Publications

*These authors contributed equally.

2014

J.K. Srimani*, G. Yao*, J. Neu, Y. Tanouchi, T.J. Lee, and L. You. Linear Population Allocation by Bistable Switches in Response to Transient Stimulation. PLoS ONE 9(8) (2014).

C. Tan, R.P. Smith, M.-C. Tsai, Russell Schwartz, and L. You. Phenotypic Signatures Arising from Unbalanced Bacterial Growth. PLoS Computational Biology 10:8 (2014).

A.J. Lee and L. You. Cells Listen to Their Inner Voice. Science 343:624 (2014).

R.P. Smith, C.M. Tan, J.K. Srimani, A. Pai, K.A. Riccione, H. Song, and L. You. Programmed Allee Effect in bacteria causes a tradeoff between population spread and survival. PNAS (2014). (Faculty of 1000 Recommended)

2013

S. Payne, B. Li, Y, Cao, D. Schaeffer, M.D. Ryser, and L. You. Temporal control of self-organized pattern formation without morphogen gradients in bacteria. Molecular Systems Biology. (2013).

S. Payne and L. You.Engineered Cell-Cell Communication and its applications. Adv Biochem Eng Biotechnol. (2013).

I. Shats, M.L. Gatza, B. Liu, S.P. Angus, L. You, and J.R. Nevins.FOXO Transcription Factors Control E2F1 Transcriptional Specificity and Apoptotic Function. Cancer Res 73(19):6056-6067 (2013).(Faculty of 1000 Recommended)

Y. Zhang, Y.P. Ho, Y.L. Chiu, H.F. Chan, B. Chlebina, T. Schumann, L. You, and K.W. Leong.A programmable microenvironment for cellular studies via microfluidics-generated double emulsions. Biomaterials34(19):4564-4572 (2013)

B.Li and L. You.Predictive Power of Cell-to-Cell Variability. Quantitative Biology1(2):131-139 (2013).

A. Pai, J.K. Srimani, Y. Tanouchi, and L. You. A Generic Metric to Quantify Quorum Sensing Activation Dynamics. ACS Synthetic Biology (2013).

Y. Tanouchi, A. J. Lee, H. Meredith, and L. You. Programmed cell death in bacteria and implications for antibiotic therapy. Trends in Microbiol. 21:6 (2013).

2012

Y. Tanouchi, A. Pai, N.E. Buchler, and L. You. Programming stress-induced altruistic death in engineered bacteria . Molecular Systems Biology 8:626 (2012).

A. Pai, Y. Tanouchi, and L. You. Optimality and Robustness in quorum sensing (QS)-mediated regulation of a costly public good enzyme. PNAS (2012).

C. Tan*, R. P. Smith*, J. K. Srimani, K. A. Riccione, S. Prasada, M. Kuehn, and L. You. The inoculum effect and band-pass bacterial response to periodic antibiotic treatment. Molecular Systems Biology 8:617 (2012).

K. A. Riccione*, R. P. Smith*, A. J. Lee, and L. You. A Synthetic Biology Approach to Understanding Cellular Information Processing. ACS Synthetic Biology 1:389-402 (2012).

Y. Tanouchi, R. P. Smith, and L. You. Engineering microbial systems to explore ecological and evolutionary dynamics. Curr. Opin. Biotech. 23:5 (2012).

J. V. Wong, B. Li, and L. You. Tension and Robustness in Multitasking Cellular Networks. PLoS Computational Biology 8:4 (2012).

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2011

F. V. Bonassi, L. You, and M. West. Bayesian Learning from Marginal Data in Bionetwork Models. Statistical Applications in Genetics and Molecular Biology 10:1 (2011).

J. V. Wong, P. Dong, J. R. Nevins, B. Mathey-Prevot, and L. You. Network Calisthenics: Control of E2F dynamics in cell cycle entry. Cell Cycle 10:18 (2011).

G. Yao, C. Tan, M. West, J. R. Nevins, and L. You. Origin of bistability underlying mammalian cell cycle entry. Molecular Systems Biology 7:485 (2011).

N. Elliott, T. J. Lee, L. You, and Fan Yuan. Proliferation Behavior of E. coli in a Three-Dimensional In-Vitro Tumor Model. Intgr. Biol. 3:6 (2011).

M. Hallen, B. Li, Y. Tanouchi, C. Tan, M. West, and L. You. Computation of Steady-State Probability Distributions in Stochastic Models of Cellular Networks. PLoS Computational Biology 7:10 (2011).

J. V. Wong, G. Yao, J. R. Nevins, and L. You. Viral-mediated noisy gene expression reveals biphasic E2f1 response to MYC. Mol. Cell. 41:3 (2011).

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2010

P. Marguet, Y. Tanouchi, E. Spitz, C. Smith, and L. You. Oscillations by Minimal Bacterial Suicide Cirucits Reveal Hidden Facets of Host-Circuit Physiology. PLoS One 5:7 (2010).

Q. Wang, J. Niemi, C. Tan, L. You, and M. West. Image segmentation and dynamic lineage analysis in single-cell flourescence microscopy. Cytometry A 77:1 (2010).

T. J. Lee, G. Yao, D. C. Bennett, J. R. Nevins, and L. You. Stochastic E2F Activation and Reconciliation of Phenomenological Cell-Cycle Models. PLoS Biology 8:9 (2010).

