Publications
Ph.D. Guangdi Li
Guangdi Li received his doctoral degree in Biomedical Sciences from the Faculty of Medicine, KU Leuven, Belgium, 2014. During his Ph.D., he received extensive training from Master of Molecular and Cellular Biophysics, Faculty of Science, KU Leuven. In 2006, he obtained his Bachelor's degree in Applied Mathematics at Hunan University. Between 2006 and 2009, he pursued his master’s degree in Computer Science at Shandong University, and received full scholarships to work as a research assistant at the Technical University of Madrid, Spain. Between 2009 and 2014, he undertook his doctorate training in the Faculty of medicine, KU Leuven, Belgium. His research interests are focused on the genome-wide diversity, coevolution and interaction of HIV, HBV and HCV, as well as the development of antiviral drugs and vaccines. Since 2013, he has published more than 10 research articles.
My Curriculum Vitae (CV)
Current address: Metabolic Syndrome Research Center, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
Email: liguangdi.research@gmail.com
My Publications
Here is my Phd thesis (418 pages):
"HIV genome-wide diversity, interaction and coevolution"
My first-author or corresponding papers are highlighted with cover images.
Title: Rheb Regulates Adipose Browning by Activating the PKA Signaling Pathway via mTORC1-depednent and -independent Mechanisms Authors: Wen Meng, Xiuci Liang, Hongzhi Chen, Hairong Luo, Juli Bai, Guangdi Li, Qinghai Zhang, Ting Xiao, Sijia He, Yacheng Zhang, Zhipeng Xu, Bo Xiao, Fang Hu, Feng Liu Journal: Diabetes, 2017, 66:1196-1213. DOI: 10.2337/db16-0886 Sources: [PDF Download] [PubMed] [Google Scholar] [Journal website] Highlights: This article discovers the role of Rheb in adipose browning by activating the PKA signaling pathway. |
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Title: Current therapy for chronic hepatitis C: The role of direct-acting antivirals Authors: Guangdi Li†, Erik De Clercq† (†: co-corresponding authors). Journal: Antiviral Research, 2017, 142:83-122. doi: 10.1016/j.antiviral.2017.02.014 Sources: [PDF Download] [Google Scholar] [Journal website] [PubMed] Highlights:We presented the first overview of the efficacy of approved HCV drugs in clinical trials. Collection of figures:  This article is the highlighted paper of Antiviral Research.  |
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Title: APPLs: More than just adiponectin receptor binding protein s Authors: Zhuoying Liu, Ting Xiao, Xiaoyu Peng, Guangdi Li, Fang Hu Journal: Cellular Signalling 32 (2017) 76–84. doi:10.1016/j.cellsig.2017.01.018 Sources: [PDF Download] [PubMed] [Google Scholar] [Journal website] Highlights: This article summarizes the latest progress of APPL (adaptor protein containing pleckstrin homology domain,phosphotyrosine binding domain and leucine zipper motif). |
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Title: Mapping the genomic diversity of HCV subtypes 1a and 1b: Implications of structural and immunological constraints for vaccine and drug development Authors: Lize Cuypers†, Guangdi Li†, Christoph Neumann-Haefelin, Supinya Piampongsant, Pieter Libin, Kristel Van Laethem, Anne-Mieke Vandamme and Kristof Theys (†: both authors contributed equally to this work). Journal: Virus Evolution, 2016, 2(2): vew024. doi: 10.1093/ve/vew024 Sources: [PDF Download] [Google Scholar] [Journal website] [PubMed] Highlights: We showed that HCV genomic divesity was driven by structural and immunological constraints. Collection of figures:  |
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Title: Impact of HCV genotype on treatment regimens and drug resistance: a snapshot in time Authors: Lize Cuypers, Francesca Ceccherini-Silberstein, Kristel Van Laethem, Guangdi Li, Anne-Mieke Vandamme, Jürgen Kurt Rockstroh Journal: Reviews in Medical Virology. doi: 10.1002/rmv.1895 Sources: [PDF Download] [PubMed] [Google Scholar] [Journal website] Highlights: This article summarizes the latest progress of HCV antiviral drugs and their resistance mutations. |
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Title: HIV Genome-Wide Protein Associations: a Review of 30 Years of Research Authors: Guangdi Li†, Erik De Clercq† (†: co-corresponding authors). Journal: Microbiology and Molecular Biology Reviews. 80(3):679-731. doi: 10.1128/MMBR.00065-15 Sources: [PDF Download] [Google Scholar] [Journal website] [PubMed] Highlights: We presented the first overview of HCV genome-wide protein associations discovered over the past 30 years. Collection of figures:  This article is highlighted as the cover paper of the journal MMBR!  |
