Publications

Please note that only the publications describing and using the tools developed by the MycoAI team are listed here. Please refer to Duong Vu’s google scholar for the full list.

2024

1. Romeijn L, Bernatavicius A, and Vu D(2024).

   Fast and Accurate Taxonomic Classification of Fungal ITS Sequences with MycoAI.

   Molecular Ecology Resources 24, e14006. https://doi.org/10.1111/1755-0998.14006

2023

1. Pagani DM, Ventura SPR, Vu D, Mendes-Pereira T, Ribeiro Tomé LM, Carvalho DSd, Costa-Rezende DH, Kato RB, García GJY, Geml J, et al.

   Unveiling Fungal Community Structure along Different Levels of Anthropic Disturbance in a South American Subtropical Lagoon (2023).

   Journal of Fungi 9(9):890. https://doi.org/10.3390/jof9090890

2. Xiao Li; José F. Muñoz; Lalitha Gade; Silvia Argimon; Marie-Elisabeth Bougnoux; Jolene R. Bowers; Nancy A. Chow; Isabel Cuesta; Rhys A. Farrer; Corinne Maufrais; Juan Monroy-Nieto; Dibyabhaba Pradhan; Jessie Uehling; Duong Vu; Corin A. Yeats; David M. Aanensen; Christophe d’Enfert; David M. Engelthaler; David W. Eyre; Matthew C. Fisher; Ferry Hagen; Wieland Meyer; Gagandeep Singh; Ana Alastruey-Izquierdo; Anastasia P. Litvintseva; Christina A. Cuomo (2023).

   Comparing genomic variant identification protocols for fungi.

   Microbial Genomics. https://doi.org/10.1099/mgen.0.000979

2022

1. Vu D, Nilsson H, Verkley G (2022).

   dnabarcoder: an open-source software package for analyzing and predicting DNA sequence similarity cut-offs for fungal sequence identification.

   Molecular Ecology Resources. https://doi.org/10.1111/1755-0998.13651

2. Isabelle AM van Thiel, Aimilia A Stavrou, Auke de Jong, Bart Theelen, Mark Davids, Theodorus Hakvoort, Iris Admiraal-van den Berg, Isabelle Weert, Martine AM de Kruijs, Duong Vu, Christine Moissl-Eichinger, Sigrid EM Heinsbroek, Daisy MAE Jonkers, Ferry Hagen, Teun Boekhout, Wouter J de Jonge, René M van den Wijngaard (2022).

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

   Sci Rep 12, 5391.https://www.nature.com/articles/s41598-022-09436-x

2021

1. Teun Boekhout, Anthony S Amend, Fouad El Baidouri, Toni Gabaldón, József Geml, Moritz Mittelbach, Vincent Robert, Chen Shuhui Tan, Benedetta Turchetti, Duong Vu, Qi-Ming Wang, Andrey Yurkov (2021b).

   Trends in yeast diversity discovery.

   Fungal Diversity, 1-47.

2. Auke W de Jong, Elaine C Francisco, João Nóbrega de Almeida, Igor B Brandão, Felicidade M Pereira, Pedro H Presta Dias, Magda M de Miranda Costa, Regiane T de Souza Jordão, Duong Vu, Arnaldo L Colombo, Ferry Hagen (2021).

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

   Mycopathologia, 1-5.

3. Ewelina Stefanovic, Colm Scully, Jimmy Roader, Finbarr Murphy, Jos Houbraken, Duong Vu (2021).

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

   Microbiology Resource Announcements 10.

4. Teun Boekhout, M Catherine Aime, Dominik Begerow, Toni Gabaldón, Joseph Heitman, Martin Kemler, Kantarawee Khayhan, Marc-André Lachance, Edward J Louis, Sheng Sun, Duong Vu, Andrey Yurkov (2021a).

   The evolving species concepts used for yeasts: from phenotypes and genomes to speciation networks.

   Fungal Diversity 109, 27–55.

5. Robert Lücking, M. Catherine Aime, Barbara Robbertse, Andrew N. Miller, Takayuki Aoki, Hiran A. Ariyawansa, Gianluigi Cardinali, Pedro W. Crous, Irina S. Druzhinina, David M. Geiser, David L. Hawksworth, Kevin D. Hyde, Laszlo Irinyi, Rajesh Jeewon, Peter R. Johnston, Paul M. Kirk, Elaine Malosso, Tom W. May, Wieland Meyer, Henrik R. Nilsson, Maarja Öpik, Vincent Robert, Marc Stadler, Marco Thines, Duong Vu, Andrey M. Yurkov, Ning Zhang & Conrad L. Schoch (2021).

   Fungal taxonomy and sequence-based nomenclature.

   Nat Microbiol 6, 540–548.https://www.nature.com/articles/s41564-021-00888-x

2020

1. D Vu, M Groenewald, G Verkley (2020).

   Convolutional neural networks improve fungal classification.

   Scientific reports 10 (1), 1-12.https://www.nature.com/articles/s41598-020-69245-y

2. Yinggai Song, Nickolas Menezes Da Silva, Vinicius Almir Weiss, Duong Vu, Leandro F Moreno, Vania Aparecida Vicente, Ruoyu Li, G Sybren de Hoog (2020).

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

   Frontiers in Microbiology 11, 586.

2019

1. Vladimiro Guarnaccia, Thies Gehrmann, Geraldo J. Silva-Junior, Paul H. Fourie, Sajeet Haridas, Duong Vu, Joseph Spatafora, Francis M. Martin, Vincent Robert, Igor V. Grigoriev, Johannes Z. Groenewald, Pedro W. Crous (2019).

   Phyllosticta citricarpa and sister species of global importance to Citrus.

   Molecular Plant Pathology. https://doi.org/10.1111/mpp.12861

2. D. Vu, M. Groenewald, M. de Vries, T. Gehrmann, B. Stielow, U. Eberhardt, A. Al-Hatmi, J.Z. Groenewald, G. Cardinali, T. Boekhout, P.W. Crous, V. Robert, and G.J.M. Verkleij (2019).

   Large-scale analysis of filamentous fungal DNA barcodes reveals thresholds for species and higher taxon delimitation.

   Studies in Mycology 92, 135-154.https://doi.org/10.1016/j.simyco.2018.05.001

2018

1. D. Vu, S. Georgievska, S. Szoke, A. Kuzniar, V. Robert (2018).

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

   Bioinformatics 34, 1577-1579.https://doi.org/10.1093/bioinformatics/btx810

2016

1. D. Vu, M. Groenewald, S. Szöke, G. Cardinali, U. Eberhardt, B. Stielow, M. de Vries, G.J.M. Verkleij, P.W. Crous, T. Boekhout, and V. Robert (2016).

   DNA barcoding analysis of more than 9000 yeast isolates contributes to quantitative thresholds for yeast species and genera delimitation.

   Studies in Mycology 85, 91-105, 2016.https://doi.org/10.1016/j.simyco.2016.11.007

2014

1. Duong Vu, Szaniszlo Szoke, Christian Wiwie, Jan Baumbach, Gianluigi Cardinali, Richard Röttger, Vincent Robert (2014).

   Massive fungal biodiversity data re-annotation with multi-level clustering.

   Nature Scientific Reports 4, 6837, 2014.https://www.nature.com/articles/srep06837