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List of works by Túlio de Oliveira

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

scientific article

A genomics network established to respond rapidly to public health threats in South Africa

scientific article published on 18 August 2020

A specific subtype C of human immunodeficiency virus type 1 circulates in Brazil

scientific article published in January 2003

A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences

scientific article (publication date: July 2009)

A1 Pairwise diversity and tMRCA as potential markers of HIV infection recency.

scientific article published on 17 April 2018

A34 Automated profiling of the human virome from raw metagenomic data.

scientific article published on 05 March 2017

Adding a Voice to the Unique Ethical Considerations in Molecular HIV Surveillance

scientific article published on 01 October 2020

An affordable HIV-1 drug resistance monitoring method for resource limited settings

scientific article

An automated genotyping system for analysis of HIV-1 and other microbial sequences

scientific article published on 2 August 2005

An outbreak of HIV-1 subtype G among Italian injecting drug users

scientific article published on May 2007

Analysis of Viral Diversity in Relation to the Recency of HIV-1C Infection in Botswana

scientific article

Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity

scientific article published in July 2006

Author Correction: T cell responses to SARS-CoV-2 spike cross-recognize Omicron

scholarly article

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

BioAfrica's HIV-1 proteomics resource: combining protein data with bioinformatics tools

scientific article

Brief Report: Virologic Monitoring Can Be a Cost-Effective Strategy to Diagnose Treatment Failure on First-Line ART.

scientific article published on 17 October 2015

CD4+ T-cell Count may not be a Useful Strategy to Monitor Antiretroviral Therapy Response in HTLV-1/HIV Co-infected Patients

scientific article published on 16 February 2017

Circulating biomarkers of immune activation distinguish viral suppression from nonsuppression in HAART-treated patients with advanced HIV-1 subtype C infection.

scientific article published on 06 April 2014

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

scientific article published in 2019

Combining Phylogenetic and Network Approaches to Identify HIV-1 Transmission Links in San Mateo County, California

article

Comparative performance of the REGA subtyping tool version 2 versus version 1.

scientific article published on 12 October 2009

Comparison of SARS-CoV-2 sequencing using the ONT GridION and the Illumina MiSeq

scientific article published on 22 April 2022

Concentrated HIV subepidemics in generalized epidemic settings

scientific article

Conserved footprints of APOBEC3G on Hypermutated human immunodeficiency virus type 1 and human endogenous retrovirus HERV-K(HML2) sequences

scientific article published on 18 June 2008

Correction for Giovanetti et al., "Yellow Fever Virus Reemergence and Spread in Southeast Brazil, 2016-2019"

scientific article published on 18 May 2020

Current Affairs of Microbial Genome-Wide Association Studies: Approaches, Bottlenecks and Analytical Pitfalls

scientific article published on 01 January 2019

Declines in HIV incidence among men and women in a South African population-based cohort

scientific article published on 02 December 2019

Deep Sequencing Analysis of Human T Cell Lymphotropic Virus Type 1 Long Terminal Repeat 5' Region from Patients with Tropical Spastic Paraparesis/Human T Cell Lymphotropic Virus Type 1-Associated Myelopathy and Asymptomatic Carriers

scientific article

Deep sequencing analysis of Human T cell lymphotropic virus type 1 (HTLV-1) long terminal repeat (LTR) region of tropical spastic paraparesis (TSP)/HTLV-1 associated myelopathy (HAM) and asymptomatic carriers

scientific article published on 7 January 2014

Detection of a SARS-CoV-2 variant of concern in South Africa

scientific article

Detection of transmission clusters of HIV-1 subtype C over a 21-year period in Cape Town, South Africa

scientific article

Development and evaluation of an affordable real-time qualitative assay for determining HIV-1 virological failure in plasma and dried blood spots

scientific article published on 17 April 2013

Different epidemic potentials of the HIV-1B and C subtypes

scientific article published in May 2005

Diversity and molecular epidemiology of HIV-1 in Cape Town; 1984 to 2010.

