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Guo Y, Kowalczyk GJ, Lee REC. Label and quantify mRNA molecules in live cell experiments using SunRISER and dNEMO. STAR Protoc. 2022 Sep 16;3(3):101630. doi: 10.1016/j.xpro.2022.101630. eCollection 2022 Sep 16. PubMed PMID: 36035802; PubMed Central PMCID: PMC9405536.
Guo Y, Lee REC. Long-term imaging of individual mRNA molecules in living cells. Cell Rep Methods. 2022 Jun 20;2(6):100226. doi: 10.1016/j.crmeth.2022.100226. eCollection 2022 Jun 20. PubMed PMID: 35784652; PubMed Central PMCID: PMC9243547.
Cruz JA, Mokashi CS, Kowalczyk GJ, Guo Y, Zhang Q, Gupta S, Schipper DL, Smeal SW, Lee REC. A variable-gain stochastic pooling motif mediates information transfer from receptor assemblies into NF-κB. Sci Adv. 2021 Jul;7(30). doi: 10.1126/sciadv.abi9410. Print 2021 Jul. PubMed PMID: 34301608; PubMed Central PMCID: PMC8302133.
Kowalczyk GJ, Cruz JA, Guo Y, Zhang Q, Sauerwald N, Lee REC. dNEMO: a tool for quantification of mRNA and punctate structures in time-lapse images of single cells. Bioinformatics. 2021 May 5;37(5):677-683. doi: 10.1093/bioinformatics/btaa874. PubMed PMID: 33051642; PubMed Central PMCID: PMC8354270.
Gupta S, Lee REC, Faeder JR. Parallel Tempering with Lasso for model reduction in systems biology. PLoS Comput Biol. 2020 Mar;16(3):e1007669. doi: 10.1371/journal.pcbi.1007669. eCollection 2020 Mar. PubMed PMID: 32150537; PubMed Central PMCID: PMC7082068.
Han F, Konkalmatt P, Mokashi C, Kumar M, Zhang Y, Ko A, Farino ZJ, Asico LD, Xu G, Gildea J, Zheng X, Felder RA, Lee REC, Jose PA, Freyberg Z, Armando I. Dopamine D(2) receptor modulates Wnt expression and control of cell proliferation. Sci Rep. 2019 Nov 14;9(1):16861. doi: 10.1038/s41598-019-52528-4. PubMed PMID: 31727925; PubMed Central PMCID: PMC6856370.
Mokashi CS, Schipper DL, Qasaimeh MA, Lee REC. A System for Analog Control of Cell Culture Dynamics to Reveal Capabilities of Signaling Networks. iScience. 2019 Sep 27;19:586-596. doi: 10.1016/j.isci.2019.08.010. Epub 2019 Aug 8. PubMed PMID: 31446223; PubMed Central PMCID: PMC6713801.
Pabon NA, Zhang Q, Cruz JA, Schipper DL, Camacho CJ, Lee REC. A network-centric approach to drugging TNF-induced NF-κB signaling. Nat Commun. 2019 Feb 26;10(1):860. doi: 10.1038/s41467-019-08802-0. PubMed PMID: 30808860; PubMed Central PMCID: PMC6391473.
Singh M, Warita K, Warita T, Faeder JR, Lee REC, Sant S, Oltvai ZN. Shift from stochastic to spatially-ordered expression of serine-glycine synthesis enzymes in 3D microtumors. Sci Rep. 2018 Jun 20;8(1):9388. doi: 10.1038/s41598-018-27266-8. PubMed PMID: 29925909; PubMed Central PMCID: PMC6010463.
Gupta S, Hainsworth L, Hogg JS, Lee REC, Faeder JR. Evaluation of Parallel Tempering to Accelerate Bayesian Parameter Estimation in Systems Biology. Proc Euromicro Int Conf Parallel Distrib Netw Based Process. 2018 Mar;2018:690-697. doi: 10.1109/PDP2018.2018.00114. Epub 2018 Jun 7. PubMed PMID: 30175326; PubMed Central PMCID: PMC6116909.
Wong VC, Bass VL, Bullock ME, Chavali AK, Lee REC, Mothes W, Gaudet S, Miller-Jensen K. NF-κB-Chromatin Interactions Drive Diverse Phenotypes by Modulating Transcriptional Noise. Cell Rep. 2018 Jan 16;22(3):585-599. doi: 10.1016/j.celrep.2017.12.080. PubMed PMID: 29346759; PubMed Central PMCID: PMC5812697.
