Timeline

Anna Zhukova

Permanent Researcher

29 May 2025

publication

Accounting for contact tracing in epidemiological birth-death models.

10 Dec 2024

publication

Genomic perspective on the bacillus causing paratyphoid B fever.

05 Nov 2024

publication

Integrating contact tracing data to enhance outbreak phylodynamic inference: a deep learning approach.

06 Sep 2024

project

Studying partner notification impact on pathogen epidemic control

06 Sep 2024

software

bdct

06 Sep 2024

software

treesimulator

05 Sep 2024

software

PyBDEI

05 Sep 2024

software

PhyloDeep

28 Aug 2024

publication

Recent evolutionary origin and localized diversity hotspots of mammalian coronaviruses.

21 Mar 2024

software

ConDor: Detection of Convergent Mutations in Large Protein Alignments

07 Mar 2024

publication

Accurate Detection of Convergent Mutations in Large Protein Alignments with ConDor.

01 Feb 2024

publication

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

03 Oct 2023

team

Evolutionary dynamics of infectious diseases

13 Sep 2023

publication

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

17 Jul 2023

publication

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

25 May 2023

publication

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

06 Jul 2022

publication

Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks.

07 May 2022

publication

BioSimulators: a central registry of simulation engines and services for recommending specific tools.

08 Feb 2022

event

DCB Seminar Series – Mary Dunlop – Cell-to-Cell Heterogeneity and Methods for Quantification and Control

01 Feb 2022

publication

A new SARS-CoV-2 variant with high lethality poorly detected by RT-PCR on nasopharyngeal samples: an observational study.

01 Jan 2022

publication

Genome-wide diversity of Zika virus: Exploring spatio-temporal dynamics to guide a new nomenclature proposal.

22 Dec 2021

course

Phylogenetics, Molecular Epidemiology and Phylodynamics – Montevideo 2021

30 Nov 2021

course

Introduction à la Phylogénie Moléculaire : Concepts, méthodes et interprétation

29 Sep 2021

course

Large phylogenies module (COVEME)

29 Sep 2021

course

Molecular evolution and phylogenetics module (IBT 2021 H3ABioNet)

28 Sep 2021

publication

Drug resistance mutations in HIV: new bioinformatics approaches and challenges.

09 Aug 2021

publication

Cuban history of CRF19 recombinant subtype of HIV-1.

09 Jun 2021

publication

Phylogenetic analysis of HIV-1 shows frequent cross-country transmission and local population expansions

01 Jun 2021

publication

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

24 Nov 2020

publication

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

22 Oct 2020

publication

The seventh pandemic of cholera in Europe revisited by microbial genomics.

01 Aug 2020

publication

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

30 Jul 2020

course

Molecular evolution and phylogenetics module (IBT 2020 H3ABioNet)

15 May 2020

course

minicourse Introduction to Phylogenetics – CentraleSupélec

15 Apr 2020

publication

Efficiently Analysing Large Viral Data Sets in Computational Phylogenomics

26 Mar 2020

project

The dynamics of HIV-1 epidemics in Cuba (Campus France)

12 Mar 2020

project

Phylogeography

12 Mar 2020

course

Introduction to Molecular Phylogenetics – ENS Paris

12 Mar 2020

event

MCEB 2020

09 Nov 2019

course

Behind Evolutionary Trees: Mathematics and Algorithms in Phylogenetics – Montevideo 2019

09 Nov 2019

course

Mathematical and Computational methods for Phylogenetics and Evolutionary Epidemiology – Havana 2019

09 Nov 2019

course

Introduction à la Phylogénie Moléculaire : Concepts, méthodes et interprétation

01 Sep 2019

publication

A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios

04 Jun 2019

event

MCEB 2019

04 Jun 2019

course

Introduction à la phylogénie moléculaire

19 Jul 2018

course

Scientific Programming in Python

19 Jul 2018

course

Introduction to Python Programming

19 Jul 2018

course

Introduction to data analysis

19 Jul 2018

software

PastML

19 Jul 2018

project

The phylodynamics of partner notification and contact tracing in HIV epidemics

19 Jul 2018

project

Bioconvert

26 Jun 2018

course

C3BI Course: Introduction to Molecular Phylogenetics – Hong Kong 2018

01 Jun 2018

project

Ancestral Reconstruction

11 Apr 2018

event

MCEB 2018

23 Oct 2017

course

INTRODUCTION À LA PHYLOGÉNIE MOLÉCULAIRE : CONCEPTS, METHODES ET OUTILS

06 Oct 2017

publication

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

10 May 2017

event

MCEB 2017

19 Jan 2017

publication

Genome-Wide Transcriptional Start Site Mapping and sRNA Identification in the Pathogen Leptospira interrogans

