2025<\/p>\n
Time-varying stimuli that prolong IKK\u00a0<\/span>activation promote nuclear remodeling and\u00a0<\/span>mechanistic switching of NF-<\/span>\u03ba<\/span>B dynamics<\/span><\/a> NEMO recruitment at single cytokine-receptor complexes shows quantized dynamics independent of ligand affinity<\/a> 2024<\/p>\n Ubiquitin: Not just a one-way ticket to the proteasome, but a therapeutic dial to fine-tune the molecular landscape of disease<\/a> 2022<\/p>\n Label and quantify mRNA molecules in live cell experiments using SunRISER and dNEMO<\/a> Long-term imaging of individual mRNA molecules in living cells<\/a> 2021<\/p>\n A variable-gain stochastic pooling motif mediates information transfer from receptor assemblies into NF-\u03baB<\/a> dNEMO: a tool for quantification of mRNA and punctate structures in time-lapse images of single cells<\/a> 2020<\/p>\n SunRISE: long-term imaging of individual mRNA molecules in living cells<\/a> Parallel Tempering with Lasso for Model Reduction in Systems Biology<\/a> 2019<\/p>\n A system for analog control of cell culture dynamics to reveal capabilities of signaling networks<\/a> Dopamine D2 receptor modulates Wnt expression and control of cell proliferation<\/a> A network-centric approach to drugging TNF-induced NF-kB signaling<\/a> 2018<\/p>\n Shift from stochastic to spatially-ordered expression of serine-glycine synthesis enzymes in 3D microtumors<\/a> Evaluation of Parallel Tempering to Accelerate Bayesian Parameter Estimation in Systems Biology<\/a> Spatial Stochastic Modeling with MCell and CellBlender<\/a> NF-\u03baB-Chromatin Interactions Drive Diverse Phenotypes by Modulating Transcriptional Noise<\/a> 2017<\/p>\n NF-\u03baB Dynamics Discriminate between TNF Doses in Single Cells<\/a> Demystifying the cytokine network: Mathematical models point the way<\/a> 2016<\/p>\n NF-\u03baB signalling and cell fate decisions in response to a short pulse of tumour necrosis factor<\/a> 2015<\/p>\n Putting it all on pigmentation: Heuristics of a bold and stochastic cell fate decision<\/a> 2014<\/p>\n Fold Change of Nuclear NF-\u03baB Determines TNF-Induced Transcription in Single Cells<\/a> Cell-to-cell variability in cell death: can systems biology help us make sense of it all?<\/a> Monitoring the Proteostasis Function of the Saccharomyces cerevisiae Metacaspase Yca1<\/a> 2013<\/p>\n A novel whole-cell lysate kinase assay identifies substrates of the p38 MAPK in differentiating myoblasts<\/a> 2010<\/p>\n Metacaspase Yca1 is required for clearance of insoluble protein aggregates<\/a> 2009<\/p>\n Reconstructing regulatory kinase pathways from phosphopeptide data: a bioinformatics approach<\/a> 2008<\/p>\n A non-death role of the yeast metacaspase: Yca1p alters cell cycle dynamics<\/a> 2006<\/p>\n Reconstructing the regulatory kinase pathways of myogenesis from phosphopeptide data<\/a> 2005<\/p>\n
SW Smeal, CM Mokashi, AH Kim, PM Chiknas, REC Lee
Nature Communications<\/p>\n
AH Kim, B Krummenacher, J Yeung, DR Koes, REC Lee
Cell Reports<\/p>\n
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AH Kim’,\u00a0<\/span><\/span>PM Chiknas’,\u00a0<\/span><\/span>REC Lee
<\/span>Clinical and Translational Medicine<\/p>\n
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Y Guo’, GJ Kowalczyk’, REC Lee
STAR Protocols<\/p>\n
Y Guo, REC Lee
Cell Reports Methods<\/p>\n
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JA Cruz’, CS Mokashi’, GJ Kowalczyk, Y Guo, Q Zhang, S Gupta, DL Schippper, REC Lee
Science Advances<\/p>\n
GJ Kowalczyk, JA Cruz, Y Guo, Q Zhang, N Sauerwald, REC Lee
Bioinformatics<\/p>\n
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Y Guo, REC Lee
bioRxiv<\/p>\n
S Gupta, REC Lee*, JR Faeder*
PLoS Computational Biology (* co-corresponding)<\/p>\n
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CS Mokashi, DL Schippper, MA Qasaimeh, REC Lee
iScience<\/p>\n
F Han, P Konkalmatt, CS Mokashi, M Kumar, Y Zhang, A Ko, Z Farino, L Asico, G Xu, J Gildea, X Zheng, R Felder, REC Lee, PA Jose, I Armando*, Z Freyberg*
Scientific Reports<\/p>\n
NA Pabon, Q Zhang, JA Cruz, DL Schipper, CJ Camacho*, REC Lee*
Nature Communications (* co-corresponding); recommended by F1000<\/a><\/p>\n
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M Singh, K Warita, T Warita, JR Faeder, REC Lee*, S Sant*, ZN Oltvai*
Scientific Reports (* co-corresponding)<\/p>\n
S Gupta*, L Hainsworth, JS Hogg, REC Lee*, JR Faeder*
IEEE, 26th Euromicro International Conference on Parallel, Distributed and Network-based Processing (PDP) (* co-corresponding)<\/p>\n
S Gupta, J Czech, R Kuczewski, TM Bartol, TJ Sejnowski, REC Lee, JR Faeder
Quantitative Biology: theory, computational methods, and models (Ed. Brian Munsky, MIT Press)<\/p>\n
VC Wong, VL Bass, ME Bullock, AK Chavali, REC Lee, W Mothes, S Gaudet, K Miller-Jensen
Cell Reports<\/p>\n
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Q Zhang, S Gupta, DL Schipper, GJ Kowalczyk, AE Mancini, JR Faeder, REC Lee
Cell Systems<\/p>\n
PA Morel, REC Lee, JR Faeder
Cytokine<\/p>\n
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REC Lee, MA Qasaimeh, X Xia, D Juncker, S Gaudet
Scientific Reports<\/p>\n
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J Xing*\u00a0and\u00a0REC Lee*
Science Signaling (* co-corresponding)<\/p>\n
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REC Lee, SR Walker, K Savery, DA Frank, S Gaudet
Molecular cell<\/p>\n
X Xia, MS Owen, REC Lee, S Gaudet
Cell death & disease<\/p>\n
A Shrestha, REC Lee, LA Megeney
Caspases, Paracaspases, and Metacaspases<\/p>\n
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JDR Knight, R Tian, REC Lee, F Wang, A Beauvais, H Zou, LA Megeney, AC Gingras, T Pawson, D Figeys, R Kothary
Skeletal Muscle<\/p>\n
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REC Lee, S Brunette, LG Puente, LA Megeney
Proceedings of the National Academy of Sciences<\/p>\n
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LG Puente, REC Lee, LA Megeney
Phospho-Proteomics<\/p>\n
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REC Lee, LG Puente, M K\u00e6rn, LA Megeney
PLoS One<\/p>\n
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LG Puente, S Voisin, REC Lee, LA Megeney
Molecular & Cellular Proteomics<\/p>\n
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