Applications of machine learning in human microbiome studies: a review on feature selection, biomarker identification, disease prediction and treatment

LJ Marcos-Zambrano… - Frontiers in …, 2021 - frontiersin.org
The number of microbiome-related studies has notably increased the availability of data on
human microbiome composition and function. These studies provide the essential material …

Environmental DNA metabarcoding: Transforming how we survey animal and plant communities

K Deiner, HM Bik, E Mächler, M Seymour… - Molecular …, 2017 - Wiley Online Library
The genomic revolution has fundamentally changed how we survey biodiversity on earth.
High‐throughput sequencing (“HTS”) platforms now enable the rapid sequencing of DNA …

The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered

K Abarenkov, RH Nilsson, KH Larsson… - Nucleic Acids …, 2024 - academic.oup.com
Abstract UNITE (https://unite. ut. ee) is a web-based database and sequence management
environment for molecular identification of eukaryotes. It targets the nuclear ribosomal …

The evolutionary drivers and correlates of viral host jumps

CCS Tan, L van Dorp, F Balloux - Nature ecology & evolution, 2024 - nature.com
Most emerging and re-emerging infectious diseases stem from viruses that naturally
circulate in non-human vertebrates. When these viruses cross over into humans, they can …

The numbers of fungi: Contributions from traditional taxonomic studies and challenges of metabarcoding

C Phukhamsakda, RH Nilsson, CS Bhunjun… - Fungal diversity, 2022 - Springer
The global diversity of fungi has been estimated using several different approaches. There is
somewhere between 2–11 million estimated species, but the number of formally described …

The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications

RH Nilsson, KH Larsson, AFS Taylor… - Nucleic acids …, 2019 - academic.oup.com
Abstract UNITE (https://unite. ut. ee/) is a web-based database and sequence management
environment for the molecular identification of fungi. It targets the formal fungal barcode—the …

High-throughput sequencing view on the magnitude of global fungal diversity

P Baldrian, T Větrovský, C Lepinay, P Kohout - Fungal Diversity, 2022 - Springer
High-throughput DNA sequencing has dramatically transformed several areas of biodiversity
research including mycology. Despite limitations, high-throughput sequencing is nowadays …

Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo

P Kapli, S Lutteropp, J Zhang, K Kobert… - …, 2017 - academic.oup.com
Motivation In recent years, molecular species delimitation has become a routine approach
for quantifying and classifying biodiversity. Barcoding methods are of particular importance …

The taxon hypothesis paradigm—on the unambiguous detection and communication of taxa

U Kõljalg, HR Nilsson, D Schigel, L Tedersoo… - Microorganisms, 2020 - mdpi.com
Here, we describe the taxon hypothesis (TH) paradigm, which covers the construction,
identification, and communication of taxa as datasets. Defining taxa as datasets of …

MIDORI2: A collection of quality controlled, preformatted, and regularly updated reference databases for taxonomic assignment of eukaryotic mitochondrial sequences

M Leray, N Knowlton, RJ Machida - Environmental Dna, 2022 - Wiley Online Library
Abstract Analysis of environmental DNA is increasingly used to characterize ecological
communities, but the effectiveness of this approach depends on the accuracy of taxonomic …