scientific article published on 3 October 2011

Dolutegravir for first-line antiretroviral therapy in low-income and middle-income countries: uncertainties and opportunities for implementation and research

article by Jienchi Dorward et al published July 2018 in The lancet. HIV

Drug resistance in children at virological failure in a rural KwaZulu-Natal, South Africa, cohort.

scientific article published on 20 January 2014

Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report

scientific article published on 30 May 2020

Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report

scientific article published on 12 November 2020

Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant

scholarly article by Andrew Pollard published in 2021

Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage

scientific article published on 08 April 2022

Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa

scientific article

Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma

scientific article

Escape of SARS-CoV-2 501Y.V2 variants from neutralization by convalescent plasma

scientific article published on 26 January 2021

Ethical issues associated with HIV molecular epidemiology: a qualitative exploratory study using inductive analytic approaches

scientific article published on 07 October 2019

Evidence of long-lived founder virus in mother-to-child HIV transmission

scientific article

Evolution and molecular epidemiology of subtype C HIV-1 in Zimbabwe

scientific article

Extensive HIV-1 intra-host recombination is common in tissues with abnormal histopathology

scientific article

Field and classroom initiatives for portable sequence-based monitoring of dengue virus in Brazil

scientific article published on 16 April 2021

Functional characteristics of HIV-1 subtype C compatible with increased heterosexual transmissibility.

scientific article

Genetic characteristics, coreceptor usage potential and evolution of Nigerian HIV-1 subtype G and CRF02_AG isolates

scientific article

Genetic variability of human immunodeficiency virus-1 in Bahia state, Northeast, Brazil: high diversity of HIV genotypes.

scientific article published on March 2009

Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes

scientific article

Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes

scientific article published on 28 February 2020

Genome Detective: An Automated System for Virus Identification from High-throughput sequencing data

article by Michael Vilsker et al published 16 August 2018 in Computer applications in the biosciences : CABIOS

Genome-Wide Association Study of HIV Whole Genome Sequences Validated using Drug Resistance

scientific article

Genomic and Epidemiological Surveillance of Zika Virus in the Amazon Region

scientific article published on 01 February 2020

Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1

scientific article published on 20 July 2023

Genomic surveillance of Rift Valley fever virus: from sequencing to lineage assignment

scientific article published on 18 July 2022

HIV-1 Drug Resistance Mutations: Potential Applications for Point-of-Care Genotypic Resistance Testing

scientific article

HIV-1 drug resistance before initiation or re-initiation of first-line antiretroviral therapy in low-income and middle-income countries: a systematic review and meta-regression analysis

scientific article published on 30 November 2017

HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences

scientific article published on 25 May 2017

HIV-1 subtypes B and C unique recombinant forms (URFs) and transmitted drug resistance identified in the Western Cape Province, South Africa

scientific article (publication date: 2014)

HTLV-1aA introduction into Brazil and its association with the trans-Atlantic slave trade.

scientific article

High Rates of Transmission of Drug-resistant HIV in Aruba Resulting in Reduced Susceptibility to the WHO Recommended First-line Regimen in Nearly Half of Newly Diagnosed HIV-infected Patients

scientific article published on 9 March 2017

High Resolution analysis of Transmission Dynamics of Sars-Cov-2 in Two Major Hospital Outbreaks in South Africa Leveraging Intrahost Diversity

scientific article published on 16 November 2020

High level of HIV-2 false positivity in KwaZulu-Natal province: a region of South Africa with a very high HIV-1 subtype C prevalence

scientific article published on 19 August 2013

High percentage of undiagnosed HIV cases within a hyperendemic South African community: a population-based study

scientific article published on 24 November 2017

High-levels of acquired drug resistance in adult patients failing first-line antiretroviral therapy in a rural HIV treatment programme in KwaZulu-Natal, South Africa

scientific article (publication date: 2013)

