Vital-IT group, Swiss Institute of Bioinformatics.

Quartier Sorge, bâtiment Amphipôle - 1015 Lausanne

Tel: +41 21 692 40 74 - Fax: +41 21 692 40 65

Email: Thuong (dot) Tran (at) sib (dot) swiss

Research interests

• Data integration
• Federated database
• Genome-scale metabolic networks
• Machine learning
• Omics data analysis
• Biomedical informatics
• MicroRNA prediction
• Protein structure prediction

Publications

• S. Li, I. Dragan, V. D. Tran, C. H. Fung, D. Kuznetsov, M. K. Hansen, J. Beulens, L. M. 't Hart, R. Slieker, L. A. Donnelly, M. J. Gerl, C. Klose, F. Mehl, K. Simons, P. J. M. Elders, E. R. Pearson, G. A. Rutter, M. Ibberson. Multi-omics subgroups associated with glycaemic deterioration in type 2 diabetes: an IMI-RHAPSODY Study, Frontiers in Endocrinology, section Diabetes: Molecular Mechanisms, 2024.
• C. Delfin, I. Dragan, D. Kuznetsov, J. F. Tajes, F. Smit, D. E. Coral, A. Farzaneh, A. Haugg, A. Hungele, A. Niknejad, C. Hall, D. Jacobs, D. Marek, D. P. Fraser, D. Thuillier, F. Ahmadizar, F. Mehl, F. Pattou, F. Burdet, G. Hawkes, I. C. W. Arts, J. Blanch, J. Van Soest, J.-M. Fernández-Real, J. Boehl, K. Fink, M. M. J. van Greevenbroek, M. Kavousi, M. Minten, N. Prinz, N. Ipsen, P. W. Franks, R. Ramos, R. W. Holl, S. Horban, T. Duarte-Salles, V. D. Tran, V. Raverdy, Y. Leal, A. Lenart, E. Pearson, T. Sparsø, G. N. Giordano, V. Ioannidis, K. Soh, T. M. Frayling, C. W. Le Roux, M. Ibberson. A Federated Database for Obesity Research: An IMI-SOPHIA Study, Life, 2024.
• K. Barreiro, A. C. Lay, G. Leparc, V. D. Tran, M. Rosler, L. Dayalan, F. Burdet, M. Ibberson, R. Coward, T. B. Huber, B. K. Kramer, D. Delic, H. Holthofer. An in vitro approach to understand contribution of kidney cells to human urinary extracellular vesicles, Journal of Extracellular Vesicles, 2023.
• S. Schrevens, E. Durandau, V. D. Tran, D. Sanglard. Using in vivo transcriptomics and RNA enrichment to identify genes involved in virulence of Candida glabrata, Virulence, 2022.
• C. Lemberg, K. M. de San Vicente, R. Frois-Martins, S. Altmeier, V. D. Tran, S. Mertens, S. Amorim-Vaz, L. S. Rai, C. d’Enfert, M. Pagni, D. Sanglard, S. LeibundGut-Landmann. Candida albicans commensalism in the oral mucosa is favoured by limited virulence and metabolic adaptation, PLOS Pathogens, 2022.
• S. Amorim-Vaz, A. T. Coste, V. D. Tran, M. Pagni, D. Sanglard. Function analysis of MBF1, a factor involved in the response to amino acid starvation and virulence in Candida albicans, Frontiers in Fungal Biology, 2021.
• S. Moretti, V. D. Tran, F. Mehl, M. Ibberson, M. Pagni. MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models, Nucleic Acids Research, 2020.
• T. Caputo, V. D. Tran, N. Bararpour, C. Winkler, G. Aguileta, K. B. Trang, G. M. P. G. Attianese, A. Wilson, A. Thomas, M. Pagni, N. Guex, B. Desvergne, F. Gilardi. Anti-adipogenic signals at the onset of obesity-related inflammation in white adipose tissue, Cellular and Molecular Life Sciences, 2020.
• F. R. Kirchner, K. Littringer, S. Altmeier, V. D. Tran, F. Schönherr, C. Lemberg, M. Pagni, D. Sanglard, N. Joller, S. LeibundGut-Landmann. Persistence of Candida albicans in the oral mucosa induces a curbed inflammatory host response that is independent of immunosuppression, Frontiers in Immunology, 2019.
• V. D. Tran, S. Moretti, A. T. Coste, S. Amorim-Vaz, D. Sanglard, M. Pagni. Condition-specific series of metabolic sub-networks and its application for gene set enrichment analysis, Bioinformatics, 2018.
• L. A. Vale-Silva, E. Beaudoing, V. D. Tran, D. Sanglard. Comparative genomics of two sequential Candida glabrata clinical isolates, G3: Genes, Genomes, Genetics, 2017.
• F. Tahi, V. D. Tran, A. Boucheham. In silico prediction of RNA secondary structure, in S. Napoli, editor, Promoter Associated RNA, volume 1543 of Methods in Molecular Biology series, Springer, 2017.
• V. D. Tran, N. De Coi, M. Feuermann, E. Schmid-Siegert, E.-T. Bagut, B. Mignon, P. Waridel, C. Peter, S. Pradervand, M. Pagni, M. Monod. RNA sequencing-based genome reannotation of the dermatophyte Arthroderma benhamiae and characterization of its secretome and whole gene expression profile during infection, mSystems, 2016.
• V. D. Tran, O. Souiai, N. Romero-Barrios, M. Crespi, D. Gautheret. Detection of generic differential RNA processing events from RNA-seq data, RNA biology, 2016.
