AIMC Topic: Genome, Fungal

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Machine Learning of Protein Interactions in Fungal Secretory Pathways.

PloS one
In this paper we apply machine learning methods for predicting protein interactions in fungal secretion pathways. We assume an inter-species transfer setting, where training data is obtained from a single species and the objective is to predict prote...

EffectorP: predicting fungal effector proteins from secretomes using machine learning.

The New phytologist
Eukaryotic filamentous plant pathogens secrete effector proteins that modulate the host cell to facilitate infection. Computational effector candidate identification and subsequent functional characterization delivers valuable insights into plant-pat...

Inferring fungal cis-regulatory networks from genome sequences via unsupervised and interpretable representation learning.

Genetics
Gene expression patterns are determined to a large extent by transcription factor (TF) binding to noncoding regulatory regions in the genome. However, gene expression cannot yet be systematically predicted from genome sequences, in part because nonfu...

The pan-genome of Saccharomyces cerevisiae.

FEMS yeast research
Understanding genotype-phenotype relationship is fundamental in biology. With the benefit from next-generation sequencing and high-throughput phenotyping methodologies, there have been generated much genome and phenome data for Saccharomyces cerevisi...

Victors: a web-based knowledge base of virulence factors in human and animal pathogens.

Nucleic acids research
Virulence factors (VFs) are molecules that allow microbial pathogens to overcome host defense mechanisms and cause disease in a host. It is critical to study VFs for better understanding microbial pathogenesis and host defense mechanisms. Victors (ht...