List of works - Ana B. Abecasis

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

scientific article

A genomic signature and the identification of new sporulation genes

scientific article published on 8 February 2013

Accidental Father-to-Son HIV-1 Transmission During the Seroconversion Period

article

An Evolutionary Model-Based Approach To Quantify the Genetic Barrier to Drug Resistance in Fast-Evolving Viruses and Its Application to HIV-1 Subtypes and Integrase Inhibitors

scientific article published on 25 July 2019

Analysis of complex HIV-1 intersubtype recombinants using a Bayesian scanning method

article

Assessing transmissibility of HIV-1 drug resistance mutations from treated and from drug-naive individuals

scientific 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

Bridging epidemiology with population genetics in a low incidence MSM-driven HIV-1 subtype B epidemic in Central Europe

scientific article

Characterization of a large cluster of HIV-1 A1 infections detected in Portugal and connected to several Western European countries

article

Characterization of an insect-specific flavivirus (OCFVPT) co-isolated from Ochlerotatus caspius collected in southern Portugal along with a putative new Negev-like virus

scientific article published on 23 July 2013

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

scientific article published on 12 October 2009

Comparison of the COBAS TAQMAN HIV-1 HPS with VERSANT HIV-1 RNA 3.0 assay (bDNA) for plasma RNA quantitation in different HIV-1 subtypes.

scientific article

Cruising Venues as a Context for HIV Risky Behavior Among Men Who Have Sex With Men.

scientific article published on 17 March 2016

Decreasing population selection rates of resistance mutation K65R over time in HIV-1 patients receiving combination therapy including tenofovir.

scientific article published on 30 September 2012

Discordant genotypic interpretation and phenotypic role of protease mutations in HIV-1 subtypes B and G.

scientific article published on 10 January 2009

Discordant predictions of residual activity could impact dolutegravir prescription upon raltegravir failure

scientific article published on 29 July 2015

Donor-Recipient Identification in Para- and Poly-phyletic Trees Under Alternative HIV-1 Transmission Hypotheses Using Approximate Bayesian Computation.

scientific article published on 14 September 2017

Effect of human immunodeficiency virus type 1 protease inhibitor therapy and subtype on development of resistance in subtypes B and G.

scientific article published on 2 July 2009

Effect of natural polymorphisms in the HIV-1 CRF02_AG protease on protease inhibitor hypersusceptibility

scientific article

Epidemic dispersion of HIV and HCV in a population of co-infected Romanian injecting drug users.

scientific article published on 9 October 2017

Geographic dispersal and genetic diversity of tick-borne phleboviruses (Phenuiviridae, Phlebovirus) as revealed by the analysis of L segment sequences

scientific article published on 03 May 2019

HIV and tuberculosis co-infection among migrants in Europe: A systematic review on the prevalence, incidence and mortality

scientific article published on 28 September 2017

HIV-1 drug resistance: where do polymorphisms fit in?

scientific article

HIV-1 genetic diversity and transmitted drug resistance in health care settings in Maputo, Mozambique

scientific article published in July 2009

HIV-1 genetic variants circulation in the North of Angola

article

HIV-1 gp120 N-linked glycosylation differs between plasma and leukocyte compartments

scientific article

HIV-1 subtype distribution and its demographic determinants in newly diagnosed patients in Europe suggest highly compartmentalized epidemics

scientific article published on 14 January 2013

HIV-2 integrase polymorphisms and longitudinal genotypic analysis of HIV-2 infected patients failing a raltegravir-containing regimen

scientific article

Impact of HIV-1 protease mutations A71V/T and T74S on M89I/V-mediated protease inhibitor resistance in subtype G isolates

scientific article

Increase in transmitted resistance to non-nucleoside reverse transcriptase inhibitors among newly diagnosed HIV-1 infections in Europe

scientific article

Increasing Prevalence of HIV-1 Transmitted Drug Resistance in Portugal: Implications for First Line Treatment Recommendations

scientific article published on 30 October 2020

Lack of evidence for the selection of E138 mutations by first-generation non-nucleoside reverse transcriptase inhibitors in patients infected with HIV-1 non-B subtypes

scientific article published in May 2015

Limited cross-border infections in patients newly diagnosed with HIV in Europe

scientific article published on 3 April 2013

Molecular Epidemiology of HIV-1 Infected Migrants Followed up in Portugal: Trends between 2001-2017

scientific article published on 28 February 2020

Molecular epidemiological analysis of paired pol/env sequences from Portuguese HIV type 1 patients

scientific article

Molecular footprints of selective pressure in the neuraminidase gene of currently circulating human influenza subtypes and lineages

article

Negeviruses found in multiple species of mosquitoes from southern Portugal: Isolation, genetic diversity, and replication in insect cell culture

scientific article published on 5 June 2015

Novel HIV-1 recombinants spreading across multiple risk groups in the United Kingdom: the identification and phylogeography of Circulating Recombinant Form (CRF) 50_A1D

scientific article (publication date: 2014)

