Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

Use of gene sequence analyses and genome comparisons for yeast systematics

(2014) C. P. Kurtzman   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Redefining the Human Oral Mycobiome with Improved Practices in Amplicon-based Taxonomy: Discovery of Malassezia as a Prominent Commensal

(2014) Amanda K. Dupuy et al.   PLoS One

Oral Mycobiome Analysis of HIV-Infected Patients: Identification of Pichia as an Antagonist of Opportunistic Fungi

(2014) Pranab K. Mukherjee et al.   PLoS Pathogens

Possible house-keeping and other draft proposals to clarify or enhance the naming of fungi within the International Code of Nomenclature for algae, fungi, and plants (Icn)

(2014) David L. Hawksworth   IMA Fungus

Cryptococcus lacticolor sp. nov. and Rhodotorula oligophaga sp. nov., novel yeasts isolated from the nasal smear microbiota of Queensland koalas kept in Japanese zoological parks

(2013) Kazuo Satoh et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Against the naming of fungi

(2013) Nicholas P. Money   Fungal Biology

Towards a unified paradigm for sequence-based identification of fungi

(2013) Urmas Kõljalg et al.   MOLECULAR ECOLOGY

Toward genome-enabled mycology

(2013) David S. Hibbett et al.   MYCOLOGIA

Filling Gaps in Biodiversity Knowledge for Macrofungi: Contributions and Assessment of an Herbarium Collection DNA Barcode Sequencing Project

(2013) Todd W. Osmundson et al.   PLoS One

StrainInfo introduces electronic passports for microorganisms

(2013) Bert Verslyppe et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

GenSeq: An updated nomenclature and ranking for genetic sequences from type and non-type sources

(2013) Prosanta Chakrabarty et al.   ZooKeys

Meeting Report: Fungal ITS Workshop (October 2012)

(2013) Scott T. Bates et al.   Standards in Genomic Sciences

Employing 454 amplicon pyrosequencing to reveal intragenomic divergence in the internal transcribed spacer rDNA region in fungi

(2013) Daniel L. Lindner et al.   Ecology and Evolution

BioNames: linking taxonomy, texts, and trees

(2013) Roderic D.M. Page   PeerJ

Taiwanascus samuelsii sp. nov., an addition to Niessliaceae from the Western ghats, Kerala, India

(2013) Kunhiraman C. Rajeshkumar et al.   IMA Fungus

A without-prejudice list of generic names of fungi for protection under the international Code of nomenclature for algae, fungi, and plants

(2013) Paul M. Kirk et al.   IMA Fungus

MycoBank gearing up for new horizons

(2013) Vincent Robert et al.   IMA Fungus

Aspergillus and Penicillium identification using DNA sequences: barcode or MLST?

(2012) Stephen W. Peterson   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

NetiNeti: discovery of scientific names from text using machine learning methods

(2012) Lakshmi Akella et al.   BMC BIOINFORMATICS

Reference databases for taxonomic assignment in metagenomics

(2012) M. Santamaria et al.   BRIEFINGS IN BIOINFORMATICS

ITS2 Database IV: Interactive taxon sampling for internal transcribed spacer 2 based phylogenies

(2012) Christian Koetschan et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The International Nucleotide Sequence Database Collaboration

(2012) Y. Nakamura et al.   NUCLEIC ACIDS RESEARCH

Darwin Core: An Evolving Community-Developed Biodiversity Data Standard

(2012) John Wieczorek et al.   PLoS One

PHYMYCO-DB: A Curated Database for Analyses of Fungal Diversity and Evolution

(2012) Stéphane Mahé et al.   PLoS One

CREST – Classification Resources for Environmental Sequence Tags

(2012) Anders Lanzén et al.   PLoS One

Limits of nuclear ribosomal DNA internal transcribed spacer (ITS) sequences as species barcodes for Fungi

(2012) L. Kiss   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

(2012) C. L. Schoch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genus Cladosporium

(2012) K. Bensch et al.   STUDIES IN MYCOLOGY

Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences

(2012) R. Henrik Nilsson et al.   MycoKeys

The Fungi: 1, 2, 3 … 5.1 million species?

