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For: Karr JR, Takahashi K, Funahashi A. The principles of whole-cell modeling. Curr Opin Microbiol 2015;27:18-24. [PMID: 26115539 DOI: 10.1016/j.mib.2015.06.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 05/25/2015] [Accepted: 06/05/2015] [Indexed: 11/17/2022]
Number Cited by Other Article(s)
1
Cui H, Tejada-Lapuerta A, Brbić M, Saez-Rodriguez J, Cristea S, Goodarzi H, Lotfollahi M, Theis FJ, Wang B. Towards multimodal foundation models in molecular cell biology. Nature 2025;640:623-633. [PMID: 40240854 DOI: 10.1038/s41586-025-08710-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/29/2025] [Indexed: 04/18/2025]
2
Li LX, Aguilar B, Gennari JH, Qin G. LM-Merger: A workflow for merging logical models with an application to gene regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.13.612961. [PMID: 39345612 PMCID: PMC11429764 DOI: 10.1101/2024.09.13.612961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
3
Kearney T, Flegg MB. Enzyme kinetics simulation at the scale of individual particles. J Chem Phys 2024;161:194111. [PMID: 39565238 DOI: 10.1063/5.0216285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 10/25/2024] [Indexed: 11/21/2024]  Open
4
Shibai A, Furusawa C. Development of specialized devices for microbial experimental evolution. Dev Growth Differ 2024;66:372-380. [PMID: 39187274 PMCID: PMC11482599 DOI: 10.1111/dgd.12940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 08/06/2024] [Accepted: 08/11/2024] [Indexed: 08/28/2024]
5
Kaizu K, Takahashi K. Technologies for whole-cell modeling: Genome-wide reconstruction of a cell in silico. Dev Growth Differ 2023;65:554-564. [PMID: 37856476 PMCID: PMC11520977 DOI: 10.1111/dgd.12897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 09/06/2023] [Accepted: 10/14/2023] [Indexed: 10/21/2023]
6
Georgouli K, Yeom JS, Blake RC, Navid A. Multi-scale models of whole cells: progress and challenges. Front Cell Dev Biol 2023;11:1260507. [PMID: 38020904 PMCID: PMC10661945 DOI: 10.3389/fcell.2023.1260507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023]  Open
7
Ponce-de-Leon M, Montagud A, Noël V, Meert A, Pradas G, Barillot E, Calzone L, Valencia A. PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks. NPJ Syst Biol Appl 2023;9:54. [PMID: 37903760 PMCID: PMC10616087 DOI: 10.1038/s41540-023-00314-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 10/11/2023] [Indexed: 11/01/2023]  Open
8
Griesemer M, Navid A. Uses of Multi-Objective Flux Analysis for Optimization of Microbial Production of Secondary Metabolites. Microorganisms 2023;11:2149. [PMID: 37763993 PMCID: PMC10536367 DOI: 10.3390/microorganisms11092149] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/07/2023] [Accepted: 08/16/2023] [Indexed: 09/29/2023]  Open
9
Khan SA, Lehmann R, Martinez-de-Morentin X, Maillo A, Lagani V, Kiani NA, Gomez-Cabrero D, Tegner J. scAEGAN: Unification of single-cell genomics data by adversarial learning of latent space correspondences. PLoS One 2023;18:e0281315. [PMID: 36735690 PMCID: PMC9897517 DOI: 10.1371/journal.pone.0281315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/19/2023] [Indexed: 02/04/2023]  Open
10
Stevens JA, Grünewald F, van Tilburg PAM, König M, Gilbert BR, Brier TA, Thornburg ZR, Luthey-Schulten Z, Marrink SJ. Molecular dynamics simulation of an entire cell. Front Chem 2023;11:1106495. [PMID: 36742032 PMCID: PMC9889929 DOI: 10.3389/fchem.2023.1106495] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/09/2023] [Indexed: 01/19/2023]  Open
11
Calzone L, Noël V, Barillot E, Kroemer G, Stoll G. Modeling signaling pathways in biology with MaBoSS: From one single cell to a dynamic population of heterogeneous interacting cells. Comput Struct Biotechnol J 2022;20:5661-5671. [PMID: 36284705 PMCID: PMC9582792 DOI: 10.1016/j.csbj.2022.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 09/30/2022] [Accepted: 10/02/2022] [Indexed: 11/24/2022]  Open
12
