Characterizing root-associated fungal communities and soils of Douglas-fir (Pseudotsuga menziesii) stands that naturally produce Oregon white truffles (Tuber oregonense and Tuber gibbosum)

FlowClus: efficiently filtering and denoising pyrosequenced amplicons

(2015) John M Gaspar et al.   BMC BIOINFORMATICS

Whose truffle is this? Distribution patterns of ectomycorrhizal fungal diversity inTuber melanosporumbrûlés developed in multi-host Mediterranean plant communities

(2015) Elisa Taschen et al.   ENVIRONMENTAL MICROBIOLOGY

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants

(2014) Gregory Bonito et al.   MOLECULAR ECOLOGY

Soil physical properties influence “black truffle” fructification in plantations

(2014) Rafael Alonso Ponce et al.   MYCORRHIZA

Global diversity and geography of soil fungi

(2014) L. Tedersoo et al.   SCIENCE

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

New North American truffles (Tuber spp.) and their ectomycorrhizal associations

(2013) Gonzalo Guevara et al.   MYCOLOGIA

Assessment of ectomycorrhizal fungal communities in the natural habitats of Tuber magnatum (Ascomycota, Pezizales)

(2013) M. Leonardi et al.   MYCORRHIZA

Assessment of ectomycorrhizal biodiversity in Tuber macrosporum productive sites

(2013) Gian Maria Niccolò Benucci et al.   MYCORRHIZA

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Historical Biogeography and Diversification of Truffles in the Tuberaceae and Their Newly Identified Southern Hemisphere Sister Lineage

(2013) Gregory Bonito et al.   PLoS One

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data

(2013) Johan Bengtsson-Palme et al.   Methods in Ecology and Evolution

Divergence in ectomycorrhizal communities with foreign Douglas-fir populations and implications for assisted migration

(2012) J. M. Kranabetter et al.   ECOLOGICAL APPLICATIONS

Comparison of ectomycorrhizal communities in natural and cultivated Tuber melanosporum truffle grounds

(2012) Beatrice Belfiori et al.   FEMS MICROBIOLOGY ECOLOGY

Mycorrhiza Reduces Adverse Effects of Dark Septate Endophytes (DSE) on Growth of Conifers

(2012) Vanessa Reininger et al.   PLoS One

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

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

New species of Chalara occupying coniferous needles

(2011) Ondřej Koukol   FUNGAL DIVERSITY

GenBank

(2011) D. A. Benson et al.   NUCLEIC ACIDS RESEARCH

Parsing the roles of abiotic and biotic factors in Douglas-fir seedling growth

(2011) Justine Karst et al.   PEDOBIOLOGIA

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

The ectomycorrhizal community in naturalTuber borchii grounds

(2010) Mirco Iotti et al.   FEMS MICROBIOLOGY ECOLOGY

Functional complementarity of Douglas-fir ectomycorrhizas for extracellular enzyme activity after wildfire or clearcut logging

(2010) Melanie D. Jones et al.   FUNCTIONAL ECOLOGY

A global meta-analysis of Tuber ITS rDNA sequences: species diversity, host associations and long-distance dispersal

(2010) GREGORY M. BONITO et al.   MOLECULAR ECOLOGY

Improved resolution of major clades within Tuber and taxonomy of species within the Tuber gibbosum complex

(2010) Gregory Bonito et al.   MYCOLOGIA

Kalapuya brunnea gen. & sp. nov. and its relationship to the other sequestrate genera in Morchellaceae

(2010) Matthew J. Trappe et al.   MYCOLOGIA

Amylocorticiales ord. nov. and Jaapiales ord. nov.: Early diverging clades of Agaricomycetidae dominated by corticioid forms

(2010) Manfred Binder et al.   MYCOLOGIA

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

Improving indicator species analysis by combining groups of sites

(2010) Miquel De Cáceres et al.   OIKOS

454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity

(2009) M. Buée et al.   NEW PHYTOLOGIST

Dark septate endophytes (DSE) of the Phialocephala fortinii s.l. – Acephala applanata species complex in tree roots: classification, population biology, and ecology

(2008) Christoph R. Grünig et al.   Botany