Metabarcoding and mitochondrial metagenomics of endogean arthropods to unveil the mesofauna of the soil

Soup to Tree: The Phylogeny of Beetles Inferred by Mitochondrial Metagenomics of a Bornean Rainforest Sample

(2015) Alex Crampton-Platt et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics

(2015) Carmelo Andújar et al.   MOLECULAR ECOLOGY

Tag jumps illuminated - reducing sequence-to-sample misidentifications in metabarcoding studies

(2015) Ida Baerholm Schnell et al.   Molecular Ecology Resources

Soil biodiversity and DNA barcodes: opportunities and challenges

(2015) Alberto Orgiazzi et al.   SOIL BIOLOGY & BIOCHEMISTRY

Validating the power of mitochondrial metagenomics for community ecology and phylogenetics of complex assemblages

(2015) Carola Gómez-Rodríguez et al.   Methods in Ecology and Evolution

High-throughput monitoring of wild bee diversity and abundance via mitogenomics

(2015) Min Tang et al.   Methods in Ecology and Evolution

Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods

(2015) Jullien M. Flynn et al.   Ecology and Evolution

Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform

(2015) Shadi Shokralla et al.   Scientific Reports

Using metabarcoding to ask if easily collected soil and leaf-litter samples can be used as a general biodiversity indicator

(2014) Chenxue Yang et al.   ECOLOGICAL INDICATORS

Bulk De Novo Mitogenome Assembly from Pooled Total DNA Elucidates the Phylogeny of Weevils (Coleoptera: Curculionoidea)

(2014) Conrad P.D.T. Gillett et al.   MOLECULAR BIOLOGY AND EVOLUTION

Belowground biodiversity and ecosystem functioning

(2014) Richard D. Bardgett et al.   NATURE

Swarm: robust and fast clustering method for amplicon-based studies

(2014) Frédéric Mahé et al.   PeerJ

Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding

(2013) Yinqiu Ji et al.   ECOLOGY LETTERS

Collembola, the biological species concept and the underestimation of global species richness

(2013) Francesco Cicconardi et al.   MOLECULAR ECOLOGY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

PyroClean: Denoising Pyrosequences from Protein-Coding Amplicons for the Recovery of Interspecific and Intraspecific Genetic Variation

(2013) Ricardo Ramirez-Gonzalez et al.   PLoS One

Regional factors rather than forest type drive the community structure of soil living oribatid mites (Acari, Oribatida)

(2012) Georgia Erdmann et al.   EXPERIMENTAL AND APPLIED ACAROLOGY

RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics

(2012) M. Lohse et al.   NUCLEIC ACIDS RESEARCH

The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna

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

Testing three pipelines for 18S rDNA-based metabarcoding of soil faunal diversity

(2012) ChenXue Yang et al.   Science China-Life Sciences

Plant–soil feedbacks mediated by humus forms: A review

(2012) Jean-François Ponge   SOIL BIOLOGY & BIOCHEMISTRY

Sequencing our way towards understanding global eukaryotic biodiversity

(2012) Holly M. Bik et al.   TRENDS IN ECOLOGY & EVOLUTION

Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering

(2011) Xiaolin Hao et al.   BIOINFORMATICS

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

Molecular study of worldwide distribution and diversity of soil animals

(2011) T. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Macroecological patterns in soil communities

(2010) Thibaud Decaëns   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Second-generation environmental sequencing unmasks marine metazoan biodiversity

(2010) Vera G. Fonseca et al.   Nature Communications

Global patterns in belowground communities

(2009) Noah Fierer et al.   ECOLOGY LETTERS

Deep phylogeographic divisions and long-term persistence of forest invertebrates (Hexapoda: Collembola) in the North-Western Mediterranean basin

(2009) F. CICCONARDI et al.   MOLECULAR ECOLOGY