Propagation, detection and correction of errors using the sequence database network

B Goudey, N Geard, K Verspoor… - Briefings in …, 2022 - academic.oup.com
Nucleotide and protein sequences stored in public databases are the cornerstone of many
bioinformatics analyses. The records containing these sequences are prone to a wide range …

The ATCC genome portal: microbial genome reference standards with data provenance

B Benton, S King, SR Greenfield… - Microbiology …, 2021 - Am Soc Microbiol
Lack of data provenance negatively impacts scientific reproducibility and the reliability of
genomic data. The ATCC Genome Portal (https://genomes. atcc. org) addresses this by …

Ten simple rules for investigating (meta) genomic data from environmental ecosystems

P Vuong, MJ Wise, AS Whiteley… - PLOS Computational …, 2022 - journals.plos.org
Metagenomics is the sequencing and study of DNA directly from environmental samples and
is an approach used in microbial ecology to explore the diversity and functions of microbial …

PPIT: an R package for inferring microbial taxonomy from nifH sequences

BJ Kapili, AE Dekas - Bioinformatics, 2021 - academic.oup.com
Motivation Linking microbial community members to their ecological functions is a central
goal of environmental microbiology. When assigned taxonomy, amplicon sequences of …

Characterizing Antarctic fish assemblages using eDNA obtained from marine sponge bycatch specimens

GJ Jeunen, M Lamare, J Devine, S Mariani… - Reviews in Fish Biology …, 2024 - Springer
International conservation goals have been set to mitigate Southern Ocean ecosystem
deterioration, with multiple monitoring programs evaluating progress towards those goals …

DFAST_QC: quality assessment and taxonomic identification tool for prokaryotic Genomes

M Elmanzalawi, T Fujisawa, H Mori, Y Nakamura… - BMC …, 2025 - Springer
Background Accurate taxonomic classification in genome databases is essential for reliable
biological research and effective data sharing. Mislabeling or inaccuracies in genome …

A machine learning framework for discovery and enrichment of metagenomics metadata from open access publications

M Nassar, AB Rogers, F Talo', S Sanchez… - …, 2022 - academic.oup.com
Metagenomics is a culture-independent method for studying the microbes inhabiting a
particular environment. Comparing the composition of samples (functionally/taxonomically) …

Concatenated 16S rRNA sequence analysis improves bacterial taxonomy

B Paul - F1000Research, 2023 - pmc.ncbi.nlm.nih.gov
Background: Microscopic, biochemical, molecular, and computer-based approaches are
extensively used to identify and classify bacterial populations. Advances in DNA sequencing …

The Australian Biosecurity Genomic Database: a new resource for high-throughput sequencing analysis based on the National Notifiable Disease List of Terrestrial …

J Batovska, ND Brohier, PT Mee, FE Constable… - Database, 2024 - academic.oup.com
Abstract The Australian Biosecurity Genomic Database (ABGD) is a curated collection of
reference viral genome sequences based on the Australian National Notifiable Disease List …

Impacts of environmental stress on resistance and resilience of algal‐associated bacterial communities

KL Morrissey, L Iveša, S Delva, S D'hondt… - Ecology and …, 2021 - Wiley Online Library
Algal‐associated bacteria are fundamental to the ecological success of marine green
macroalgae such as Caulerpa. The resistance and resilience of algal‐associated microbiota …