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WholeCellKB: model organism databases for comprehensive whole-cell models.
Nucleic Acids Res. 2013 Jan;41(Database issue):D787-92. doi: 10.1093/nar/gks1108. Epub 2012 Nov 21.
Nucleic Acids Res. 2013.
PMID: 23175606
Free PMC article.
A whole-cell computational model predicts phenotype from genotype.
Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM, Bolival B Jr, Assad-Garcia N, Glass JI, Covert MW.
Karr JR, et al. Among authors: macklin dn.
Cell. 2012 Jul 20;150(2):389-401. doi: 10.1016/j.cell.2012.05.044.
Cell. 2012.
PMID: 22817898
Free PMC article.
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The future of whole-cell modeling.
Macklin DN, Ruggero NA, Covert MW.
Macklin DN, et al.
Curr Opin Biotechnol. 2014 Aug;28:111-5. doi: 10.1016/j.copbio.2014.01.012. Epub 2014 Feb 17.
Curr Opin Biotechnol. 2014.
PMID: 24556244
Free PMC article.
Review.
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Competing pathways control host resistance to virus via tRNA modification and programmed ribosomal frameshifting.
Maynard ND, Macklin DN, Kirkegaard K, Covert MW.
Maynard ND, et al. Among authors: macklin dn.
Mol Syst Biol. 2012 Jan 31;8:567. doi: 10.1038/msb.2011.101.
Mol Syst Biol. 2012.
PMID: 22294093
Free PMC article.
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Simultaneous cross-evaluation of heterogeneous E. coli datasets via mechanistic simulation.
Macklin DN, Ahn-Horst TA, Choi H, Ruggero NA, Carrera J, Mason JC, Sun G, Agmon E, DeFelice MM, Maayan I, Lane K, Spangler RK, Gillies TE, Paull ML, Akhter S, Bray SR, Weaver DS, Keseler IM, Karp PD, Morrison JH, Covert MW.
Macklin DN, et al.
Science. 2020 Jul 24;369(6502):eaav3751. doi: 10.1126/science.aav3751.
Science. 2020.
PMID: 32703847
Free PMC article.
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Measuring Signaling and RNA-Seq in the Same Cell Links Gene Expression to Dynamic Patterns of NF-κB Activation.
Lane K, Van Valen D, DeFelice MM, Macklin DN, Kudo T, Jaimovich A, Carr A, Meyer T, Pe'er D, Boutet SC, Covert MW.
Lane K, et al. Among authors: macklin dn.
Cell Syst. 2017 Apr 26;4(4):458-469.e5. doi: 10.1016/j.cels.2017.03.010. Epub 2017 Apr 5.
Cell Syst. 2017.
PMID: 28396000
Free PMC article.
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Live-cell measurements of kinase activity in single cells using translocation reporters.
Kudo T, Jeknić S, Macklin DN, Akhter S, Hughey JJ, Regot S, Covert MW.
Kudo T, et al. Among authors: macklin dn.
Nat Protoc. 2018 Jan;13(1):155-169. doi: 10.1038/nprot.2017.128. Epub 2017 Dec 21.
Nat Protoc. 2018.
PMID: 29266096
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Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments.
Van Valen DA, Kudo T, Lane KM, Macklin DN, Quach NT, DeFelice MM, Maayan I, Tanouchi Y, Ashley EA, Covert MW.
Van Valen DA, et al. Among authors: macklin dn.
PLoS Comput Biol. 2016 Nov 4;12(11):e1005177. doi: 10.1371/journal.pcbi.1005177. eCollection 2016 Nov.
PLoS Comput Biol. 2016.
PMID: 27814364
Free PMC article.
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