Metagenome sequence ofElaphomyces granulatusfrom sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and aProteobacteria-rich microbiome

Bacteria associated with truffle-fruiting bodies contribute to truffle aroma

(2014) Richard Splivallo et al.   ENVIRONMENTAL MICROBIOLOGY

Complete Genome sequence of Burkholderia phymatum STM815T, a broad host range and efficient nitrogen-fixing symbiont of Mimosa species

(2014) Lionel Moulin et al.   Standards in Genomic Sciences

Detection and quantification of a mycorrhization helper bacterium and a mycorrhizal fungus in plant-soil microcosms at different levels of complexity

(2013) Florence Kurth et al.   BMC MICROBIOLOGY

Comprehensive annotation of secondary metabolite biosynthetic genes and gene clusters of Aspergillus nidulans, A. fumigatus, A. niger and A. oryzae

(2013) Diane O Inglis et al.   BMC MICROBIOLOGY

Black truffle-associated bacterial communities during the development and maturation ofTuber melanosporumascocarps and putative functional roles

(2013) Sanjay Antony-Babu et al.   ENVIRONMENTAL MICROBIOLOGY

Detection of a novel intracellular microbiome hosted in arbuscular mycorrhizal fungi

(2013) Alessandro Desirò et al.   ISME Journal

antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers

(2013) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

MycoCosm portal: gearing up for 1000 fungal genomes

(2013) Igor V. Grigoriev et al.   NUCLEIC ACIDS RESEARCH

Endohyphal Bacterium Enhances Production of Indole-3-Acetic Acid by a Foliar Fungal Endophyte

(2013) Michele T. Hoffman et al.   PLoS One

The Genome and Development-Dependent Transcriptomes of Pyronema confluens: A Window into Fungal Evolution

(2013) Stefanie Traeger et al.   PLoS Genetics

Nonribosomal Peptide Synthetase GenespesLandpes1Are Essential for Fumigaclavine C Production in Aspergillus fumigatus

(2012) Karen A. O'Hanlon et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

EVOLUTIONARY STABILITY IN A 400-MILLION-YEAR-OLD HERITABLE FACULTATIVE MUTUALISM

(2012) Stephen J. Mondo et al.   EVOLUTION

A molecular phylogeny of thermophilic fungi

(2012) Ingo Morgenstern et al.   Fungal Biology

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Sequestrate fungi of New Zealand:Elaphomyces(Ascomycota, Eurotiales, Elaphomycetaceae)

(2012) Michael A Castellano et al.   NEW ZEALAND JOURNAL OF BOTANY

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

The Irreversible Loss of a Decomposition Pathway Marks the Single Origin of an Ectomycorrhizal Symbiosis

(2012) Benjamin E. Wolfe et al.   PLoS One

Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla

(2012) K. C. Wrighton et al.   SCIENCE

A quest for indigenous truffle helper prokaryotes

(2012) Milan Gryndler et al.   Environmental Microbiology Reports

Australian species of Elaphomyces (Elaphomycetaceae, Eurotiales, Ascomycota)

(2011) Michael A. Castellano et al.   AUSTRALIAN SYSTEMATIC BOTANY

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Bacterial-Fungal Interactions: Hyphens between Agricultural, Clinical, Environmental, and Food Microbiologists

(2011) P. Frey-Klett et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Next Generation Sequencing Provides Rapid Access to the Genome of Puccinia striiformis f. sp. tritici, the Causal Agent of Wheat Stripe Rust

(2011) Dario Cantu et al.   PLoS One

Phylogeny and nomenclature of the genus Talaromyces and taxa accommodated in Penicillium subgenus Biverticillium

(2011) R.A. Samson et al.   STUDIES IN MYCOLOGY

Phylogeny of Penicillium and the segregation of Trichocomaceae into three families

(2011) J. Houbraken et al.   STUDIES IN MYCOLOGY

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Comparative Genomic Analysis of Human Fungal Pathogens Causing Paracoccidioidomycosis

(2011) Christopher A. Desjardins et al.   PLoS Genetics

Soil beneficial bacteria and their role in plant growth promotion: a review

(2010) Rifat Hayat et al.   ANNALS OF MICROBIOLOGY

Phylogenomics reveals subfamilies of fungal nonribosomal peptide synthetases and their evolutionary relationships

(2010) Kathryn E Bushley et al.   BMC EVOLUTIONARY BIOLOGY

SMURF: Genomic mapping of fungal secondary metabolite clusters

(2010) Nora Khaldi et al.   FUNGAL GENETICS AND BIOLOGY

Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis

(2010) Francis Martin et al.   NATURE

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

Genome Expansion and Gene Loss in Powdery Mildew Fungi Reveal Tradeoffs in Extreme Parasitism

(2010) P. D. Spanu et al.   SCIENCE

Three Genomes from the Phylum Acidobacteria Provide Insight into the Lifestyles of These Microorganisms in Soils

(2009) N. L. Ward et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The relative ages of ectomycorrhizal mushrooms and their plant hosts estimated using Bayesian relaxed molecular clock analyses

(2009) David S Hibbett et al.   BMC BIOLOGY

Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives

(2009) T. J. Sharpton et al.   GENOME RESEARCH

Ectomycorrhizal lifestyle in fungi: global diversity, distribution, and evolution of phylogenetic lineages

(2009) Leho Tedersoo et al.   MYCORRHIZA

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

Complete genome sequence of Catenulispora acidiphila type strain (ID 139908T)

(2009) Alex Copeland et al.   Standards in Genomic Sciences

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

Secondary metabolism: regulation and role in fungal biology

(2008) Ellen M Fox et al.   CURRENT OPINION IN MICROBIOLOGY

Microdiversity of Burkholderiales associated with mycorrhizal and nonmycorrhizal roots of Medicago truncatula

(2008) Pierre Offre et al.   FEMS MICROBIOLOGY ECOLOGY

Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training

(2008) V. Ter-Hovhannisyan et al.   GENOME RESEARCH

The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis

(2008) F. Martin et al.   NATURE

Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum

(2008) Marco A van den Berg et al.   NATURE BIOTECHNOLOGY

Assessing the gene space in draft genomes

(2008) Genis Parra et al.   NUCLEIC ACIDS RESEARCH

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

(2008) B. L. Cantarel et al.   NUCLEIC ACIDS RESEARCH

Genomic Islands in the Pathogenic Filamentous Fungus Aspergillus fumigatus

(2008) Natalie D. Fedorova et al.   PLoS Genetics