A graph neural network-based model with out-of-distribution robustness for enhancing antiretroviral therapy outcome prediction for HIV-1.

Anne-Mieke Vandamme https://orcid.org/0000-0002-6594-2766 https://www.wikidata.org/entity/Q28743834 https://www.researcherid.com/rid/I-4127-2012 https://id.loc.gov/authorities/names/n2002153128

Giulia Di Teodoro Federico Siciliano Valerio Guarrasi Anne-Mieke Vandamme Valeria Ghisetti Anders Sönnerborg Maurizio Zazzi Fabrizio Silvestri Laura Palagi A graph neural network-based model with out-of-distribution robustness for enhancing antiretroviral therapy outcome prediction for HIV-1. 102484 2025 120 Comput. Medical Imaging Graph. https://doi.org/10.1016/j.compmedimag.2024.102484 db/journals/cmig/cmig120.html#TeodoroSGVGSZSP25 streams/journals/cmig

Giulia Di Teodoro Federico Siciliano Valerio Guarrasi Anne-Mieke Vandamme Valeria Ghisetti Anders Sönnerborg Maurizio Zazzi Fabrizio Silvestri Laura Palagi A graph neural network-based model with Out-of-Distribution Robustness for enhancing Antiretroviral Therapy Outcome Prediction for HIV-1. 2023 abs/2312.17506 CoRR https://doi.org/10.48550/arXiv.2312.17506 db/journals/corr/corr2312.html#abs-2312-17506

Kristof Decock Koenraad Debackere Anne-Mieke Vandamme Bart Van Looy Scenario-driven forecasting: modeling peaks and paths. Insights from the COVID-19 pandemic in Belgium. 2703-2715 2020 124 Scientometrics 3 https://doi.org/10.1007/s11192-020-03591-6 https://www.wikidata.org/entity/Q98659283 db/journals/scientometrics/scientometrics124.html#DecockDVL20

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 Genome Detective: an automated system for virus identification from high-throughput sequencing data. 871-873 2019 35 Bioinform. 5 https://doi.org/10.1093/bioinformatics/bty695 https://www.wikidata.org/entity/Q62670770 db/journals/bioinformatics/bioinformatics35.html#VilskerMNFGDPAE19

Pieter Libin Ewout Vanden Eynden Francesca Incardona Ann Nowé Antonia Bezenchek EucoHIV Study Group Anders Sönnerborg Anne-Mieke Vandamme Kristof Theys Guy Baele PhyloGeoTool: interactively exploring large phylogenies in an epidemiological context. 3993-3995 2017 33 Bioinform. 24 https://doi.org/10.1093/bioinformatics/btx535 https://www.wikidata.org/entity/Q41927860 db/journals/bioinformatics/bioinformatics33.html#LibinEINBGSVTB17

Bram Vrancken Andrew Rambaut Marc A. Suchard Alexei J. Drummond Guy Baele Inge Derdelinckx Eric Van Wijngaerden Anne-Mieke Vandamme Kristel Van Laethem Philippe Lemey The Genealogical Population Dynamics of HIV-1 in a Large Transmission Chain: Bridging within and among Host Evolutionary Rates. 2014 10 PLoS Comput. Biol. 4 https://doi.org/10.1371/journal.pcbi.1003505 https://www.wikidata.org/entity/Q28541827 db/journals/ploscb/ploscb10.html#VranckenRSDBDWVLL14

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 Stefan Wesner Joke Snoeck Jean Ruelle Annelies De Bel Patrick Lacor Paul De Munter Eric Van Wijngaerden Maurizio Zazzi Rolf Kaiser Ahidjo Ayouba Martine Peeters Tulio de Oliveira Luiz Carlos Júnior Alcântara Zehava Grossman Peter M. A. Sloot Dan Otelea Simona Paraschiv Charles A. Boucher Ricardo Camacho Anne-Mieke Vandamme RegaDB: community-driven data management and analysis for infectious diseases. 1477-1480 2013 29 Bioinform. 11 https://doi.org/10.1093/bioinformatics/btt162 https://www.wikidata.org/entity/Q30621161 db/journals/bioinformatics/bioinformatics29.html#LibinBDIFLTCCLTAWSRBLMWZKAPOAGSOPBCV13

Bram Vrancken Andrew Rambaut Guy Baele Anne-Mieke Vandamme Kristel Van Laethem Eric Van Wijngaerden Alexei J. Drummond Marc A. Suchard Philippe Lemey Reconstruction of an HIV Transmission History in a Bayesian Coalescent Framework. 555-556 2013 IWBBIO http://iwbbio.ugr.es/papers/iwbbio_091.pdf conf/iwbbio/2013 db/conf/iwbbio/iwbbio2013.html#VranckenRBVLWDSL13

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 Estimating the individualized HIV-1 genetic barrier to resistance using a nelfinavir fitness landscape. 409 2010 11 BMC Bioinform. https://doi.org/10.1186/1471-2105-11-409 https://www.wikidata.org/entity/Q33648513 db/journals/bmcbi/bmcbi11.html#TheysDBMLLCRSWV10

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 A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences. 634-642 2009 37 Nucleic Acids Res. Web-Server-Issue https://doi.org/10.1093/nar/gkp455 https://www.wikidata.org/entity/Q27488863 db/journals/nar/nar37.html#AlcantaraCLDPRGVO09

