Abstract:
:While elementary flux mode (EFM) analysis is now recognized as a cornerstone computational technique for cellular pathway analysis and engineering, EFM application to genome-scale models remains computationally prohibitive. This article provides a review of aspects of EFM computation that elucidates bottlenecks in scaling EFM computation. First, algorithms for computing EFMs are reviewed. Next, the impact of redundant constraints, sensitivity to constraint ordering and network compression are evaluated. Then, the advantages and limitations of recent parallelization and GPU-based efforts are highlighted. The article then reviews alternative pathway analysis approaches that aim to reduce the EFM solution space. Despite advances in EFM computation, our review concludes that continued scaling of EFM computation is necessary to apply EFM to genome-scale models. Further, our review concludes that pathway analysis methods that target specific pathway properties can provide powerful alternatives to EFM analysis.
journal_name
Brief Bioinformjournal_title
Briefings in bioinformaticsauthors
Ullah E,Yosafshahi M,Hassoun Sdoi
10.1093/bib/bbz094subject
Has Abstractpub_date
2020-12-01 00:00:00pages
1875-1885issue
6eissn
1467-5463issn
1477-4054pii
5622691journal_volume
21pub_type
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journal_title:Briefings in bioinformatics
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