Towards the fully automated monitoring of ecological communities

M Besson, J Alison, K Bjerge, TE Gorochowski… - Ecology …, 2022 - Wiley Online Library
High‐resolution monitoring is fundamental to understand ecosystems dynamics in an era of
global change and biodiversity declines. While real‐time and automated monitoring of …

[HTML][HTML] Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods

J Pawlowski, K Bruce, K Panksep, FI Aguirre… - Science of the Total …, 2022 - Elsevier
Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for
identification of whole communities within a targeted group) is revolutionizing the field of …

Deep learning and computer vision will transform entomology

TT Høye, J Ärje, K Bjerge… - Proceedings of the …, 2021 - National Acad Sciences
Most animal species on Earth are insects, and recent reports suggest that their abundance is
in drastic decline. Although these reports come from a wide range of insect taxa and regions …

Environmental DNA: What's behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring

J Pawlowski, L Apothéloz‐Perret‐Gentil… - Molecular …, 2020 - Wiley Online Library
The last decade brought a spectacular development of so‐called environmental (e) DNA
studies. In general,“environmental DNA” is defined as DNA isolated from environmental …

Machine learning applications in microbial ecology, human microbiome studies, and environmental monitoring

RB Ghannam, SM Techtmann - Computational and Structural …, 2021 - Elsevier
Advances in nucleic acid sequencing technology have enabled expansion of our ability to
profile microbial diversity. These large datasets of taxonomic and functional diversity are key …

Biases in bulk: DNA metabarcoding of marine communities and the methodology involved

LM van der Loos, R Nijland - Molecular Ecology, 2021 - Wiley Online Library
With the growing anthropogenic pressure on marine ecosystems, the need for efficient
monitoring of biodiversity grows stronger. DNA metabarcoding of bulk samples is …

Ecosystems monitoring powered by environmental genomics: a review of current strategies with an implementation roadmap

T Cordier, L Alonso‐Sáez… - Molecular …, 2021 - Wiley Online Library
A decade after environmental scientists integrated high‐throughput sequencing
technologies in their toolbox, the genomics‐based monitoring of anthropogenic impacts on …

Machine learning in marine ecology: an overview of techniques and applications

P Rubbens, S Brodie, T Cordier… - ICES Journal of …, 2023 - academic.oup.com
Abstract Machine learning covers a large set of algorithms that can be trained to identify
patterns in data. Thanks to the increase in the amount of data and computing power …

Embracing environmental genomics and machine learning for routine biomonitoring

T Cordier, A Lanzén, L Apothéloz-Perret-Gentil… - Trends in …, 2019 - cell.com
Genomics is fast becoming a routine tool in medical diagnostics and cutting-edge
biotechnologies. Yet, its use for environmental biomonitoring is still considered a futuristic …

Improving metabarcoding taxonomic assignment: A case study of fishes in a large marine ecosystem

Z Gold, EE Curd, KD Goodwin, ES Choi… - Molecular ecology …, 2021 - Wiley Online Library
DNA metabarcoding is an important tool for molecular ecology. However, its effectiveness
hinges on the quality of reference sequence databases and classification parameters …