Thibaut Jombart
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Mathematics Biology
Thibaut Jombart's Degrees
- Bachelors Biology University of Strasbourg
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(Suggest an Edit or Addition)Thibaut Jombart's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- adegenet: a R package for the multivariate analysis of genetic markers (2008) (5437)
- Discriminant analysis of principal components: a new method for the analysis of genetically structured populations (2010) (3672)
- adegenet 1.3-1: new tools for the analysis of genome-wide SNP data (2011) (2148)
- Pandemic Potential of a Strain of Influenza A (H1N1): Early Findings (2009) (1932)
- The effect of control strategies to reduce social mixing on outcomes of the COVID-19 epidemic in Wuhan, China: a modelling study (2020) (1748)
- Ebola virus disease in West Africa--the first 9 months of the epidemic and forward projections. (2014) (1078)
- Global, regional, and national estimates of the population at increased risk of severe COVID-19 due to underlying health conditions in 2020: a modelling study (2020) (706)
- How to measure and test phylogenetic signal (2012) (693)
- An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia (2011) (675)
- Effectiveness of isolation, testing, contact tracing, and physical distancing on reducing transmission of SARS-CoV-2 in different settings: a mathematical modelling study (2020) (663)
- Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 (2021) (656)
- Effects of non-pharmaceutical interventions on COVID-19 cases, deaths, and demand for hospital services in the UK: a modelling study (2020) (654)
- Increased transmissibility and global spread of SARS-CoV-2 variants of concern as at June 2021 (2021) (551)
- Revealing cryptic spatial patterns in genetic variability by a new multivariate method (2008) (519)
- Community ecology in the age of multivariate multiscale spatial analysis (2012) (504)
- Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity (2010) (484)
- COVID-19 length of hospital stay: a systematic review and data synthesis (2020) (443)
- Improved inference of time-varying reproduction numbers during infectious disease outbreaks (2019) (359)
- Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis (2012) (340)
- Adephylo: New Tools for Investigating the Phylogenetic Signal in Biological Traits (2010) (290)
- Genetic markers in the playground of multivariate analysis (2009) (288)
- Estimation and Tests of Hierarchical F-Statistics (2015) (258)
- Routine childhood immunisation during the COVID-19 pandemic in Africa: a benefit–risk analysis of health benefits versus excess risk of SARS-CoV-2 infection (2020) (220)
- The impact of non-pharmaceutical interventions on SARS-CoV-2 transmission across 130 countries and territories (2020) (211)
- Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data (2014) (202)
- A Timescale for Evolution, Population Expansion, and Spatial Spread of an Emerging Clone of Methicillin-Resistant Staphylococcus aureus (2010) (181)
- A tutorial for Discriminant Analysis of Principal Components ( DAPC ) using adegenet 1 . 4-0 (2011) (163)
- Using a real-world network to model localized COVID-19 control strategies (2020) (153)
- After Ebola in West Africa--Unpredictable Risks, Preventable Epidemics. (2016) (152)
- Reconstructing disease outbreaks from genetic data: a graph approach (2010) (144)
- Climate shaped the worldwide distribution of human mitochondrial DNA sequence variation (2009) (134)
- Plasmodium falciparum Accompanied the Human Expansion out of Africa (2010) (128)
- The Ecological Dynamics of Fecal Contamination and Salmonella Typhi and Salmonella Paratyphi A in Municipal Kathmandu Drinking Water (2016) (121)
- Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis (2015) (121)
- treespace: Statistical exploration of landscapes of phylogenetic trees (2017) (120)
- Reconstructing the early global dynamics of under-ascertained COVID-19 cases and infections (2020) (114)
- Outbreak analytics: a developing data science for informing the response to emerging pathogens (2019) (111)
