K. Deforche

发表

Bayesian network analysis of resistance pathways against HIV-1 protease inhibitors.

T. Silander, D. Katzenstein, Y. Moreau, 2007, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

Bayesian network analyses of resistance pathways against efavirenz and nevirapine

D. Katzenstein, R. Shafer, M. Soares, 2008, AIDS.

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

Pieter J. K. Libin, M. Poljak, A. Wensing, 2012, Retrovirology.

Estimating an In Vivo Fitness Landscape During Protease and Reverse Transcriptase Treatment from Observed Genetic Evolution to Predict Accumulation of Mutations under Selective Pressure

Yves Moreau, Kristof Theys, Anne-Mieke Vandamme, 2007 .

APOBEC3G-Induced Hypermutation of Human Immunodeficiency Virus Type-1 Is Typically a Discrete “All or Nothing” Phenomenon

J. Welch, A. Rambaut, L. Fugger, 2012, PLoS genetics.

Automated subtyping of HIV-1 genetic sequences for clinical and surveillance

Anne-Mieke Vandamme, Stijn Imbrechts, Tulio de Oliveira, 2013 .

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

M. Debruyne, K. Theys, A. Vandamme, 2008, Retrovirology.

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

K. Deforche, T. de Oliveira, L. Alcântara, 2020, bioRxiv.

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

A. Vandamme, K. Deforche, L. Alcântara, 2018, Bioinform..

Possible Footprints of APOBEC3F and/or Other APOBEC3 Deaminases, but Not APOBEC3G, on HIV-1 from Patients with Acute/Early and Chronic Infections

J. Welch, A. Rambaut, K. Deforche, 2014, Journal of Virology.

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

K. Theys, A. Vandamme, K. Deforche, 2008, Virology Journal.

Behavioral changes before lockdown, and decreased retail and recreation mobility during lockdown, contributed most to the successful control of the COVID-19 epidemic in 35 Western countries

A. Vandamme, K. Deforche, V. Müller, 2020, medRxiv.

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

A. Vandamme, K. Deforche, V. Müller, 2020, BMC Public Health.

An age-structured epidemiological model of the Belgian COVID-19 epidemic

K. Deforche, 2020, medRxiv.

HIV-1 fitness landscape models for indinavir treatment pressure using observed evolution in longitudinal sequence data are predictive for treatment failure.

Pieter J. K. Libin, R. Shafer, P. Libin, 2013, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

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

P. Libin, K. Theys, A. Vandamme, 2009, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

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

Tulio de Oliveira, Pieter Libin, Anne-Mieke Vandamme, 2009, Nucleic Acids Res..

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

Tulio de Oliveira, Christopher J. Seebregts, David A. van de Vijver, 2005, Bioinform..

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

M. Kraemer, O. Pybus, L. du Plessis, 2021, Nature.

An automated genotyping tool for enteroviruses and noroviruses.

K. Deforche, J. Vinjé, H. Vennema, 2011, Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology.

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

Tulio de Oliveira, Anne-Mieke Vandamme, Sam Nooij, 2018, Bioinform..

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

Ann Nowé, Kristof Theys, Anne-Mieke Vandamme, 2019, PLoS neglected tropical diseases.

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

Kristof Theys, Koen Deforche, Pieter J. K. Libin, 2018, bioRxiv.

Prevalence and epidemiology of HIV type 1 drug resistance among newly diagnosed therapy-naive patients in Belgium from 2003 to 2006.

Anne-Mieke Vandamme, Katrien Fransen, Inge Derdelinckx, 2008, AIDS research and human retroviruses.

Investigation of Baseline Susceptibility to Protease Inhibitors in HIV-1 Subtypes C, F, G and Crf02_Ag

Anne-Mieke Vandamme, Koen Deforche, Ricardo Jorge Camacho, 2005, Antiviral therapy.

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

Anne-Mieke Vandamme, Koen Deforche, Joke Snoeck, 2005, AIDS.

Resistance pathways of human immunodeficiency virus type 1 against the combination of zidovudine and lamivudine.

P. Libin, K. Theys, K. Deforche, 2010, The Journal of general virology.

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

Kristof Theys, Alexei J Drummond, Andrew Rambaut, 2018, bioRxiv.

Rise and Fall of the RT K65R Incidence in the Portuguese Resistance Database

K. Theys, A. Vandamme, K. Deforche, 2006 .

SlidingBayes: exploring recombination using a sliding window approach based on Bayesian phylogenetic inference

Anne-Mieke Vandamme, Philippe Lemey, Koen Deforche, 2005, Bioinform..

A Public HTLV-1 Molecular Epidemiology Database for Sequence Management and Data Mining

Anne-Mieke Vandamme, Luiz Carlos Junior Alcantara, Koen Deforche, 2012, PloS one.

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

Lynn Morris, Anne-Mieke Vandamme, Praphan Phanuphak, 2006, Antimicrobial Agents and Chemotherapy.

A genotypic assay for the amplification and sequencing of gag and protease from diverse human immunodeficiency virus type 1 group M subtypes.

M. Van Ranst, A. Vandamme, K. Deforche, 2006, Journal of virological methods.

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

Jean Ruelle, Peter M. A. Sloot, Stefan Wesner, 2013, Bioinform..

Modelled in vivo HIV Fitness under drug Selective Pressure and Estimated Genetic Barrier Towards Resistance are Predictive for Virological Response

Yves Moreau, Kristof Theys, Anne-Mieke Vandamme, 2008, Antiviral therapy.

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

Tulio de Oliveira, Sara Cleemput, Koen Deforche, 2020, Bioinform..

Discordances between interpretation algorithms for genotypic resistance to protease and reverse transcriptase inhibitors are subtype dependent

Lynn Morris, Anne-Mieke Vandamme, Praphan Phanuphak, 2004 .

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

A. Vandamme, K. Deforche, R. Camacho, 2005, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

Estimation of an in vivo fitness landscape experienced by HIV-1 under drug selective pressure useful for prediction of drug resistance evolution during treatment

Yves Moreau, Anne-Mieke Vandamme, Ricardo Camacho, 2008, Bioinform..

An alignment method for nucleic acid sequences against annotated genomes

Koen Deforche, K. Deforche, 2017, bioRxiv.

Estimating the Relative Contribution of dNTP Pool Imbalance and APOBEC3G/3F Editing to HIV Evolution In Vivo

Yves Moreau, Anne-Mieke Vandamme, Beth Shapiro, 2007, J. Comput. Biol..

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

P. Libin, K. Theys, A. Vandamme, 2009, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

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

Pieter J. K. Libin, A. Vandamme, K. Deforche, 2013, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

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

Anne-Mieke Vandamme, Paul Kellam, David Dunn, 2007 .