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List of works by Nuno Rodrigues Faria

A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage

scientific article published on 31 March 2020

A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes

scientific article

A sensitive assay for virus discovery in respiratory clinical samples

scientific article

A10 The evolution and molecular epidemiology of epidemic GII.17 noroviruses.

scientific article

Air travel is associated with intracontinental spread of dengue virus serotypes 1-3 in Brazil

scientific article

An integrated map of HIV genome-wide variation from a population perspective.

scientific article

Author Correction: Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance

scientific article published on 01 March 2020

Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: performance evaluation of the new REGA version 3 and seven other tools

scientific article published on 7 May 2013

Challenges in dengue research: A computational perspective.

scientific article

Characterisation of HIV-1 Molecular Epidemiology in Nigeria: Origin, Diversity, Demography and Geographic Spread

scientific article published on 26 February 2020

Characterisation of the HIV-1 Molecular Epidemiology in Nigeria: Origin, Diversity, Demography and Geographic Spread

scientific article published on 7 September 2018

Chikungunya virus outbreak in the Amazon region: replacement of the Asian genotype by an ECSA lineage

article

Circulation of chikungunya virus East/Central/South African lineage in Rio de Janeiro, Brazil

scientific article published in 2019

Clearance of Persistent SARS-CoV-2 RNA Detection in a NFκB-Deficient Patient in Association with the Ingestion of Human Breast Milk: A Case Report

scientific article published on 13 May 2022

Clusters of SARS-CoV-2 Lineage B.1.1.7 Infection after Vaccination with Adenovirus-Vectored and Inactivated Vaccines

scientific article published on 22 October 2021

Discovery of a persistent Zika virus lineage in Bahia, Brazil

article

Dispersion of the HIV-1 Epidemic in Men Who Have Sex with Men in the Netherlands: A Combined Mathematical Model and Phylogenetic Analysis

scientific article

Distinct Zika Virus Lineage in Salvador, Bahia, Brazil

scientific article

Distinct rates and patterns of spread of the major HIV-1 subtypes in Central and East Africa

scientific article published on 06 December 2019

Early Genomic Detection of Cosmopolitan Genotype of Dengue Virus Serotype 2, Angola, 2018

scientific article published on 01 April 2019

Early genomic detection of the Cosmopolitan Genotype of Dengue Virus 2 in Angola, 2018

scientific article published on 28 September 2018

Early identification of dengue virus lineage replacement in Brazil using portable genomic surveillance

scientific article published on 28 July 2019

Effect of Live Poultry Market Interventions on Influenza A(H7N9) Virus, Guangdong, China

scientific article published on December 2016

Emergence and persistence of the Chikungunya virus East-Central-South-African genotype in Northeast Brazil

scientific article (publication date: 27 February 2017)

Emergence and potential for spread of Chikungunya virus in Brazil

scientific article

Emergence of the Asian lineage of Zika virus in Angola: an outbreak investigation

scientific article published on 01 October 2019

Emergence of the Zika virus Asian lineage in Angola

scientific article published on 18 January 2019

Epidemic establishment and cryptic transmission of Zika virus in Brazil and the Americas

scientific article

Epidemiological and clinical characteristics of the COVID-19 epidemic in Brazil

scientific article published on 31 July 2020

Epidemiological and clinical characteristics of the early phase of the COVID-19 epidemic in Brazil

scientific article published on 29 April 2020

Epidemiological and ecological determinants of Zika virus transmission in an urban setting

scientific article published on 20 January 2017

Epidemiological and ecological determinants of Zika virus transmission in an urban setting.

scientific article published on 9 September 2017

Epidemiological history and genomic characterization of non-D1 HBV strains identified in Iran

scientific article published on 17 December 2014

Epidemiology of Chikungunya Virus in Bahia, Brazil, 2014-2015

scientific article

Epidemiology of the Zika Virus Outbreak in the Cabo Verde Islands, West Africa.

scientific article published on 15 March 2018

Epidemiology of the Zika virus outbreak in the Cabo Verde Islands, West Africa

scientific article published on 6 October 2017

Establishment and cryptic transmission of Zika virus in Brazil and the Americas

scientific article (publication date: 24 May 2017)

Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK

scientific article published on 08 January 2021

Evolution and epidemic spread of SARS-CoV-2 in Brazil

scientific article published on 23 July 2020

Evolution and epidemic spread of SARS-CoV-2 in Brazil

preprint article published on 12 June 2020

Evolutionary Dynamics of Oropouche Virus in South America

scientific article published on 14 February 2020

First report of Aedes albopictus infected by Dengue and Zika virus in a rural outbreak in Brazil

scientific article published on 12 March 2020

First report of multiple lineages of dengue viruses type 1 in Rio de Janeiro, Brazil

scientific article published on 03 August 2011

Genomic Epidemiology Reconstructs the Introduction and Spread of Zika Virus in Central America and Mexico.

scientific article published on 24 May 2018

Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China

scientific article published on 28 April 2020

Genomic Insights into Zika Virus Emergence and Spread

scientific article published in March 2018

Genomic Surveillance of Yellow Fever Virus Epizootic in São Paulo, Brazil, 2016 - 2018

scientific article published on 07 August 2020

Genomic Surveillance of Yellow Fever Virus Epizootic in São Paulo, Brazil, 2016 – 2018

scientific article published on 22 May 2019

Genomic and Epidemiological Surveillance of Zika Virus in the Amazon Region

scientific article published on 01 February 2020

Genomic and epidemiological characterisation of a dengue virus outbreak among blood donors in Brazil

scientific article published on 9 November 2017

Genomic and epidemiological monitoring of yellow fever virus transmission potential

scientific article published in Science

Genomic and epidemiological monitoring of yellow fever virus transmission potential

article

Genomic epidemiology of SARS-CoV-2 in Guangdong Province, China

scientific article published on 04 April 2020

Genomic epidemiology reveals multiple introductions of Zika virus into the United States ⬇️

scientific article

Genomic evidence of yellow fever virus in Aedes scapularis, southeastern Brazil, 2016

scientific article published on 07 February 2020

Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California ⬇️

scientific article published on 08 June 2020

Genomic, epidemiological and digital surveillance of Chikungunya virus in the Brazilian Amazon

article

Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil

scientific article

HIV Maintains an Evolving and Dispersed Population in Multiple Tissues during Suppressive Combined Antiretroviral Therapy in Individuals with Cancer.

scientific article published on 27 July 2016

HIV Type 1 transmission networks among men having sex with men and heterosexuals in Kenya

scientific article published on 17 September 2013

HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations

scientific article

Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci

scientific article (publication date: March 2013)

Increasing airline travel may facilitate co-circulation of multiple dengue virus serotypes in Asia

scientific article

Longitudinal Genetic Characterization Reveals That Cell Proliferation Maintains a Persistent HIV Type 1 DNA Pool During Effective HIV Therapy

scientific article

MVSE: An R-package that estimates a climate-driven mosquito-borne viral suitability index

scientific article published on 19 June 2019

MVSE: an R-package that estimates a climate-driven mosquito-borne viral suitability index

scientific article published on 5 July 2018

Madariaga and Venezuelan equine encephalitis virus seroprevalence in rodent enzootic hosts in Eastern and Western Panama

scientific article published on 29 August 2023

Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance

scientific article published on 13 January 2020

Mobile real-time surveillance of Zika virus in Brazil

scientific article published on 29 September 2016

Molecular archaeoparasitology identifies cultural changes in the Medieval Hanseatic trading centre of Lübeck

scientific article published on 03 October 2018

Molecular epidemiology reveals the role of war in the spread of HIV in Ukraine.

scientific article published on 16 January 2018

Monitoring social distancing and SARS-CoV-2 transmission in Brazil using cell phone mobility data

scientific article published on 05 May 2020

Multiple introductions of Zika virus into the United States revealed through genomic epidemiology

scientific article

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples

scientific article (publication date: 9 January 2017)

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples.

scientific article

Opsoclonus-myoclonus-ataxia syndrome associated with chikungunya and dengue virus co-infection

scientific article published on 01 August 2018

Past and future spread of the arbovirus vectors Aedes aegypti and Aedes albopictus

scientific article published on 04 March 2019

Persistence of chikungunya ECSA genotype and local outbreak in an upper medium class neighborhood in Northeast Brazil

scientific article published on 08 January 2020

Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak

Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak.

scientific article

Phylodynamics of influenza A(H3N2) in South America, 1999-2012.

