RT Journal Article
SR Electronic
T1 Multi –omics and metabolic modelling pipelines: challenges and tools for systems microbiology
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 013532
DO 10.1101/013532
A1 Marco Fondi
A1 Pietro Liò
YR 2015
UL http://biorxiv.org/content/early/2015/01/07/013532.abstract
AB Integrated -omics approaches are quickly spreading across microbiology research labs, leading to i) the possibility of detecting previously hidden features of microbial cells like multi-scale spatial organisation and ii) tracing molecular components across multiple cellular functional states. This promises to reduce the knowledge gap between genotype and phenotype and poses new challenges for computational microbiologists. We underline how the capability to unravel the complexity of microbial life will strongly depend on the integration of the huge and diverse amount of information that can be derived today from - omics experiments. In this work, we present opportunities and challenges of multi –omics data integration in current systems biology pipelines. We here discuss which layers of biological information are important for biotechnological and clinical purposes, with a special focus on bacterial metabolism and modelling procedures. A general review of the most recent computational tools for performing large-scale datasets integration is also presented, together with a possible framework to guide the design of systems biology experiments by microbiologists.