Markus Willard Covert - Publications

Affiliations: 
2003 University of California, San Diego, La Jolla, CA 

50 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 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, ... ... Covert MW, et al. Simultaneous cross-evaluation of heterogeneous datasets via mechanistic simulation. Science (New York, N.Y.). 369. PMID 32703847 DOI: 10.1126/science.aav3751  0.68
2020 Bodner K, Melkonian AL, Barth AIM, Kudo T, Tanouchi Y, Covert MW. Engineered Fluorescent E. coli Lysogens Allow Live-Cell Imaging of Functional Prophage Induction Triggered inside Macrophages. Cell Systems. PMID 32191875 DOI: 10.1016/j.cels.2020.02.006  0.56
2019 DeFelice MM, Clark HR, Hughey JJ, Maayan I, Kudo T, Gutschow MV, Covert MW, Regot S. NF-κB signaling dynamics is controlled by a dose-sensing autoregulatory loop. Science Signaling. 12. PMID 31040261 DOI: 10.1126/scisignal.aau3568  0.68
2019 Jeknić S, Kudo T, Covert MW. Techniques for Studying Decoding of Single Cell Dynamics. Frontiers in Immunology. 10: 755. PMID 31031756 DOI: 10.3389/fimmu.2019.00755  0.56
2019 Lane K, Andres-Terre M, Kudo T, Monack DM, Covert MW. Escalating Threat Levels of Bacterial Infection Can Be Discriminated by Distinct MAPK and NF-κB Signaling Dynamics in Single Host Cells. Cell Systems. PMID 30904375 DOI: 10.1016/j.cels.2019.02.008  0.56
2018 Gutschow MV, Mason JC, Lane KM, Maayan I, Hughey JJ, Bajar BT, Amatya DN, Valle SD, Covert MW. Combinatorial processing of bacterial and host-derived innate immune stimuli at the single-cell level. Molecular Biology of the Cell. mbcE18070423. PMID 30462580 DOI: 10.1091/mbc.E18-07-0423  0.68
2018 Kudo T, Jeknić S, Macklin DN, Akhter S, Hughey JJ, Regot S, Covert MW. Live-cell measurements of kinase activity in single cells using translocation reporters. Nature Protocols. 13: 155-169. PMID 29266096 DOI: 10.1038/nprot.2017.128  0.68
2017 Lane K, Van Valen D, DeFelice MM, Macklin DN, Kudo T, Jaimovich A, Carr A, Meyer T, Pe'er D, Boutet SC, Covert MW. Measuring Signaling and RNA-Seq in the Same Cell Links Gene Expression to Dynamic Patterns of NF-κB Activation. Cell Systems. PMID 28396000 DOI: 10.1016/j.cels.2017.03.010  0.68
2016 Van Valen DA, Kudo T, Lane KM, Macklin DN, Quach NT, DeFelice MM, Maayan I, Tanouchi Y, Ashley EA, Covert MW. Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments. Plos Computational Biology. 12: e1005177. PMID 27814364 DOI: 10.1371/journal.pcbi.1005177  0.68
2016 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. High-resolution imaging and computational analysis of haematopoietic cell dynamics in vivo. Nature Communications. 7: 12169. PMID 27425143 DOI: 10.1038/ncomms12169  1
2015 Carrera J, Covert MW. Why Build Whole-Cell Models? Trends in Cell Biology. PMID 26471224 DOI: 10.1016/j.tcb.2015.09.004  1
2015 Karr JR, Williams AH, Zucker JD, Raue A, Steiert B, Timmer J, Kreutz C, Wilkinson S, Allgood BA, Bot BM, Hoff BR, Kellen MR, Covert MW, Stolovitzky GA, et al. Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models. Plos Computational Biology. 11: e1004096. PMID 26020786 DOI: 10.1371/journal.pcbi.1004096  1
2015 Karr JR, Guturu H, Chen EY, Blair SL, Irish JM, Kotecha N, Covert MW. NetworkPainter: dynamic intracellular pathway animation in Cytobank. Bmc Bioinformatics. 16: 172. PMID 26003204 DOI: 10.1186/s12859-015-0602-4  1
2015 Hughey JJ, Gutschow MV, Bajar BT, Covert MW. Single-cell variation leads to population invariance in NF-κB signaling dynamics. Molecular Biology of the Cell. 26: 583-90. PMID 25473117 DOI: 10.1091/mbc.E14-08-1267  1
2014 Karr JR, Phillips NC, Covert MW. WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions. Database : the Journal of Biological Databases and Curation. 2014. PMID 25231498 DOI: 10.1093/database/bau095  1
