Personal information

Websites & social links

personal page @ Institut Pasteur
Google scholar

Other IDs

SciProfiles: 2899907

Keywords

phylogenetics, phylogeography, phylodynamics, mathematical modelling, algorithms, ontologies, metabolic modelling

Countries

France, United Kingdom, Russia

Activities

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Employment (8)

Institut Pasteur: Paris, FR

2024-04 to present | Research Fellow (Chargée de Recherche) (Computational Biology)
Employment
Source: Self-asserted source
Anna Zhukova

Institut Pasteur: Paris, FR

2015-11 to 2024-03 | Research Engineer (Computational Biology)
Employment
Source: Self-asserted source
Anna Zhukova

Institut de Biochimie et Génétique Cellulaires: Bordeaux, Nouvelle-Aquitaine, FR

2014-10 to 2015-11 | Postdoc
Employment
Source: Self-asserted source
Anna Zhukova

Inria Centre de recherche Bordeaux Sud-Ouest: Talence, Aquitaine, FR

2011-10 to 2014-12 | PhD researcher
Employment
Source: Self-asserted source
Anna Zhukova

European Bioinformatics Institute: Cambridge, GB

2011-03 to 2011-08 | trainee
Employment
Source: Self-asserted source
Anna Zhukova

Inria Bordeaux - Sud-Ouest Research Centre: Talence, FR

2010-09 to 2010-12 | intern
Employment
Source: Self-asserted source
Anna Zhukova

SwiftTeams: St. Petersburg, RU

2008 to 2010 | Junior software developer
Employment
Source: Self-asserted source
Anna Zhukova

European Bioinformatics Institute: Cambridge, GB

2009-08 to 2009-09 | trainee
Employment
Source: Self-asserted source
Anna Zhukova

Education and qualifications (2)

University of Bordeaux: Bordeaux, FR

2011-10 to 2014-12 | PhD
Qualification
Source: Self-asserted source
Anna Zhukova

Saint Petersburg State University: St. Petersburg, RU

2005-09 to 2010-06 | Specialist (eq. BSc+MSc) (Mathematics and Mechanics)
Qualification
Source: Self-asserted source
Anna Zhukova

Works (37)

Genomic perspective on the bacillus causing paratyphoid B fever

Nature Communications
2024-12-10 | Journal article
DOI: 10.1038/s41467-024-54418-4
Contributors: Jane Hawkey; Lise Frézal; Alicia Tran Dien; Anna Zhukova; Derek Brown; Marie Anne Chattaway; Sandra Simon; Hidemasa Izumiya; Patricia I. Fields; Niall De Lappe et al.
Source: check_circle
Crossref

Integrating Contact Tracing Data to Enhance Outbreak Phylodynamic Inference: A Deep Learning Approach

Molecular Biology and Evolution
2024-11-01 | Journal article
DOI: 10.1093/molbev/msae232
Contributors: Ruopeng Xie; Dillon C Adam; Shu Hu; Benjamin J Cowling; Olivier Gascuel; Anna Zhukova; Vijaykrishna Dhanasekaran; Tal Pupko
Source: check_circle
Crossref

Accounting for partner notification in epidemiological birth-death models

2024-09-09 | Preprint
DOI: 10.1101/2024.09.09.24313296
Contributors: Anna Zhukova; Olivier Gascuel
Source: check_circle
Crossref

Recent evolutionary origin and localized diversity hotspots of mammalian coronaviruses

2024-07-24 | Preprint
DOI: 10.7554/eLife.91745.2
Contributors: Renan Maestri; Benoît Perez-Lamarque; Anna Zhukova; Hélène Morlon
Source: check_circle
Crossref

Recent evolutionary origin and localized diversity hotspots of mammalian coronaviruses

2024-07-24 | Preprint
DOI: 10.7554/eLife.91745
Contributors: Renan Maestri; Benoît Perez-Lamarque; Anna Zhukova; Hélène Morlon
Source: check_circle
Crossref

Genomic perspective on the bacillus causing paratyphoid B fever

2024-06-18 | Preprint
DOI: 10.21203/rs.3.rs-4502330/v1
Contributors: François-Xavier Weill; Lise Frézal; Alicia Tran-Dien; Anna Zhukova; Derek Brown; Marie Chattaway; Sandra Simon; Hidemasa izumiya; Patricia Fields; Niall de Lappe et al.
Source: check_circle
Crossref

Recent evolutionary origin and localized diversity hotspots of mammalian coronaviruses

2024-02-28 | Preprint
DOI: 10.7554/eLife.91745.1
Contributors: Renan Maestri; Benoît Perez-Lamarque; Anna Zhukova; Hélène Morlon
Source: check_circle
Crossref

The multiplicity of thioredoxin systems meets the specific lifestyles of Clostridia.

