L You

Summary

Affiliation: Duke University Medical Center
Country: USA

Publications

  1. pmc A synthetic Escherichia coli predator-prey ecosystem
    Frederick K Balagadde
    Department of Bioengineering, Stanford University and Howard Hughes Medical Institute, Stanford, CA, USA
    Mol Syst Biol 4:187. 2008
  2. pmc Sensing and integration of Erk and PI3K signals by Myc
    Tae Lee
    Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
    PLoS Comput Biol 4:e1000013. 2008
  3. pmc Spatiotemporal modulation of biodiversity in a synthetic chemical-mediated ecosystem
    Hao Song
    Department of Biomedical Engineering and Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, USA
    Nat Chem Biol 5:929-35. 2009
  4. pmc Noise reduction by diffusional dissipation in a minimal quorum sensing motif
    Yu Tanouchi
    Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
    PLoS Comput Biol 4:e1000167. 2008
  5. pmc Optimal tuning of bacterial sensing potential
    Anand Pai
    Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
    Mol Syst Biol 5:286. 2009
  6. pmc Oscillations by minimal bacterial suicide circuits reveal hidden facets of host-circuit physiology
    Philippe Marguet
    Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, United States of America
    PLoS ONE 5:e11909. 2010
  7. pmc Stochastic E2F activation and reconciliation of phenomenological cell-cycle models
    Tae J Lee
    Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
    PLoS Biol 8:. 2010
  8. pmc Computation of steady-state probability distributions in stochastic models of cellular networks
    Mark Hallen
    Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
    PLoS Comput Biol 7:e1002209. 2011
  9. pmc Tension and robustness in multitasking cellular networks
    Jeffrey V Wong
    Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
    PLoS Comput Biol 8:e1002491. 2012
  10. pmc The inoculum effect and band-pass bacterial response to periodic antibiotic treatment
    Cheemeng Tan
    Department of Biomedical Engineering, Duke University, Durham, NC, USA
    Mol Syst Biol 8:617. 2012

Collaborators

  • Guang Yao
  • Hao Song
  • Jeffrey V Wong
  • Quanli Wang
  • Nicolas E Buchler
  • Cheemeng Tan
  • Yu Tanouchi
  • Frederick K Balagadde
  • Anand Pai
  • Philippe Marguet
  • Stephen Payne
  • Bochong Li
  • Mark Hallen
  • Tae J Lee
  • Farren J Isaacs
  • Tae Lee
  • Stephen R Quake
  • Frances H Arnold
  • David Schaeffer
  • Yangxiaolu Cao
  • Marc D Ryser
  • Sameer Prasada
  • META KUEHN
  • Jaydeep K Srimani
  • Robert Phillip Smith
  • Katherine A Riccione
  • Mike West
  • Dorothy C Bennett
  • Eric Spitz
  • Joseph R Nevins
  • Cameron Smith
  • Dennis Tu
  • Jun Ozaki
  • Matthew Barnet
  • Jungsang Kim
  • Joseph Nevins
  • Cynthia H Collins
  • Faisal Reza
  • Jarad Niemi
  • Carl L Hansen

