Chapter 11: Modelling cellular interactions #
Host–pathogen systems biology
Forst (2006) Drug Discovery TodayA nice review on host–pathogen systems biology.
Modelling Viral and Immune System Dynamics
Perelson (2002) Nature Reviews ImmunologyAn authoritative review on modelling the dynamics of viral infections e.g. HIV/HCV.
Immunology for physicists
Perelson (1997) Reviews of Modern PhysicsA detailed review of an extraordinary variety of models of the immune system, from a physicist’s perspective.
Boolean models of within-host immune interactions
Thakar and Albert (2010) Current Opinion in MicrobiologyAn excellent application of Boolean network modelling to study host–pathogen interactions.
Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction
Raghunathan et al. (2009) BMC Systems BiologyA nice application of constraint-based modelling to study host–pathogen interactions.
A systems perspective of host–pathogen interactions: predicting disease outcome in tuberculosis
Raman et al. (2010) Molecular BioSystemsA detailed systems-level model of TB infection, capturing a large number of interactions between the pathogen and the host immune system.
Current trends in modeling host–pathogen interactions
Mukherjee et al. (2013) Wiley Interdisciplinary Reviews: Data Mining and Knowledge DiscoveryAnother nice review on host–pathogen systems biology.
Metabolic modeling of a mutualistic microbial community
Stolyar et al. (2007) Molecular Systems BiologyThe classic paper on applying FBA to model microbial communities.
Enumerating all possible biosynthetic pathways in metabolic networks
Ravikrishnan et al. (2018) Scientific ReportsDetails the MetQuest approach to enumerate biosynthetic pathways, which can span even across microbes.
SteadyCom: Predicting microbial abundances while ensuring community stability
Chan et al. (2017) PLoS Computational BiologyAn excellent paper detailing the background of community modelling approaches, and focussing on the SteadyCom approach, one of the best approaches based on constraint-based modelling.
Investigating metabolic interactions in a microbial co-culture through integrated modelling and experiments
Ravikrishnan et al. (2020) Computational and Structural Biotechnology JournalAn integrated experimental and computational approach, defining an index measuring the metabolic dependency between organisms.
Modelling approaches for studying the microbiome
Kumar et al. (2019) Nature MicrobiologyA detailed review on metabolic modelling of microbial communities.