PLoS pathogens
2024-02-08 | Journal article
DOI: 10.1101/2023.09.14.557728
DOI: 10.1371/journal.ppat.1012001
PMID: 38330058
Contributors: Anjou C; Lotoux A; Anna Zhukova; Royer M; Caulat LC; Capuzzo E; Morvan C; Isabelle Martin-verstraete
Source: Self-asserted source
Anna Zhukova
grade
Preferred source (of 2)‎

Fast and Accurate Maximum-Likelihood Estimation of Multi-Type Birth–Death Epidemiological Models from Phylogenetic Trees

Systematic Biology
2023-12-30 | Journal article
DOI: 10.1093/sysbio/syad059
Contributors: Anna Zhukova; Frédéric Hecht; Yvon Maday; Olivier Gascuel
Source: check_circle
Crossref

Integrating full and partial genome sequences to decipher the global spread of canine rabies virus

Nature Communications
2023-07-17 | Journal article
DOI: 10.1038/s41467-023-39847-x
Contributors: Andrew Holtz; Guy Baele; Hervé Bourhy; Anna Zhukova
Source: check_circle
Crossref
grade
Preferred source (of 3)‎

Modeling Drug Resistance Emergence and Transmission in HIV-1 in the UK

Viruses
2023-05 | Journal article | Author
DOI: 10.3390/v15061244
Contributors: Anna Zhukova; David Dunn; Olivier GASCUEL
Source: check_circle
Multidisciplinary Digital Publishing Institute
grade
Preferred source (of 4)‎

Recent evolutionary origin and localized diversity hotspots of mammalian coronaviruses

2023-03-09 | Preprint
DOI: 10.1101/2023.03.09.531875
Contributors: Renan Maestri; Benoît Perez-Lamarque; Anna Zhukova; Hélène Morlon
Source: check_circle
Crossref

Fast and Accurate Maximum-Likelihood Estimation of Multi-Type Birth-Death Epidemiological Models from Phylogenetic Trees

2022-08-03 | Preprint
DOI: 10.1101/2022.08.02.22278328
Contributors: Anna Zhukova; Frédéric Hecht; Yvon Maday; Olivier Gascuel
Source: check_circle
Crossref

Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks

Nature Communications
2022-07-06 | Journal article
DOI: 10.1101/2021.03.11.435006
DOI: 10.1038/s41467-022-31511-0
Part of ISSN: 2041-1723
Contributors: J. Voznica; A. Zhukova; V. Boskova; E. Saulnier; Frédéric Lemoine; M. Moslonka-Lefebvre; Olivier GASCUEL
Source: Self-asserted source
Anna Zhukova
grade
Preferred source (of 2)‎

Drug resistance mutations in HIV: new bioinformatics approaches and challenges

Current Opinion in Virology
2021-12 | Journal article
DOI: 10.1016/j.coviro.2021.09.009
Contributors: Luc Blassel; Anna Zhukova; Christian J Villabona-Arenas; Katherine E Atkins; Stéphane Hué; Olivier Gascuel
Source: check_circle
Crossref

A new SARS-CoV-2 variant poorly detected by RT-PCR on nasopharyngeal samples, with high lethality

Clinical Microbiology and Infection
2021-09-09 | Journal article
DOI: 10.1101/2021.05.05.21256690
Source: Self-asserted source
Anna Zhukova

Cuban history of CRF19 recombinant subtype of HIV-1

PLoS Pathogens
2021-08-09 | Journal article
DOI: 10.1371/journal.ppat.1009786
DOI: 10.1371/journal.ppat.1009786
HAL: hal-03228076
Contributors: Anna Zhukova; Jakub Voznica; Miraine Davila Felipe; Thu-Hien To; Lissette Pérez; Yenisleidys Martínez; Yanet Pintos; Melissa Méndez; Olivier Gascuel; Vivian Kouri
Source: Self-asserted source
Anna Zhukova via HAL
grade
Preferred source (of 4)‎

Accurate Detection of Convergent Mutations in Large Protein Alignments with ConDor

2021-07-01 | Preprint
DOI: 10.1101/2021.06.30.450558
Contributors: Marie Morel; Frédéric Lemoine; Anna Zhukova; Olivier Gascuel
Source: check_circle
Crossref

Maternal and neonatal outcomes related to Zika virus in pregnant women in Southern Vietnam: An epidemiological and virological prospective analysis

The Lancet Regional Health - Western Pacific
2021-06 | Journal article
DOI: 10.1016/j.lanwpc.2021.100163
Part of ISSN: 2666-6065
Source: Self-asserted source
Anna Zhukova

Phylogenetic Analysis of HIV-1 Shows Frequent Cross-Country Transmission and Local Population Expansions

Virus Evolution
2021-06-09 | Journal article
DOI: 10.1093/ve/veab055
Part of ISSN: 2057-1577
Source: Self-asserted source
Anna Zhukova

Efficiently Analysing Large Viral Data Sets in Computational Phylogenomics

2020 | Book chapter
HAL: hal-02536435
Contributors: Anna Zhukova; Olivier Gascuel; Sebastián Duchene; Daniel Ayres; Philippe Lemey; Guy Baele
Source: Self-asserted source
Anna Zhukova via HAL

Origin, evolution and global spread of SARS-CoV-2

Comptes Rendus Biologies
2020-11-24 | Journal article
DOI: 10.5802/crbiol.29
HAL: pasteur-03038752
PMID: 33274614
Contributors: Anna Zhukova; Luc Blassel; Frédéric Lemoine; Marie Morel; Jakub Voznica; Olivier Gascuel
Source: Self-asserted source
Anna Zhukova via HAL