Matthias Assel David A. van de Vijver Pieter Libin Kristof Theys Daniel Harezlak Breanndán Ó Nualláin Piotr Nowakowski Marian Bubak Anne-Mieke Vandamme Stijn Imbrechts Raphael Sangeda Tao Jiang Dineke Frentz Peter M. A. Sloot A Collaborative Environment Allowing Clinical Investigations on Integrated Biomedical Databases. 51-61 2009 HealthGrid https://doi.org/10.3233/978-1-60750-027-8-51 conf/healthgrid/2009 db/conf/healthgrid/healthgrid2009.html#AsselVLTHNNBVISJFS09

Koen Deforche Ricardo Camacho Kristel Van Laethem Philippe Lemey Andrew Rambaut Yves Moreau Anne-Mieke Vandamme Estimation of an in vivo fitness landscape experienced by HIV-1 under drug selective pressure useful for prediction of drug resistance evolution during treatment. 34-41 2008 24 Bioinform. 1 https://doi.org/10.1093/bioinformatics/btm540 https://www.wikidata.org/entity/Q46891926 db/journals/bioinformatics/bioinformatics24.html#DeforcheCLLRMV08

Peter M. A. Sloot Peter V. Coveney Marian Bubak Anne-Mieke Vandamme Breanndán Ó Nualláin David A. van de Vijver Charles A. Boucher Multi-Science Decision Support for HIV Drug Resistance Treatment. 188-198 2008 HealthGrid http://www.booksonline.iospress.nl/Content/View.aspx?piid=9171 conf/healthgrid/2008 db/conf/healthgrid/healthgrid2008.html#SlootCBVNVB08

Koen Deforche Ricardo Camacho Kristel Van Laethem Beth Shapiro Yves Moreau Andrew Rambaut Anne-Mieke Vandamme Philippe Lemey Estimating the Relative Contribution of dNTP Pool Imbalance and APOBEC3G/3F Editing to HIV Evolution In Vivo. 1105-1114 2007 14 J. Comput. Biol. 8 https://doi.org/10.1089/cmb.2007.0073 https://www.wikidata.org/entity/Q46912380 db/journals/jcb/jcb14.html#DeforcheCLSMRVL07

Koen Deforche Tomi Silander Ricardo Camacho Zehava Grossman M. A. Soares Kristel Van Laethem Rami Kantor Yves Moreau Anne-Mieke Vandamme Analysis of HIV-1 pol sequences using Bayesian Networks: implications for drug resistance. 2975-2979 2006 22 Bioinform. 24 https://doi.org/10.1093/bioinformatics/btl508 https://www.wikidata.org/entity/Q40281796 db/journals/bioinformatics/bioinformatics22.html#DeforcheSCGSLKMV06

Dimitris Paraskevis Koen Deforche Philippe Lemey Gkikas Magiorkinis Angelos Hatzakis Anne-Mieke Vandamme SlidingBayes: exploring recombination using a sliding window approach based on Bayesian phylogenetic inference. 1274-1275 2005 21 Bioinform. 7 https://doi.org/10.1093/bioinformatics/bti139 https://www.wikidata.org/entity/Q51984121 db/journals/bioinformatics/bioinformatics21.html#ParaskevisDLMHV05

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 Anne-Mieke Vandamme An automated genotyping system for analysis of HIV-1 and other microbial sequences. 3797-3800 2005 21 Bioinform. 19 https://doi.org/10.1093/bioinformatics/bti607 https://www.wikidata.org/entity/Q33220974 db/journals/bioinformatics/bioinformatics21.html#ValenteDCSPSSRWVBCV05

Luiz Carlos Júnior AlcântaraLuiz Carlos Alcantara Matthias Assel Ahidjo Ayouba Guy Baele Gertjan Beheydt Annelies De Bel Antonia Bezenchek Charles A. Boucher Marian Bubak Ricardo Camacho Ana Patricia Carvalho Sharon Cassol Joana Cavaco-Silva Peter V. Coveney Koenraad Debackere Kristof Decock Koen Deforche Inge Derdelinckx Alexei J. Drummond Korneel Dumon Ewout Vanden Eynden Fossie Ferreira Vagner Fonseca Dineke Frentz Bernardo Galvão-Castro Valeria Ghisetti Yoika Ghysens Zehava Grossman EucoHIV Study Group Valerio Guarrasi Daniel Harezlak Angelos Hatzakis Stijn Imbrechts Francesca Incardona Tao Jiang Rolf Kaiser Rami Kantor Patrick Lacor Kristel Van Laethem Giuseppe Lapadula Philippe Lemey Pieter Libin Bart Van Looy Gkikas Magiorkinis Yumna Moosa Yves Moreau Paul De Munter Sam Nooij Piotr Nowakowski Ann Nowé Breanndán Ó Nualláin Tulio de Oliveira Dan Otelea Laura Palagi Simona Paraschiv Dimitris Paraskevis Raf Pauwels Martine Peeters Oliver G. Pybus Andrew Rambaut Marc Van Ranst Estrelita J. Janse van Rensburg Soo-Yon Rhee Jean Ruelle Mika Salminen Raphael Zozimus SangedaRaphael Sangeda Christopher J. SeebregtsChris Seebregts Robert W. Shafer Beth Shapiro Federico Siciliano Tomi Silander Fabrizio Silvestri Peter M. A. Sloot Joke Snoeck M. A. Soares Anders Sönnerborg Marc A. Suchard Giulia Di Teodoro Kristof Theys Carlo Torti David A. van de Vijver Michael Vilsker Bram Vrancken Annemarie M. J. Wensing Stefan Wesner Eric Van Wijngaerden Maurizio Zazzi