SlidingBayes: exploring recombination using a sliding window approach based on Bayesian phylogenetic inference. - Dimitris Paraskevis; Koen Deforche; Philippe Lemey; Gkikas Magiorkinis; Angelos Hatzakis; Anne-Mieke Vandamme (Bioinform., 2005)

An automated genotyping system for analysis of HIV-1 and other microbial sequences. - Tulio de Oliveira; Koen Deforche; Sharon Cassol; Mika Salminen; Dimitris Paraskevis; Chris Seebregts; Joke Snoeck; Estrelita J. Janse van Rensburg; Annemarie M. J. Wensing; David A. van de Vijver; Charles A. Boucher; Ricardo Camacho; et al. (Bioinform., 2005)

Analysis of HIV-1 pol sequences using Bayesian Networks: implications for drug resistance. - Koen Deforche; Tomi Silander; Ricardo Camacho; Zehava Grossman; M. A. Soares; Kristel Van Laethem; Rami Kantor; Yves Moreau; Anne-Mieke Vandamme (Bioinform., 2006)

Estimating the Relative Contribution of dNTP Pool Imbalance and APOBEC3G/3F Editing to HIV Evolution In Vivo. - Koen Deforche; Ricardo Camacho; Kristel Van Laethem; Beth Shapiro; Yves Moreau; Andrew Rambaut; Anne-Mieke Vandamme; Philippe Lemey (J. Comput. Biol., 2007)

Estimation of an in vivo fitness landscape experienced by HIV-1 under drug selective pressure useful for prediction of drug resistance evolution during treatment. - Koen Deforche; Ricardo Camacho; Kristel Van Laethem; Philippe Lemey; Andrew Rambaut; Yves Moreau; Anne-Mieke Vandamme (Bioinform., 2008)

A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences. - Luiz Carlos Júnior Alcântara; Sharon Cassol; Pieter Libin; Koen Deforche; Oliver G. Pybus; Marc Van Ranst; Bernardo Galvão-Castro; Anne-Mieke Vandamme; Tulio de Oliveira (Nucleic Acids Res., 2009)

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; Philippe Lemey; Ricardo Camacho; Soo-Yon Rhee; Robert W. Shafer; Eric Van Wijngaerden; Anne-Mieke Vandamme (BMC Bioinform., 2010)

RegaDB: community-driven data management and analysis for infectious diseases. - Pieter Libin; Gertjan Beheydt; Koen Deforche; Stijn Imbrechts; Fossie Ferreira; Kristel Van Laethem; Kristof Theys; Ana Patricia Carvalho; Joana Cavaco-Silva; Giuseppe Lapadula; Carlo Torti; Matthias Assel; et al. (Bioinform., 2013)

VIRULIGN: fast codon-correct alignment and annotation of viral genomes. - Pieter J. K. Libin; Koen Deforche; Ana B. Abecasis; Kristof Theys (Bioinform., 2019)

Genome Detective: an automated system for virus identification from high-throughput sequencing data. - Michael Vilsker; Yumna Moosa; Sam Nooij; Vagner Fonseca; Yoika Ghysens; Korneel Dumon; Raf Pauwels; Luiz Carlos Alcantara; Ewout Vanden Eynden; Anne-Mieke Vandamme; Koen Deforche; Tulio de Oliveira (Bioinform., 2019)

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; Luiz Carlos Alcantara; Koen Deforche; Tulio de Oliveira (Bioinform., 2020)