TY  - JOUR
A1  - Bartoszewicz, Jakub M.
A1  - Nasri, Ferdous
A1  - Nowicka, Melania
A1  - Renard, Bernhard Y.
T1  - Detecting DNA of novel fungal pathogens using ResNets and a curated fungi-hosts data collection
JF  - Bioinformatics
N2  - Background: 
Emerging pathogens are a growing threat, but large data collections and approaches for predicting the risk associated with novel agents are limited to bacteria and viruses. Pathogenic fungi, which also pose a constant threat to public health, remain understudied. 
Relevant data remain comparatively scarce and scattered among many different sources, hindering the development of sequencing-based detection workflows for novel fungal pathogens. 
No prediction method working for agents across all three groups is available, even though the cause of an infection is often difficult to identify from symptoms alone.

Results: 
We present a curated collection of fungal host range data, comprising records on human, animal and plant pathogens, as well as other plant-associated fungi, linked to publicly available genomes. 
We show that it can be used to predict the pathogenic potential of novel fungal species directly from DNA sequences with either sequence homology or deep learning. 
We develop learned, numerical representations of the collected genomes and visualize the landscape of fungal pathogenicity. 
Finally, we train multi-class models predicting if next-generation sequencing reads originate from novel fungal, bacterial or viral threats. 

Conclusions: 
The neural networks trained using our data collection enable accurate detection of novel fungal pathogens.
A curated set of over 1400 genomes with host and pathogenicity metadata supports training of machine-learning models and sequence comparison, not limited to the pathogen detection task.
Y1  - 2022
U6  - https://doi.org/10.1093/bioinformatics/btac495
SN  - 1367-4803
SN  - 1367-4811
VL  - 38
SP  - ii168
EP  - ii174
PB  - Oxford Univ. Press
CY  - Oxford
ER  -