High-resolution molecular epidemiology and evolutionary history of HIV-1 subtypes in Albania

scientific article

History and origin of the HIV-1 subtype C epidemic in South Africa and the greater southern African region

scientific article

Human Retrovirus Codon Usage from tRNA Point of View: Therapeutic Insights

scientific article published on 10 October 2013

Human T cell lymphotropic virus type 1 (HTLV-1) infection increases the CD4 count in human immunodeficiency virus type 1 (HIV-1) infected patients submitted to antiretroviral therapy (ARV). ⬇️

scientific article published on 7 January 2014

Identification and characterization of previously described epitopes in HIV-1 subtypes B, C, F and BF in Brazil

article

Identifying Recent HIV Infections: From Serological Assays to Genomics

scientific article

Impact of drug resistance-associated amino acid changes in HIV-1 subtype C on susceptibility to newer nonnucleoside reverse transcriptase inhibitors

scientific article

Impact of next generation sequencing defined HIV pre-treatment drug resistance on virological outcomes in the ANRS 12249 treatment as prevention trial

article

Impact of pretreatment low-abundance HIV-1 drug-resistant variants on virological failure among HIV-1/TB-co-infected individuals

scientific article published on 08 August 2020

Implementing HIV-1 genotypic resistance testing in antiretroviral therapy programs in Africa: needs, opportunities, and challenges

scientific article published on October 2013

Implementing antiretroviral resistance testing in a primary health care HIV treatment programme in rural KwaZulu-Natal, South Africa: early experiences, achievements and challenges

scientific article

Improving HIV proteome annotation: new features of BioAfrica HIV Proteomics Resource

scientific article published on 17 April 2016

Incidence rate estimation, periodic testing and the limitations of the mid-point imputation approach

scientific article published on 9 August 2017

Increasing HIV-1 Drug Resistance Between 2010 and 2012 in Adults Participating in Population-Based HIV Surveillance in Rural KwaZulu-Natal, South Africa

scientific article published on 22 March 2016

Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis

article

Libya should stop denying scientific evidence on HIV

scientific article published in Nature

Managing and assembling population-scale data streams, tools and workflows to plan for future pandemics within the INFORM-Africa Consortium

scientific article published in 2023

Mapping sites of positive selection and amino acid diversification in the HIV genome: an alternative approach to vaccine design?

scientific article

Modeling HIV-1 drug resistance as episodic directional selection

scientific article

Moderate to high levels of pre-treatment HIV drug resistance in KwaZulu-Natal Province, South Africa

article

Molecular Characterization of the Human Immunodeficiency Virus Type 1 in Women and Their Vertically Infected Children

scientific article

Molecular epidemiology: HIV-1 and HCV sequences from Libyan outbreak

scientific article published on December 2006

Mosaic genomes of the six major primate lentivirus lineages revealed by phylogenetic analyses

scientific article published on July 2003

Mutational Correlates of Virological Failure in Individuals Receiving a WHO-Recommended Tenofovir-Containing First-Line Regimen: An International Collaboration

scientific article published on 19 March 2017

New SARS-CoV-2 Variants - Clinical, Public Health, and Vaccine Implications

scientific article

Next Generation Sequencing and Bioinformatics Analysis of Family Genetic Inheritance

scientific article published on 23 October 2020

Next-Generation Whole Genome Sequencing: Opportunities and Challenges

scientific article published on 09 December 2018

Novel evolutionary analyses of full-length HIV type 1 subtype C molecular clones from Cape Town, South Africa

scientific article published on November 2002

Occult HIV-1 drug resistance to thymidine analogues following failure of first-line tenofovir combined with a cytosine analogue and nevirapine or efavirenz in sub Saharan Africa: a retrospective multi-centre cohort study