Detail Information

Publications26

  1. pmc A synthetic Escherichia coli predator-prey ecosystem
    Frederick K Balagadde
    Department of Bioengineering, Stanford University and Howard Hughes Medical Institute, Stanford, CA, USA
    Mol Syst Biol 4:187. 2008
    ..A simple mathematical model is developed to capture these system dynamics. Coherent interplay between experiments and mathematical analysis enables exploration of the dynamics of interacting populations in a predictable manner...
  2. pmc Sensing and integration of Erk and PI3K signals by Myc
    Tae Lee
    Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
    PLoS Comput Biol 4:e1000013. 2008
    ..We further propose that these characteristics of the protein stability control module in Myc may be commonly utilized in various cell types and classes of proteins...
  3. pmc Spatiotemporal modulation of biodiversity in a synthetic chemical-mediated ecosystem
    Hao Song
    Department of Biomedical Engineering and Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, USA
    Nat Chem Biol 5:929-35. 2009
    ..Otherwise, biodiversity was insensitive to cellular motility. Our results suggested a simple criterion for predicting the modulation of biodiversity by habitat partitioning and cellular motility in chemical-mediated ecosystems...
  4. pmc Noise reduction by diffusional dissipation in a minimal quorum sensing motif
    Yu Tanouchi
    Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
    PLoS Comput Biol 4:e1000167. 2008
    ..Our results suggest that, in a QS system, an unstable transcriptional regulator may be favored for regulating expression of costly proteins that generate public goods...
  5. pmc Optimal tuning of bacterial sensing potential
    Anand Pai
    Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
    Mol Syst Biol 5:286. 2009
    ..As an example, we show how QS characteristics uniquely determine the scenarios in which regulation of a typical QS-controlled function, such as exoenzyme secretion, becomes advantageous...
  6. pmc Oscillations by minimal bacterial suicide circuits reveal hidden facets of host-circuit physiology
    Philippe Marguet
    Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, United States of America
    PLoS ONE 5:e11909. 2010
    ..As synthetic biology grows as a discipline, increasing value may be derived from tools that enable the assessment of parts in their final context...
  7. pmc Stochastic E2F activation and reconciliation of phenomenological cell-cycle models
    Tae J Lee
    Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
    PLoS Biol 8:. 2010
    ..It also suggests a potential utility of the TP or GC models in defining concise, quantitative phenotypes of cell physiology. This may have implications in classifying cell types or states...
  8. pmc Computation of steady-state probability distributions in stochastic models of cellular networks
    Mark Hallen
    Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
    PLoS Comput Biol 7:e1002209. 2011
    ..Evaluation and illustrations are given in analysis of two well-characterized synthetic gene circuits, as well as a signaling network underlying the mammalian cell cycle entry...
  9. pmc Tension and robustness in multitasking cellular networks
    Jeffrey V Wong
    Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
    PLoS Comput Biol 8:e1002491. 2012
    ..Such analysis would suggest new ways to interfere with network elements to elucidate the design principles of cellular networks...
  10. pmc The inoculum effect and band-pass bacterial response to periodic antibiotic treatment
    Cheemeng Tan
    Department of Biomedical Engineering, Duke University, Durham, NC, USA
    Mol Syst Biol 8:617. 2012
    ..Our proposed mechanism for the IE may be generally applicable to other bacterial species treated with antibiotics targeting the ribosomes...
  11. pmc Programming stress-induced altruistic death in engineered bacteria
    Yu Tanouchi
    Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
    Mol Syst Biol 8:626. 2012
    ..Our findings fill a critical conceptual gap in the analysis of the evolution of bacterial programmed death, and have implications for a design of antibiotic treatment...
  12. pmc Temporal control of self-organized pattern formation without morphogen gradients in bacteria
    Stephen Payne
    Department of Biomedical Engineering, Duke University, Durham, NC, USA
    Mol Syst Biol 9:697. 2013
    ..Our work defines a novel mechanism of pattern formation that has implications for understanding natural developmental processes. ..
  13. pmc A brave new synthetic world
    Farren J Isaacs
    Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
    Genome Biol 10:302. 2009
    ..A report of the first meeting on 'Frontiers in Synthetic Biology', Boston, USA, 1-2 December 2008...
  14. ncbi request reprint Evolutionary design on a budget: robustness and optimality of bacteriophage T7
    L You
    Department of Biomedical Engineering and Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
    Syst Biol (Stevenage) 153:46-52. 2006