2014 Bird SW, Maynard ND, Covert MW, Kirkegaard K. Nonlytic viral spread enhanced by autophagy components. Proceedings of the National Academy of Sciences of the United States of America. 111: 13081-6. PMID 25157142 DOI: 10.1073/pnas.1401437111  0.64
2014 Regot S, Hughey JJ, Bajar BT, Carrasco S, Covert MW. High-sensitivity measurements of multiple kinase activities in live single cells. Cell. 157: 1724-34. PMID 24949979 DOI: 10.1016/j.cell.2014.04.039  1
2014 Covert MW. Simulating a living cell. Scientific American. 310: 44-51. PMID 24616970 DOI: 10.1038/scientificamerican0114-44  1
2014 Macklin DN, Ruggero NA, Covert MW. The future of whole-cell modeling. Current Opinion in Biotechnology. 28: 111-5. PMID 24556244 DOI: 10.1016/j.copbio.2014.01.012  1
2014 Birch EW, Udell M, Covert MW. Incorporation of flexible objectives and time-linked simulation with flux balance analysis. Journal of Theoretical Biology. 345: 12-21. PMID 24361328 DOI: 10.1016/j.jtbi.2013.12.009  1
2014 Bird SW, Maynard ND, Covert MW, Kirkegaard K. Nonlytic viral spread enhanced by autophagy components Proceedings of the National Academy of Sciences of the United States of America. 111: 13081-13086. DOI: 10.1073/pnas.1401437111  1
2013 Sanghvi JC, Regot S, Carrasco S, Karr JR, Gutschow MV, Bolival B, Covert MW. Accelerated discovery via a whole-cell model. Nature Methods. 10: 1192-5. PMID 24185838 DOI: 10.1038/nmeth.2724  1
2013 Lee R, Karr JR, Covert MW. WholeCellViz: data visualization for whole-cell models. Bmc Bioinformatics. 14: 253. PMID 23964998 DOI: 10.1186/1471-2105-14-253  1
2013 Purcell O, Jain B, Karr JR, Covert MW, Lu TK. Towards a whole-cell modeling approach for synthetic biology. Chaos (Woodbury, N.Y.). 23: 025112. PMID 23822510 DOI: 10.1063/1.4811182  1
2013 Gutschow MV, Hughey JJ, Ruggero NA, Bajar BT, Valle SD, Covert MW. Single-cell and population NF-κB dynamic responses depend on lipopolysaccharide preparation. Plos One. 8: e53222. PMID 23301045 DOI: 10.1371/journal.pone.0053222  1
2013 Karr JR, Sanghvi JC, Macklin DN, Arora A, Covert MW. WholeCellKB: model organism databases for comprehensive whole-cell models. Nucleic Acids Research. 41: D787-92. PMID 23175606 DOI: 10.1093/nar/gks1108  1
2012 Birch EW, Ruggero NA, Covert MW. Determining host metabolic limitations on viral replication via integrated modeling and experimental perturbation. Plos Computational Biology. 8: e1002746. PMID 23093930 DOI: 10.1371/journal.pcbi.1002746  1
2012 Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM, Bolival B, Assad-Garcia N, Glass JI, Covert MW. A whole-cell computational model predicts phenotype from genotype. Cell. 150: 389-401. PMID 22817898 DOI: 10.1016/j.cell.2012.05.044  1
2012 Maynard ND, Macklin DN, Kirkegaard K, Covert MW. Competing pathways control host resistance to virus via tRNA modification and programmed ribosomal frameshifting. Molecular Systems Biology. 8: 567. PMID 22294093 DOI: 10.1038/msb.2011.101  1
2010 Lee TK, Covert MW. High-throughput, single-cell NF-κB dynamics. Current Opinion in Genetics & Development. 20: 677-83. PMID 20846851 DOI: 10.1016/j.gde.2010.08.005  1
2010 Hughey JJ, Lee TK, Covert MW. Computational modeling of mammalian signaling networks. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 2: 194-209. PMID 20836022 DOI: 10.1002/wsbm.52  1
2010 Maynard ND, Gutschow MV, Birch EW, Covert MW. The virus as metabolic engineer. Biotechnology Journal. 5: 686-94. PMID 20665642 DOI: 10.1002/biot.201000080  1
2010 Maynard ND, Birch EW, Sanghvi JC, Chen L, Gutschow MV, Covert MW. A forward-genetic screen and dynamic analysis of lambda phage host-dependencies reveals an extensive interaction network and a new anti-viral strategy. Plos Genetics. 6: e1001017. PMID 20628568 DOI: 10.1371/journal.pgen.1001017  1