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2009

C. Tan, P. Marguet, and L. You. Emergent bistability by a growth-modulating positive feedback circuit. Nat. Chem. Biol. 5:11 (2009).

A. Pai, Y. Tanouchi, C. H. Collins, and L. You. Engineering multicellular systems by cell-cell communication. Curr. Opin. Biotechnol. 20:4 (2009).

A. Pai, and L. You. Optimal tuning of bacterial sensing potential. Molecular Systems Biology 5:286 (2009).

H. Song, S. Payne, M. Gray, and L. You. Spatiotemporal modulation of biodiversity in a synthetic chemical-mediated ecosystem. Nat. Chem. Biol. 5:12 (2009).

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Previous

G. Yao, T. J. Lee, S. Mori, J. Nevins, and L. You. A bistable Rb-E2F switch underlies the restriction point. Nature Cell Biology 10:4 (2008).

K. Brenner, L. You, and F. H. Arnold. Engineering microbial consortia: a new frontier in synthetic biology. Trends in Biotechnology 26:9 (2008).

T. J. Lee, G. Yao, J. Nevins, and L. You. Sensing and Integration of Erk and PI3K Signals by Myc. PLoS Computational Biology 4:2 (2008).

Y. Tanouchi, D. Tu, J. Kim, and L. You. Noise Reduction by Diffusional Dissipation in a Minimal Quorum Sensing Motif. PLoS Computational Biology 4:8 (2008).

F. K. Balagadde, H. Song, J. Ozaki, C. H. Collins, M. Barnet, F. H. Arnold, S.R. Quake, and L. You. A syntehtic Eschichia coli predator-prey ecosystem. Molecular Systems Biology 4:187 (2008).

C. Smith, H. Song, and l. You. Signal discrimination by differential regulation of protein stability in quorum sensing. J. Mol. Biol. 382:5 (2008).

C. Tan, F. Reza, and L. You. Noise-limited frequency signal transmission in gene circuits. Biophysical J. Published online (2007)

C. Tan, H. Song, J. Niemi, and L. You. A synthetic biology challenge: making cells compute. Molecular BioSystems. 3:343 (2007).

P. Marguet, F. Balagadde, C. Tan, and L. You. Biology by design: reduction and synthesis of cellular components and behavior. J. Royal Society Interface. 4:607(2007)

H. Song and L. You. Evolving Sensitivity (Point of View). ACS Chemical Biology. In press (2006).

D. Tu, J. Lee, T. Ozdere, T. Lee, and L. You. Engineering gene circuits: foundations and applications. In Nanotechnology in Biology and Medicine Methods, Devices and Applications, Ed. T. Vo-Dinh. CRC Press. In press (2006)

T. Lee, C. M. Tan, D. Tu, and L. You. Modeling cellular networks. In Bioinformatics: An Engineering Case-Based Approach, Eds.  G. Alterovitz & M. Ramoni. In press (2006).

L. You and J. Yin. (2006). Evolutionary design on a budget: robustness and optimality of bacteriophage T7. IEE. Systems Biology. 153:46-52.

F. K. Balagadde *, L. You*, C. Hansen, F. H. Arnold and S. Quake. (2005). Long-term monitoring of bacteria undergoing programmed population control in a microchemostat, Science. 309: 137-140 (* contributed equally).

L. You, R. S. Cox III, R. Weiss, and F. H. Arnold. (2004). Programmed population control by cell-cell communication and regulated killing. Nature428: 868-871. Featured in ScienceNow (405:3).

L. You, (2004) Towards computational systems biology. Cell Biochemistry and Biophysics. 40: 167-184

L. You, A. Hoonlor, and J. Yin. (2003) Modeling biological systems using Dynetica – a simulator of dynamic networks. Bioinformatics. 19: 435-436.

R. Srivastava, L. You, J. Summers, and J. Yin. (2002) Stochastic versus deterministic modeling of intracellular viral kinetics. J. Theor. Biol. 218: 309-321.

L. You and J. Yin (2002). Dependence of epistasis on environment and mutation severity as revealed by in silico mutagenesis of phage T7. Genetics. 160: 1273-1281

L. You, P. F. Suthers, and J. Yin (2002). Effects of E. coli physiology on growth of phage T7 in vivo and in silico. J. Bacteriology. 184: 1888-1894. (Highlighted in Editors’ Choice of Science (2002), 296: 219)

L. You and J. Yin (2001). Simulating the growth of viruses. Proceedings of the Pacific Symposium on Biocomputing: 532-543.

L. You and J. Yin (2000). Patterns of regulation from mRNA and protein time-series Metabolic Engineering. 2: 210-217.

D. Endy, L. You, J. Yin, and I. J. Molineux (2000). Computation, prediction, and experimental tests of fitness for bacteriophage T7 mutants with permuted genomes. Proc. Nat. Acad. Sci. USA. 97: 5375-5380.

L. You and J. Yin (1999). Amplification and spread of viruses in a growing plaque. J. Theor. Biol. 200(4): 365-373.

L. You, Q. Liu, Y. Shi, C. X. Wang, M. Lahaye, and V. Tran (1997). The conformational study of b-D-GlcA-(1,4)-L-Rha in solution by NMR and molecular dynamics simulations. Chemical Physics. 224: 81-94.

 

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