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Items: 46

1.

NF-κB signaling dynamics is controlled by a dose-sensing autoregulatory loop.

DeFelice MM, Clark HR, Hughey JJ, Maayan I, Kudo T, Gutschow MV, Covert MW, Regot S.

Sci Signal. 2019 Apr 30;12(579). pii: eaau3568. doi: 10.1126/scisignal.aau3568.

PMID:
31040261
2.

Techniques for Studying Decoding of Single Cell Dynamics.

Jeknić S, Kudo T, Covert MW.

Front Immunol. 2019 Apr 11;10:755. doi: 10.3389/fimmu.2019.00755. eCollection 2019. Review.

3.

Escalating Threat Levels of Bacterial Infection Can Be Discriminated by Distinct MAPK and NF-κB Signaling Dynamics in Single Host Cells.

Lane K, Andres-Terre M, Kudo T, Monack DM, Covert MW.

Cell Syst. 2019 Mar 27;8(3):183-196.e4. doi: 10.1016/j.cels.2019.02.008. Epub 2019 Mar 20.

PMID:
30904375
4.

Combinatorial processing of bacterial and host-derived innate immune stimuli at the single-cell level.

Gutschow MV, Mason JC, Lane KM, Maayan I, Hughey JJ, Bajar BT, Amatya DN, Valle SD, Covert MW.

Mol Biol Cell. 2019 Jan 15;30(2):282-292. doi: 10.1091/mbc.E18-07-0423. Epub 2018 Nov 21.

5.

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.

Nat Protoc. 2018 Jan;13(1):155-169. doi: 10.1038/nprot.2017.128. Epub 2017 Dec 21.

PMID:
29266096
6.
7.

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.

Cell Syst. 2017 Apr 26;4(4):458-469.e5. doi: 10.1016/j.cels.2017.03.010. Epub 2017 Apr 5.

8.

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.

PLoS Comput Biol. 2016 Nov 4;12(11):e1005177. doi: 10.1371/journal.pcbi.1005177. eCollection 2016 Nov.

9.

High-resolution imaging and computational analysis of haematopoietic cell dynamics in vivo.

Koechlein CS, Harris JR, Lee TK, Weeks J, Fox RG, Zimdahl B, Ito T, Blevins A, Jung SH, Chute JP, Chourasia A, Covert MW, Reya T.

Nat Commun. 2016 Jul 18;7:12169. doi: 10.1038/ncomms12169.

10.

Why Build Whole-Cell Models?

Carrera J, Covert MW.

Trends Cell Biol. 2015 Dec;25(12):719-722. doi: 10.1016/j.tcb.2015.09.004. Epub 2015 Oct 21.

11.

Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models.

Karr JR, Williams AH, Zucker JD, Raue A, Steiert B, Timmer J, Kreutz C; DREAM8 Parameter Estimation Challenge Consortium, Wilkinson S, Allgood BA, Bot BM, Hoff BR, Kellen MR, Covert MW, Stolovitzky GA, Meyer P.

PLoS Comput Biol. 2015 May 28;11(5):e1004096. doi: 10.1371/journal.pcbi.1004096. eCollection 2015 May.

12.

NetworkPainter: dynamic intracellular pathway animation in Cytobank.

Karr JR, Guturu H, Chen EY, Blair SL, Irish JM, Kotecha N, Covert MW.

BMC Bioinformatics. 2015 May 25;16:172. doi: 10.1186/s12859-015-0602-4.

13.

Single-cell variation leads to population invariance in NF-κB signaling dynamics.

Hughey JJ, Gutschow MV, Bajar BT, Covert MW.

Mol Biol Cell. 2015 Feb 1;26(3):583-90. doi: 10.1091/mbc.E14-08-1267. Epub 2014 Dec 3.

14.

WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions.

Karr JR, Phillips NC, Covert MW.

Database (Oxford). 2014 Sep 16;2014. pii: bau095. doi: 10.1093/database/bau095. Print 2014.

15.

Nonlytic viral spread enhanced by autophagy components.