scientific article

Omicron extensively but incompletely escapes Pfizer BNT162b2 neutralization

scientific article

Omicron extensively but incompletely escapes Pfizer BNT162b2 neutralization

scientific article published in February 2022

Omicron infection enhances Delta antibody immunity in vaccinated persons

scientific article published in July 2022

Origin, imports and exports of HIV-1 subtype C in South Africa: A historical perspective

scientific article published on 12 July 2016

PANGEA-HIV: phylogenetics for generalised epidemics in Africa

scientific article published on March 2015

Pairwise diversity and tMRCA as potential markers for HIV infection recency

scientific article published on February 2017

Pervasive and non-random recombination in near full-length HIV genomes from Uganda

scientific article published on 01 January 2020

Phylogenetic studies of transmission dynamics in generalized HIV epidemics: an essential tool where the burden is greatest?

scientific article

Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of human immunodeficiency virus type 1.

scientific article

Predicted antiviral activity of tenofovir versus abacavir in combination with a cytosine analogue and the integrase inhibitor dolutegravir in HIV-1-infected South African patients initiating or failing first-line ART

article

Prevalence of HIV type-1 drug-associated mutations in pre-therapy patients in the Free State, South Africa

scientific article published in January 2009

Primary HIV-1 Drug Resistant Minority Variants

scientific article

Primary drug resistance in South Africa: data from 10 years of surveys

scientific article

Protocol: Leveraging a demographic and health surveillance system for Covid-19 Surveillance in rural KwaZulu-Natal

scientific article published on 29 May 2020

Public database for HIV drug resistance in southern Africa

scientific article published on April 2010

Quantifying HIV transmission flow between high-prevalence hotspots and surrounding communities: a population-based study in Rakai, Uganda

scientific article published on 14 January 2020

Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

scientific article

Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

scientific article published on 07 January 2022

Rates of virological suppression and drug resistance in adult HIV-1-positive patients attending primary healthcare facilities in KwaZulu-Natal, South Africa

scientific article published on 3 August 2017

Rates of virological suppression and drug resistance in adult HIV-1-positive patients attending primary healthcare facilities in KwaZulu-Natal, South Africa

scientific article published in November 2017

Re-mapping the molecular features of the human immunodeficiency virus type 1 and human T-cell lymphotropic virus type 1 Brazilian sequences using a bioinformatics unit established in Salvador, Bahia, Brazil, to give support to the viral epidemiology

scientific article published on May 2007

Reduced efficacy of HIV-1 integrase inhibitors in patients with drug resistance mutations in reverse transcriptase

scientific article published on 01 December 2020

RegaDB: community-driven data management and analysis for infectious diseases

scientific article

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

SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma

scientific article

SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse

scientific article published in 2021

SARS-CoV-2 prolonged infection during advanced HIV disease evolves extensive immune escape

publication published on 14 January 2022

SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy

scientific article published on 21 April 2021

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

scientific article published on 07 May 2020

Searching for virus phylotypes ⬇️

scientific article published on January 17, 2013

Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function

scientific article published on 01 April 2022

Sensitive Next-Generation Sequencing Method Reveals Deep Genetic Diversity of HIV-1 in the Democratic Republic of the Congo

scientific article

Sequencing and phylogenetic analysis of near full-length HIV-1 subtypes A, B, G and unique recombinant AC and AD viral strains identified in South Africa

scientific article

Sixteen novel lineages of SARS-CoV-2 in South Africa

scientific article

Social Disequilibrium and the Risk of HIV Acquisition: A Multilevel Study in Rural KwaZulu-Natal Province, South Africa

scientific article published on 10 March 2017

Sociobehavioral and community predictors of unsuppressed HIV viral load: multilevel results from a hyperendemic rural South African population

scientific article published on 01 March 2019

Southern African Treatment Resistance Network (SATuRN) RegaDB HIV drug resistance and clinical management database: supporting patient management, surveillance and research in southern Africa

scientific article published on 6 February 2014

Space-time clustering of recently-diagnosed tuberculosis and impact of ART scale-up: Evidence from an HIV hyper-endemic rural South African population

scientific article published on 24 July 2019

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)

