Systems Biology Approaches for Host-Fungal Interactions: An Expanding Multi-Omics Frontier

Omics : a Journal of Integrative Biology
Luka CulibrkScott J Tebbutt

Abstract

Opportunistic fungal infections are an increasing threat for global health, and for immunocompromised patients in particular. These infections are characterized by interaction between fungal pathogen and host cells. The exact mechanisms and the attendant variability in host and fungal pathogen interaction remain to be fully elucidated. The field of systems biology aims to characterize a biological system, and utilize this knowledge to predict the system's response to stimuli such as fungal exposures. A multi-omics approach, for example, combining data from genomics, proteomics, metabolomics, would allow a more comprehensive and pan-optic "two systems" biology of both the host and the fungal pathogen. In this review and literature analysis, we present highly specialized and nascent methods for analysis of multiple -omes of biological systems, in addition to emerging single-molecule visualization techniques that may assist in determining biological relevance of multi-omics data. We provide an overview of computational methods for modeling of gene regulatory networks, including some that have been applied towards the study of an interacting host and pathogen. In sum, comprehensive characterizations of host-fungal pathogen systems ...Continue Reading

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Citations

Apr 20, 2016·Frontiers in Microbiology·Carys A CroftScott J Tebbutt
Oct 27, 2017·Science China. Life Sciences·Dongyu WangLushan Wang
Oct 20, 2017·Omics : a Journal of Integrative Biology·Aryashree ArunimaMrutyunjay Suar
Jan 23, 2018·Omics : a Journal of Integrative Biology·Manousos E KambourisGeorge P Patrinos
Aug 15, 2018·Omics : a Journal of Integrative Biology·Arun H PatilThottethodi Subrahmanya Keshava Prasad
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Jul 3, 2021·Frontiers in Cell and Developmental Biology·Adam JaremekStephen J Renaud
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Jun 28, 2019·Journal of Proteome Research·Paniz JasbiHaiwei Gu
Jan 25, 2022·Applied Microbiology and Biotechnology·Zeling ZhangWeihong Zhong

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Methods Mentioned

BETA
gene knockdown
gene knockout
immunoprecipitation
RNA-seq
PCR
transfection
proximity ligation assay
two-hybrid
protein exchange
size-exclusion chromatography

Software Mentioned

GEne Network Inference with Ensemble of GENIE3
DREAM
trans
FISSEQ
SILAC
MIMS
GENIE3
iTRAQ
Hi
PUNCH

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