Duong Vu

Research output

Research output per year 2009 2009 2011 2013 2021 2022 2023 2023

• 22 Article
• 11 Software
• 2 Poster
• 2 Book/Film/Article review
• 1 More
  • 1 Chapter

Research output per year

Research output per year

Search results

• 2023

  A transformer architecture for retention time prediction in liquid chromatography mass spectrometry-based proteomics

  Pham, T. V., Nguyen, V. V., Vu, D., Henneman, A. A., Richardson, R. A., Piersma, S. R. & Jimenez, C. R., Apr 2023, In: Proteomics. 23, 7-8, p. e2200041

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

  Open Access

  • Liquid Chromatography 100%
  • Deep Learning 98%
  • Proteomics 88%
  • Retention Time 87%
  • Mass Spectrometry 86%
  2 Citations (Scopus)

• Comparing genomic variant identification protocols for Candida auris

  Li, X., Muñoz, J. F., Gade, L., Argimon, S., Bougnoux, M-E., Bowers, J. R., Chow, N. A., Cuesta, I., Farrer, R. A., Maufrais, C., Monroy-Nieto, J., Pradhan, D., Uehling, J., Vu, D., Yeats, C. A., Aanensen, D. M., d'Enfert, C., Engelthaler, D. M., Eyre, D. W., Fisher, M. C., & 6 othersHagen, F., Meyer, W., Singh, G., Alastruey-Izquierdo, A., Litvintseva, A. P. & Cuomo, C. A., 13 Apr 2023, In: Microbial genomics. 9, 4

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

  Open Access

  • Candida 100%
  • Single Nucleotide Polymorphism 81%
  • Practice Guidelines 36%
  • Disease Outbreaks 34%
  • Genome 26%

• How, not if, is the question mycologists should be asking about DNA-based typification

  Nilsson, R. H., Ryberg, M., Wurzbacher, C., Tedersoo, L., Anslan, S., Põlme, S., Spirin, V., Mikryukov, V., Svantesson, S., Hartmann, M., Lennartsdotter, C., Belford, P., Khomich, M., Retter, A., Corcoll, N., Martinez, D. G., Jansson, T., Ghobad-Nejhad, M., Vu, D., Sanchez-Garcia, M., & 2 othersKristiansson, E. & Abarenkov, K., 2023, In: MycoKeys. 96, p. 143-157 15 p.

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

  Open Access

  • Fungi 100%
  • DNA 91%
  • plant and fungus 82%
  • fungi 66%
  • code 64%
  3 Citations (Scopus)
• 2022

  Dnabarcoder: An open‐source software package for analysing and predicting DNA sequence similarity cutoffs for fungal sequence identification

  Vu, D., Nilsson, R. H. & Verkley, G. J. M., 20 Jun 2022, In: Molecular Ecology Resources.

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

  Open Access
  2 Citations (Scopus)

• Genetic and phenotypic diversity of fecal Candida albicans strains in irritable bowel syndrome

  van Thiel, I. A. M., Stavrou, A. A., de Jong, A., Theelen, B., Davids, M., Hakvoort, T. B. M., Admiraal-van den Berg, I., Weert, I. C. M., de Kruijs, M. A. M. H., Vu, D., Moissl-Eichinger, C., Heinsbroek, S. E. M., Jonkers, D. M. A. E., Hagen, F., Boekhout, T., de Jonge, W. J. & van den Wijngaard, R. M., 30 Mar 2022, In: Scientific Reports. 12, 1, p. 5391

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

  Open Access

  • Irritable Bowel Syndrome 100%
  • Candida albicans 88%
  • Genetic Variation 84%
  • Candida albicans ECE1 protein 31%
  • Fungi 26%
  4 Citations (Scopus)
• 2021

  Author Correction: Fungal taxonomy and sequence-based nomenclature

  Lücking, R., Aime, M. C., Robbertse, B., Miller, A. N., Aoki, T., Ariyawansa, H. A., Cardinali, G., Crous, P. W., Druzhinina, I. S., Geiser, D. M., Hawksworth, D. L., Hyde, K. D., Irinyi, L., Jeewon, R., Johnston, P. R., Kirk, P. M., Malosso, E., May, T. W., Meyer, W., Nilsson, H. R., & 8 othersÖpik, M., Robert, V., Stadler, M., Thines, M., Vu, D., Yurkov, A. M., Zhang, N. & Schoch, C. L., 27 May 2021, In: Nature Microbiology.

