VLDB 2026 Research / reviewers in the wild / expert
Matthew D. Johnston
dblp:09/9974
· DBLP profile ↗
2ranked-venue papers
0as first author
2since 2021 · last 2025
—ORCID · unresolved
Domains — the database's venue-derived domains; a paper can count in several
Theory of computation · 1 · 1 since 2021Applied, interdisciplinary, general and emerging computing · 1 · 1 since 2021
| Year | Publication | Venue | Position |
|---|---|---|---|
| 2025 | Absolute concentration robustness: Algebra and geometry
Luis David García-Puente, Elizabeth Gross, Heather A. Harrington, Matthew D. Johnston, Nicolette Meshkat, Mercedes Pérez Millán, Anne Shiu |
J. Symb. Comput. | 4 |
| 2023 | A framework for deriving analytic steady states of biochemical reaction networksabstractThe long-term behaviors of biochemical systems are often described by their steady states. Deriving these states directly for complex networks arising from real-world applications, however, is often challenging. Recent work has consequently focused on network-based approaches. Specifically, biochemical reaction networks are transformed into weakly reversible and deficiency zero generalized networks, which allows the derivation of their analytic steady states. Identifying this transformation, however, can be challenging for large and complex networks. In this paper, we address this difficulty by breaking the complex network into smaller independent subnetworks and then transforming the subnetworks to derive the analytic steady states of each subnetwork. We show that stitching these solutions together leads to the analytic steady states of the original network. To facilitate this process, we develop a user-friendly and publicly available package, COMPILES (COMPutIng anaLytic stEady States). With COMPILES, we can easily test the presence of bistability of a CRISPRi toggle switch model, which was previously investigated via tremendous number of numerical simulations and within a limited range of parameters. Furthermore, COMPILES can be used to identify absolute concentration robustness (ACR), the property of a system that maintains the concentration of particular species at a steady state regardless of any initial concentrations. Specifically, our approach completely identifies all the species with and without ACR in a complex insulin model. Our method provides an effective approach to analyzing and understanding complex biochemical systems. Bryan S. Hernandez, Patrick Vincent N. Lubenia, Matthew D. Johnston, Jae Kyoung Kim |
PLoS Comput. Biol. | 3 |