Publications, talks, and presentations (Lingchong You)

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

Peer reviewed articles

F. K. Balagadde *, L. You*, C. Hanson, F. H. Arnold and S. Quake. (2005). Long-term monitoring of bacteria undergoing programmed oscillations in a microchemostat, submitted. (* 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

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

Synthetic gene circuits for decoding and controlling cellular behavior. Duke Bioengineering Initiative Forum. (October, 2004). Duke University, Durham, North Carolina.

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

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

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

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

Beyond single cells: Programming population dynamics by engineered cell-cell communication (June 2004). UCSD, California.

Beyond single cells: Programming population dynamics by engineered cell-cell communication (May 2004). Harvard Medical School, Massachusetts.

Beyond single cells: Programming population dynamics by engineered cell-cell communication (April 2004). UCSF, California.

Beyond single cells: Programming population dynamics by engineered cell-cell communication (March 2004). Duke University, North Carolina.

Beyond single cells: Programming population dynamics by engineered cell-cell communication (Janurary 2004). Lehigh University, Pennsylvania.

 

Other conference presentations    

L. You (speaker) 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.

L. You (speaker), 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.

L. You and J. Yin (speaker) (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.

L. You (speaker) 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.

L. You (speaker), 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.

L. You (presenter) 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.

L. You (speaker), 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.

R. Srivastava (presenter), 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.

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

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

D. Endy (speaker), 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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