Diatom metabarcoding and microscopic analyses from sediment samples at Lake Nam Co, Tibet: The effect of sample-size and bioinformatics on the identified communities

Seasonal stratification of a deep, high-altitude, dimictic lake: Nam Co, Tibetan Plateau

(2020) Junbo Wang et al.   JOURNAL OF HYDROLOGY

Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA

(2019) Krista M. Ruppert et al.   Global Ecology and Conservation

Morphological reconsideration of the araphid genus Pseudostaurosira (Bacillariophyceae), a revision of Gedaniella, Popovskayella and Serratifera, and a description of a new Nanofrustulum species

(2019) Eduardo A. Morales et al.   Plant Ecology and Evolution

Applicability of DNA metabarcoding approach in the bioassessment of Portuguese rivers using diatoms

(2019) Andreia Mortágua et al.   ECOLOGICAL INDICATORS

Bioinformatics matters: The accuracy of plant and soil fungal community data is highly dependent on the metabarcoding pipeline

(2019) Charlie Pauvert et al.   Fungal Ecology

Diatom DNA Metabarcoding for Biomonitoring: Strategies to Avoid Major Taxonomical and Bioinformatical Biases Limiting Molecular Indices Capacities

(2019) Kálmán Tapolczai et al.   Frontiers in Ecology and Evolution

Diatom metabarcoding applied to large scale monitoring networks: Optimization of bioinformatics strategies using Mothur software

(2019) Sinziana F. Rivera et al.   ECOLOGICAL INDICATORS

The potential of High-Throughput Sequencing (HTS) of natural samples as a source of primary taxonomic information for reference libraries of diatom barcodes

(2018) Frederic Rimet et al.   Fottea

Optimal extraction methods for the simultaneous analysis of DNA from diverse organisms and sample types

(2018) Syrie M. Hermans et al.   Molecular Ecology Resources

Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of operational taxonomic units’ ecological profiles

(2018) François Keck et al.   Molecular Ecology Resources

Do we similarly assess diversity with microscopy and high-throughput sequencing? Case of microalgae in lakes

(2018) Frédéric Rimet et al.   ORGANISMS DIVERSITY & EVOLUTION

Avoiding quantification bias in metabarcoding: Application of a cell biovolume correction factor in diatom molecular biomonitoring

(2018) Valentin Vasselon et al.   Methods in Ecology and Evolution

Lindavia biswashanti, a new diatom species (Bacillariophyta) from Gokyo Cho, Himalayan Range, Nepal

(2018) JOSEPH MOHAN et al.   Phytotaxa

Sample size effects on the assessment of eukaryotic diversity and community structure in aquatic sediments using high-throughput sequencing

(2018) Francisco J. A. Nascimento et al.   Scientific Reports

Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding

(2018) Sten Anslan et al.   MycoKeys

The impact of OTU sequence similarity threshold on diatom-based bioassessment: A case study of the rivers of Mayotte (France, Indian Ocean)

(2018) Kálmán Tapolczai et al.   Ecology and Evolution

Assessing the impact of long-term changes in climate and atmospheric deposition on a shallow alpine lake from southeast Tibet

(2018) Wengang Kang et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Metabarcoding of lake benthic diatoms: from structure assemblages to ecological assessment

(2017) S. F. Rivera et al.   HYDROBIOLOGIA

Impact of sequence processing and taxonomic classification approaches on eukaryotic community structure from environmental samples with emphasis on diatoms

(2017) Kristin Hardge et al.   Molecular Ecology Resources

PipeCraft: Flexible open-source toolkit for bioinformatics analysis of custom high-throughput amplicon sequencing data

(2017) Sten Anslan et al.   Molecular Ecology Resources

Taxonomy-free molecular diatom index for high-throughput eDNA biomonitoring

(2017) Laure Apothéloz-Perret-Gentil et al.   Molecular Ecology Resources

Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium

(2017) Rashmi Sinha et al.   NATURE BIOTECHNOLOGY

Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates

(2017) Tobias Guldberg Frøslev et al.   Nature Communications

Aerosol-weakened summer monsoons decrease lake fertilization on the Chinese Loess Plateau

(2017) Jianbao Liu et al.   Nature Climate Change

Application of high-throughput sequencing (HTS) metabarcoding to diatom biomonitoring: Do DNA extraction methods matter?

(2017) Valentin Vasselon et al.   Freshwater Science

Application of high-throughput sequencing (HTS) metabarcoding to diatom biomonitoring: Do DNA extraction methods matter?

(2017) Valentin Vasselon et al.   Freshwater Science

Accuracy of microbial community diversity estimated by closed- and open-reference OTUs

(2017) Robert C. Edgar   PeerJ

Sedimentary DNA versus morphology in the analysis of diatom-environment relationships

(2016) Katharina Dulias et al.   JOURNAL OF PALEOLIMNOLOGY

A comparison of DNA extraction methods for high-throughput DNA analyses

(2016) Lauren M. Schiebelhut et al.   Molecular Ecology Resources

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring

(2016) Frédéric Rimet et al.   Database-The Journal of Biological Databases and Curation

Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons

(2016) C. Ryan Penton et al.   Frontiers in Microbiology

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Environmental Monitoring: Inferring the Diatom Index from Next-Generation Sequencing Data

(2015) Joana Amorim Visco et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Meiofaunal community analysis by high-throughput sequencing: Comparison of extraction, quality filtering, and clustering methods

(2015) Pamela M. Brannock et al.   Marine Genomics

Bioinformatic Amplicon Read Processing Strategies Strongly Affect Eukaryotic Diversity and the Taxonomic Composition of Communities

(2015) Markus Majaneva et al.   PLoS One

Industrial arsenic contamination causes catastrophic changes in freshwater ecosystems

(2015) Guangjie Chen et al.   Scientific Reports

A combined paleolimnological/genetic analysis of diatoms reveals divergent evolutionary lineages of Staurosira and Staurosirella (Bacillariophyta) in Siberian lake sediments along a latitudinal transect

(2014) Kathleen R. Stoof-Leichsenring et al.   JOURNAL OF PALEOLIMNOLOGY

Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies

(2014) Jonas Zimmermann et al.   Molecular Ecology Resources

Transport Distance of Invertebrate Environmental DNA in a Natural River

(2014) Kristy Deiner et al.   PLoS One

Increased mass over the Tibetan Plateau: From lakes or glaciers?

(2013) Guoqing Zhang et al.   GEOPHYSICAL RESEARCH LETTERS

Next-generation sequencing to inventory taxonomic diversity in eukaryotic communities: a test for freshwater diatoms

(2013) L. Kermarrec et al.   Molecular Ecology Resources

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Observations on Hippodonta (Bacillariophyceae) in selected ancient lakes

(2013) ALEKSANDAR PAVLOV et al.   Phytotaxa

Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing

(2012) DONALD J. BAIRD et al.   MOLECULAR ECOLOGY

Flickering gives early warning signals of a critical transition to a eutrophic lake state

(2012) Rong Wang et al.   NATURE

Comparisons between the chemical compositions of lake water, inflowing river water, and lake sediment in Nam Co, central Tibetan Plateau, China and their controlling mechanisms

(2010) Junbo Wang et al.   JOURNAL OF GREAT LAKES RESEARCH

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The NCBI BioSystems database

(2009) Lewis Y. Geer et al.   NUCLEIC ACIDS RESEARCH

Hydrological and geomorphological basin and catchment characteristics of Lake Nam Co, South-Central Tibet

(2009) A. Keil et al.   QUATERNARY INTERNATIONAL