Publications, talks, and presentations

Publications (click on the title to get a PDF for each paper)

Peer reviewed articles

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. Hanson, F. H. Arnold and S. Quake. (2005). Long-term monitoring of bacteria undergoing programmed population control in a microchemostat, Science. In press(* 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. Nature.  Published online April 4th 2004. 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.

Ph.D. Thesis

Lingchong You (May 2002) The extension, application, and generalization of a phage T7 intracellular growth model. Department of Chemical Engineering. University of Wisconsin, Madison, WI.  Download [PDF]

Recent Invited Talks

1.      Programming bacterial dynamics by synthetic killer circuits. The First Duke Systems Biology Symposium, Durham, NC, September 2006.

2.      Modeling complex dynamic cellular networks. SAMSI workshop on “Development, Assessment, and Utilization of Complex Computer Models”, Durham, NC, September 2006

3.      Control of the mammalian cell cycle entry by a bistable switch. Workshop on "Exploring the Mechanisms and Landscapes of Cellular Networks". Telluride Science Research Center, CO, August 2006.

4.      Control of the mammalian cell cycle entry by a bistable switch. SIAM Life Sciences Symposium. Raleigh, NC. August 2006.

5.      Programming bacterial dynamics by synthetic killer circuits. American Physical Society Annual Meeting. Baltimore, MD. March 2006.

6.      Synthetic Biology: Rewiring a bug’s life. Center for Nonlinear and Complex Systems seminar series. Duke University, NC. November 2005.

7.      Designer cells: “what I cannot create, I do not understand”. IGSP Computation Biology and Bioinformatics seminar series. Duke University. September 2005.

8.      Biology by design: reduction and synthesis of cellular networks. IGSP Genomes@4 seminar series, Duke University. NC. March 2005.

9.    Synthetic gene circuits for decoding life. UPGG/IGSP seminar series. Duke University, NC February 2005.

10.  Homeostasis, oscillations, and ecological interactions in reprogrammed bacterial populations. Workshop on Regulatory Networks. Mathematical Biosciences Institute, The Ohio State University, Columbus, Ohio. November 2004

11.  Synthetic gene circuits for decoding and controlling cellular behavior. Duke Bioengineering Initiative Forum. Duke University, Durham, NC. October, 2004

12.  Beyond single cells: programming population dynamics by cell-cell communication. Computational Bioengineering -- Synthetic Cell Communication Systems. BMES Annual Meeting.. Philadelphia, PA. October, 2004.

13.  Homeostasis, oscillations, and ecological interactions in reprogrammed bacterial populations. Center for Biological Circuit Design. California Institute of Technology, CA. October, 2004.

14.  Integrated understanding of biological networks by modeling. Integrating Disparate Data to Simulate Lymphocyte Function. The Banbury Center, Cold Spring Harbor Laboratory, NY. September, 2004.

15.  Beyond single cells: Programming population dynamics by engineered cell-cell communication. SIAM Life Sciences Symposium. Portland, OR. July 2004.

16.  Beyond single cells: Programming population dynamics by engineered cell-cell communication. UCSD, CA. June 2004.

17.  Beyond single cells: Programming population dynamics by engineered cell-cell communication. Harvard Medical School, MA. May 2004.

18.  Beyond single cells: Programming population dynamics by engineered cell-cell communication. UCSF, CA. April 2004.

19.  Beyond single cells: Programming population dynamics by engineered cell-cell communication. Duke University, NC. March 2004.

20.  Beyond single cells: Programming population dynamics by engineered cell-cell communication. Lehigh University, PA. January 2004.

 

Past Invited Talks

L. You. From bacteriophage T7 toPhenoBank”: Mathematical modeling for integrated understanding of biological systems, Texas A&M University, University of Houston, Eli Lilly & Company, University of Massachusetts at Amherst, University of Norte Dame, Johns Hopkins University, Purdue University, University of Pennsylvania, Lehigh University, UCSD, and Duke University (Jan-Apr 2002).