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

  Open Access

• Draft Genome Sequences of Two Cadophora Strains Isolated from Water and a Nonalcoholic Beverage Ingredient Auteurs

  Stefanovic, E., Scully, C., Roader, J., Murphy, F., Houbraken, J. & Vu, D., 01 Jul 2021, In: Genome Announcements. 10, 26

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

  Open Access

  • Beverages 100%
  • Soil 93%
  • Food 60%
  • Genome 58%
  • Water 57%

• Fungal Planet description sheets: 1284-1382

  Crous, P. W., Osieck, E. R., Jurjević, Ž., Boers, J., van Iperen, A. L., Starink-Willemse, M., Dima, B., Balashov, S., Bulgakov, T. S., Johnston, P. R., Morozova, O. V., Pinruan, U., Sommai, S., Alvarado, P., Decock, C. A., Lebel, T., McMullan-Fisher, S., Moreno, G., Shivas, R. G., Zhao, L., & 161 othersAbdollahzadeh, J., Abrinbana, M., Ageev, D. V., Akhmetova, G., Alexandrova, A. V., Altés, A., Amaral, A. G. G., Angelini, C., Antonín, V., Arenas, F., Asselman, P., Badali, F., Baghela, A., Bañares, A., Barreto, R. W., Baseia, I. G., Bellanger, J-M., Berraf-Tebbal, A., Biketova, A. Y., Bukharova, N. V., Burgess, T. I., Cabero, J., Câmara, M. P. S., Cano-Lira, J. F., Ceryngier, P., and Chávez, R., Cowan, D. A., de Lima, A. F., Oliveira, R. L., Denman, S., Dang, Q. N., Dovana, F., Duarte, I. G., Eichmeier, A., Erhard, A., Esteve-Raventós, F., Fellin, A., Ferisin, G., Ferreira, R. J., Ferrer, A., Finy, P., Gaya, E., Geering, A. D. W., Gil-Durán, C., Glässnerová, K., Glushakova, A. M., Gramaje, D., Guard, F. E., Guarnizo, A. L., Haelewaters, D., Halling, R. E., Hill, R., Hirooka, Y., Hubka, V., Iliushin, V. A., Ivanova, D. D., Ivanushkina, N. E., Jangsantear, P., Justo, A., Kachalkin, A. V., Kato, S., Khamsuntorn, P., Kirtsideli, I. Y., Knapp, D. G., Kochkina, G. A., Koukol, O., Kovács, G. M., Kruse, J., Kumar, T. K. A., Kušan, I., Læssøe, T., Larsson, E., Lebeuf, R., Levicán, G., Loizides, M., Marinho, P., Luangsa-ard, J. J., Lukina, E. G., Magaña-Dueñas, V., Maggs-Kölling, G., Malysheva, E. F., Malysheva, V. F., Martín, B., Martín, M. P., Matočec, N., McTaggart, A. R., Mehrabi-Koushki, M., Mešić, A., Miller, A. N., Mironova, P., Moreau, P-A., Morte, A., Müller, K., Nagy, L. G., Nanu, S., Navarro-Ródenas, A., Nel, W. J., Nguyen, T. H., Nóbrega, T. F., Noordeloos, M. E., Olariaga, I., Overton, B. E., Ozerskaya, A. M., Palani, P., Pancorbo, F., Papp, V., Pawłowska, J., Pham, T. Q., Phosri, C., Popov, E. S., Portugal, A., Pošta, A., Reschke, K., Reul, M., Ricci, G. M., Rodríguez, A., Romanowski, J., Ruchikachorn, N., Saar, I., Safi, A., Sakolrak, B., Salzmann, F., Sandoval-Denis, M., Sangwichein, E., Sanhueza, L., Sato, T., Sastoque, A., Senn-Irlet, B., Shibata, A., Siepe, K., Somrithipol, S., Spetik, M., Sridhar, P., Stchigel, A. M., Stuskova, K., Suwannasai, N., Tan, Y. P., Thangavel, R., Tiago, I., Tiwari, S., Tkalčec, Z., Tomashevskaya, M. A., Tonegawa, C., Tran, H. X., Tran, N. T., Trovão, J., Trubitsyn, V. E., Van Wyk, J., Vieira, W. A. S., Vila, J., Visagie, C. M., Vizzini, A., Volobuev, S. V., Vu, D. T., Wangsawat, N., Yaguchi, T., Ercole, E., Ferreira, B. W., de Souza, A. P., Vieira, B. S. & Groenewald, J. Z., 31 Dec 2021, In: Persoonia. 47, p. 178-374 197 p.

