Publications (feel free to contact me for PDF preprints or reprints)

 

2012

1.     H. Song and L. YouModeling spatiotemporal dynamics of bacterial populations. Methods in Molecular Biology (edited by Xuedong Liu and Meredith Betterton). In press

2.     J. W. Chin and L. You, A different life? (Editorial for a special issue on Synthetic Biology). Current Opinion in Chemical Biology. 2012 Aug;16(3-4):243-4. 

3.     J. V. Wong,  B. Li, and L. You, Tension and robustness in multitasking cellular networks.  PLoS Computation Biology. 2012;8(4):e1002491. Epub 2012 Apr 26.

4.     K. A. Riccione, R. P. Smith, A. J. Lee, and L. You,  A synthetic biology approach to understanding cellular information processing. ACS Synthetic Biology published online. DOI: 10.1021/sb300044r.

5.     Y. Tanouchi, R. P. Smith,  L. You. Engineering microbial systems to explore ecological and evolutionary dynamics. Current Opinion in Biotechnology. 2012 Feb 4 [Epub ahead of print].

6.     S. Payne, R. Smith, and L. YouQuantitative Analysis of the Spatiotemporal Dynamics of a Synthetic Predator-Prey Ecosystem. Methods in Molecular Biology (edited by Wilfried Weber and MartinFussenegger).  2012; 813:315-30.

2011

7.     F. V. BonassiL. You, and M. West (2011). Bayesian Learning from Marginal Data in Bionetwork Models. Statistical Applications in Genetics and Molecular Biology. 10 (1), Article 49. doi:10.2202/1544-6115.1684

8.     M. Hallen, B. Li, Y. Tanouchi, C. Tan, M. West, and L. You (2011). Computation of Steady-State Probability Distributions in Stochastic Models of Cellular Networks. PLoS Computational Biology7: e1002209. doi:10.1371/journal.pcbi.1002209

9.     J.V. Wong, P. Dong, J. R. Nevins, B. Mathey-PrevotL. You (2011). Network calisthenics: Control of E2F dynamics in cell cycle entry. Cell Cycle. 10: 3086-3094

10.  H. Song, S. Payne, C. Tan, and L. You (2011). Programming microbial population dynamics by engineered cell-cell communication. Biotechnology Journal. 6:837-849

11.  N. Elliott, T. Lee, L. You, and F. Yuan (2011). Proliferation behavior of E. coli in a three-dimensional in vitro tumor model. Integrative Biology3: 696-705

12.  J. V. Wong, G. Yao, J. R. Nevins, L. You (2011). Using noisy gene expression mediated by engineered adenovirus to probe signaling dynamics in mammalian cells. Methods in Enzymology (edited by Christopher Voigt). 497:221-37.

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

14.  J. V. Wong, G. Yao, J. R. Nevins, and L. You (2011). Viral-mediated noisy gene expression reveals biphasic E2F1 response to MYC. Molecular Cell. 41: 275-285.

15.  B. Li and L. You (2011). Synthetic Biology: Division of Logic Labor (News & Views). Nature. 469: 171-2

 

2010

16.  T. J. Lee, G. Yao, D. C. Bennett, J. R. Nevins, and L. You (2010). Stochastic E2F Activation and Reconciliation of Phenomenological Cell-Cycle Models. PLoS Biology 8(9): e1000488.

17.  P. Marguet, Y. Tanouchi, E. Spitz, C. Smith, and L. You (2010) Oscillations by Minimal Bacterial Suicide Circuits Reveal Hidden Facets of Host-Circuit Physiology. PLoS ONE. 5(7):e11909. PMID: 20689598

18.  Q. Wang, J Niemi, C. Tan, L. You and M. West (2010), Image segmentation and dynamic lineage analysis in single-cell fluorescence microscopy. Cytometry A. Published online. DOI:10.1002/cyto.a.20812

 

2009

19.  H. Song, S. Payne, M. Gray, and L. You (2009). Spatiotemporal modulation of biodiversity in a synthetic chemical-mediated ecosystem. Nature Chemical Biology. 5:929-935

20.  C. Tan, P. Marguet, and L. You (2009). Emergent bistability by a growth-modulating positive feedback circuit. Nature Chemical Biology. 5, 842 - 848. [News & Views: Slow growth leads to a switch]

21.  A. Pai, Y. Tanouchi, C. Collins, and L. You (2009). Engineering multicellular systems by cell-cell communication. Current Opinion in Biotechnology. DOI:10.1016/j.copbio.2009.08.006    

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

23.  Y. Tanouchi, A. Pai, and L. You (2009). Decoding biological principles using gene circuits . Molecular BioSystems. DOI: 10.1039/b901584c

24.  F. J. Isaacs, and L. You (2009). A brave new synthetic world (Meeting report). Genome Biology10:302

 

