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Fungi

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Deep learning approach to describe and classify fungi microscopic images.

PloS one
Preliminary diagnosis of fungal infections can rely on microscopic examination. However, in many cases, it does not allow unambiguous identification of the species due to their visual similarity. Therefore, it is usually necessary to use additional b...

Its2vec: Fungal Species Identification Using Sequence Embedding and Random Forest Classification.

BioMed research international
Fungi play essential roles in many ecological processes, and taxonomic classification is fundamental for microbial community characterization and vital for the study and preservation of fungal biodiversity. To cope with massive fungal barcode data, t...

Optimization of fungi co-fermentation for improving anthraquinone contents and antioxidant activity using artificial neural networks.

Food chemistry
The fermentation products of edible fungi are rich in anthraquinones and have a variety of activities, including the antioxidant activity. Because of the large number of combinations, it is very difficult to obtain the optimal multi-strains co-fermen...

Assigning the Origin of Microbial Natural Products by Chemical Space Map and Machine Learning.

Biomolecules
Microbial natural products (NPs) are an important source of drugs, however, their structural diversity remains poorly understood. Here we used our recently reported MinHashed Atom Pair fingerprint with diameter of four bonds (MAP4), a fingerprint sui...

Scalable classification of organisms into a taxonomy using hierarchical supervised learners.

Journal of bioinformatics and computational biology
Accurately identifying organisms based on their partially available genetic material is an important task to explore the phylogenetic diversity in an environment. Specific fragments in the DNA sequence of a living organism have been defined as DNA ba...

Deep learning-based quantification of arbuscular mycorrhizal fungi in plant roots.

The New phytologist
Soil fungi establish mutualistic interactions with the roots of most vascular land plants. Arbuscular mycorrhizal (AM) fungi are among the most extensively characterised mycobionts to date. Current approaches to quantifying the extent of root colonis...

Comprehensive assessment of machine learning-based methods for predicting antimicrobial peptides.

Briefings in bioinformatics
Antimicrobial peptides (AMPs) are a unique and diverse group of molecules that play a crucial role in a myriad of biological processes and cellular functions. AMP-related studies have become increasingly popular in recent years due to antimicrobial r...

A NLP Pipeline for the Automatic Extraction of Microorganisms Names from Microbiological Notes.

Studies in health technology and informatics
According to the "Istituto Superiore di Sanita'" (ISS), hospital infections are the most frequent and serious complication of health care. This constitutes a real health emergency which requires incisive and joint action at all levels of the local an...