(2011) Meredith Blackwell   AMERICAN JOURNAL OF BOTANY

Accurate, Rapid Taxonomic Classification of Fungal Large-Subunit rRNA Genes

(2011) Kuan-Liang Liu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Species delimitation in fungal endophyte diversity studies and its implications in ecological and biogeographic inferences

(2011) ROMINA GAZIS et al.   MOLECULAR ECOLOGY

A new lineage in Pucciniomycotina: class Tritirachiomycetes, order Tritirachiales, family Tritirachiaceae

(2011) Wiley A. Schell et al.   MYCOLOGIA

The diversity of Terfezia desert truffles: new species and a highly variable species complex with intrasporocarpic nrDNA ITS heterogeneity

(2011) Gábor M. Kovács et al.   MYCOLOGIA

The NCBI Taxonomy database

(2011) S. Federhen   NUCLEIC ACIDS RESEARCH

Zymoseptoria gen. nov.: a new genus to accommodate Septoria-like species occurring on graminicolous hosts

(2011) W. Quaedvlieg et al.   PERSOONIA

Tasting Soil Fungal Diversity with Earth Tongues: Phylogenetic Test of SATé Alignments for Environmental ITS Data

(2011) Zheng Wang et al.   PLoS One

Comparing COI and ITS as DNA Barcode Markers for Mushrooms and Allies (Agaricomycotina)

(2011) Bryn T. M. Dentinger et al.   PLoS One

Data Partitions, Bayesian Analysis and Phylogeny of the Zygomycetous Fungal Family Mortierellaceae, Inferred from Nuclear Ribosomal DNA Sequences

(2011) Tamás Petkovits et al.   PLoS One

Evolutionary informatics: unifying knowledge about the diversity of life

(2011) Cynthia S. Parr et al.   TRENDS IN ECOLOGY & EVOLUTION

The Amsterdam Declaration on Fungal Nomenclature

(2011) David L. Hawksworth et al.   IMA Fungus

Successful DNA sequencing of a 75 year-old herbarium specimen of Aspicilia aschabadensis (J. Steiner) Mereschk.

(2010) Mohammad Sohrabi et al.   LICHENOLOGIST

Taxonomic position of Mucor hiemalis f. luteus

(2010) J. Budziszewska et al.   MYCOTAXON

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota)

(2010) M. Öpik et al.   NEW PHYTOLOGIST

DNA barcoding of arbuscular mycorrhizal fungi

(2010) Herbert Stockinger et al.   NEW PHYTOLOGIST

Cyber infrastructure for Fusarium: three integrated platforms supporting strain identification, phylogenetics, comparative genomics and knowledge sharing

(2010) B. Park et al.   NUCLEIC ACIDS RESEARCH

Names are key to the big new biology

(2010) D.J. Patterson et al.   TRENDS IN ECOLOGY & EVOLUTION

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Comments on the paper by Pleijel et al. (2008): Vouching for GenBank

(2009) Scott Federhen et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Comparative taxonomy of desert truffles of the Australian outback and the African Kalahari

(2009) James M. Trappe et al.   MYCOLOGICAL PROGRESS

Using heterozygosity to estimate a percentage DNA sequence similarity for environmental species’ delimitation across basidiomycete fungi

(2009) Karen W. Hughes et al.   NEW PHYTOLOGIST

Intergeneric transfer of ribosomal genes between two fungi

(2008) Jiatao Xie et al.   BMC EVOLUTIONARY BIOLOGY

Intragenomic Variation of Fungal Ribosomal Genes Is Higher than Previously Thought

(2008) U. K. Simon et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenies without roots? A plea for the use of vouchers in molecular phylogenetic studies

(2008) F. Pleijel et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

How to know unknown fungi: the role of a herbarium

(2008) Patrick M. Brock et al.   NEW PHYTOLOGIST