- When are pathogen genome sequences informative of transmission events? (2018) (111)
- Genome sequencing defines phylogeny and spread of methicillin-resistant Staphylococcus aureus in a high transmission setting (2015) (108)
- Deciphering the complex: Methodological overview of statistical models to derive OMICS‐based biomarkers (2013) (107)
- The role of rapid diagnostics in managing Ebola epidemics (2015) (103)
- Estimating the effectiveness of routine asymptomatic PCR testing at different frequencies for the detection of SARS-CoV-2 infections (2020) (102)
- Multiple independent introductions of Plasmodium falciparum in South America (2011) (101)
- Heterogeneities in the case fatality ratio in the West African Ebola outbreak 2013–2016 (2017) (97)
- Unraveling the drivers of MERS-CoV transmission (2016) (96)
- A high-resolution genomic analysis of multidrug-resistant hospital outbreaks of Klebsiella pneumoniae (2015) (95)
- Prospective use of whole genome sequencing (WGS) detected a multi-country outbreak of Salmonella Enteritidis (2016) (94)
- The impact of COVID-19 control measures on social contacts and transmission in Kenyan informal settlements (2020) (89)
- Response strategies for COVID-19 epidemics in African settings: a mathematical modelling study (2020) (89)
- Phylogenetic diversity and historical patterns of pandemic spread of Yersinia pestis (2010) (80)
- A fast likelihood solution to the genetic clustering problem (2018) (78)
- Exposure Patterns Driving Ebola Transmission in West Africa: A Retrospective Observational Study (2016) (75)
- Key data for outbreak evaluation: building on the Ebola experience (2017) (70)
- A simple approach to measure transmissibility and forecast incidence (2017) (68)
- Phylogenetic structure of European Salmonella Enteritidis outbreak correlates with national and international egg distribution network (2016) (68)
- High Levels of Antimicrobial Resistance among Escherichia coli Isolates from Livestock Farms and Synanthropic Rats and Shrews in the Mekong Delta of Vietnam (2014) (67)
- Ebola virus disease among children in West Africa. (2015) (66)
- Nonrandom Distribution of Azole Resistance across the Global Population of Aspergillus fumigatus (2019) (59)
- Putting phylogeny into the analysis of biological traits: a methodological approach. (2010) (59)
- Finding essential scales of spatial variation in ecological data: a multivariate approach. (2009) (58)
- The effect of travel restrictions on the geographical spread of COVID-19 between large cities in China: a modelling study (2020) (54)
- outbreaker2: a modular platform for outbreak reconstruction (2018) (51)
- Climate forcing of an emerging pathogenic fungus across a montane multi-host community (2016) (50)
- Bayesian inference of transmission chains using timing of symptoms, pathogen genomes and contact data (2019) (49)
- Phylogeography of Toxoplasma gondii points to a South American origin. (2017) (49)
- Ebola Virus Disease among Male and Female Persons in West Africa. (2016) (47)
- Estimating Potential Incidence of MERS-CoV Associated with Hajj Pilgrims to Saudi Arabia, 2014 (2014) (43)
- The impact of local and national restrictions in response to COVID-19 on social contacts in England: a longitudinal natural experiment (2021) (42)
- OutbreakTools: A new platform for disease outbreak analysis using the R software (2014) (41)
- A cross-sectional analysis of meteorological factors and SARS-CoV-2 transmission in 409 cities across 26 countries (2021) (41)
- Estimating the Severity and Subclinical Burden of Middle East Respiratory Syndrome Coronavirus Infection in the Kingdom of Saudi Arabia (2016) (39)
- Epidemic curves made easy using the R package incidence (2019) (38)
- Revisiting Guerry’s data: Introducing spatial constraints in multivariate analysis (2011) (36)
- A systematic review of MERS-CoV seroprevalence and RNA prevalence in dromedary camels: Implications for animal vaccination (2019) (36)