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

  Open Access

  • planet 100%
  • Entoloma 50%
  • leaves 49%
  • branches 41%
  • air 40%
  46 Citations (Scopus)

• Nanopore Genome Sequencing and Variant Analysis of the Susceptible Candida auris Strain L1537/2020, Salvador, Brazil

  de Jong, A. W., Francisco, E. C., de Almeida, J. N., Brandão, I. B., Pereira, F. M., Dias, P. H. P., de Miranda Costa, M. M., de Souza Jordão, R. T., Vu, D., Colombo, A. L. & Hagen, F., 20 Oct 2021, In: Mycopathologia.

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

  Open Access

  • Nanopore Sequencing 100%
  • nanopores 89%
  • Candida 64%
  • Brazil 53%
  • Genome 40%
  4 Citations (Scopus)
• 2020

  Comparative genomic analysis of capsule-producing black yeasts Exophiala dermatitidis and Exophiala spinifera, potential agents of disseminated mycoses

  Song, Y., Menezes da Silva, N., Almir Weiss, V., Vu, D., F Moreno, L. & de Hoog, S., 08 Apr 2020, In: Frontiers in Microbiology. 11

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

  Open Access

  • Exophiala 100%
  • Mycoses 61%
  • Genomics 61%
  • Capsules 54%
  • Virulence 52%
  8 Citations (Scopus)

• Convolutional neural networks improve fungal classification

  Vu, D., Groenewald, M. & Verkley, G. J. M., 28 Jul 2020, In: Scientific Reports. 10

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

  Open Access

  • Datasets 100%
  • Metagenomics 62%
  • Machine Learning 57%
  • Deep Learning 34%
  • Big Data 34%
  12 Citations (Scopus)
• 2019

  Large-scale generation and analysis of filamentous fungal DNA barcodes boosts coverage for kingdom fungi and reveals thresholds for fungal species and higher taxon delimitation

  Vu, D., Groenewald, M., de Vries, M., Gehrmann, T., Stielow, B., Eberhardt, U., Al-Hatmi, A., Groenewald, J. Z., Cardinali, G., Houbraken, J., Boekhout, T., Crous, P. W., Robert, V. & Verkley, G. J. M., Mar 2019, In: Studies in Mycology. 92, p. 135-154 20 p.

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

  Open Access

  • Fungal DNA 100%
  • Fungi (Kingdom) 97%
  • DNA barcoding 65%
  • Genetic Markers 63%
  • Fungi 54%
  555 Citations (Scopus)
• 2018

  Early Ongoing Speciation of Ogataea uvarum Sp. Nov. Within the Grape Ecosystem Revealed by the Internal Variability Among the rDNA Operon Repeats

  Roscini, L., Tristezza, M., Corte, L., Colabella, C., Perrotta, C., Rampino, P., Robert, V. A. R. G., Vu, D., Cardinali, G. & Grieco, F., 03 Aug 2018, In: Frontiers in Microbiology. p. 1687

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

  Open Access

  • Vitis 100%
  • Ribosomal DNA 90%
  • Ecosystem 85%
  • Operon 84%
  • Yeasts 62%
  10 Citations (Scopus)

• NGS barcode sequencing in taxonomy and diagnostics, an application in "Candida" pathogenic yeasts with a metagenomic perspective

  Colabella, C., Corte, L., Roscini, L., Bassetti, M., Mellor, J. C., Meyer, W., Robert, V. A. R. G., Vu, D. & Cardinali, G., 09 Jun 2018, In: IMA Fungus. p. 91-105 15 p.

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

  Open Access

  • Metagenomics 100%
  • Ribosomal DNA 94%
  • barcoding 90%
  • Candida 88%
  • ribosomal DNA 79%
  21 Citations (Scopus)
• 2017

  fMLC: Fast Multi-Level Clustering and Visualization of Large Molecular Datasets

  Vu, D., Georgievska, S., Szoke, S., Kuzniar, A. & Robert, V., 15 Dec 2017, In: Bioinformatics.

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

  • Visualization 100%
  • Clustering 87%
  • Cluster Analysis 82%
  • Datasets 72%
  • Data Visualization 67%
  11 Citations (Scopus)
• 2016

  DNA barcoding analysis of more than 9 000 yeast isolates contributes to quantitative thresholds for yeast species and genera delimitation

  Vu, D., Groenewald, M., Szöke, S., Cardinali, G., Eberhardt, U., Stielow, B., de Vries, M., Verkleij, G. J. M., Crous, P. W., Boekhout, T. & Robert, V., Sept 2016, In: Studies in Mycology. 85, p. 91-105 15 p.

