| Modeling sample variables with an Experimental Factor Ontology J Malone, E Holloway, T Adamusiak, M Kapushesky, J Zheng, ... Bioinformatics 26 (8), 1112-1118, 2010 | 574 | 2010 |
| Controlled vocabularies and semantics in systems biology M Courtot, N Juty, C Knüpfer, D Waltemath, A Zhukova, A Dräger, ... Molecular systems biology 7 (1), 543, 2011 | 341 | 2011 |
| SBML Level 3: an extensible format for the exchange and reuse of biological models SM Keating, D Waltemath, M König, F Zhang, A Dräger, C Chaouiya, ... Molecular systems biology 16 (8), e9110, 2020 | 228 | 2020 |
| A fast likelihood method to reconstruct and visualize ancestral scenarios SA Ishikawa, A Zhukova, W Iwasaki, O Gascuel Molecular biology and evolution 36 (9), 2069-2085, 2019 | 194 | 2019 |
| Toward community standards and software for whole-cell modeling D Waltemath, JR Karr, FT Bergmann, V Chelliah, M Hucka, M Krantz, ... IEEE Transactions on Biomedical Engineering 63 (10), 2007-2014, 2016 | 65 | 2016 |
| Genome-Wide Transcriptional Start Site Mapping and sRNA Identification in the Pathogen Leptospira interrogans A Zhukova, LG Fernandes, P Hugon, CJ Pappas, O Sismeiro, JY Coppée, ... Frontiers in cellular and infection microbiology 7, 10, 2017 | 53 | 2017 |
| Drug resistance mutations in HIV: new bioinformatics approaches and challenges L Blassel, A Zhukova, CJ Villabona-Arenas, KE Atkins, S Hué, O Gascuel Current opinion in virology 51, 56-64, 2021 | 41 | 2021 |
| Origin, evolution and global spread of SARS-CoV-2 A Zhukova, L Blassel, F Lemoine, M Morel, J Voznica, O Gascuel Comptes Rendus. Biologies 344 (1), 57-75, 2021 | 40 | 2021 |
| Pantograph: A template-based method for genome-scale metabolic model reconstruction N Loira, A Zhukova, DJ Sherman Journal of bioinformatics and computational biology 13 (02), 1550006, 2015 | 40 | 2015 |
| Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks J Voznica, A Zhukova, V Boskova, E Saulnier, F Lemoine, ... Nature Communications 13 (1), 3896, 2022 | 39* | 2022 |
| The seventh pandemic of cholera in Europe revisited by microbial genomics M Oprea, E Njamkepo, D Cristea, A Zhukova, CG Clark, AN Kravetz, ... Nature Communications 11 (1), 5347, 2020 | 27 | 2020 |
| BioSimulators: a central registry of simulation engines and services for recommending specific tools B Shaikh, LP Smith, D Vasilescu, G Marupilla, M Wilson, E Agmon, ... Nucleic acids research 50 (W1), W108-W114, 2022 | 21 | 2022 |
| A new SARS-CoV-2 variant poorly detected by RT-PCR on nasopharyngeal samples, with high lethality P Fillatre, MJ Dufour, S Behillil, R Vatan, P Reusse, A Gabellec, ... Clinical Microbiology and Infection, 2021 | 14* | 2021 |
| The multiplicity of thioredoxin systems meets the specific lifestyles of Clostridia C Anjou, A Lotoux, A Zhukova, M Royer, LC Caulat, E Capuzzo, C Morvan, ... PLoS Pathogens 20 (2), e1012001, 2024 | 10 | 2024 |
| The role of phylogenetics as a tool to predict the spread of resistance A Zhukova, T Cutino-Moguel, O Gascuel, D Pillay The Journal of Infectious Diseases 216 (suppl_9), S820-S823, 2017 | 8 | 2017 |
| Phylogenetic analysis of HIV-1 shows frequent cross-country transmission and local population expansions M Bennedbæk, A Zhukova, MHE Tang, J Bennet, P Munderi, ... Virus evolution 7 (2), veab055, 2021 | 7 | 2021 |
| Genome-wide diversity of Zika virus: Exploring spatio-temporal dynamics to guide a new nomenclature proposal SG Seabra, PJK Libin, K Theys, A Zhukova, BI Potter, ... Virus evolution 8 (1), veac029, 2022 | 6 | 2022 |
| Differing impacts of global and regional responses on SARS-CoV-2 transmission cluster dynamics BR Magalis, A Ramirez-Mata, A Zhukova, C Mavian, S Marini, F Lemoine, ... bioRxiv, 2020 | 6 | 2020 |
| Integrating full and partial genome sequences to decipher the global spread of canine rabies virus A Holtz, G Baele, H Bourhy, A Zhukova Nature Communications 14 (1), 4247, 2023 | 5* | 2023 |
| Knowledge-based generalization of metabolic models A Zhukova, DJ Sherman Journal of Computational Biology 21 (7), 534-547, 2014 | 5 | 2014 |
Olivier GascuelCNRS & Muséum National d'Histoire NaturelleVerified email at mnhn.fr
