Joining and decomposing reaction networks
In systems and synthetic biology, much research has focused on the behavior and design of single pathways, while, more recently, experimental efforts have focused on how cross-talk (coupling two or more pathways) or inhibiting molecular function (isolating one part of the pathway) affects systems-le...
| Main Authors: | , , , |
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| Format: | Journal article |
| Language: | English |
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Springer
2020
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| _version_ | 1826259246594916352 |
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| author | Gross, E Harrington, H Meshkat, N Shiu, A |
| author_facet | Gross, E Harrington, H Meshkat, N Shiu, A |
| author_sort | Gross, E |
| collection | OXFORD |
| description | In systems and synthetic biology, much research has focused on the behavior and design of single pathways, while, more recently, experimental efforts have focused on how cross-talk (coupling two or more pathways) or inhibiting molecular function (isolating one part of the pathway) affects systems-level behavior. However, the theory for tackling these larger systems in general has lagged behind. Here, we analyze how joining networks (e.g., cross-talk) or decomposing networks (e.g., inhibition or knock-outs) affects three properties that reaction networks may possess—identifiability (recoverability of parameter values from data), steady-state invariants (relationships among species concentrations at steady state, used in model selection), and multistationarity (capacity for multiple steady states, which correspond to multiple cell decisions). Specifically, we prove results that clarify, for a network obtained by joining two smaller networks, how properties of the smaller networks can be inferred from or can imply similar properties of the original network. Our proofs use techniques from computational algebraic geometry, including elimination theory and differential algebra. |
| first_indexed | 2024-03-06T18:46:51Z |
| format | Journal article |
| id | oxford-uuid:0ecdfd7f-216d-498e-b7c4-919fb9d1a1be |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-06T18:46:51Z |
| publishDate | 2020 |
| publisher | Springer |
| record_format | dspace |
| spelling | oxford-uuid:0ecdfd7f-216d-498e-b7c4-919fb9d1a1be2022-03-26T09:47:54ZJoining and decomposing reaction networksJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:0ecdfd7f-216d-498e-b7c4-919fb9d1a1beEnglishSymplectic ElementsSpringer2020Gross, EHarrington, HMeshkat, NShiu, AIn systems and synthetic biology, much research has focused on the behavior and design of single pathways, while, more recently, experimental efforts have focused on how cross-talk (coupling two or more pathways) or inhibiting molecular function (isolating one part of the pathway) affects systems-level behavior. However, the theory for tackling these larger systems in general has lagged behind. Here, we analyze how joining networks (e.g., cross-talk) or decomposing networks (e.g., inhibition or knock-outs) affects three properties that reaction networks may possess—identifiability (recoverability of parameter values from data), steady-state invariants (relationships among species concentrations at steady state, used in model selection), and multistationarity (capacity for multiple steady states, which correspond to multiple cell decisions). Specifically, we prove results that clarify, for a network obtained by joining two smaller networks, how properties of the smaller networks can be inferred from or can imply similar properties of the original network. Our proofs use techniques from computational algebraic geometry, including elimination theory and differential algebra. |
| spellingShingle | Gross, E Harrington, H Meshkat, N Shiu, A Joining and decomposing reaction networks |
| title | Joining and decomposing reaction networks |
| title_full | Joining and decomposing reaction networks |
| title_fullStr | Joining and decomposing reaction networks |
| title_full_unstemmed | Joining and decomposing reaction networks |
| title_short | Joining and decomposing reaction networks |
| title_sort | joining and decomposing reaction networks |
| work_keys_str_mv | AT grosse joininganddecomposingreactionnetworks AT harringtonh joininganddecomposingreactionnetworks AT meshkatn joininganddecomposingreactionnetworks AT shiua joininganddecomposingreactionnetworks |