Publications (feel
free to contact me for PDF preprints or reprints)
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. 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). In
press.
2011
3. 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
4. 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
5. 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
6. H.
Song, S. Payne, C. Tan, and L. You (2011). Programming
microbial population dynamics by engineered cell-cell communication. Biotechnology
Journal. 6:837-849
7. 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
8. 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.
9. 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
10. 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.
11. B.
Li and L. You (2011). Synthetic Biology:
Division of Logic Labor (News & Views). Nature. 469:
171-2
2010
12. 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.
13. 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
14. 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
15. 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
16. 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]
17. 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
18. A. Pai and L.
You (2009). Optimal tuning of bacterial sensing potential. Molecular Systems Biology. 5:286.
19. Y. Tanouchi, A. Pai, and L. You (2009). Decoding
biological principles using gene circuits . Molecular BioSystems. DOI: 10.1039/b901584c
20. F. J. Isaacs, and L. You (2009). A brave new synthetic world (Meeting report). Genome
Biology. 10:302
2008
21. 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
22. 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
23. K.
Brenner, L. You, and F. H. Arnold (2008). Engineering
microbial consortia: a new frontier for synthetic biology. Trends in Biotechnology. 26: 483-489
24. 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.
25. 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.
26. 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
27. 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.
28. C. Tan, F. Reza,
and L. You (2007). Noise-limited
frequency signal transmission in gene circuits. Biophysical J. 93(11):3753-61.
29. C.
Tan, H. Song, J. Niemi, and L. You (2007). A synthetic
biology challenge: making cells compute. Molecular BioSystems. 3:343.
30. H. Song, C. Tan,
and L. You (2007). Living
computers (Perspective). Chemical Biology. Published
online
31. 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 .
32. 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
33. 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.
34. 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.
35. H.
Song and L. You (2006). Evolving Sensitivity (Point of View). ACS Chemical Biology. 1:681.
36. L. You and J. Yin.
(2006). Evolutionary design on a budget: robustness and optimality
of bacteriophage T7. IEE. Systems Biology. 153:46-52.
37. 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.
38. 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).
39. L. You (2004). Towards computational systems biology. Cell
Biochemistry and Biophysics. 40: 167-184
40. L. You, A. Hoonlor, and J.
Yin. (2003) Modeling biological systems using Dynetica: a
simulator of dynamic networks. Bioinformatics. 19: 435-436.
41. 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
42. 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)
43. 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.
44. L. You and J. Yin (2001). Simulating
the growth of viruses. Proceedings of the Pacific Symposium on
Biocomputing: 532-543.
45. L. You and J. Yin (2000). Patterns of regulation from mRNA and protein time-series. Metabolic
Engineering. 2: 210-217.
46. 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.
47. L. You and J. Yin (1999). Amplification
and spread of viruses in a growing plaque. Journal of Theoretical Biology 200(4):
365-373.
48. 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.