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)

Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase. - Pascale Gaudet; Lydie Lane; Petra Fey; Alan J. Bridge; Sylvain Poux; Andrea H. Auchincloss; Kristian B. Axelsen; Silvia Braconi-Quintaje; Emmanuel Boutet; P. Brown; Elisabeth Coudert; Ruchira S. Datta; et al. (Database J. Biol. Databases Curation, 2009)

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)

The RNA Virus Database. - Robert Belshaw; Tulio de Oliveira; Sidney Markowitz; Andrew Rambaut (Nucleic Acids Res., 2009)

Modeling HIV-1 Drug Resistance as Episodic Directional Selection. - Ben Murrell; Tulio de Oliveira; Chris Seebregts; Sergei L. Kosakovsky Pond; Konrad Scheffler (PLoS Comput. Biol., 2012)

An Investigation of Classification Algorithms for Predicting HIV Drug Resistance without Genotype Resistance Testing. - Pascal S. Brandt; Deshendran Moodley; Anban W. Pillay; Christopher J. Seebregts; Tulio de Oliveira (FHIES, 2013)

Searching for virus phylotypes. - François Chevenet; Matthieu Jung; Martine Peeters; Tulio de Oliveira; Olivier Gascuel (Bioinform., 2013)

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)

Southern African Treatment Resistance Network (SATuRN) RegaDB HIV drug resistance and clinical management database: supporting patient management, surveillance and research in southern Africa. - Justen Manasa; Richard Lessells; Theresa Rossouw; Kevindra Naidu; Cloete Van Vuuren; Dominique Goedhals; Gert van Zyl; P. Armand Bester; Andrew Skingsley; Katharine Stott; Siva Danaviah; Terusha Chetty; et al. (Database J. Biol. Databases Curation, 2014)

Human immunodeficiency virus (HIV) proteomics resource at BioAfrica. - Megan Druce; Paula Sommer; Philippe Le Mercier; Chantal Hulo; Patrick Masson; Tulio de Oliveira (BCB, 2015)

Improving HIV proteome annotation: new features of BioAfrica HIV Proteomics Resource. - Megan Druce; Chantal Hulo; Patrick Masson; Paula Sommer; Ioannis Xenarios; Philippe Le Mercier; Tulio de Oliveira (Database J. Biol. Databases Curation, 2016)

The Development of Computational Biology in South Africa: Successes Achieved and Lessons Learnt. - Nicola J. Mulder; Alan Christoffels; Tulio de Oliveira; Junaid Gamieldien; Scott Hazelhurst; Fourie Joubert; Judit Kumuthini; Ché S. Pillay; Jacky L. Snoep; Özlem Tastan Bishop; Nicki Tiffin (PLoS Comput. Biol., 2016)

Renewing Felsenstein's phylogenetic bootstrap in the era of big data. - Frédéric Lemoine 002; Jean-Baka Domelevo Entfellner; Eduan Wilkinson; Damien Correia; Miraine Dávila Felipe; Tulio de Oliveira; Olivier Gascuel (Nat., 2018)

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)

SeqPanther: Sequence manipulation and mutation statistics toolset. - James Emmanuel San; Stephanie van Wyk; Houriiyah Tegally; Simeon Eche; Eduan Wilkinson; Aquillah M. Kanzi; Tulio de Oliveira; Anmol M. Kiran (J. Open Source Softw., 2023)