Publications (feel free to contact me
for PDF preprints or reprints)
2012
1. H. Song and L. You. Modeling
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. You. Quantitative
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. Bonassi, L. 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
Biology, 7:
e1002209. doi:10.1371/journal.pcbi.1002209
9.
J.V.
Wong, P. Dong, J. R. Nevins, B. Mathey-Prevot, L. 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 Biology. 3: 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 Biology. 10:302
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.
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, OŐBrien 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.
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 Biology. 153:46-52.
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 microchemostat, Science. 309:
137-140 (* contributed equally). Faculty of 1000 Biology, Recommended.
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 Biophysics. 40: 167-184
44. L. You, A. Hoonlor, and J.
Yin. (2003) Modeling biological systems using Dynetica: a
simulator of dynamic networks. Bioinformatics. 19:
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 silico. J.
Bacteriology. 184: 1888-1894. (Highlighted in EditorŐs 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 Biocomputing: 532-543.
49. L. You and J. Yin (2000). Patterns of regulation
from mRNA and protein time-series. Metabolic Engineering. 2:
210-217.
50. 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.
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.