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Genome Detective: an automated system for virus identification from high-throughput sequencing data

Bioinformatics, 2019-03, Vol.35 (5), p.871-873

2019

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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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Behavioral changes before lockdown and decreased retail and recreation mobility during lockdown contributed most to controlling COVID-19 in Western countries

BMC public health, 2021-04, Vol.21 (1), p.654-654, Article 654

2021

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

Infection, genetics and evolution, 2013-10, Vol.19, p.337-348

2013

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APOBEC3G-induced hypermutation of human immunodeficiency virus type-1 is typically a discrete "all or nothing" phenomenon

PLoS genetics, 2012-03, Vol.8 (3), p.e1002550-e1002550

2012

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A public HTLV-1 molecular epidemiology database for sequence management and data mining

PloS one, 2012-09, Vol.7 (9), p.e42123-e42123

2012

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

Bioinformatics, 2020-06, Vol.36 (11), p.3552-3555

2020

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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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A16 A distributed pan-viral typing framework

Virus evolution, 2017-03, Vol.3 (suppl_1)

2017

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Development of HTLV-1 Database for data management and datamining HTLV-1 sequences

Retrovirology, 2011-06, Vol.8 (S1), p.A79-A79, Article A79

2011

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

Bioinformatics, 2005-10, Vol.21 (19), p.3797-3800

2005

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

Nucleic acids research, 2009-07, Vol.37 (Web Server issue), p.W634

2009

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

PLoS neglected tropical diseases, 2019-05, Vol.13 (5), p.e0007231-e0007231

2019

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Possible footprints of APOBEC3F and/or other APOBEC3 deaminases, but not APOBEC3G, on HIV-1 from patients with acute/early and chronic infections

Journal of virology, 2014-11, Vol.88 (21), p.12882-12894

2014

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SANTA-SIM: simulating viral sequence evolution dynamics under selection and recombination

Virus evolution, 2019-01, Vol.5 (1), p.vez003-vez003

2019

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Analysis of HIV-1 pol sequences using Bayesian Networks: implications for drug resistance

Bioinformatics, 2006-12, Vol.22 (24), p.2975-2979

2006

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A34 Automated profiling of the human virome from raw metagenomic data

Virus evolution, 2017-03, Vol.3 (suppl_1)

2017

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Protease mutation M89I/V is linked to therapy failure in patients infected with the HIV-1 non-B subtypes C, F or G

AIDS (London), 2005-11, Vol.19 (16), p.1799-1806

2005

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Discordances between Interpretation Algorithms for Genotypic Resistance to Protease and Reverse Transcriptase Inhibitors of Human Immunodeficiency Virus Are Subtype Dependent

Antimicrobial Agents and Chemotherapy, 2006-02, Vol.50 (2), p.694-701

2006

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Bayesian network analyses of resistance pathways against efavirenz and nevirapine

AIDS (London), 2008-10, Vol.22 (16), p.2107-2115

2008

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Treatment-associated polymorphisms in protease are significantly associated with higher viral load and lower CD4 count in newly diagnosed drug-naive HIV-1 infected patients

Retrovirology, 2012-10, Vol.9 (1), p.81-81, Article 81

2012

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Investigation of baseline susceptibility to protease inhibitors in HIV-1 subtypes C, F, G and CRF02_AG

Antiviral therapy, 2006-01, Vol.11 (5), p.581-589

2006

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Genome Detective: an automated system for virus identification from high-throughput sequencing data

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

Behavioral changes before lockdown and decreased retail and recreation mobility during lockdown contributed most to controlling COVID-19 in Western countries

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

APOBEC3G-induced hypermutation of human immunodeficiency virus type-1 is typically a discrete "all or nothing" phenomenon

A public HTLV-1 molecular epidemiology database for sequence management and data mining

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

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

A16 A distributed pan-viral typing framework

Development of HTLV-1 Database for data management and datamining HTLV-1 sequences

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

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

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

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

Possible footprints of APOBEC3F and/or other APOBEC3 deaminases, but not APOBEC3G, on HIV-1 from patients with acute/early and chronic infections

SANTA-SIM: simulating viral sequence evolution dynamics under selection and recombination

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

Analysis of HIV-1 pol sequences using Bayesian Networks: implications for drug resistance

A34 Automated profiling of the human virome from raw metagenomic data

Protease mutation M89I/V is linked to therapy failure in patients infected with the HIV-1 non-B subtypes C, F or G

Discordances between Interpretation Algorithms for Genotypic Resistance to Protease and Reverse Transcriptase Inhibitors of Human Immunodeficiency Virus Are Subtype Dependent

Bayesian network analyses of resistance pathways against efavirenz and nevirapine

Treatment-associated polymorphisms in protease are significantly associated with higher viral load and lower CD4 count in newly diagnosed drug-naive HIV-1 infected patients

Investigation of baseline susceptibility to protease inhibitors in HIV-1 subtypes C, F, G and CRF02_AG

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