Publications by authors named "Koen Deforche"

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A method for in-depth analysis of circular DNA virus populations by unambiguously profiling the low abundant virus variants and partial genomic components.
Victor Golyaev, Sam Dierickx, Koen Deforche, Wim Dumon, Hervé Vanderschuren

Nucleic Acids Res· March 2025

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Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa.
Raquel Viana, Sikhulile Moyo, Daniel G Amoako, Houriiyah Tegally, Cathrine Scheepers, Koen Deforche

Nature· March 2022

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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.
Koen Deforche, Jurgen Vercauteren, Viktor Müller, Anne-Mieke Vandamme

BMC Public Health· April 2021

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Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes.
Sara Cleemput, Wim Dumon, Vagner Fonseca, Wasim Abdool Karim, Marta Giovanetti, Koen Deforche

Bioinformatics· June 2020

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Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes.
Sara Cleemput, Wim Dumon, Vagner Fonseca, Wasim Abdool Karim, Marta Giovanetti, Koen Deforche

bioRxiv· February 2020

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VIRULIGN: fast codon-correct alignment and annotation of viral genomes.
Pieter J K Libin, Koen Deforche, Ana B Abecasis, Kristof Theys

Bioinformatics· May 2019

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A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes.
Vagner Fonseca, Pieter J K Libin, Kristof Theys, Nuno R Faria, Marcio R T Nunes, Koen Deforche

PLoS Negl Trop Dis· May 2019

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Genome Detective: an automated system for virus identification from high-throughput sequencing data.
Michael Vilsker, Yumna Moosa, Sam Nooij, Vagner Fonseca, Yoika Ghysens, Koen Deforche

Bioinformatics· March 2019

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SANTA-SIM: simulating viral sequence evolution dynamics under selection and recombination.
Abbas Jariani, Christopher Warth, Koen Deforche, Pieter Libin, Alexei J Drummond

Virus Evol· January 2019

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A16 A distributed pan-viral typing framework.
Michael Vilsker, Koen Deforche

Virus Evol· March 2017

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A34 Automated profiling of the human virome from raw metagenomic data.
Yumna Moosa, Michael Vilsker, Ewout Vanden Eyden, Vagner Fonseca, Sam Nooij, Koen Deforche

Virus Evol· March 2017

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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.
Andrew E Armitage, Koen Deforche, John J Welch, Kristel Van Laethem, Ricardo Camacho

J Virol· November 2014

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HIV-1 fitness landscape models for indinavir treatment pressure using observed evolution in longitudinal sequence data are predictive for treatment failure.
Raphael Z Sangeda, Kristof Theys, Gertjan Beheydt, Soo-Yon Rhee, Koen Deforche

Infect Genet Evol· October 2013

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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.
Andrea-Clemencia Pineda-Peña, Nuno Rodrigues Faria, Stijn Imbrechts, Pieter Libin, Ana Barroso Abecasis, Koen Deforche

Infect Genet Evol· October 2013

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RegaDB: community-driven data management and analysis for infectious diseases.
Pieter Libin, Gertjan Beheydt, Koen Deforche, Stijn Imbrechts, Fossie Ferreira

Bioinformatics· June 2013

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A public HTLV-1 molecular epidemiology database for sequence management and data mining.
Thessika Hialla Almeida Araujo, Leandro Inacio Souza-Brito, Pieter Libin, Koen Deforche, Dustin Edwards

PLoS One· May 2013

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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.
Kristof Theys, Koen Deforche, Jurgen Vercauteren, Pieter Libin, David Amc van de Vijver

Retrovirology· October 2012

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APOBEC3G-induced hypermutation of human immunodeficiency virus type-1 is typically a discrete "all or nothing" phenomenon.
Andrew E Armitage, Koen Deforche, Chih-Hao Chang, Edmund Wee, Beatrice Kramer

PLoS Genet· September 2012

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Estimating the individualized HIV-1 genetic barrier to resistance using a nelfinavir fitness landscape.
Kristof Theys, Koen Deforche, Gertjan Beheydt, Yves Moreau, Kristel van Laethem

BMC Bioinformatics· August 2010

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The rise and fall of K65R in a Portuguese HIV-1 Drug Resistance database, despite continuously increasing use of tenofovir.
Kristof Theys, Jurgen Vercauteren, Ana B Abecasis, Pieter Libin, Koen Deforche

Infect Genet Evol· July 2009

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A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences.
Luiz Carlos Junior Alcantara, Sharon Cassol, Pieter Libin, Koen Deforche, Oliver G Pybus

Nucleic Acids Res· July 2009

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Bayesian network analyses of resistance pathways against efavirenz and nevirapine.
Koen Deforche, Ricardo J Camacho, Zehave Grossman, Marcelo A Soares, Kristel Van Laethem

AIDS· October 2008

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Modelled in vivo HIV fitness under drug selective pressure and estimated genetic barrier towards resistance are predictive for virological response.
Koen Deforche, Alessandro Cozzi-Lepri, Kristof Theys, Bonaventura Clotet, Ricardo J Camacho

Antivir Ther· July 2008

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Impact of HIV-1 protease mutations A71V/T and T74S on M89I/V-mediated protease inhibitor resistance in subtype G isolates.
Luis M F Gonzalez, André F Santos, Ana B Abecasis, Kristel Van Laethem, Esmeralda A Soares, Koen Deforche

J Antimicrob Chemother· June 2008

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Prevalence and epidemiology of HIV type 1 drug resistance among newly diagnosed therapy-naive patients in Belgium from 2003 to 2006.
Jurgen Vercauteren, Inge Derdelinckx, André Sasse, Marleen Bogaert, Helga Ceunen, Koen Deforche

AIDS Res Hum Retroviruses· March 2008

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