Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden)

Kessy Abarenkov; Rachel I. Adams; Irinyi Laszlo; Ahto Agan; Elia Ambrosio; Alexandre Antonelli; Mohammad Bahram; Johan Bengtsson-Palme; Gunilla Bok; Patrik Cangren; Victor Coimbra; Claudia Coleine; Claes Gustafsson; Jinhong He; Tobias Hofmann; Erik Kristiansson; Ellen Larsson; Tomas Larsson; Yingkui Liu; Svante Martinsson; Wieland Meyer; Marina Panova; Nuttapon Pombubpa; Camila Ritter; Martin Ryberg; Sten Svantesson; Ruud Scharn; Ola Svensson; Mats Töpel; Martin Unterseher; Cobus Visagie; Christian Wurzbacher; Andy F.S. Taylor; Urmas Kõljalg; Lynn Schriml; R. Henrik Nilsson

doi:10.3897/mycokeys.16.10000

Barbara Robbertse, Pooja K Strope, Priscila Chaverri, Romina Gazis, Stacy Ciufo, Michael Domrachev, Conrad L Schoch (2017)
Improving taxonomic accuracy for fungi in public sequence databases: applying ‘one name one species’ in well-defined genera with Trichoderma/Hypocrea as a test case. Database 2017: .

DOI: 10.1093/database/bax072

R. Henrik Nilsson, Sten Anslan, Mohammad Bahram, Christian Wurzbacher, Petr Baldrian, Leho Tedersoo (2019)
Mycobiome diversity: high-throughput sequencing and identification of fungi. Nature Reviews Microbiology 17: 95.

DOI: 10.1038/s41579-018-0116-y

Sebastian Gnat, Dominik Łagowski, Mariusz Dyląg, Aneta Nowakiewicz (2021)
Human Mycobiome In Normobiosis And Dysbiosis States Characteristics And Analysis Methods. Postępy Mikrobiologii - Advancements of Microbiology 60: 31.

DOI: 10.21307/PM-2021.60.1.04

Abu Bakar Siddique, Anis Mahmud Khokon, Martin Unterseher (2017)
What do we learn from cultures in the omics age? High-throughput sequencing and cultivation of leaf-inhabiting endophytes from beech (Fagus sylvatica L.) revealed complementary community composition but similar correlations with local habitat conditions. MycoKeys 20: 1.

DOI: 10.3897/mycokeys.20.11265

R. Henrik Nilsson, Marisol Sánchez-García, Martin K. Ryberg, Kessy Abarenkov, Christian Wurzbacher, Erik Kristiansson (2017)
Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory. MycoKeys 26: 13.

DOI: 10.3897/mycokeys.26.14591

Mathew Andrew Harris, Bernard Slippers, Martin Kemler, Michelle Greve (2023)
Opportunities for diversified usage of metabarcoding data for fungal biogeography through increased metadata quality. Fungal Biology Reviews 46: 100329.

DOI: 10.1016/j.fbr.2023.100329

Martin Unterseher, Samantha C Karunarathna, García Roberto Cruz, Nikki H Dagamac, Mathilde B Dahl, Serena E Dool, Michelle Galla, Lina Herbst, R Henrik Nilsson, Sébastien J. Puechmaille, Caroline Schöner, Michael Schöner, Abu B Siddique, Annette Teltewskoi, Kristina Wicke, David G Würth, Christian Wurzbacher, Kevin D Hyde (2018)
Mycobiomes of sympatric Amorphophallus albispathus (Araceae) and Camellia sinensis (Theaceae) – a case study reveals clear tissue preferences and differences in diversity and composition. Mycological Progress 17: 489.

DOI: 10.1007/s11557-018-1375-8

Rolf Henrik Nilsson, Karl-Henrik Larsson, Andy F S Taylor, Johan Bengtsson-Palme, Thomas S Jeppesen, Dmitry Schigel, Peter Kennedy, Kathryn Picard, Frank Oliver Glöckner, Leho Tedersoo, Irja Saar, Urmas Kõljalg, Kessy Abarenkov (2019)
The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Research 47: D259.

DOI: 10.1093/nar/gky1022

J.B. Tanney, C.M. Visagie, N. Yilmaz, K.A. Seifert (2017)
AspergillussubgenusPolypaecilumfrom the built environment. Studies in Mycology 88: 237.

DOI: 10.1016/j.simyco.2017.11.001

Kessy Abarenkov, Erik Kristiansson, Martin Ryberg, Sandra Nogal-Prata, Daniela Gómez-Martínez, Katrin Stüer-Patowsky, Tobias Jansson, Sergei Põlme, Masoomeh Ghobad-Nejhad, Natàlia Corcoll, Ruud Scharn, Marisol Sánchez-García, Maryia Khomich, Christian Wurzbacher, R. Henrik Nilsson (2022)
The curse of the uncultured fungus. MycoKeys 86: 177.

DOI: 10.3897/mycokeys.86.76053

Duong Vu, R. Henrik Nilsson, Gerard J. M. Verkley (2022)
Dnabarcoder: An open‐source software package for analysing and predicting DNA sequence similarity cutoffs for fungal sequence identification. Molecular Ecology Resources 22: 2793.

DOI: 10.1111/1755-0998.13651

Pei Yee Tiew, Micheál Mac Aogain, Nur A’tikah Binte Mohamed Ali, Kai Xian Thng, Karlyn Goh, Kenny J. X. Lau, Sanjay H. Chotirmall (2020)
The Mycobiome in Health and Disease: Emerging Concepts, Methodologies and Challenges. Mycopathologia : .

DOI: 10.1007/s11046-019-00413-z

Cobus M. Visagie, Teun Boekhout, Bart Theelen, Jan Dijksterhuis, Neriman Yilmaz, Keith A. Seifert (2023)
Da Vinci's yeast: Blastobotrys davincii f.a., sp. nov. Yeast 40: 7.

DOI: 10.1002/yea.3816

Rodney T. Richardson, Johan Bengtsson‐Palme, Reed M. Johnson (2017)
Evaluating and optimizing the performance of software commonly used for the taxonomic classification of DNA metabarcoding sequence data. Molecular Ecology Resources 17: 760.

DOI: 10.1111/1755-0998.12628

R. Henrik Nilsson, Andy F.S. Taylor, Rachel I. Adams, Christiane Baschien, Johan Bengtsson-Palme, Patrik Cangren, Claudia Coleine, Heide-Marie Daniel, Sydney I. Glassman, Yuuri Hirooka, Irinyi Laszlo, Reda Iršėnaitė, Pedro M. Martin-Sanchez, Wieland Meyer, Seung-Yoon Oh, Jose Paulo Sampaio, Keith Seifert, Frantisek Sklenář, Dirk Stubbe Dirk Stubbe, Sung-Oui Suh, Richard Summerbell, Sten Svantesson, Martin Unterseher, Cobus Visagie, Michael Weiss, Joyce Woudenberg, Christian Wurzbacher, Silke Van den Wyngaert, Neriman Yilmaz, Andrey Yurkov, Urmas Kõljalg, Kessy Abarenkov (2018)
Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK). MycoKeys 28: 65.

DOI: 10.3897/mycokeys.28.20887

John P. Springston, Elliott Horner, Joseph Lstiburek (2021)
Patty's Industrial Hygiene. : 1.

DOI: 10.1002/0471435139.hyg065.pub3

Masoomeh Ghobad-Nejhad, R. Henrik Nilsson, Alexander Ordynets (2024)
Microbial Genomics: Clinical, Pharmaceutical, and Industrial Applications. : 173.

DOI: 10.1016/B978-0-443-18866-4.00007-9