Integrative modeling of the cell
A whole-cell model represents certain aspects of the cell structure and/or function. Due to the high complexity of the cell, an integrative modeling approach is often taken to utilize all available information including experimental data, prior knowledge and prior models. In this review, we summariz...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
China Science Publishing & Media Ltd.
2022-08-01
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| Series: | Acta Biochimica et Biophysica Sinica |
| Subjects: | |
| Online Access: | https://www.sciengine.com/doi/10.3724/abbs.2022115 |
| _version_ | 1797635374924693504 |
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| author | Zhong Xianni Zhao Jihui Sun Liping |
| author_facet | Zhong Xianni Zhao Jihui Sun Liping |
| author_sort | Zhong Xianni |
| collection | DOAJ |
| description | A whole-cell model represents certain aspects of the cell structure and/or function. Due to the high complexity of the cell, an integrative modeling approach is often taken to utilize all available information including experimental data, prior knowledge and prior models. In this review, we summarize an emerging workflow of whole-cell modeling into five steps: (i) gather information; (ii) represent the modeled system into modules; (iii) translate input information into scoring function; (iv) sample the whole-cell model; (v) validate and interpret the model. In particular, we propose the integrative modeling of the cell by combining available (whole-cell) models to maximize the accuracy, precision, and completeness. In addition, we list quantitative predictions of various aspects of cell biology from existing whole-cell models. Moreover, we discuss the remaining challenges and future directions, and highlight the opportunity to establish an integrative spatiotemporal multi-scale whole-cell model based on a community approach. |
| first_indexed | 2024-03-11T12:21:11Z |
| format | Article |
| id | doaj.art-d47f882611fb4e1a87ed107cc10225ce |
| institution | Directory Open Access Journal |
| issn | 1672-9145 |
| language | English |
| last_indexed | 2024-03-11T12:21:11Z |
| publishDate | 2022-08-01 |
| publisher | China Science Publishing & Media Ltd. |
| record_format | Article |
| series | Acta Biochimica et Biophysica Sinica |
| spelling | doaj.art-d47f882611fb4e1a87ed107cc10225ce2023-11-07T01:01:27ZengChina Science Publishing & Media Ltd.Acta Biochimica et Biophysica Sinica1672-91452022-08-01541213122110.3724/abbs.202211520d259ccIntegrative modeling of the cellZhong Xianni0Zhao Jihui1Sun Liping2["iHuman Institute, ShanghaiTech University, Shanghai 201210, China","School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China"]["iHuman Institute, ShanghaiTech University, Shanghai 201210, China"]["iHuman Institute, ShanghaiTech University, Shanghai 201210, China"]A whole-cell model represents certain aspects of the cell structure and/or function. Due to the high complexity of the cell, an integrative modeling approach is often taken to utilize all available information including experimental data, prior knowledge and prior models. In this review, we summarize an emerging workflow of whole-cell modeling into five steps: (i) gather information; (ii) represent the modeled system into modules; (iii) translate input information into scoring function; (iv) sample the whole-cell model; (v) validate and interpret the model. In particular, we propose the integrative modeling of the cell by combining available (whole-cell) models to maximize the accuracy, precision, and completeness. In addition, we list quantitative predictions of various aspects of cell biology from existing whole-cell models. Moreover, we discuss the remaining challenges and future directions, and highlight the opportunity to establish an integrative spatiotemporal multi-scale whole-cell model based on a community approach.https://www.sciengine.com/doi/10.3724/abbs.2022115whole-cell modelingintegrative modelingcompartment modelcell biology |
| spellingShingle | Zhong Xianni Zhao Jihui Sun Liping Integrative modeling of the cell Acta Biochimica et Biophysica Sinica whole-cell modeling integrative modeling compartment model cell biology |
| title | Integrative modeling of the cell |
| title_full | Integrative modeling of the cell |
| title_fullStr | Integrative modeling of the cell |
| title_full_unstemmed | Integrative modeling of the cell |
| title_short | Integrative modeling of the cell |
| title_sort | integrative modeling of the cell |
| topic | whole-cell modeling integrative modeling compartment model cell biology |
| url | https://www.sciengine.com/doi/10.3724/abbs.2022115 |
| work_keys_str_mv | AT zhongxianni integrativemodelingofthecell AT zhaojihui integrativemodelingofthecell AT sunliping integrativemodelingofthecell |