ArticleFrontiers in genetics2024
CAMDA 2023: Finding patterns in urban microbiomes.
Article in Frontiers in genetics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed.
- MicroAgroBiome: a toolkit for exploring specialized metabolism and ecological interactions in rhizosphere microbiomes of cultivated crops.Nucleic acids research · 2026Article
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Authors and funding
13 authors.
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Abstract
The Critical Assessment of Massive Data Analysis (CAMDA) addresses the complexities of harnessing Big Data in life sciences by hosting annual competitions that inspire research groups to develop innovative solutions. In 2023, the Forensic Challenge focused on identifying the city of origin for 365 metagenomic samples collected from public transportation systems and identifying associations between bacterial distribution and other covariates. For microbiome classification, we incorporated both taxonomic and functional annotations as features. To identify the most informative Operational Taxonomic Units, we selected features by fitting negative binomial models. We then implemented supervised models conducting 5-fold cross-validation (CV) with a 4:1 training-to-validation ratio. After variable selection, which reduced the dataset to fewer than 300 OTUs, the Support Vector Classifier achieved the highest F1 score (0.96). When using functional features from MIFASER, the Neural Network model outperformed other models. When considering climatic and demographic variables of the cities, Dirichlet regression over
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