Ye C, Wei X, Shi T, Sun X, Xu N, Gao C, Zou W. Genome-scale metabolic network models: from first-generation to next-generation. Appl Microbiol Biotechnol 2022;106:4907-4920. [PMID: 35829788 DOI: 10.1007/s00253-022-12066-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 06/24/2022] [Accepted: 07/02/2022] [Indexed: 11/26/2022]
13
Bi X, Liu Y, Li J, Du G, Lv X, Liu L. Construction of Multiscale Genome-Scale Metabolic Models: Frameworks and Challenges. Biomolecules 2022;12:biom12050721. [PMID: 35625648 PMCID: PMC9139095 DOI: 10.3390/biom12050721] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/15/2022] [Accepted: 05/16/2022] [Indexed: 12/04/2022]  Open
14
A multiscale model of the regulation of aquaporin 2 recycling. NPJ Syst Biol Appl 2022;8:16. [PMID: 35534498 PMCID: PMC9085758 DOI: 10.1038/s41540-022-00223-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 03/24/2022] [Indexed: 11/08/2022]  Open
15
Shallom D, Naiger D, Weiss S, Tuller T. Accelerating Whole-Cell Simulations of mRNA Translation Using a Dedicated Hardware. ACS Synth Biol 2021;10:3489-3506. [PMID: 34813269 PMCID: PMC8689694 DOI: 10.1021/acssynbio.1c00415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
16
Tourigny DS, Goldberg AP, Karr JR. Simulating single-cell metabolism using a stochastic flux-balance analysis algorithm. Biophys J 2021;120:5231-5242. [PMID: 34757076 DOI: 10.1016/j.bpj.2021.10.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 10/01/2021] [Accepted: 10/26/2021] [Indexed: 10/19/2022]  Open
17
Panikov NS. Genome-Scale Reconstruction of Microbial Dynamic Phenotype: Successes and Challenges. Microorganisms 2021;9:2352. [PMID: 34835477 PMCID: PMC8621822 DOI: 10.3390/microorganisms9112352] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/18/2021] [Accepted: 10/27/2021] [Indexed: 12/04/2022]  Open
18
Budde K, Smith J, Wilsdorf P, Haack F, Uhrmacher AM. Relating simulation studies by provenance-Developing a family of Wnt signaling models. PLoS Comput Biol 2021;17:e1009227. [PMID: 34351901 PMCID: PMC8407594 DOI: 10.1371/journal.pcbi.1009227] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 08/31/2021] [Accepted: 06/29/2021] [Indexed: 12/28/2022]  Open
19
Matthews ML, Marshall-Colón A. Multiscale plant modeling: from genome to phenome and beyond. Emerg Top Life Sci 2021;5:231-237. [PMID: 33543231 PMCID: PMC8166335 DOI: 10.1042/etls20200276] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 01/08/2023]
20
Santibáñez R, Garrido D, Martin AJM. Atlas: automatic modeling of regulation of bacterial gene expression and metabolism using rule-based languages. Bioinformatics 2021;36:5473-5480. [PMID: 33367504 PMCID: PMC8016457 DOI: 10.1093/bioinformatics/btaa1040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 11/19/2020] [Accepted: 12/12/2020] [Indexed: 12/31/2022]  Open
21
Lawlor B, Sleator RD. The roles of code in biology. Sci Prog 2021;104:368504211010570. [PMID: 33856939 PMCID: PMC10454959 DOI: 10.1177/00368504211010570] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
22
Roth YD, Lian Z, Pochiraju S, Shaikh B, Karr JR. Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior. Nucleic Acids Res 2021;49:D516-D522. [PMID: 33174603 PMCID: PMC7779073 DOI: 10.1093/nar/gkaa1008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/12/2020] [Accepted: 10/21/2020] [Indexed: 12/23/2022]  Open
23
Prediction of Cellular Burden with Host-Circuit Models. Methods Mol Biol 2021;2229:267-291. [PMID: 33405227 DOI: 10.1007/978-1-0716-1032-9_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
24
Noll P, Henkel M. History and Evolution of Modeling in Biotechnology: Modeling & Simulation, Application and Hardware Performance. Comput Struct Biotechnol J 2020;18:3309-3323. [PMID: 33240472 PMCID: PMC7670204 DOI: 10.1016/j.csbj.2020.10.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/15/2020] [Accepted: 10/17/2020] [Indexed: 12/17/2022]  Open
25
Marucci L, Barberis M, Karr J, Ray O, Race PR, de Souza Andrade M, Grierson C, Hoffmann SA, Landon S, Rech E, Rees-Garbutt J, Seabrook R, Shaw W, Woods C. Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology. Front Bioeng Biotechnol 2020;8:942. [PMID: 32850764 PMCID: PMC7426639 DOI: 10.3389/fbioe.2020.00942] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/21/2020] [Indexed: 01/03/2023]  Open
