Identification of Habitat-Specific Biomes of Aquatic Fungal Communities Using a Comprehensive Nearly Full-Length 18S rRNA Dataset Enriched with Contextual Data

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Stream-dwelling fungal decomposer communities along a gradient of eutrophication unraveled by 454 pyrosequencing

(2014) S. Duarte et al.   FUNGAL DIVERSITY

Phylogenetic detection of novel Cryptomycota in an Iowa (United States) aquifer and from previously collected marine and freshwater targeted high-throughput sequencing sets

(2013) Joshua A. Livermore et al.   ENVIRONMENTAL MICROBIOLOGY

Fungal diversity from various marine habitats deduced through culture-independent studies

(2013) Cathrine Sumathi Manohar et al.   FEMS MICROBIOLOGY LETTERS

Families of Dothideomycetes

(2013) Kevin D. Hyde et al.   FUNGAL DIVERSITY

Elemental composition and degree of homeostasis of fungi: are aquatic hyphomycetes more like metazoans, bacteria or plants?

(2013) Michael Danger et al.   Fungal Ecology

Diversity, ecological role and potential biotechnological applications of marine fungi associated to the seagrass Posidonia oceanica

(2013) Luigi Panno et al.   New Biotechnology

Deep Sequencing of Subseafloor Eukaryotic rRNA Reveals Active Fungi across Marine Subsurface Provinces

(2013) William Orsi et al.   PLoS One

Phylogenetic Affiliation of SSU rRNA Genes Generated by Massively Parallel Sequencing: New Insights into the Freshwater Protist Diversity

(2013) Najwa Taib et al.   PLoS One

Temporal variation of the small eukaryotic community in two freshwater lakes: emphasis on zoosporic fungi

(2012) E Lefèvre et al.   AQUATIC MICROBIAL ECOLOGY

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

Fungal palaeodiversity revealed using high-throughput metabarcoding of ancient DNA from arctic permafrost

(2012) Eva Bellemain et al.   ENVIRONMENTAL MICROBIOLOGY

Diversity and distribution of fungal communities in lakes of Antarctica

(2012) Vívian N. Gonçalves et al.   FEMS MICROBIOLOGY ECOLOGY

Ecosystem processes and interactions in a morass of diversity

(2012) James I. Prosser   FEMS MICROBIOLOGY ECOLOGY

Phylogenetic conservatism of functional traits in microorganisms

(2012) Adam C Martiny et al.   ISME Journal

The phylogenetic Kantorovich-Rubinstein metric for environmental sequence samples

(2012) Steven N. Evans et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

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

Fungal soil communities in a young transgenic poplar plantation form a rich reservoir for fungal root communities

(2012) L. Danielsen et al.   Ecology and Evolution

Marine Fungi: Their Ecology and Molecular Diversity

(2011) Thomas A. Richards et al.   Annual Review of Marine Science

Molecular evidence that deep-branching fungi are major fungal components in deep-sea methane cold-seep sediments

(2011) Takahiko Nagahama et al.   ENVIRONMENTAL MICROBIOLOGY

Exploring and quantifying fungal diversity in freshwater lake ecosystems using rDNA cloning/sequencing and SSU tag pyrosequencing

(2011) Sébastien Monchy et al.   ENVIRONMENTAL MICROBIOLOGY

Multiple markers pyrosequencing reveals highly diverse and host-specific fungal communities on the mangrove trees Avicennia marina and Rhizophora stylosa

(2011) Yonathan Arfi et al.   FEMS MICROBIOLOGY ECOLOGY

Fungal diversity in anoxic-sulfidic sediments in a mangrove soil

(2011) Yonathan Arfi et al.   Fungal Ecology

Coral-associated marine fungi form novel lineages and heterogeneous assemblages

(2011) Anthony S Amend et al.   ISME Journal

Phylogenetic Identification of Fungi Isolated from the Marine Sponge Tethya aurantium and Identification of Their Secondary Metabolites

(2011) Jutta Wiese et al.   Marine Drugs

Community Structure of Planktonic Fungi and the Impact of Parasitic Chytrids on Phytoplankton in Lake Inba, Japan

(2011) Maiko Kagami et al.   MICROBIAL ECOLOGY

Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments

(2011) HOLLY M. BIK et al.   MOLECULAR ECOLOGY

Discovery of novel intermediate forms redefines the fungal tree of life

(2011) Meredith D. M. Jones et al.   NATURE

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

(2011) Pelin Yilmaz et al.   NATURE BIOTECHNOLOGY

Diversity and Vertical Distribution of Microbial Eukaryotes in the Snow, Sea Ice and Seawater Near the North Pole at the End of the Polar Night

(2011) Charles Bachy et al.   Frontiers in Microbiology

Diversity and functions of microscopic fungi: a missing component in pelagic food webs

(2010) Marlène Jobard et al.   AQUATIC SCIENCES

The response of dissolved organic carbon (DOC) and the ecosystem carbon balance to experimental drought in a temperate shrubland

(2010) A. Sowerby et al.   EUROPEAN JOURNAL OF SOIL SCIENCE

Phylogenetic diversity of endophyte assemblages associated with the tropical seagrass Enhalus acoroides in Thailand

(2010) J. Sakayaroj et al.   FUNGAL DIVERSITY

Composition, uniqueness and variability of the epiphytic bacterial community of the green alga Ulva australis

(2010) Catherine Burke et al.   ISME Journal

The role of fungi in processing marine organic matter in the upwelling ecosystem off Chile

(2010) M. H. Gutiérrez et al.   MARINE BIOLOGY

Fungal Community Analysis in the Deep-Sea Sediments of the Central Indian Basin by Culture-Independent Approach

(2010) Purnima Singh et al.   MICROBIAL ECOLOGY

Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water

(2010) THORSTEN STOECK et al.   MOLECULAR ECOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Fungal Diversity in Deep-Sea Hydrothermal Ecosystems

(2009) T. Le Calvez et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Diversity of culturable marine filamentous fungi from deep-sea hydrothermal vents

(2009) Gaëtan Burgaud et al.   ENVIRONMENTAL MICROBIOLOGY

Fungal diversity in oxygen-depleted regions of  the Arabian Sea revealed by targeted environmental sequencing combined with cultivation

(2009) Cathrine S. Jebaraj et al.   FEMS MICROBIOLOGY ECOLOGY

Molecular characterization of the spatial diversity and novel lineages of mycoplankton in Hawaiian coastal waters

(2009) Zheng Gao et al.   ISME Journal

Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data

(2009) Micah Hamady et al.   ISME Journal

What is microbial community ecology?

(2009) Allan Konopka   ISME Journal

Infrequent marine–freshwater transitions in the microbial world

(2009) Ramiro Logares et al.   TRENDS IN MICROBIOLOGY

Phylocom: software for the analysis of phylogenetic community structure and trait evolution

(2008) Campbell O. Webb et al.   BIOINFORMATICS

Bacterial, archaeal and eukaryotic diversity in Arctic sediment as revealed by 16S rRNA and 18S rRNA gene clone libraries analysis

(2008) Fei Tian et al.   POLAR BIOLOGY

The ecology of chytrids in aquatic ecosystems: roles in food web dynamics

(2008) Frank H. Gleason et al.   Fungal Biology Reviews