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Title: Approved Antiviral Drugs over the Past 50 Years Authors: Erik De Clercq, Guangdi Li. Journal: Clinical Microbiology Reviews. Jul;29(3):695-747. doi: 10.1128/CMR.00102-15. Sources: [PDF Download] [Google Scholar] [Journal website] [PubMed] Highlights: We presented the first overview of 90 antiviral drugs approved over the past 50 years. Collection of figures:  This article is highlighted as the cover paper of the journal CMR!  |
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Title: A functional FAS polymorphism links CD4 T stem cell memory levels and IFN induced apoptosis in both healthy controls and Adult T-cell Leukemia patients Authors: Ricardo Khouri, Daniele Decanine, Gilvaneia Silva-Santos, Kristof Theys, Guangdi Li, Aline Clara Silva, Lourdes Farre, Achilea Bittencourt, Massimo Mangino, Mario Roederer, Johan Van Weyenbergh. Journal: Cytokine. 76 66–112. doi: 10.1016/j.cyto.2015.08.242 Sources: [PDF Download] [Google Scholar] [Journal website] Highlights: A genetically determined IFN/STAT1/FAS axis underscores the CD4 Tscm ATL model and helps explain the observed in vivo IFN + AZT responsiveness and chemotherapy resistance in ATL patients. |
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Title: Genetic Diversity and Selective Pressure in Hepatitis C Virus Genotypes 1-6: Significance for Direct-Acting Antiviral Treatment and Drug Resistance Authors: Lize Cuypers†, Guangdi Li†, Pieter Libin, Supinya Piampongsant, Anne-Mieke Vandamme, Kristof Theys (†: both authors contributed equally to this work). Journal: Viruses. 7(9):5018-5039. Sources: [PDF Download] [Google Scholar] [Journal website] [PubMed] Highlights: We presented a large-scale study to characterize HCV genomic diversity using 1415 full-length genome sequences. Collection of figures:  |
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Title: High-Throughput Analysis of Human Cytomegalovirus Genome Diversity Highlights the Widespread Occurrence of Gene-Disrupting Mutations and Pervasive Recombination Authors: Steven Sijmons, Kim Thys, Mirabeau Mbong Ngwese, Ellen Van Damme, Jan Dvorak, Marnix Van Loock, Guangdi Li, Ruth Tachezy, Laurent Busson, Jeroen Aerssens, Marc Van Ranst, Piet Maes. Journal: Journal of Virology. Vol. 89 no. 15 7673-7695. doi: 10.1128/JVI.00578-15 Sources: [PDF Download] [Google Scholar] [PubMed] [Journal website] Highlights: We presented the first high-resolution analysis of interhost genome diversity, providing an unbiased and comprehensive overview of cytomegalovirus variability. |
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Title: An integrated map of HIV genome-wide diversity from a population perspective Authors: Guangdi Li*, Supinya Piampongsant, Nuno Rodrigues Faria, Arnout Voet, Andrea-Clemencia Pineda-Peña, Ricardo Khouri, Philippe Lemey, Anne-Mieke Vandamme, Kristof Theys* (*: corresponding authors) Journal: Retrovirology. 12:18. doi: 10.1186/s12977-015-0148-6. Sources: [PDF Download] [Our Software & Dataset] [Google Scholar] [PubMed] Highlights: We presented the first study to characterize HIV genomic diversity using large-scale genomic datasets including approximately 3000 full-length genome sequences, all HIV protein structures, detailed HIV-human protein interaction data, human immunological data and all peptide inhibitors derived from the HIV genome. Collection of figures:  |
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Title: A new ensemble coevolution system for detecting HIV-1 protein coevolution Authors: Guangdi Li, Kristof Theys, Jens Verheyen, Andrea-Clemencia Pineda-Peña, Ricardo Khouri, Supinya Piampongsant, Mónica Eusébio, Jan Ramon, Anne-Mieke Vandamme Journal: Biology Direct 10:1. doi: 10.1186/s13062-014-0031-8. Sources: [PDF Download] [Our Software & Dataset] [Google Scholar] [PubMed] Highlights: We introduced the first ensemble coevolution system, which integrates 27 sequence-based methods published in the past decade, to predict the intra- and inter-protein coevolution in the HIV-1 genome. Collection of figures:  |