- Estimating number of cases and spread of coronavirus disease (COVID-19) using critical care admissions, United Kingdom, February to March 2020 (2020) (34)
- Modelling that shaped the early COVID-19 pandemic response in the UK (2021) (33)
- Inferring the number of COVID-19 cases from recently reported deaths (2020) (32)
- Consensus genetic structuring and typological value of markers using multiple co-inertia analysis (2007) (31)
- Within-population genetic diversity of Plasmodium falciparum vaccine candidate antigens reveals geographic distance from a Central sub-Saharan African origin. (2013) (30)
- Explosive nosocomial outbreak of SARS-CoV-2 in a rehabilitation clinic: the limits of genomics for outbreak reconstruction (2021) (29)
- How reliable are morphological and anatomical characters to distinguish European wildcats, domestic cats and their hybrids in France? (2014) (29)
- Contact tracing is an imperfect tool for controlling COVID-19 transmission and relies on population adherence (2021) (28)
- West African Ebola epidemic after one year--slowing but not yet under control. (2015) (28)
- Recommendations for the COVID-19 Response at the National Level Based on Lessons Learned from the Ebola Virus Disease Outbreak in the Democratic Republic of the Congo (2020) (28)
- Short-term forecasts to inform the response to the COVID-19 epidemic in the UK (2020) (28)
- The potential for vaccination-induced herd immunity against the SARS-CoV-2 B.1.1.7 variant (2021) (24)
- Estimating the impact of reopening schools on the reproduction number of SARS-CoV-2 in England, using weekly contact survey data (2021) (24)
- A graph-based evidence synthesis approach to detecting outbreak clusters: An application to dog rabies (2018) (24)
- Regular treatments of praziquantel do not impact on the genetic make-up of Schistosoma mansoni in Northern Senegal. (2013) (23)
- epicontacts: Handling, visualisation and analysis of epidemiological contacts. (2018) (22)
- An Eigenvalue test for spatial principal component analysis (2017) (22)
- apex: phylogenetics with multiple genes (2016) (20)
- Modelling the medium-term dynamics of SARS-CoV-2 transmission in England in the Omicron era (2022) (19)
- Statistical Exploration of Landscapes of Phylogenetic Trees (2015) (19)
- Characterising within-hospital SARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves (2022) (19)
- What questions we should be asking about COVID-19 in humanitarian settings: perspectives from the Social Sciences Analysis Cell in the Democratic Republic of the Congo (2020) (18)
- projections: Project Future Case Incidence (2020) (17)
- Implications of the school-household network structure on SARS-CoV-2 transmission under school reopening strategies in England (2021) (17)
- Linking genomics and population genetics with R (2017) (17)
- Population substructure and signals of divergent adaptive selection despite admixture in the sponge Dendrilla antarctica from shallow waters surrounding the Antarctic Peninsula (2019) (16)
- The cost of insecurity: from flare-up to control of a major Ebola virus disease hotspot during the outbreak in the Democratic Republic of the Congo, 2019 (2020) (16)
- Plasmodium falciparum mitochondrial genetic diversity exhibits isolation-by-distance patterns supporting a sub-Saharan African origin. (2013) (16)
- Patterns and dynamics of genetic diversity in Plasmodium falciparum: what past human migrations tell us about malaria. (2015) (16)
- Spatiotemporal dynamics in the early stages of the 2009 A/H1N1 influenza pandemic (2009) (15)
- Importance of patient bed pathways and length of stay differences in predicting COVID-19 hospital bed occupancy in England (2021) (14)
- Inferring the number of COVID-19 cases from recently reported deaths (2020) (14)
- A mathematical model of the transmission of middle East respiratory syndrome coronavirus in dromedary camels (Camelus dromedarius) (2019) (12)
- Towards an integrated ecosystem of R packages for the analysis of population genetic data (2017) (11)
- Real-time monitoring of COVID-19 dynamics using automated trend fitting and anomaly detection (2020) (11)