14 Oct 2016

project

HIV-1 Drug Resistance Mutation analysis

14 Oct 2016

project

Virogenesis

10 Jun 2016

publication

Toward community standards and software for whole-cell modeling

10 May 2016

project

Systems biology of cell infection by the bacterial pathogen Listeria monocytogenes

26 Jun 2015

team

Bioinformatics and Biostatistics HUB

26 Feb 2015

publication

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

08 Jan 2015

publication

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

25 Apr 2014

publication

Knowledge-based generalization of metabolic models

06 Mar 2014

publication

Knowledge-based generalization of metabolic networks: a practical study

24 Sep 2012

publication

LibKiSAO: a Java library for Querying KiSAO

25 Oct 2011

publication

Controlled vocabularies and semantics in systems biology

03 Mar 2010

publication

A little guide for advanced search:

Accounting for contact tracing in epidemiological birth-death models.

Genomic perspective on the bacillus causing paratyphoid B fever.

Integrating contact tracing data to enhance outbreak phylodynamic inference: a deep learning approach.

Studying partner notification impact on pathogen epidemic control

bdct

treesimulator

PyBDEI

PhyloDeep

Recent evolutionary origin and localized diversity hotspots of mammalian coronaviruses.

ConDor: Detection of Convergent Mutations in Large Protein Alignments

Accurate Detection of Convergent Mutations in Large Protein Alignments with ConDor.

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

Evolutionary dynamics of infectious diseases

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

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

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

Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks.

BioSimulators: a central registry of simulation engines and services for recommending specific tools.

DCB Seminar Series – Mary Dunlop – Cell-to-Cell Heterogeneity and Methods for Quantification and Control

A new SARS-CoV-2 variant with high lethality poorly detected by RT-PCR on nasopharyngeal samples: an observational study.

Genome-wide diversity of Zika virus: Exploring spatio-temporal dynamics to guide a new nomenclature proposal.

Phylogenetics, Molecular Epidemiology and Phylodynamics – Montevideo 2021

Introduction à la Phylogénie Moléculaire : Concepts, méthodes et interprétation

Large phylogenies module (COVEME)

Molecular evolution and phylogenetics module (IBT 2021 H3ABioNet)

Drug resistance mutations in HIV: new bioinformatics approaches and challenges.

Cuban history of CRF19 recombinant subtype of HIV-1.

Phylogenetic analysis of HIV-1 shows frequent cross-country transmission and local population expansions

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

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

The seventh pandemic of cholera in Europe revisited by microbial genomics.

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

Molecular evolution and phylogenetics module (IBT 2020 H3ABioNet)

minicourse Introduction to Phylogenetics – CentraleSupélec

Efficiently Analysing Large Viral Data Sets in Computational Phylogenomics

The dynamics of HIV-1 epidemics in Cuba (Campus France)

Phylogeography

Introduction to Molecular Phylogenetics – ENS Paris

MCEB 2020

Behind Evolutionary Trees: Mathematics and Algorithms in Phylogenetics – Montevideo 2019

Mathematical and Computational methods for Phylogenetics and Evolutionary Epidemiology – Havana 2019

Introduction à la Phylogénie Moléculaire : Concepts, méthodes et interprétation

A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios

MCEB 2019

Introduction à la phylogénie moléculaire

Scientific Programming in Python

Introduction to Python Programming

Introduction to data analysis

PastML

The phylodynamics of partner notification and contact tracing in HIV epidemics

Bioconvert

C3BI Course: Introduction to Molecular Phylogenetics – Hong Kong 2018

Ancestral Reconstruction

MCEB 2018

INTRODUCTION À LA PHYLOGÉNIE MOLÉCULAIRE : CONCEPTS, METHODES ET OUTILS

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

MCEB 2017

Genome-Wide Transcriptional Start Site Mapping and sRNA Identification in the Pathogen Leptospira interrogans

HIV-1 Drug Resistance Mutation analysis

Virogenesis

Toward community standards and software for whole-cell modeling

Systems biology of cell infection by the bacterial pathogen Listeria monocytogenes

Bioinformatics and Biostatistics HUB

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

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

Knowledge-based generalization of metabolic models

Knowledge-based generalization of metabolic networks: a practical study

LibKiSAO: a Java library for Querying KiSAO

Controlled vocabularies and semantics in systems biology

Modeling sample variables with an Experimental Factor Ontology