Differing impacts of global and regional responses on SARS-CoV-2 transmission cluster dynamics

2020-11-06 | Preprint
DOI: 10.1101/2020.11.06.370999
Contributors: Brittany Rife Magalis; Andrea Ramirez-Mata; Anna Zhukova; Carla Mavian; Simone Marini; Frederic Lemoine; Mattia Prosperi; Olivier Gascuel; Marco Salemi
Source: check_circle
Crossref

The seventh pandemic of cholera in Europe revisited by microbial genomics

Nature Communications
2020-10-22 | Journal article
DOI: 10.1038/s41467-020-19185-y
HAL: pasteur-03036907
PMC: PMC7582136
PMID: 33093464
Contributors: Mihaela Oprea; Elisabeth Njamkepo; Daniela Cristea; Anna Zhukova; Clifford Clark; Anatoly Kravetz; Elena Monakhova; Adriana Ciontea; Radu Cojocaru; Jean Rauzier et al.
Source: Self-asserted source
Anna Zhukova via HAL

SBML Level 3: an extensible format for the exchange and reuse of biological models

Molecular Systems Biology
2020-08 | Journal article
DOI: 10.15252/msb.20199110
HAL: hal-02924909
Contributors: Sarah Keating; Frank Bergmann; Tomáš Helikar; Rahuman Malik‐sheriff; Ion Moraru; Martin Meier‐schellersheim; Richard Adams; Nicholas Allen; Bastian Angermann; Marco Antoniotti et al.
Source: Self-asserted source
Anna Zhukova via HAL

A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios

Molecular Biology and Evolution
2019-09-01 | Journal article
DOI: 10.1093/molbev/msz131
HAL: pasteur-02405083
PMID: 31127303
Contributors: Sohta Ishikawa; Anna Zhukova; Wataru Iwasaki; Olivier Gascuel
Source: Self-asserted source
Anna Zhukova via HAL

Genome-wide transcriptional start site mapping and sRNA identification in the pathogen Leptospira interrogans

Frontiers in cellular and infection microbiology
2017 | Journal article
Source: Self-asserted source
Anna Zhukova

The Role of Phylogenetics as a Tool to Predict the Spread of Resistance

Journal of Infectious Diseases
2017-11-15 | Journal article
DOI: 10.1093/infdis/jix411
HAL: lirmm-02078446
Contributors: Anna Zhukova; Teresa Cutino-Moguel; Olivier Gascuel; Deenan Pillay
Source: Self-asserted source
Anna Zhukova via HAL

Referee report. For: Finding the shortest path with PesCa: a tool for network reconstruction [version 2; referees: 1 approved, 2 approved with reservations]
Source: Self-asserted source
Anna Zhukova via BASE - Bielefeld Academic Search Engine

Toward community standards and software for whole-cell modeling

IEEE Transactions on Biomedical Engineering
2016 | Journal article
Source: Self-asserted source
Anna Zhukova

Mimoza: web-based semantic zooming and navigation in metabolic networks

BMC systems biology
2015 | Journal article
Source: Self-asserted source
Anna Zhukova

Pantograph: A template-based method for genome-scale metabolic model reconstruction

Journal of Bioinformatics and Computational Biology
2015-01-09 | Journal article
DOI: 10.1142/S0219720015500067
HAL: hal-01123733
Contributors: Nicolás Loira; Anna Zhukova; David James Sherman
Source: Self-asserted source
Anna Zhukova via HAL

Knowledge-based generalization of metabolic models

Journal of Computational Biology
2014 | Journal article
Source: Self-asserted source
Anna Zhukova

Knowledge-based generalization of metabolic networks: a practical study

Journal of bioinformatics and computational biology
2014 | Journal article
Source: Self-asserted source
Anna Zhukova

LibKiSAO: a Java Library for Querying KiSAO

BMC Research Notes
2012-09-24 | Journal article
DOI: 10.1186/1756-0500-5-520
HAL: hal-00734673
Contributors: Anna Zhukova; Richard Adams; Camille Laibe; Nicolas Le Novère
Source: Self-asserted source
Anna Zhukova via HAL

Controlled vocabularies and semantics in systems biology

Molecular systems biology
2011 | Journal article
Source: Self-asserted source
Anna Zhukova

Modeling sample variables with an Experimental Factor Ontology

Bioinformatics
2010 | Journal article
Source: Self-asserted source
Anna Zhukova

Peer review (21 reviews for 13 publications/grants)

Review activity for Bioinformatics (1)
Review activity for Biotechnology for biofuels (1)
Review activity for BMC systems biology. (1)
Review activity for F1000Research. (1)
Review activity for Genome biology and evolution. (1)
Review activity for Genome biology. (1)
Review activity for Methods in ecology and evolution. (1)
Review activity for Philosophical transactions. (1)
Review activity for PLoS computational biology. (6)
Review activity for PloS one. (1)
Review activity for Systematic biology. (4)
Review activity for Virus evolution. (1)
Review activity for Wellcome open research. (1)
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