 

Conference Presentations

  1. T. Lee, G. Yao, J. Nevins, and L. You (2006). Signal patterns of Ras effector pathways that yield precise modulation of Myc expression. BMES Annual Meeting, October. Chicago, IL
  2. I-C. Liao, M. Kluenger, L. You, K. Leong (2006). Micro/nano fibers embedded with live cell and viral vectors. BMES Annual Meeting, October, Chicago, IL
  3. C. M. Tan, F. Reza, and L. You (2006). Fidelity and speed of signal transmission limited by cellular noise. BMES Annual meeting, October. Chicago, IL
  4. C.M. Tan, M. Salahi, and L. You (2006). Bistability in an integrated gene and protein regulatory network. BMES Annual meeting, October. Chicago, IL
  5. J. Niemi, L. You, and M. West (2006). Bayesian parameter estimation for systems biological models of dynamic cellular networks. Valencia International Meeting on Bayesian Statistics. June. Universitat de València, Spain
  6. T. Lee, G. Yao, J. Nevins, and L. You (2006). Signal patterns of Ras effector pathways that yield precise modulation of Myc expression. Dynamics Days 2006. Bethesda, MD
  7. G. Yao, T. Lee, S. Mori, J. Nevins, and L. You (2005). Control of cell cycle entry by a Myc/Rb/E2F bistable switch. NIH/NCI ICBP Workshop.  Washington, DC.

8.      J. Ozaki (speaker), M. Barnet, C. Collins, F. H. Arnold, and L. You (2005). A Synthetic E. coli predator-prey system. Synthetic Systems Biology. AIChE Annual Meeting (November), Cincinnati, OH

9.      F.K. Balagadde, L. You, C. Hansen, F.H. Arnold and S.R. Quake (2005). Programmed Population Control by Cell-Cell Communication in a Microfluidic Chemostat. NSTI Nanotechnology conference and trade show. Anaheim, CA

10.  L. You, R. S. Cox III, R. Weiss and F. H. Arnold (2004). Programmed population control by engineered cell-cell communication (poster). The 1st International Conference of Synthetic Biology (June). MIT, MA. 

11.  L. You and F. H. Arnold (2003). Design and construction of a synthetic population control circuit. Advances in Biotechnology Genomics I. AIChE Annual Meeting (November), San Francisco, CA.

12.  L. You, R. S. Cox III, and F. H. Arnold (2003). Computational design of a synthetic E. coli predator-prey ecosystem. Advances in Metabolic Engineering and Bioinformatics I. AIChE Annual Meeting (November), San Francisco, CA.

13.  L. You and J. Yin (2002). Environmental constraints on genomic design: insights from in silico mutagenesis of virus-host interactions (oral presentation). Advances in Bioinformatics: Networks and Pathways. AIChE Annual Meeting (November), Indianapolis, IN.

14.  L. You and J. Yin (2001). Quantifying genetic interactions using in silico mutagenesis (oral presentation). Food, Pharmaceutical, Bioengineering & Fundamentals in Life Science. AIChE Annual Meeting (November), Reno, NV.

15.  L. You, A. Hoonlor, Y.-F. Chen, and J. Yin (2001). Modeling biological systems using Dynetica – a simulator of dynamic networks. Bioinformatics and Genomics, AIChE Annual Meeting (November), Reno, NV.

16.  L. You and J. Yin (2001). From Genome to Organism: Computing the Dynamics of Phage T7 Growth and Exploring the Interactions Among Deleterious Mutations (poster). Pacific Symposium on Biocomputing (January). The Big Island, Hawaii.

17.  L. You, P. Suthers, and J. Yin (2000). Effects of E. coli physiology on bacteriophage T7 growth (oral presentation). Advances in Bioinformatics. AIChE Annual Meeting (November), Los Angeles, CA.

18.  R. Srivastava, L. You, J. Summers and J. Yin (2000). Stochastic versus deterministic modeling of hepatitis B virus intracellular kinetics (poster). Food, Pharmaceutical and Bioengineering, AIChE Annual Meeting (November), Los Angeles, CA.

19.  L. You, D. Endy, and J. Yin (2000). Functional genomics of bacteriophage T7 (poster). Quantitative Challenges in the Post-Genomic Sequence Era: A Workshop and Symposium (January). San Diego, CA.

20.  L. You and J. Yin (1999). Discovering patterns of biochemical function from mRNA and protein time-series (poster). AIChE Annual Meeting (November), Dallas, TX.

21.  D. Endy, L. You, I. J. Molineux, and J. Yin (1999). Prediction, design, and characterization of alternative genetic element orders for bacteriophage T7 (oral presentation). ACS National Meeting (March), Anaheim, CA.

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