Bird SW, Maynard ND, Covert MW, Kirkegaard K.

Proc Natl Acad Sci U S A. 2014 Sep 9;111(36):13081-6. doi: 10.1073/pnas.1401437111. Epub 2014 Aug 25.

16.

High-sensitivity measurements of multiple kinase activities in live single cells.

Regot S, Hughey JJ, Bajar BT, Carrasco S, Covert MW.

Cell. 2014 Jun 19;157(7):1724-34. doi: 10.1016/j.cell.2014.04.039.

17.

Simulating a living cell.

Covert MW.

Sci Am. 2014 Jan;310(1):44-51. No abstract available.

PMID:
24616970
18.

The future of whole-cell modeling.

Macklin DN, Ruggero NA, Covert MW.

Curr Opin Biotechnol. 2014 Aug;28:111-5. doi: 10.1016/j.copbio.2014.01.012. Epub 2014 Feb 17. Review.

19.

Incorporation of flexible objectives and time-linked simulation with flux balance analysis.

Birch EW, Udell M, Covert MW.

J Theor Biol. 2014 Mar 21;345:12-21. doi: 10.1016/j.jtbi.2013.12.009. Epub 2013 Dec 17.

20.

Accelerated discovery via a whole-cell model.

Sanghvi JC, Regot S, Carrasco S, Karr JR, Gutschow MV, Bolival B Jr, Covert MW.

Nat Methods. 2013 Dec;10(12):1192-5. doi: 10.1038/nmeth.2724. Epub 2013 Nov 3.

21.

WholeCellViz: data visualization for whole-cell models.

Lee R, Karr JR, Covert MW.

BMC Bioinformatics. 2013 Aug 21;14:253. doi: 10.1186/1471-2105-14-253.

22.

Towards a whole-cell modeling approach for synthetic biology.

Purcell O, Jain B, Karr JR, Covert MW, Lu TK.

Chaos. 2013 Jun;23(2):025112. doi: 10.1063/1.4811182.

23.

Single-cell and population NF-κB dynamic responses depend on lipopolysaccharide preparation.

Gutschow MV, Hughey JJ, Ruggero NA, Bajar BT, Valle SD, Covert MW.

PLoS One. 2013;8(1):e53222. doi: 10.1371/journal.pone.0053222. Epub 2013 Jan 3.

24.

WholeCellKB: model organism databases for comprehensive whole-cell models.

Karr JR, Sanghvi JC, Macklin DN, Arora A, Covert MW.

Nucleic Acids Res. 2013 Jan;41(Database issue):D787-92. doi: 10.1093/nar/gks1108. Epub 2012 Nov 21.

25.

Determining host metabolic limitations on viral replication via integrated modeling and experimental perturbation.

Birch EW, Ruggero NA, Covert MW.

PLoS Comput Biol. 2012;8(10):e1002746. doi: 10.1371/journal.pcbi.1002746. Epub 2012 Oct 18.

26.

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.

Cell. 2012 Jul 20;150(2):389-401. doi: 10.1016/j.cell.2012.05.044.

27.

Competing pathways control host resistance to virus via tRNA modification and programmed ribosomal frameshifting.

Maynard ND, Macklin DN, Kirkegaard K, Covert MW.

Mol Syst Biol. 2012 Jan 31;8:567. doi: 10.1038/msb.2011.101.

28.

High-throughput, single-cell NF-κB dynamics.

Lee TK, Covert MW.

Curr Opin Genet Dev. 2010 Dec;20(6):677-83. doi: 10.1016/j.gde.2010.08.005. Epub 2010 Sep 16. Review.

29.

Computational modeling of mammalian signaling networks.

Hughey JJ, Lee TK, Covert MW.

Wiley Interdiscip Rev Syst Biol Med. 2010 Mar-Apr;2(2):194-209. doi: 10.1002/wsbm.52. Review.

30.

Genome-scale metabolic networks.

Terzer M, Maynard ND, Covert MW, Stelling J.

Wiley Interdiscip Rev Syst Biol Med. 2009 Nov-Dec;1(3):285-297. doi: 10.1002/wsbm.37. Review.

