2022
Label and quantify mRNA molecules in live cell experiments using SunRISER and dNEMO
Y Guo’, GJ Kowalczyk’, REC Lee
STAR Protocols
Long-term imaging of individual mRNA molecules in living cells
Y Guo, REC Lee
Cell Reports Methods
2021
A variable-gain stochastic pooling motif mediates information transfer from receptor assemblies into NF-κB
JA Cruz’, CS Mokashi’, GJ Kowalczyk, Y Guo, Q Zhang, S Gupta, DL Schippper, REC Lee
Science Advances
dNEMO: a tool for quantification of mRNA and punctate structures in time-lapse images of single cells
GJ Kowalczyk, JA Cruz, Y Guo, Q Zhang, N Sauerwald, REC Lee
Bioinformatics
2020
SunRISE: long-term imaging of individual mRNA molecules in living cells
Y Guo, REC Lee
bioRxiv
Parallel Tempering with Lasso for Model Reduction in Systems Biology
S Gupta, REC Lee*, JR Faeder*
PLoS Computational Biology (* co-corresponding)
2019
A system for analog control of cell culture dynamics to reveal capabilities of signaling networks
CS Mokashi, DL Schippper, MA Qasaimeh, REC Lee
iScience
Dopamine D2 receptor modulates Wnt expression and control of cell proliferation
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
A network-centric approach to drugging TNF-induced NF-kB signaling
NA Pabon, Q Zhang, JA Cruz, DL Schipper, CJ Camacho*, REC Lee*
Nature Communications (* co-corresponding); recommended by F1000
2018
Shift from stochastic to spatially-ordered expression of serine-glycine synthesis enzymes in 3D microtumors
M Singh, K Warita, T Warita, JR Faeder, REC Lee*, S Sant*, ZN Oltvai*
Scientific Reports (* co-corresponding)
Evaluation of Parallel Tempering to Accelerate Bayesian Parameter Estimation in Systems Biology
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)
Spatial Stochastic Modeling with MCell and CellBlender
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)
NF-κB-Chromatin Interactions Drive Diverse Phenotypes by Modulating Transcriptional Noise
VC Wong, VL Bass, ME Bullock, AK Chavali, REC Lee, W Mothes, S Gaudet, K Miller-Jensen
Cell Reports
2017
NF-κB Dynamics Discriminate between TNF Doses in Single Cells
Q Zhang, S Gupta, DL Schipper, GJ Kowalczyk, AE Mancini, JR Faeder, REC Lee
Cell Systems
Demystifying the cytokine network: Mathematical models point the way
PA Morel, REC Lee, JR Faeder
Cytokine
2016
NF-κB signalling and cell fate decisions in response to a short pulse of tumour necrosis factor
REC Lee, MA Qasaimeh, X Xia, D Juncker, S Gaudet
Scientific Reports
2015
Putting it all on pigmentation: Heuristics of a bold and stochastic cell fate decision
J Xing* and REC Lee*
Science Signaling (* co-corresponding)
2014
Fold Change of Nuclear NF-κB Determines TNF-Induced Transcription in Single Cells
REC Lee, SR Walker, K Savery, DA Frank, S Gaudet
Molecular cell
Cell-to-cell variability in cell death: can systems biology help us make sense of it all?
X Xia, MS Owen, REC Lee, S Gaudet
Cell death & disease
Monitoring the Proteostasis Function of the Saccharomyces cerevisiae Metacaspase Yca1
A Shrestha, REC Lee, LA Megeney
Caspases, Paracaspases, and Metacaspases
2013
A novel whole-cell lysate kinase assay identifies substrates of the p38 MAPK in differentiating myoblasts
JDR Knight, R Tian, REC Lee, F Wang, A Beauvais, H Zou, LA Megeney, AC Gingras, T Pawson, D Figeys, R Kothary
Skeletal Muscle
2010
Metacaspase Yca1 is required for clearance of insoluble protein aggregates
REC Lee, S Brunette, LG Puente, LA Megeney
Proceedings of the National Academy of Sciences
2009
Reconstructing regulatory kinase pathways from phosphopeptide data: a bioinformatics approach
LG Puente, REC Lee, LA Megeney
Phospho-Proteomics
2008
A non-death role of the yeast metacaspase: Yca1p alters cell cycle dynamics
REC Lee, LG Puente, M Kærn, LA Megeney
PLoS One
2006
Reconstructing the regulatory kinase pathways of myogenesis from phosphopeptide data
LG Puente, S Voisin, REC Lee, LA Megeney
Molecular & Cellular Proteomics
2005
The yeast kinome displays scale free topology with functional hub clusters
REC Lee, LA Megeney
BMC bioinformatics