    ..In particular, the strong correlation between fitness and growth efficiency suggests that T7 may have evolved to maximise its growth rate by minimising waste of finite resources...
  15. pmc Image segmentation and dynamic lineage analysis in single-cell fluorescence microscopy
    Quanli Wang
    Department of Statistical Science, Duke University, Durham, North Carolina 27708 0251, USA
    Cytometry A 77:101-10. 2010
    ..The automated methods are implemented in freely available, open-source software...
  16. doi request reprint A whole more than the sum of its synthetic parts
    Jeffrey V Wong
    Department of Biomedical Engineering and the Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina 27708, USA
    ACS Chem Biol 3:27-9. 2008
    ..This bacterial "consensus" system, functional in liquid, solid, and biofilm niches, represents a novel strategy that raises the bar in terms of the specificity and complexity of tasks performed by engineered organisms...
  17. pmc Emergent bistability by a growth-modulating positive feedback circuit
    Cheemeng Tan
    Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
    Nat Chem Biol 5:842-8. 2009
    ..Our results reveal a new mechanism of generating bistability and underscore the need to account for host physiology modulation when engineering gene circuits...
  18. ncbi request reprint A synthetic biology challenge: making cells compute
    Cheemeng Tan
    Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
    Mol Biosyst 3:343-53. 2007
    ..We conclude with discussion of challenges involved in a typical design cycle, as well as those specific to cellular computation...
  19. pmc Effects of Escherichia coli physiology on growth of phage T7 in vivo and in silico
    Lingchong You
    Department of Chemical Engineering, University of Wisconsin Madison, Madison, Wisconsin 53706 1691, USA
    J Bacteriol 184:1888-94. 2002
    ..Finally, the simulation was used to follow how bottlenecks to phage growth shift in response to variations in host or phage functions...
  20. ncbi request reprint Evolving sensitivity
    Hao Song
    Department of Biomedical Engineering and Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina 27708, USA
    ACS Chem Biol 1:681-2. 2006
    ..Directed evolution complements rational design as an important strategy for optimizing gene circuits and circuit elements...
  21. pmc Noise-limited frequency signal transmission in gene circuits
    Cheemeng Tan
    Department of Biomedical Engineering, and Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, USA
    Biophys J 93:3753-61. 2007
    ..Our results may have implications for understanding signal processing in natural biological networks and for engineering synthetic gene circuits...
  22. ncbi request reprint Long-term monitoring of bacteria undergoing programmed population control in a microchemostat
    Frederick K Balagadde
    Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA
    Science 309:137-40. 2005
    ..The microfluidic bioreactor enabled long-term monitoring of unnatural behavior programmed by the synthetic circuit, which included sustained oscillations in cell density and associated morphological changes, over hundreds of hours...
  23. ncbi request reprint Programmed population control by cell-cell communication and regulated killing
    Lingchong You
    Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
    Nature 428:868-71. 2004
    ..This circuit incorporates a mechanism for programmed death in response to changes in the environment, and allows us to probe the design principles of its more complex natural counterparts...
  24. ncbi request reprint Toward computational systems biology
    Lingchong You
    Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
    Cell Biochem Biophys 40:167-84. 2004
    ..Here I give an overview of current mainstream approaches in modeling biological systems, highlight specific applications of modeling in various settings, and point out future research opportunities and challenges...
  25. ncbi request reprint Modeling biological systems using Dynetica--a simulator of dynamic networks
    Lingchong You
    Division of Chemistry and Chemical Engineering, California Institute of Technology, USA
    Bioinformatics 19:435-6. 2003
    ..AVAILABILITY AND SUPPLEMENTARY INFORMATION: Dynetica 1.0, example models, and the user's guide are available at http://www.its.caltech.edu/~you/Dynetica/Dynetica_page.htm..
  26. pmc Dependence of epistasis on environment and mutation severity as revealed by in silico mutagenesis of phage t7
    Lingchong You
    Department of Chemical Engineering, University of Wisconsin, Madison, Wisconsin 53706, USA
    Genetics 160:1273-81. 2002
    ..Our approach demonstrates how computer simulations of developmental processes can be used to quantitatively study genetic interactions at the population level...

Research Grants1

  1. Coordinating Cell Killing by Communication: Biological Control and Cancer Therapy
    Lingchong You; Fiscal Year: 2010
    ..This approach will offer the extremely high targeting selectivity and bacterial containment efficiency needed for effective and safe cancer therapy. ..