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

  Open Access

  • DNA barcoding 100%
  • Yeasts 74%
  • yeasts 60%
  • DNA 51%
  • barcoding 41%
  175 Citations (Scopus)
• 2015

  One fungus , which genes ? Development and assessment of universal primers for potential secondary fungal DNA barcodes

  Stielow, J. B., Lévesque, C. A., Seifert, K. A., Meyer, W., Irinyi, L., Smits, D., Renfurm, R., Verkley, G. J. M., Groenewald, M., Chaduli, D., Lomascolo, A., Welti, S., Lesage-Meessen, L., Favel, A., Al-Hatmi, A. M. S., Damm, U., Yilmaz, N., Houbraken, J., Lombard, L., Quaedvlieg, W., & 43 othersBinder, M., Vaas, L. A. I., Vu, D., Yurkov, A., Begerow, D., Roehl, O., Guerreiro, M., Fonseca, A., Samerpitak, K., Diepeningen, A. D. V., Dolatabadi, S., Moreno, L. F., Casaregola, S., Mallet, S., Jacques, N., Roscini, L., Egidi, E., Bizet, C., Garcia-Hermoso, D., Martín, M. P., Deng, S., Groenewald, J. Z., Boekhout, T., Beer, Z. W. D., Barnes, I., Duong, T. A., Wingfield, M. J., Hoog, G. S. D., Crous, P. W., Lewis, C. T., Hambleton, S., Moussa, T. A. A., Al-Zahrani, H. S., Almaghrabi, O. A., Louis-Seize, G., Assabgui, R., McCormick, W., Omer, G., Dukik, K., Cardinali, G., Eberhardt, U., Vries, M. D. & Robert, V., 2015, In: Persoonia. 35, p. 242-263 22 p.

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

  Open Access

  • DNA barcoding 100%
  • DNA topoisomerase 93%
  • fungus 79%
  • translation (genetics) 79%
  • barcoding 76%
  359 Citations (Scopus)
• 2014

  Susceptibility and Diversity in the Therapy-Refractory Genus Scedosporium

  Lackner, M., Hagen, F., Meis, JF., Gerrits van den Ende, B., Vu, D., Robert, V., Fritz, J., Moussa, TAA. & de Hoog, GS., Oct 2014, In: Antimicrobial Agents and Chemotherapy. 58, 10, p. 5877-5885 9 p.

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

  Open Access

  • Scedosporium 100%
  • Pseudallescheria 23%
  • Ribosomal DNA 10%
  • Therapeutics 10%
  • Sympatry 8%
  51 Citations (Scopus)
• 2013

  MycoBank gearing up for new horizons.

  Robert, V., Vu, D., Ben Hadj Amor, A., van de Wiele, N., Brouwer, C. P. J. M., de Cock, A. W., Stalpers, J. A., Stalpers, D., Verkley, G. J. M., Groenewald, M., Borges dos Santos, F., Stegehuis, G. J., Crous, P. W. & et al., N. V., 2013, In: IMA Fungus. 4, 2, p. 371-379

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

  148 Citations (Scopus)

• Sympatric Evolution of the Therapy-Refractory Fungus Scedosporium

  Lackner, M., de Hoog, G. S., Gerrits van den Ende, A. H. G., Meis, J., Vu, D., Robert, V. A. R. G. & Klaassen, C. H. W., 2013, In: Clinical Infectious Diseases.

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review
• 2012

  A laboratory information management system for DNA barcoding workflows

  Vu, D., Eberhardt, U., Szöke, S., Groenewald, M. & Robert, V., 2012, In: Integrative Biology. 4, 7, p. 744-755

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review

  • Clinical Laboratory Information Systems 100%
  • Information Management 84%
  • Workflow 71%
  • DNA Sequence 66%
  • Strain 44%
  20 Citations (Scopus)
• 2011

  BioloMICS software, Biological data Management, Identification, Classification and Statistics

  Robert, V., Szoke, S., Jabas, B., Vu, D., Chouchen, O., Blom, E. & Cardinali, G., 2011, In: The Open Applied Informatics Journal. 5, p. 87-98

  Research output: Contribution to journal/periodical › Article › Scientific › peer-review