mimoza: web-based semantic zooming and navigation in metabolic networks, BMC Syst Biol 2015;9:10.
• 2015
  Loira N, Zhukova A, Sherman DJ, Pantograph: A template-based method for genome-scale metabolic model reconstruction, J Bioinform Comput Biol 2015 Apr;13(2):1550006.
• 2014
  Zhukova A, Sherman DJ, Knowledge-based generalization of metabolic models, J. Comput. Biol. 2014 Jul;21(7):534-47.
• 2014
  Zhukova A, Sherman DJ, Knowledge-based generalization of metabolic networks: a practical study, J Bioinform Comput Biol 2014 Apr;12(2):1441001.
• 2012
  Zhukova A, Adams R, Laibe C, Le Novère N, LibKiSAO: a Java library for Querying KiSAO, BMC Res Notes 2012;5:520.
• 2011
  Courtot* M, Juty* N, Knüpfer* C, Waltemath* D, Zhukova* A, Dräger A, Dumontier M, Finney A, Golebiewski M, Hastings J, Hoops S, Keating S, Kell DB, Kerrien S, Lawson J, Lister A, Lu J, Machne R, Mendes P, Pocock M, Rodriguez N, Villeger A, Wilkinson DJ, Wimalaratne S, Laibe C, Hucka M, Le Novère N, Controlled vocabularies and semantics in systems biology, Mol. Syst. Biol. 2011;7:543.
• 2010
  Malone J, Holloway E, Adamusiak T, Kapushesky M, Zheng J, Kolesnikov N, Zhukova A, Brazma A, Parkinson H, Modeling sample variables with an Experimental Factor Ontology, Bioinformatics 2010 Apr;26(8):1112-8.