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Title: A stably expressed llama single-domain intrabody targeting Rev displays broad-spectrum anti-HIV activity Authors: Eline Boons, Guangdi Li, Els Vanstreels, Thomas Vercruysse, Christophe Pannecouque, Anne-Mieke Vandamme, Dirk Daelemans. Journal: Antiviral Research. 112:91-102. doi: 10.1016/j.antiviral.2014.10.007. Sources: [PDF Download] [Google Scholar] [PubMed] [Journal website] Highlights: This study reports that the single-domain intrabody Nb190 targeting Rev displays broad-spectrum anti-HIV activity. |
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Title: HIV-1 Gag C-terminal amino acid substitutions emerging under selective pressure of protease inhibitors in patient populations infected with different HIV-1 subtypes Authors: Guangdi Li, Jens Verheyen, Kristof Theys, Supinya Piampongsant, Kristel Van Laethem, Anne-Mieke Vandamme Journal: Retrovirology. 11:79. doi: 10.1186/s12977-014-0079-7. Sources: [PDF Download] [Our Software & Dataset] [Google Scholar] [PubMed] Highlights: This study reports the first large-scale analysis which evaluates protease inhibitor (PI) associated Gag mutations emerging during the PI treatment using 11613 patients infected with different HIV-1 subtypes. Collection of figures and tables:  |
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Title: Trends and predictors of transmitted drug resistance (TDR) and clusters with TDR in a local Belgian HIV-1 epidemic. Authors: Andrea-Clemencia Pineda, Nuno Rodrigues Faria, Francisco-Javier Diaz, Patricia Olaya, Casper Møller Frederiksen, Guangdi Li, Arley Gomez-Lopez, Philippe Lemey, Anne-Mieke Vandamme Journal: PLoS One. 9(7):e101738. doi: 10.1371/journal.pone.0101738. Sources: [PDF Download] [Google Scholar] [PubMed] [Journal website] Collection of figures: Highlights: This study reports that transmitted drug resistance remained stable and a NNRTI up-and-down trend was observed in Belgian patient populations. |
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Title: Learning Ancestral Polytrees Authors: Guangdi Li, Anne-Mieke Vandamme, Jan Ramon Computer Science Conference: The 1st workshop of Learning Tractable Probabilistic Model co-located with the 31st International Conference on Machine Learning (ICML 2014), Beijing, China. Sources: [PDF] [Our Software & Dataset] [Google Scholar] [Conference website] Highlights: This study for the first time proposed a new causal model, so-called ancestral polytree, to evaluate causal patterns in the context of latent variables. Collection of figures:  |
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Title: Horizontal gene transfer from human host to HIV-1 reverse transcriptase confers drug resistance and partly compensates for replication deficits Authors: Sarah Megens, Dolores Vaira, Greet De Baets, Nathalie Dekeersmaeker, Yoeri Schrooten, Guangdi Li, Joost Schymkowitz, Frederic Rousseau, Anne-Mieke Vandamme, Michel Moutschen, Kristel Van Laethem, Journal: Virology. 456-457:310-8. doi: 10.1016/j.virol.2014.03.023 Sources: [PDF Download] [Google Scholar] [PubMed] [Journal website] Highlights: This study reports a particular sequence within human chromosome 17, which is prone to horizontal gene transfer into the HIV-1 RT finger subdomain. |
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Title: Functional conservation of HIV-1 Gag: implications for rational drug design Authors: Guangdi Li, Jens Verheyen, Soo-Yon Rhee, Arnout Voet, Anne-Mieke Vandamme, Kristof Theys Journal: Retrovirology. 10:126. doi: 10.1186/1742-4690-10-126. Sources: [PDF Download] [Our Software & Dataset] [Google Scholar] [PubMed] Highlights: We introduced the first ensemble coevolution system, which integrates 27 sequence-based methods published in the past decade, to predict the intra- and inter-protein coevolution in the HIV-1 genome. Collection of figures:  |
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Title: Multi-Dimensional Classification with Bayesian Networks Authors: Concha Bielza (my supervisor), Guangdi Li, Pedro Larrañaga. Journal: International Journal of Approximate Reasoning, 52:6, 705–727. Sources: [PDF Download] [Google Scholar] [Journal website] Highlights: We introduced new algorithms to perform multi-dimensional classification with Bayesian networks, which outperformed known algorithms. Collection of figures and algorithms:  |
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Title: Energy saving design for central air-conditioning systems (in Chinease) Authors: Yanwei Wang, Zhifei Ji, Guangdi Li Journal: Mathematics in Practice and Theory, 16. Highlights: We introduced a new algorithm to optimize the stategy of energy saving in central air-conditioninig systems. |