- Age-structured SEIR model for COVID-19 outbreak in Wuhan, China (2020) (11)
- pegas: Population and Evolutionary Genetics Analysis System (2020) (11)
- Population and Evolutionary Genetics Analysis System (2015) (11)
- epicontacts: Handling, visualisation and analysis of epidemiological contacts (2018) (9)
- Influenza: Making Privileged Data Public Response (2009) (8)
- epiflows: an R package for risk assessment of travel-related spread of disease. (2018) (8)
- Revealing cryptic genetic structuring in an urban population of stray cats (Felis silvestris catus). (2009) (8)
- Analysis of temporal trends in potential COVID-19 cases reported through NHS Pathways England (2020) (8)
- EpiJSON: A unified data-format for epidemiology (2015) (7)
- Erratum: Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis (2015) (6)
- Characterising within-hospital SARS-CoV-2 transmission events: a retrospective analysis integrating epidemiological and viral genomic data from a UK tertiary care setting across two pandemic waves (2021) (6)
- Publisher Correction: Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis (2019) (5)
- Why development of outbreak analytics tools should be valued, supported, and funded (2021) (4)
- Estimation and Tests of Hierarchical F-Statistics [R package hierfstat version 0.5-7] (2020) (4)
- Worldwide routine immunisation coverage regressed during the first year of the COVID-19 pandemic (2021) (4)
- The role of animals as a source of antimicrobial resistant nontyphoidal Salmonella causing invasive and non-invasive human disease in Vietnam (2020) (4)
- Measuring the unknown: An estimator and simulation study for assessing case reporting during epidemics (2021) (3)
- Exploratory Analysis of Genetic and Genomic Data [R package adegenet version 2.1.3] (2020) (3)
- Differential antimicrobial susceptibility profiles between symptomatic and asymptomatic non-typhoidal Salmonella infections in Vietnamese children (2020) (3)
- Estimating number of cases and spread of Coronavirus disease 2019 (COVID-19) in the United Kingdom using critical care admissions, February to March 2020 (2020) (3)
- Phylogenetic Methods for Multiple Gene Data (2015) (3)
- reconhub/incidence: Incidence version 1.7.2 (2020) (3)
- SARS-CoV-2 infection risk during delivery of childhood vaccination campaigns: a modelling study (2021) (3)
- How to improve outbreak response: a case study of integrated outbreak analytics from Ebola in Eastern Democratic Republic of the Congo (2021) (3)
- Relating Species Traits to Environment (2018) (2)
- mvmapper: Interactive spatial mapping of genetic structures (2018) (2)
- epiflows: an R package for risk assessment of travel-related spread of disease (2019) (2)
- Global and national estimates of the number of healthcare workers at high risk of SARS-CoV-2 infection (2021) (2)
- Using a real-world network to model localized COVID-19 control strategies (2020) (1)
- Perspective Piece Recommendations for the COVID-19 Response at the National Level Based on Lessons Learned from the Ebola Virus Disease Outbreak in the Democratic Republic of the Congo (2020) (1)
- Estimation of Transmissibility in the Early Stages of a Disease Outbreak [R package earlyR version 0.0.5] (2020) (1)
- Description of Species-Environment Relationships (2018) (1)
- Project Future Case Incidence [R package projections version 0.5.1] (2020) (1)
- Supplementary material from "Climate forcing of an emerging pathogenic fungus across a montane multihost community" (2016) (1)
- Useful R Functions and Data Structures (2018) (1)
- outbreak evaluation : building on the Ebola experience (2019) (1)
- Description of Environmental Variables Structures (2018) (1)
- epiflows: an R package for risk assessment of travel-related spread of disease. (2019) (1)
- Inferring COVID-19 cases from recent death (2020) (1)
- Modelling Vaccination Strategies for the Control of Marburg Virus Disease Outbreaks (2022) (1)
- and Andrea Manica mitochondrial DNA sequence variation Climate shaped the worldwide distribution of human (2009) (1)
- Multivariate Analysis Graphs (2018) (1)