PMID:
20835998
31.

The virus as metabolic engineer.

Maynard ND, Gutschow MV, Birch EW, Covert MW.

Biotechnol J. 2010 Jul;5(7):686-94. doi: 10.1002/biot.201000080. Review.

32.

A forward-genetic screen and dynamic analysis of lambda phage host-dependencies reveals an extensive interaction network and a new anti-viral strategy.

Maynard ND, Birch EW, Sanghvi JC, Chen L, Gutschow MV, Covert MW.

PLoS Genet. 2010 Jul 8;6(7):e1001017. doi: 10.1371/journal.pgen.1001017.

33.

Single-cell NF-kappaB dynamics reveal digital activation and analogue information processing.

Tay S, Hughey JJ, Lee TK, Lipniacki T, Quake SR, Covert MW.

Nature. 2010 Jul 8;466(7303):267-71. doi: 10.1038/nature09145. Epub 2010 Jun 27.

34.

A noisy paracrine signal determines the cellular NF-kappaB response to lipopolysaccharide.

Lee TK, Denny EM, Sanghvi JC, Gaston JE, Maynard ND, Hughey JJ, Covert MW.

Sci Signal. 2009 Oct 20;2(93):ra65. doi: 10.1126/scisignal.2000599.

35.

A dynamic network of transcription in LPS-treated human subjects.

Seok J, Xiao W, Moldawer LL, Davis RW, Covert MW.

BMC Syst Biol. 2009 Jul 28;3:78. doi: 10.1186/1752-0509-3-78.

36.

Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli.

Covert MW, Xiao N, Chen TJ, Karr JR.

Bioinformatics. 2008 Sep 15;24(18):2044-50. doi: 10.1093/bioinformatics/btn352. Epub 2008 Jul 10.

37.

Achieving stability of lipopolysaccharide-induced NF-kappaB activation.

Covert MW, Leung TH, Gaston JE, Baltimore D.

Science. 2005 Sep 16;309(5742):1854-7.

38.

Integrating high-throughput and computational data elucidates bacterial networks.

Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO.

Nature. 2004 May 6;429(6987):92-6.

PMID:
15129285
39.

Reconstruction of microbial transcriptional regulatory networks.

Herrgård MJ, Covert MW, Palsson BØ.

Curr Opin Biotechnol. 2004 Feb;15(1):70-7. Review.

PMID:
15102470
40.

Identifying constraints that govern cell behavior: a key to converting conceptual to computational models in biology?

Covert MW, Famili I, Palsson BO.

Biotechnol Bioeng. 2003 Dec 30;84(7):763-72. Review.

PMID:
14708117
41.

Reconciling gene expression data with known genome-scale regulatory network structures.

Herrgård MJ, Covert MW, Palsson BØ.

Genome Res. 2003 Nov;13(11):2423-34. Epub 2003 Oct 14.

42.

Constraints-based models: regulation of gene expression reduces the steady-state solution space.

Covert MW, Palsson BO.

J Theor Biol. 2003 Apr 7;221(3):309-25.

PMID:
12642111
43.

Genome-scale metabolic model of Helicobacter pylori 26695.

Schilling CH, Covert MW, Famili I, Church GM, Edwards JS, Palsson BO.

J Bacteriol. 2002 Aug;184(16):4582-93.

44.

Transcriptional regulation in constraints-based metabolic models of Escherichia coli.

Covert MW, Palsson BØ.

J Biol Chem. 2002 Aug 2;277(31):28058-64. Epub 2002 May 10.

45.

Regulation of gene expression in flux balance models of metabolism.

Covert MW, Schilling CH, Palsson B.

J Theor Biol. 2001 Nov 7;213(1):73-88.

PMID:
11708855
46.

Metabolic modeling of microbial strains in silico.

Covert MW, Schilling CH, Famili I, Edwards JS, Goryanin II, Selkov E, Palsson BO.

Trends Biochem Sci. 2001 Mar;26(3):179-86. Review.

PMID:
11246024

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