26
Keating SM, Waltemath D, König M, Zhang F, Dräger A, Chaouiya C, Bergmann FT, Finney A, Gillespie CS, Helikar T, Hoops S, Malik‐Sheriff RS, Moodie SL, Moraru II, Myers CJ, Naldi A, Olivier BG, Sahle S, Schaff JC, Smith LP, Swat MJ, Thieffry D, Watanabe L, Wilkinson DJ, Blinov ML, Begley K, Faeder JR, Gómez HF, Hamm TM, Inagaki Y, Liebermeister W, Lister AL, Lucio D, Mjolsness E, Proctor CJ, Raman K, Rodriguez N, Shaffer CA, Shapiro BE, Stelling J, Swainston N, Tanimura N, Wagner J, Meier‐Schellersheim M, Sauro HM, Palsson B, Bolouri H, Kitano H, Funahashi A, Hermjakob H, Doyle JC, Hucka M. SBML Level 3: an extensible format for the exchange and reuse of biological models. Mol Syst Biol 2020;16:e9110. [PMID: 32845085 PMCID: PMC8411907 DOI: 10.15252/msb.20199110] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 06/24/2020] [Accepted: 07/09/2020] [Indexed: 12/25/2022]  Open
27
Ye C, Xu N, Gao C, Liu G, Xu J, Zhang W, Chen X, Nielsen J, Liu L. Comprehensive understanding of Saccharomyces cerevisiae phenotypes with whole-cell model WM_S288C. Biotechnol Bioeng 2020;117:1562-1574. [PMID: 32022245 DOI: 10.1002/bit.27298] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 01/28/2020] [Accepted: 02/03/2020] [Indexed: 02/01/2023]
28
Feig M, Sugita Y. Whole-Cell Models and Simulations in Molecular Detail. Annu Rev Cell Dev Biol 2019;35:191-211. [PMID: 31299173 PMCID: PMC6783340 DOI: 10.1146/annurev-cellbio-100617-062542] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
29
Liu F, Heiner M, Gilbert D. Coloured Petri nets for multilevel, multiscale and multidimensional modelling of biological systems. Brief Bioinform 2019;20:877-886. [PMID: 29112705 PMCID: PMC6585149 DOI: 10.1093/bib/bbx150] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/22/2017] [Indexed: 01/25/2023]  Open
30
Liu F, Heiner M, Gilbert D. Fuzzy Petri nets for modelling of uncertain biological systems. Brief Bioinform 2018;21:198-210. [PMID: 30590430 DOI: 10.1093/bib/bby118] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 10/09/2018] [Accepted: 11/16/2018] [Indexed: 12/28/2022]  Open
31
Furusawa C, Horinouchi T, Maeda T. Toward prediction and control of antibiotic-resistance evolution. Curr Opin Biotechnol 2018;54:45-49. [DOI: 10.1016/j.copbio.2018.01.026] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 01/23/2018] [Accepted: 01/28/2018] [Indexed: 11/30/2022]
32
Gómez-Schiavon M, El-Samad H. Complexity-aware simple modeling. Curr Opin Microbiol 2018;45:47-52. [PMID: 29494832 DOI: 10.1016/j.mib.2018.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 01/07/2018] [Indexed: 11/19/2022]
33
Multi-Algorithm Particle Simulations with Spatiocyte. Methods Mol Biol 2018;1611:219-236. [PMID: 28451982 DOI: 10.1007/978-1-4939-7015-5_16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
34
Goldberg AP, Szigeti B, Chew YH, Sekar JA, Roth YD, Karr JR. Emerging whole-cell modeling principles and methods. Curr Opin Biotechnol 2017;51:97-102. [PMID: 29275251 DOI: 10.1016/j.copbio.2017.12.013] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 12/07/2017] [Accepted: 12/11/2017] [Indexed: 11/16/2022]
35
Sarma GP, Faundez V. Integrative biological simulation praxis: Considerations from physics, philosophy, and data/model curation practices. CELLULAR LOGISTICS 2017;7:e1392400. [PMID: 29296511 PMCID: PMC5739097 DOI: 10.1080/21592799.2017.1392400] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 10/02/2017] [Accepted: 10/10/2017] [Indexed: 01/06/2023]
36
Szigeti B, Roth YD, Sekar JAP, Goldberg AP, Pochiraju SC, Karr JR. A blueprint for human whole-cell modeling. ACTA ACUST UNITED AC 2017;7:8-15. [PMID: 29806041 DOI: 10.1016/j.coisb.2017.10.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
37
Babtie AC, Stumpf MPH. How to deal with parameters for whole-cell modelling. J R Soc Interface 2017;14:20170237. [PMID: 28768879 PMCID: PMC5582120 DOI: 10.1098/rsif.2017.0237] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 06/22/2017] [Indexed: 11/12/2022]  Open