On the contribution of Angola to the initial spread of HIV-1.

scientific article

Origin and epidemiological history of HIV-1 CRF14_BG.

scientific article

Patterns of transmitted HIV drug resistance in Europe vary by risk group

scientific article (publication date: 2014)

Phylodynamics of the HIV-1 CRF02_AG clade in Cameroon

scientific article

Phylogenetic analysis as a forensic tool in HIV transmission investigations: a literature review.

scientific article published on 26 December 2017

Phylogeography and invasion history of Aedes aegypti, the Dengue and Zika mosquito vector in Cape Verde islands (West Africa) ⬇️

scientific article published on 03 August 2019

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

scientific article published on November 2012

Quantifying differences in the tempo of human immunodeficiency virus type 1 subtype evolution

scientific article published on 30 September 2009

Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: subtype G is a circulating recombinant form

scientific article

Science in court: the myth of HIV fingerprinting

scientific article

Short communication: prevalence of HIV type 1 transmitted drug resistance in Slovenia: 2005-2010.

scientific article published on 29 August 2012

Sub-Epidemics Explain Localized High Prevalence of Reduced Susceptibility to Rilpivirine in Treatment-Naive HIV-1-Infected Patients: Subtype and Geographic Compartmentalization of Baseline Resistance Mutations

scientific article published on 13 December 2015

Superinfection with drug-resistant HIV is rare and does not contribute substantially to therapy failure in a large European cohort

scientific article

The characteristics of the HIV subtype B epidemic in Slovenia

article

The impact of HIV-1 within-host evolution on transmission dynamics

scientific article published on 21 December 2017

The rise and fall of K65R in a Portuguese HIV-1 Drug Resistance database, despite continuously increasing use of tenofovir

scientific article published on 6 November 2008

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

article

Transmission of HIV-2

article

Tuberculosis care for migrant patients in Portugal: a mixed methods study with primary healthcare providers

article

VIRULIGN: fast codon-correct alignment and annotation of viral genomes

scientific article

Women in the European Virus Bioinformatics Center

scientific article published on 13 July 2022

Zika genomics urgently need standardized and curated reference sequences

scientific article published on 7 September 2017

inTB - a data integration platform for molecular and clinical epidemiological analysis of tuberculosis.

scientific article

List of works by Ana B. Abecasis

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

A genomic signature and the identification of new sporulation genes

Accidental Father-to-Son HIV-1 Transmission During the Seroconversion Period

An Evolutionary Model-Based Approach To Quantify the Genetic Barrier to Drug Resistance in Fast-Evolving Viruses and Its Application to HIV-1 Subtypes and Integrase Inhibitors

Analysis of complex HIV-1 intersubtype recombinants using a Bayesian scanning method

Assessing transmissibility of HIV-1 drug resistance mutations from treated and from drug-naive individuals

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

Bridging epidemiology with population genetics in a low incidence MSM-driven HIV-1 subtype B epidemic in Central Europe

Characterization of a large cluster of HIV-1 A1 infections detected in Portugal and connected to several Western European countries

Characterization of an insect-specific flavivirus (OCFVPT) co-isolated from Ochlerotatus caspius collected in southern Portugal along with a putative new Negev-like virus

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

Comparison of the COBAS TAQMAN HIV-1 HPS with VERSANT HIV-1 RNA 3.0 assay (bDNA) for plasma RNA quantitation in different HIV-1 subtypes.

Cruising Venues as a Context for HIV Risky Behavior Among Men Who Have Sex With Men.

Decreasing population selection rates of resistance mutation K65R over time in HIV-1 patients receiving combination therapy including tenofovir.

Discordant genotypic interpretation and phenotypic role of protease mutations in HIV-1 subtypes B and G.