• S. Amorim-vaz, V. D. Tran, S. Pradervand, M. Pagni, A. T. Coste, D. Sanglard. Characterization of a new virulence gene in Candida albicans, Clinical Chemistry and Laboratory Medicine, 2016.
• S. Altmeier, F. Schonherr, S. Amorim-vaz, V. D. Tran, A. T. Coste, D. Sanglard, S. Leibundgut-landmann. Transcriptomic approach to determine the interaction between Candida albicans and the host mucosa in vivo, Clinical Chemistry and Laboratory Medicine, 2016.
• SIB Swiss Institute of Bioinformatics Members. The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases, Nucleic Acids Research, 2015.
• S. Moretti, O. Martin, V. D. Tran, A. Bridge, A. Morgat, M. Pagni. MetaNetX/MNXref - reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks, Nucleic Acids Research, 2015.
• S. Amorim-Vaz, V. D. Tran, S. Pradervand, M. Pagni, A. T. Coste, D. Sanglard. RNA enrichment method for quantitative transcriptional analysis of pathogens in vivo applied to the fungus Candida albicans, mBio, 2015.
• V. D. Tran, S. Tempel, B. Zerath, F. Zehraoui, F. Tahi. miRBoost: boosting support vector machines for microRNA precursor classification, RNA, 2015.
• F. Tahi, V. D. Tran, S. Tempel, E. Mahe. Bioinformatics of noncoding RNAs and GPUs. A case study: prediction at large scale of microRNAs in genomes, in F. Magoules, editor, Patterns for Parallel Programming on GPUs, Saxe Coburg Publications, 2014.
• V. D. Tran, P. Chassignet, J.-M. Steyaert. On permuted super-secondary structures of transmembrane beta-barrel proteins, Theoretical Computer Science, 2014.
• V. D. Tran, P. Chassignet, J.-M. Steyaert. Supersecondary structure prediction of transmembrane beta-barrel proteins, in A. E. Kister, editor, Protein Supersecondary Structure, volumn 932 of Methods in Molecular Biology series, Humana Press, 2013.
• V. D. Tran, B. Zerath, S. Tempel, F. Zehraoui, F. Tahi. BoostSVM: A miRNA classifier with high accuracy using boosting SVM, 13e Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), 2012.
• S. Sheikh, V. D. Tran, P. Chassignet, J.-M. Steyaert. Knowledge-based consensus methods for secondary structure prediction of transmembrane beta-barrel proteins. BICoB'12: International Conference on Bioinformatics and Computational Biology, 2012.
• V. D. Tran, P. Chassignet, S. Sheikh, J.-M. Steyaert. A graph-theoretic approach for classification and structure prediction of transmembrane beta-barrel proteins. BMC Genomics, 13(Suppl 2):S5, 2012.
• V. D. Tran, P. Chassignet, J.-M. Steyaert. Prediction of permuted super-secondary structures in beta-barrel proteins. SAC'11: ACM Symposium on Applied Computing, 2011.
• V. D. Tran, P. Chassignet, S. Sheikh, J.-M. Steyaert. Energy-based classification and structure prediction of transmembrane beta-barrel proteins, ICCABS'11: IEEE International Conference on Computational Advances in Bio and Medical Sciences, 2011.
• V. D. Tran, P. Chassignet, J.-M. Steyaert. Prediction of super-secondary structure in alpha-helical and beta-barrel transmembrane proteins, BMC Bioinformatics, 10(Suppl 13):O3, 2009.

Thesis

• Modeling and predicting super-secondary structures of transmembrane beta-barrel proteins, PhD thesis, Ecole Polytechnique, France, 2011
  

Teaching

• SIB Swiss Institute of Bioinformatics, 2016-present: R in Life Sciences, Deep Learning for Life Sciences, Multiomics Data Analysis and Integration, Multivariate Analysis for Omics Data Integration, Introduction to Machine Learning, Biochemical pathways and Metabolic networks
• Université d'Evry Val d'Essonne, 2012: Advanced Network
• Université Paris Sud, 2007-2011: Internet Programming, Unix, Java, C, C++, Formal Languages and Syntactic Analysis, Algorithm and Complexity, Algorithm and Complexity in Biology
• Ecole Polytechnique, 2007-2009: Scilab

Software

• dsMO: non-disclosive federated Multi-Omics analysis
• metaboGSE: gene set enrichment analysis via integration of metabolic networks and RNA-seq data
• RNAprof (RNA Profile Analysis): identification of differential processing events from RNA-seq data
• miRBoost: microRNA precursor prediction with boosting SVM
• BBP (Beta-Barrel Predictor): prediction of super-secondary structures of transmembrane beta-barrel proteins