38
Rejc Ž, Magdevska L, Tršelič T, Osolin T, Vodopivec R, Mraz J, Pavliha E, Zimic N, Cvitanović T, Rozman D, Moškon M, Mraz M. Computational modelling of genome-scale metabolic networks and its application to CHO cell cultures. Comput Biol Med 2017;88:150-160. [PMID: 28732234 DOI: 10.1016/j.compbiomed.2017.07.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/04/2017] [Accepted: 07/05/2017] [Indexed: 01/30/2023]
39
Gábor A, Villaverde AF, Banga JR. Parameter identifiability analysis and visualization in large-scale kinetic models of biosystems. BMC SYSTEMS BIOLOGY 2017;11:54. [PMID: 28476119 PMCID: PMC5420165 DOI: 10.1186/s12918-017-0428-y] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 04/25/2017] [Indexed: 01/13/2023]
40
Loewe L, Scheuer KS, Keel SA, Vyas V, Liblit B, Hanlon B, Ferris MC, Yin J, Dutra I, Pietsch A, Javid CG, Moog CL, Meyer J, Dresel J, McLoone B, Loberger S, Movaghar A, Gilchrist-Scott M, Sabri Y, Sescleifer D, Pereda-Zorrilla I, Zietlow A, Smith R, Pietenpol S, Goldfinger J, Atzen SL, Freiberg E, Waters NP, Nusbaum C, Nolan E, Hotz A, Kliman RM, Mentewab A, Fregien N, Loewe M. Evolvix BEST Names for semantic reproducibility across code2brain interfaces. Ann N Y Acad Sci 2016;1387:124-144. [PMID: 27918836 PMCID: PMC5299481 DOI: 10.1111/nyas.13192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 07/12/2016] [Indexed: 11/30/2022]
41
Waltemath D, Karr JR, Bergmann FT, Chelliah V, Hucka M, Krantz M, Liebermeister W, Mendes P, Myers CJ, Pir P, Alaybeyoglu B, Aranganathan NK, Baghalian K, Bittig AT, Burke PEP, Cantarelli M, Chew YH, Costa RS, Cursons J, Czauderna T, Goldberg AP, Gomez HF, Hahn J, Hameri T, Gardiol DFH, Kazakiewicz D, Kiselev I, Knight-Schrijver V, Knupfer C, Konig M, Lee D, Lloret-Villas A, Mandrik N, Medley JK, Moreau B, Naderi-Meshkin H, Palaniappan SK, Priego-Espinosa D, Scharm M, Sharma M, Smallbone K, Stanford NJ, Song JH, Theile T, Tokic M, Tomar N, Toure V, Uhlendorf J, Varusai TM, Watanabe LH, Wendland F, Wolfien M, Yurkovich JT, Zhu Y, Zardilis A, Zhukova A, Schreiber F. Toward Community Standards and Software for Whole-Cell Modeling. IEEE Trans Biomed Eng 2016;63:2007-14. [PMID: 27305665 PMCID: PMC5451320 DOI: 10.1109/tbme.2016.2560762] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Metabolic flux analyses of Pseudomonas aeruginosa cystic fibrosis isolates. Metab Eng 2016;38:251-263. [PMID: 27637318 DOI: 10.1016/j.ymben.2016.09.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 06/07/2016] [Accepted: 09/11/2016] [Indexed: 01/22/2023]
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Current state and challenges for dynamic metabolic modeling. Curr Opin Microbiol 2016;33:97-104. [PMID: 27472025 DOI: 10.1016/j.mib.2016.07.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 06/28/2016] [Accepted: 07/06/2016] [Indexed: 01/06/2023]
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Medley JK, Goldberg AP, Karr JR. Guidelines for Reproducibly Building and Simulating Systems Biology Models. IEEE Trans Biomed Eng 2016;63:2015-20. [PMID: 27429432 DOI: 10.1109/tbme.2016.2591960] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Santero E, Floriano B, Govantes F. Harnessing the power of microbial metabolism. Curr Opin Microbiol 2016;31:63-69. [DOI: 10.1016/j.mib.2016.03.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 03/15/2016] [Accepted: 03/16/2016] [Indexed: 01/12/2023]
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Big Data in Plant Science: Resources and Data Mining Tools for Plant Genomics and Proteomics. Methods Mol Biol 2016;1415:533-47. [PMID: 27115651 DOI: 10.1007/978-1-4939-3572-7_27] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Outters P, Jaeger S, Zaarour N, Ferrier P. Long-Range Control of V(D)J Recombination & Allelic Exclusion: Modeling Views. Adv Immunol 2015;128:363-413. [PMID: 26477371 DOI: 10.1016/bs.ai.2015.08.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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