Discordant predictions of residual activity could impact dolutegravir prescription upon raltegravir failure

Donor-Recipient Identification in Para- and Poly-phyletic Trees Under Alternative HIV-1 Transmission Hypotheses Using Approximate Bayesian Computation.

Effect of human immunodeficiency virus type 1 protease inhibitor therapy and subtype on development of resistance in subtypes B and G.

Effect of natural polymorphisms in the HIV-1 CRF02_AG protease on protease inhibitor hypersusceptibility

Epidemic dispersion of HIV and HCV in a population of co-infected Romanian injecting drug users.

Geographic dispersal and genetic diversity of tick-borne phleboviruses (Phenuiviridae, Phlebovirus) as revealed by the analysis of L segment sequences

HIV and tuberculosis co-infection among migrants in Europe: A systematic review on the prevalence, incidence and mortality

HIV-1 drug resistance: where do polymorphisms fit in?

HIV-1 genetic diversity and transmitted drug resistance in health care settings in Maputo, Mozambique

HIV-1 genetic variants circulation in the North of Angola

HIV-1 gp120 N-linked glycosylation differs between plasma and leukocyte compartments

HIV-1 subtype distribution and its demographic determinants in newly diagnosed patients in Europe suggest highly compartmentalized epidemics

HIV-2 integrase polymorphisms and longitudinal genotypic analysis of HIV-2 infected patients failing a raltegravir-containing regimen

Impact of HIV-1 protease mutations A71V/T and T74S on M89I/V-mediated protease inhibitor resistance in subtype G isolates

Increase in transmitted resistance to non-nucleoside reverse transcriptase inhibitors among newly diagnosed HIV-1 infections in Europe

Increasing Prevalence of HIV-1 Transmitted Drug Resistance in Portugal: Implications for First Line Treatment Recommendations

Lack of evidence for the selection of E138 mutations by first-generation non-nucleoside reverse transcriptase inhibitors in patients infected with HIV-1 non-B subtypes

Limited cross-border infections in patients newly diagnosed with HIV in Europe

Molecular Epidemiology of HIV-1 Infected Migrants Followed up in Portugal: Trends between 2001-2017

Molecular epidemiological analysis of paired pol/env sequences from Portuguese HIV type 1 patients

Molecular footprints of selective pressure in the neuraminidase gene of currently circulating human influenza subtypes and lineages

Negeviruses found in multiple species of mosquitoes from southern Portugal: Isolation, genetic diversity, and replication in insect cell culture

Novel HIV-1 recombinants spreading across multiple risk groups in the United Kingdom: the identification and phylogeography of Circulating Recombinant Form (CRF) 50_A1D

On the contribution of Angola to the initial spread of HIV-1.

Origin and epidemiological history of HIV-1 CRF14_BG.

Patterns of transmitted HIV drug resistance in Europe vary by risk group

Phylodynamics of the HIV-1 CRF02_AG clade in Cameroon

Phylogenetic analysis as a forensic tool in HIV transmission investigations: a literature review.

Phylogeography and invasion history of Aedes aegypti, the Dengue and Zika mosquito vector in Cape Verde islands (West Africa) ⬇️

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

Quantifying differences in the tempo of human immunodeficiency virus type 1 subtype evolution

Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: subtype G is a circulating recombinant form

Science in court: the myth of HIV fingerprinting

Short communication: prevalence of HIV type 1 transmitted drug resistance in Slovenia: 2005-2010.

Sub-Epidemics Explain Localized High Prevalence of Reduced Susceptibility to Rilpivirine in Treatment-Naive HIV-1-Infected Patients: Subtype and Geographic Compartmentalization of Baseline Resistance Mutations

Superinfection with drug-resistant HIV is rare and does not contribute substantially to therapy failure in a large European cohort

The characteristics of the HIV subtype B epidemic in Slovenia

The impact of HIV-1 within-host evolution on transmission dynamics

The rise and fall of K65R in a Portuguese HIV-1 Drug Resistance database, despite continuously increasing use of tenofovir

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

Transmission of HIV-2

Tuberculosis care for migrant patients in Portugal: a mixed methods study with primary healthcare providers

VIRULIGN: fast codon-correct alignment and annotation of viral genomes

Women in the European Virus Bioinformatics Center

Zika genomics urgently need standardized and curated reference sequences

inTB - a data integration platform for molecular and clinical epidemiological analysis of tuberculosis.