2010 Tay S, Hughey JJ, Lee TK, Lipniacki T, Quake SR, Covert MW. Single-cell NF-B dynamics reveal digital activation and analogue information processing Nature. 466: 267-271. PMID 20581820 DOI: 10.1038/nature09145  1
2009 Terzer M, Maynard ND, Covert MW, Stelling J. Genome-scale metabolic networks. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 1: 285-97. PMID 20835998 DOI: 10.1002/wsbm.37  1
2009 Lee TK, Denny EM, Sanghvi JC, Gaston JE, Maynard ND, Hughey JJ, Covert MW. A noisy paracrine signal determines the cellular NF-kappaB response to lipopolysaccharide. Science Signaling. 2: ra65. PMID 19843957 DOI: 10.1126/scisignal.2000599  1
2009 Seok J, Xiao W, Moldawer LL, Davis RW, Covert MW. A dynamic network of transcription in LPS-treated human subjects. Bmc Systems Biology. 3: 78. PMID 19638230 DOI: 10.1186/1752-0509-3-78  1
2008 Covert MW, Xiao N, Chen TJ, Karr JR. Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli. Bioinformatics (Oxford, England). 24: 2044-50. PMID 18621757 DOI: 10.1093/bioinformatics/btn352  1
2006 Covert MW. Integrated regulatory and metabolic models Computational Systems Biology. 191-204. DOI: 10.1016/B978-012088786-6/50029-0  1
2005 Covert MW, Leung TH, Gaston JE, Baltimore D. Achieving stability of lipopolysaccharide-induced NF-kappaB activation. Science (New York, N.Y.). 309: 1854-7. PMID 16166516 DOI: 10.1126/science.1112304  1
2004 Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO. Integrating high-throughput and computational data elucidates bacterial networks. Nature. 429: 92-6. PMID 15129285 DOI: 10.1038/nature02456  1
2004 Herrgård MJ, Covert MW, Palsson BØ. Reconstruction of microbial transcriptional regulatory networks. Current Opinion in Biotechnology. 15: 70-7. PMID 15102470 DOI: 10.1016/j.copbio.2003.11.002  1
2003 Covert MW, Famili I, Palsson BO. Identifying constraints that govern cell behavior: a key to converting conceptual to computational models in biology? Biotechnology and Bioengineering. 84: 763-72. PMID 14708117 DOI: 10.1002/bit.10849  1
2003 Herrgård MJ, Covert MW, Palsson BØ. Reconciling gene expression data with known genome-scale regulatory network structures. Genome Research. 13: 2423-34. PMID 14559784 DOI: 10.1101/gr.1330003  1
2003 Covert MW, Palsson BO. Constraints-based models: regulation of gene expression reduces the steady-state solution space. Journal of Theoretical Biology. 221: 309-25. PMID 12642111 DOI: 10.1006/jtbi.2003.3071  1
2002 Schilling CH, Covert MW, Famili I, Church GM, Edwards JS, Palsson BO. Genome-scale metabolic model of Helicobacter pylori 26695. Journal of Bacteriology. 184: 4582-93. PMID 12142428 DOI: 10.1128/JB.184.16.4582-4593.2002  1
2002 Covert MW, Palsson BØ. Transcriptional regulation in constraints-based metabolic models of Escherichia coli. The Journal of Biological Chemistry. 277: 28058-64. PMID 12006566 DOI: 10.1074/jbc.M201691200  1
2002 Edwards JS, Covert M, Palsson B. Metabolic modelling of microbes: the flux-balance approach. Environmental Microbiology. 4: 133-40. PMID 12000313 DOI: 10.1046/j.1462-2920.2002.00282.x  1
2001 Covert MW, Schilling CH, Palsson B. Regulation of gene expression in flux balance models of metabolism. Journal of Theoretical Biology. 213: 73-88. PMID 11708855 DOI: 10.1006/jtbi.2001.2405  1
2001 Covert MW, Schilling CH, Famili I, Edwards JS, Goryanin II, Selkov E, Palsson BO. Metabolic modeling of microbial strains in silico. Trends in Biochemical Sciences. 26: 179-86. PMID 11246024 DOI: 10.1016/S0968-0004(00)01754-0  1
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