2008

25.  C. Smith, H. Song, and L. You (2008). Signal discrimination by differential regulation of protein stability in quorum sensing. J. Molecular Biology. 382(5):1290-7

26.  Y. Tanouchi, D. Tu, J. Kim, and L. You (2008). Noise reduction by diffusional dissipation in a minimal quorum sensing motif. PLoS Computational Biology. 4: e1000167. doi:10.1371/journal.pcbi.1000167

27.  K. Brenner, L. You, and F. H. Arnold (2008). Engineering microbial consortia: a new frontier for synthetic biology. Trends in Biotechnology. 26: 483-489

28.  F. Balagadde, H. Song, J. Ozaki, C. Collins, M. Barnet, F. H. Arnold, S. Quake, and L. You (2008). A synthetic Escherichia coli predator-prey ecosystem. Molecular Systems Biology.  4:187.  Faculty of 1000 Biology, Must Read. 

29.  G. Yao, T. Lee, S. Mori, J. Nevins#, and L. You# (2008). A bistable Rb-E2F switch underlies the restriction point. Nature Cell Biology. Published online. Faculty of 1000 Biology, Must Read. 

30.  T. Lee, G. Yao, J. Nevins, and L. You (2008).  Sensing and integration of Erk and PI3K signals by Myc. PLoS Computational Biology. 4(2): e1000013. doi:10.1371/journal.pcbi.1000013

31.  J. V. Wong, H. Song, and L. You (2008). A whole more than the sum of its synthetic parts (Point of View). ACS Chemical Biology. 3(1):27-9.

 

2007

32.  C. Tan, F. Reza, and L. You (2007). Noise-limited frequency signal transmission in gene circuits. Biophysical J. 93(11):3753-61.

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

34.  H. Song, C. Tan, and L. You (2007). Living computers (Perspective). Chemical Biology. Published online

35.  Reza F, Chandran K, Feltz M, Heinz A, Josephs E, OBrien P, Dyke B, Chung H, Indurkhya S, lakhani N, Lee J, Lin S, Tang N, LaBean T, You L, Yuan F, and Tian J (2007). Engineering novel synthetic biological systems, IET Synthetic Biology, vol. 1, pp. 48-52 .

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

37.  D. Tu, J. Lee, T. Ozdere, T. Lee, and L. You (2007)Engineering gene circuits: foundations and applications. In Nanotechnology in Biology and Medicine Methods, Devices and Applications, Ed. T. Vo-Dinh. CRC Press. Chapter 21.

38.  T. Lee, C. M. Tan, D. Tu, and L. You (2007). Modeling cellular networks. In Bioinformatics: An Engineering Case-Based Approach, Eds.  G. Alterovitz & M. Ramoni. Chapter 6.

 

2006

39.  H. Song and L. You (2006)Evolving Sensitivity (Point of View). ACS Chemical Biology. 1:681.

40.  L. You and J. Yin. (2006). Evolutionary design on a budget: robustness and optimality of bacteriophage T7. IEE. Systems Biology153:46-52.

 

2005

41.  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 microchemostatScience. 309: 137-140 (* contributed equally).  Faculty of 1000 Biology, Recommended.

 

2004 and before

42.  L. You, R. S. Cox III, R. Weiss, and F. H. Arnold. (2004). Programmed population control by cell-cell communication and regulated killing. Nature.  428: 868-871. Featured in ScienceNow (405:3).

43.  L. You (2004). Towards computational systems biology. Cell Biochemistry and Biophysics40: 167-184

44.  L. You, A. Hoonlor, and J. Yin. (2003) Modeling biological systems using Dynetica: a simulator of dynamic networks. Bioinformatics19: 435-436. 

45.  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

46.  L. You, P. F. Suthers, and J. Yin (2002). Effects of E. coli physiology on growth of phage T7 in vivo and in silicoJ. Bacteriology184: 1888-1894. (Highlighted in Editors Choice of Science (2002), 296: 219)

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

48.  L. You and J. Yin (2001). Simulating the growth of viruses. Proceedings of the Pacific Symposium on Biocomputing532-543.

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

50.  D. EndyL. 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.

51.  L. You and J. Yin (1999). Amplification and spread of viruses in a growing plaque. Journal of Theoretical Biology  200(4): 365-373.

52.  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.

st:l0 level1 lfo1;background: white'>46.  R. Srivastava, L. You, J. Summers, and J. Yin (2002). Stochastic versus deterministic modeling of intracellular viral kinetics. Journal of Theoretical Biology 218: 309-321.

47.  L. You and J. Yin (2001). Simulating the growth of viruses. Proceedings of the Pacific Symposium on Biocomputing532-543.

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

49.  D. EndyL. 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.

50.  L. You and J. Yin (1999). Amplification and spread of viruses in a growing plaque. Journal of Theoretical Biology  200(4): 365-373.

51.  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.