T cell responses to SARS-CoV-2 spike cross-recognize Omicron

scientific article published in March 2022

The Art of HIV Elimination: Past and Present Science

scientific article

The Development of Computational Biology in South Africa: Successes Achieved and Lessons Learnt

scientific article published on 4 February 2016

The HIV type 1 epidemic in Bulgaria involves multiple subtypes and is sustained by continuous viral inflow from West and East European countries

scientific article

The HIV-1 subtype C epidemic in South America is linked to the United Kingdom

scientific article

The RNA virus database

scientific article published on 23 October 2008

The biological and clinical significance of emerging SARS-CoV-2 variants

scientific article

The effect of interventions on the transmission and spread of HIV in South Africa: a phylodynamic analysis

article

The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages

The ongoing COVID-19 epidemic in Minas Gerais, Brazil: insights from epidemiological data and SARS-CoV-2 whole genome sequencing

scientific article published on 29 July 2020

The ongoing COVID-19 epidemic in Minas Gerais, Brazil: insights from epidemiological data and SARS-CoV-2 whole genome sequencing.

scientific article published on 11 May 2020

Tracing the origin of Brazilian HTLV-1 as determined by analysis of host and viral genes

scientific article published in March 2006

Track Omicron’s spread with molecular data

scientific article

Tracking external introductions of HIV using phylodynamics reveals a major source of infections in rural KwaZulu-Natal, South Africa

article

Tracking the 2022 monkeypox outbreak with epidemiological data in real-time

scientific article published on 09 June 2022

Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2

scientific article

Transmission dynamics of SARS-CoV-2 within-host diversity in two major hospital outbreaks in South Africa

scientific article published on 01 January 2021

Transmission networks and risk of HIV infection in KwaZulu-Natal, South Africa: a community-wide phylogenetic study

scientific article published on 30 November 2016

Trends in Genotypic HIV-1 Antiretroviral Resistance between 2006 and 2012 in South African Patients Receiving First- and Second-Line Antiretroviral Treatment Regimens

scientific article (publication date: 2013)

Trends in HIV Prevention, Treatment, and Incidence in a Hyperendemic Area of KwaZulu-Natal, South Africa

scientific article published on 01 November 2019

Trends in Pretreatment HIV-1 Drug Resistance in Antiretroviral Therapy-naive Adults in South Africa, 2000-2016: A Pooled Sequence Analysis

article

Understanding Specific Contexts of Antiretroviral Therapy Adherence in Rural South Africa: A Thematic Analysis of Digital Stories from a Community with High HIV Prevalence

scientific article

Undetectable proviral deoxyribonucleic acid in an adolescent perinatally infected with human immunodeficiency virus-1C and on long-term antiretroviral therapy resulted in viral rebound following antiretroviral therapy termination: A case report with

scientific article published on 01 November 2019

Universal test and treat and the HIV epidemic in rural South Africa: a phase 4, open-label, community cluster randomised trial

scientific article published on 30 November 2017

Unlocking the efficiency of genomics laboratories with robotic liquid-handling

scientific article published on 20 October 2020

Variability at human immunodeficiency virus type 1 subtype C protease cleavage sites: an indication of viral fitness?

scientific article published on September 2003

Virological Outcomes of Second-line Protease Inhibitor-Based Treatment for Human Immunodeficiency Virus Type 1 in a High-Prevalence Rural South African Setting: A Competing-Risks Prospective Cohort Analysis

scientific article

Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic

scientific article published on 17 August 2020

Whole genome sequencing for drug-resistant tuberculosis management in South Africa: What gaps would this address and what are the challenges to implementation?

scientific article published on 09 July 2019

Will climate change amplify epidemics and give rise to pandemics?

scientific article published on 24 August 2023

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)

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