Gupta S, Czech J, Kuczewski R, Bartol TM, Sejnowski TJ, Lee RE, Faeder JR. Spatial Stochastic Modeling with MCell and CellBlender. In: Munsky B, Hlavacek WS, Tsimring LS, editors. Quantitative Biology: Theory, Computational Methods, and Models Cambridge, MA: MIT Press; 2018. Chapter 24; p.485-511.
Zhang Q, Gupta S, Schipper DL, Kowalczyk GJ, Mancini AE, Faeder JR, Lee REC. NF-κB Dynamics Discriminate between TNF Doses in Single Cells. Cell Syst. 2017 Dec 27;5(6):638-645.e5. doi: 10.1016/j.cels.2017.10.011. Epub 2017 Nov 8. PubMed PMID: 29128333; PubMed Central PMCID: PMC5746429.
Morel PA, Lee REC, Faeder JR. Demystifying the cytokine network: Mathematical models point the way. Cytokine. 2017 Oct;98:115-123. doi: 10.1016/j.cyto.2016.11.013. Epub 2016 Dec 3. Review. PubMed PMID: 27919524; PubMed Central PMCID: PMC5457394.
Lee RE, Qasaimeh MA, Xia X, Juncker D, Gaudet S. NF-κB signalling and cell fate decisions in response to a short pulse of tumour necrosis factor. Sci Rep. 2016 Dec 22;6:39519. doi: 10.1038/srep39519. PubMed PMID: 28004761; PubMed Central PMCID: PMC5177917.
Xing J, Lee RE. Putting it all on pigmentation: Heuristics of a bold and stochastic cell fate decision. Sci Signal. 2015 Oct 6;8(397):fs17. doi: 10.1126/scisignal.aad2816. PubMed PMID: 26443702.
Xia X, Owen MS, Lee RE, Gaudet S. Cell-to-cell variability in cell death: can systems biology help us make sense of it all?. Cell Death Dis. 2014 May 29;5(5):e1261. doi: 10.1038/cddis.2014.199. Review. PubMed PMID: 24874733; PubMed Central PMCID: PMC4047886.
Lee RE, Walker SR, Savery K, Frank DA, Gaudet S. Fold change of nuclear NF-κB determines TNF-induced transcription in single cells. Mol Cell. 2014 Mar 20;53(6):867-79. doi: 10.1016/j.molcel.2014.01.026. Epub 2014 Feb 13. PubMed PMID: 24530305; PubMed Central PMCID: PMC3977799.
Shrestha A, Lee RE, Megeney LA. Monitoring the proteostasis function of the Saccharomyces cerevisiae metacaspase Yca1. Methods Mol Biol. 2014;1133:223-35. doi: 10.1007/978-1-4939-0357-3_14. PubMed PMID: 24567105.
Knight JD, Tian R, Lee RE, Wang F, Beauvais A, Zou H, Megeney LA, Gingras AC, Pawson T, Figeys D, Kothary R. A novel whole-cell lysate kinase assay identifies substrates of the p38 MAPK in differentiating myoblasts. Skelet Muscle. 2012 Mar 6;2:5. doi: 10.1186/2044-5040-2-5. PubMed PMID: 22394512; PubMed Central PMCID: PMC3350448.
Lee RE, Brunette S, Puente LG, Megeney LA. Metacaspase Yca1 is required for clearance of insoluble protein aggregates. Proc Natl Acad Sci U S A. 2010 Jul 27;107(30):13348-53. doi: 10.1073/pnas.1006610107. Epub 2010 Jul 12. PubMed PMID: 20624963; PubMed Central PMCID: PMC2922170.
Puente LG, Lee RE, Megeney LA. Reconstructing regulatory kinase pathways from phosphopeptide data: a bioinformatics approach. Methods Mol Biol. 2009;527:311-9, x. doi: 10.1007/978-1-60327-834-8_23. Review. PubMed PMID: 19241023.
Lee RE, Puente LG, Kaern M, Megeney LA. A non-death role of the yeast metacaspase: Yca1p alters cell cycle dynamics. PLoS One. 2008 Aug 13;3(8):e2956. doi: 10.1371/journal.pone.0002956. PubMed PMID: 18698411; PubMed Central PMCID: PMC2493032.
Puente LG, Voisin S, Lee RE, Megeney LA. Reconstructing the regulatory kinase pathways of myogenesis from phosphopeptide data. Mol Cell Proteomics. 2006 Dec;5(12):2244-51. doi: 10.1074/mcp.M600134-MCP200. Epub 2006 Sep 13. PubMed PMID: 16971385.
Lee RE, Megeney LA. The yeast kinome displays scale free topology with functional hub clusters. BMC Bioinformatics. 2005 Nov 9;6:271. doi: 10.1186/1471-2105-6-271. PubMed PMID: 16283924; PubMed Central PMCID: PMC1310538.
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