• 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.