scientific article

Phylodynamics of the HIV-1 CRF02_AG clade in Cameroon

scientific article

Phylogeographical footprint of colonial history in the global dispersal of human immunodeficiency virus type 2 group A.

scientific article published on 21 December 2011

Phylogeography of dengue virus serotype 4, Brazil, 2010-2011.

scientific article published on November 2012

Phylogeography of foot-and-mouth disease virus serotype O in Ecuador

scientific article published on 15 September 2012

Publisher Correction: Past and future spread of the arbovirus vectors Aedes aegypti and Aedes albopictus

scientific article published on 01 May 2019

Publisher Correction: Past and future spread of the arbovirus vectors Aedes aegypti and Aedes albopictus

correction of a scholarly article

Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases ⬇️

scientific article

Reconstruction and prediction of viral disease epidemics

scientific article published on 05 November 2018

Reconstruction of the Genetic History and the Current Spread of HIV-1 Subtype A in Germany

scientific article published on 29 May 2019

Report 21: Estimating COVID-19 cases and reproduction number in Brazil

scientific article published on 18 May 2020

Return of the founder Chikungunya virus to its place of introduction into Brazil is revealed by genomic characterization of exanthematic disease cases

scientific article published on 27 December 2019

Rooting human parechovirus evolution in time

scientific article (publication date: 15 July 2009)

Routes for COVID-19 importation in Brazil

scientific article (preprint)

Routes for COVID-19 importation in Brazil

scientific article published on 23 March 2020

SERAPHIM: studying environmental rasters and phylogenetically informed movements

scientific article published on 22 June 2016

Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable

scientific article published on 07 May 2020

Serial Interval Distribution of SARS-CoV-2 Infection in Brazil

scientific article published on 25 July 2020

Serial Interval Distribution of SARS-CoV-2 Infection in Brazil

scientific article published on 12 June 2020

Simultaneously reconstructing viral cross-species transmission history and identifying the underlying constraints

scientific article

Single cell analysis of lymph node tissue from HIV-1 infected patients reveals that the majority of CD4+ T-cells contain one HIV-1 DNA molecule

scientific article

Spread of Chikungunya Virus East/Central/South African Genotype in Northeast Brazil

scientific article published on October 2017

Spread of yellow fever virus outbreak in Angola and the Democratic Republic of the Congo 2015–16: a modelling study

scientific article (publication date: December 2016)

The Evolution and Transmission of Epidemic GII.17 Noroviruses

scientific article published on 24 May 2016

The HIV-1 reservoir in eight patients on long-term suppressive antiretroviral therapy is stable with few genetic changes over time

scientific article published on 25 November 2013

The changing epidemiological profile of HIV-1 subtype B epidemic in Ukraine

article

The effect of human mobility and control measures on the COVID-19 epidemic in China

scientific article (preprint)

The effect of human mobility and control measures on the COVID-19 epidemic in China

scientific article

The evolutionary dynamics of Oropouche Virus (OROV) in South America

scientific article published on 26 June 2019

Three-quarters attack rate of SARS-CoV-2 in the Brazilian Amazon during a largely unmitigated epidemic

scientific article

Toward a quantitative understanding of viral phylogeography

scientific article published on 28 October 2011

Tracing the Impact of Public Health Interventions on HIV-1 Transmission in Portugal Using Molecular Epidemiology

article

Unifying viral genetics and human transportation data to predict the global transmission dynamics of human influenza H3N2.

scientific article

Using viral gene sequences to compare and explain the heterogeneous spatial dynamics of virus epidemics

scientific article

Utilizing general human movement models to predict the spread of emerging infectious diseases in resource poor settings

scientific article published on 26 March 2019

Virus genomes reveal factors that spread and sustained the Ebola epidemic

scientific article (publication date: 12 April 2017)

Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic

article published in 2016

Yellow Fever Virus Reemergence and Spread in Southeast Brazil, 2016-2019

scientific article published on 12 December 2019

Yellow fever virus spread in Rio de Janeiro and Espírito Santo, 2016-2019: Phylodynamic assessment to improve intervention strategies

scientific article published on 23 July 2019

Zika virus complete genome from Salvador, Bahia, Brazil

scientific article (publication date: July 2016)

Zika virus in the Americas: Early epidemiological and genetic findings

scientific article

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