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

Bioinformatics, 2019-05, Vol.35 (10), p.1763-1765

2019

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Within-patient mutation frequencies reveal fitness costs of CpG dinucleotides and drastic amino acid changes in HIV

PLoS genetics, 2018-06, Vol.14 (6), p.e1007420-e1007420

2018

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Genetic Diversity and Selective Pressure in Hepatitis C Virus Genotypes 1-6: Significance for Direct-Acting Antiviral Treatment and Drug Resistance

Viruses, 2015-09, Vol.7 (9), p.5018-5039

2015

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Drivers of HIV-1 transmission: The Portuguese case

PloS one, 2019-09, Vol.14 (9), p.e0218226-e0218226

2019

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

PloS one, 2017-10, Vol.12 (10), p.e0185866-e0185866

2017

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Functional conservation of HIV-1 Gag: implications for rational drug design

Retrovirology, 2013-10, Vol.10 (1), p.126-126, Article 126

2013

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Correction: Within-patient mutation frequencies reveal fitness costs of CpG dinucleotides and drastic amino acid changes in HIV

PLoS genetics, 2018-12, Vol.14 (12), p.e1007855-e1007855

2018

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Zika genomics urgently need standardized and curated reference sequences

PLoS pathogens, 2017-09, Vol.13 (9), p.e1006528-e1006528

2017

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

Viruses, 2020-10, Vol.12 (11), p.1238

2020

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Advances in Visualization Tools for Phylogenomic and Phylodynamic Studies of Viral Diseases

Frontiers in public health, 2019-08, Vol.7, p.208-208

2019

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Analyses of Early ZIKV Genomes Are Consistent with Viral Spread from Northeast Brazil to the Americas

Viruses, 2023-05, Vol.15 (6), p.1236

2023

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HIV-1 Infection in Cyprus, the Eastern Mediterranean European Frontier: A Densely Sampled Transmission Dynamics Analysis from 1986 to 2012

Scientific reports, 2018-01, Vol.8 (1), p.1702-14, Article 1702

2018

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Time to Harmonize Dengue Nomenclature and Classification

Viruses, 2018-10, Vol.10 (10), p.569

2018

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A genetic IFN/STAT1/FAS axis determines CD4 T stem cell memory levels and apoptosis in healthy controls and Adult T-cell Leukemia patients

Oncoimmunology, 2018-05, Vol.7 (5), p.e1426423-e1426423

2018

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CRF19_cpx is an Evolutionary fit HIV-1 Variant Strongly Associated With Rapid Progression to AIDS in Cuba

EBioMedicine, 2015-03, Vol.2 (3), p.244-254

2015

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Characterization of Nucleoside Reverse Transcriptase Inhibitor-Associated Mutations in the RNase H Region of HIV-1 Subtype C Infected Individuals

Viruses, 2017-11, Vol.9 (11), p.330

2017

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The incidence of multidrug and full class resistance in HIV-1 infected patients is decreasing over time (2001-2006) in Portugal

Retrovirology, 2008-02, Vol.5 (1), p.12-12

2008

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Estimating the individualized HIV-1 genetic barrier to resistance using a nelfinavir fitness landscape

BMC bioinformatics, 2010-08, Vol.11 (1), p.409-409, Article 409

2010

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Molecular epidemiology of HIV-1 infection in Cyprus: onward transmission is predominantly driven by young adults

Journal of Virus Eradication, 2016-05, Vol.2, p.23-23

2016

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Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research

Briefings in bioinformatics, 2020-11, Vol.22 (2), p.642-663

2020

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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

Antimicrobial agents and chemotherapy, 2019-08, Vol.63 (8)

2019

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A Bayesian network approach to study host and viral genetic correlates of HIV-1 disease progression

Retrovirology, 2011-10, Vol.8 (S2), p.P70-P70, Article P70

2011

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HIV-1 genotypic drug resistance testing: digging deep, reaching wide?

Current opinion in virology, 2015-10, Vol.14, p.16-23

2015

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

Retrovirology, 2015-02, Vol.12 (1), p.18-18, Article 18

2015

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

Virology journal, 2008-01, Vol.5 (1), p.14-14, Article 14

2008

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

Within-patient mutation frequencies reveal fitness costs of CpG dinucleotides and drastic amino acid changes in HIV

Genetic Diversity and Selective Pressure in Hepatitis C Virus Genotypes 1-6: Significance for Direct-Acting Antiviral Treatment and Drug Resistance

Drivers of HIV-1 transmission: The Portuguese case

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

Functional conservation of HIV-1 Gag: implications for rational drug design

Correction: Within-patient mutation frequencies reveal fitness costs of CpG dinucleotides and drastic amino acid changes in HIV

Zika genomics urgently need standardized and curated reference sequences

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

Advances in Visualization Tools for Phylogenomic and Phylodynamic Studies of Viral Diseases

Analyses of Early ZIKV Genomes Are Consistent with Viral Spread from Northeast Brazil to the Americas

HIV-1 Infection in Cyprus, the Eastern Mediterranean European Frontier: A Densely Sampled Transmission Dynamics Analysis from 1986 to 2012

Time to Harmonize Dengue Nomenclature and Classification

A genetic IFN/STAT1/FAS axis determines CD4 T stem cell memory levels and apoptosis in healthy controls and Adult T-cell Leukemia patients

CRF19_cpx is an Evolutionary fit HIV-1 Variant Strongly Associated With Rapid Progression to AIDS in Cuba

Characterization of Nucleoside Reverse Transcriptase Inhibitor-Associated Mutations in the RNase H Region of HIV-1 Subtype C Infected Individuals

The incidence of multidrug and full class resistance in HIV-1 infected patients is decreasing over time (2001-2006) in Portugal

Estimating the individualized HIV-1 genetic barrier to resistance using a nelfinavir fitness landscape

Molecular epidemiology of HIV-1 infection in Cyprus: onward transmission is predominantly driven by young adults

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research

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

A Bayesian network approach to study host and viral genetic correlates of HIV-1 disease progression

HIV-1 genotypic drug resistance testing: digging deep, reaching wide?

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

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

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