- Functions to Work with 'incidence2' Objects [R package i2extras version 0.0.2] (2020) (0)
- reconhub/projections: 0.5.1 (2020) (0)
- A multivariate method to investigate the spatial patterns of the genetic variability (2008) (0)
- Evaluate Trending Models [R package trendeval version 0.0.1] (2020) (0)
- adegenet: adegenet version 2.0.1 (2016) (0)
- Tools for Handling EpiJSON (Epidemiology Data) Files (2015) (0)
- Time series analysis of routine immunisation coverage during the COVID-19 pandemic in 2021 shows continued global decline and increases in Zero Dose children (2023) (0)
- Description of Species Structures (2018) (0)
- Comparative methods in R hackathon (2008) (0)
- Analysing Patterns of Biodiversity (2018) (0)
- Handling, Visualisation and Analysis of Epidemiological Contacts [R package epicontacts version 1.1.0] (2017) (0)
- Bayesian reconstruction of household transmissions to infer the serial interval of COVID-19 by variants of concern: analysis from a prospective community cohort study (Virus Watch) (2022) (0)
- Analysing Spatial Structures (2018) (0)
- Title: Worldwide routine immunisation coverage regressed during the first year of the COVID-19 pandemic (2021) (0)
- R package epiflows: Predicting Disease Spread from Flow Data (2018) (0)
- Bayesian reconstruction of household transmissions to infer the serial interval of COVID-19 by variants of concern: analysis from a prospective community cohort study (Virus Watch). (2022) (0)
- Compute, Handle, Plot and Model Incidence of Dated Events [R package incidence version 1.7.3] (2020) (0)
- Analysing Changes in Co-structures (2018) (0)
- Identifying and Addressing 6 Key Questions when Using Data Driven Scrum (2021) (0)
- Erratum: Publisher Correction: Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis (Nature communications (2015) 6 (6740)) (2019) (0)
- Comparative assessment of methods for short-term forecasts of COVID-19 hospital admissions in England at the local level (2022) (0)
- Characterising within-hospital SARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves (2022) (0)
- trendbreaker 0.1.0: Detect Changes in Temporal Trends (2020) (0)
- Taking into Account Groups of Sites (2018) (0)
- Model Temporal Trends [R package trending version 0.0.1.0] (2020) (0)
- Population and Evolutionary Genetics Analysis System [R package pegas version 0.14] (2020) (0)
- Assessing the feasibility of Phase 3 vaccine trials against Marburg Virus Disease: a modelling study (2023) (0)
- An Eigenvalue test for spatial principal component analysis (2017) (0)
- apex: First release on CRAN (2015) (0)
- Publisher Correction: Characterising within-hospital SARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves (2022) (0)
- Inferring COVID-19 cases from deaths of confirmed cases (2020) (0)
- adegenet: New major version (2015) (0)
- The origin of Aboriginal Australians as inferred from the genomic sequence of a hundred-year-old lock of hair (2011) (0)
- apex: Version 1.0.1 submitted to CRAN (2015) (0)
- A Collection of Disease Outbreak Data [R package outbreaks version 1.9.0] (2019) (0)
- Compute, Handle and Plot Incidence of Dated Events [R package incidence2 version 0.2.0] (2020) (0)
- Bayesian reconstruction of household transmissions to infer the serial interval of COVID-19 by variants of concern: analysis from a prospective community cohort study (Virus Watch) (2022) (0)
- outbreaker2: a modular platform for outbreak reconstruction (2018) (0)
- thibautjombart/covid19_bed_occupancy: Second major release (2020) (0)
- Publisher Correction: Characterising within-hospital SARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves (2022) (0)
- The dudi Class (2018) (0)
- Analysing Phylogenetic Structures (2018) (0)
- A systematic review of MERS-CoV (Middle East Respiratory Syndrome Coronavirus) seroprevalence and viral RNA prevalence in dromedary camels: implications for animal vaccination (2019) (0)
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What Schools Are Affiliated With Thibaut Jombart?
Thibaut Jombart is affiliated with the following schools:
