Lingchong You

Research Themes

Biomaterials, Biomedical & Health Data Sciences, Computational Modeling of Biological Systems, Drug & Gene Delivery, Synthetic & Systems Biology

Research Interests

Quantitative biology, synthetic biology, machine learning, antibiotic resistance, microbiome

Bio

The You lab uses a combination of mathematical modeling, machine learning, and quantitative experiments to elucidate principles underlying the dynamics of microbial communities in time and space and to control these dynamics for applications in computation, engineering, and medicine.

Education

• B.S.E. Chengdu University of Science and Technology (China), 1994
• M.S. University of Science and Technology of China (China), 1997
• Ph.D. University of Wisconsin, Madison, 2002

Positions

• James L. Meriam Distinguished Professor of Biomedical Engineering
• Professor of Biomedical Engineering
• Director of the Center for Quantitative Biology and Machine Learning
• Professor in Molecular Genetics and Microbiology

Awards, Honors, and Distinctions

• Fellow. American Institute for Medical and Biological Engineering. 2019
• Faculty Early Career Development (CAREER) Program. National Science Foundation. 2010
• Young Professor Award. DuPont. 2008
• Fellowships for Science and Engineering. David and Lucile Packard Foundation. 2006

Courses Taught

• PHARM 394: Research Independent Study
• MGM 593: Research Independent Study
• EGR 393: Research Projects in Engineering
• CBB 574: Modeling and Engineering Gene Circuits (GE, MC)
• BME 792: Continuation of Graduate Independent Study
• BME 791: Graduate Independent Study
• BME 713S: QBio Seminar Series
• BME 590: Special Topics in Biomedical Engineering
• BME 574: Modeling and Engineering Gene Circuits (GE, MC)
• BME 494: Projects in Biomedical Engineering (GE)
• BME 493: Projects in Biomedical Engineering (GE)
• BME 394: Projects in Biomedical Engineering (GE)
• BIOLOGY 293-1: Research Independent Study

Publications

• Ma HR, Xu HZ, Kim K, Anderson DJ, You L. Private benefit of β-lactamase dictates selection dynamics of combination antibiotic treatment. Nat Commun. 2024 Sep 27;15(1):8337.
• Dai Y, Zhou Z, Yu W, Ma Y, Kim K, Rivera N, et al. Biomolecular condensates regulate cellular electrochemical equilibria. Cell. 2024 Sep;S0092-8674(24)00909-7.
• Şimşek E, Kim K, Lu J, Silver A, Luo N, Lee CT, et al. A 'rich-get-richer' mechanism drives patchy dynamics and resistance evolution in antibiotic-treated bacteria. Molecular systems biology. 2024 Aug;20(8):880–97.
• Ha Y, Ma HR, Wu F, Weiss A, Duncker K, Xu HZ, et al. Data-driven learning of structure augments quantitative prediction of biological responses. PLoS computational biology. 2024 Jun;20(6):e1012185.
• Luo N, Lu J, Şimşek E, Silver A, Yao Y, Ouyang X, et al. The collapse of cooperation during range expansion of Pseudomonas aeruginosa. Nature microbiology. 2024 May;9(5):1220–30.
• Hamrick GS, Maddamsetti R, Son H-I, Wilson ML, Davis HM, You L. Programming Dynamic Division of Labor Using Horizontal Gene Transfer. ACS synthetic biology. 2024 Apr;13(4):1142–51.
• Wang T, Weiss A, You L. A generic approach to infer community-level fitness of microbial genes. Proceedings of the National Academy of Sciences of the United States of America. 2024 Apr;121(17):e2318380121.
• Li Z, Shen Q, Usher ET, Anderson AP, Iburg M, Lin R, et al. Phase transition of GvpU regulates gas vesicle clustering in bacteria. Nature microbiology. 2024 Apr;9(4):1021–35.
• Maddamsetti R, Yao Y, Wang T, Gao J, Huang VT, Hamrick GS, et al. Duplicated antibiotic resistance genes reveal ongoing selection and horizontal gene transfer in bacteria. Nature communications. 2024 Feb;15(1):1449.
• Baig Y, Ma HR, Xu H, You L. Autoencoder neural networks enable low dimensional structure analyses of microbial growth dynamics. Nature communications. 2023 Dec;14(1):7937.
• Weiss A, Wang T, You L. Promotion of plasmid maintenance by heterogeneous partitioning of microbial communities. Cell systems. 2023 Oct;14(10):895-905.e5.
• Kim K, Wang T, Ma HR, Şimşek E, Li B, Andreani V, et al. Mapping single-cell responses to population-level dynamics during antibiotic treatment. Molecular Systems Biology. 2023 Jul 11;19(7).
• Dai Y, Chamberlayne CF, Messina MS, Chang CJ, Zare RN, You L, et al. Interface of biomolecular condensates modulates redox reactions. Chem. 2023 Jun;9(6):1594–609.
• Şimşek E, Yao Y, Lee D, You L. Toward predictive engineering of gene circuits. Trends in biotechnology. 2023 Jun;41(6):760–8.
• Silver A, You L. A change of phase. Nature chemical biology. 2023 Apr;19(4):397–8.
• Dai Y, Farag M, Lee D, Zeng X, Kim K, Son H-I, et al. Programmable synthetic biomolecular condensates for cellular control. Nature chemical biology. 2023 Apr;19(4):518–28.
• Luo J, Chen J, Huang Y, You L, Dai Z. Engineering living materials by synthetic biology. Biophysics reviews. 2023 Mar;4(1):011305.
• Bethke JH, Ma HR, Tsoi R, Cheng L, Xiao M, You L. Vertical and horizontal gene transfer tradeoffs direct plasmid fitness. Molecular systems biology. 2023 Feb;19(2):e11300.
• Wang T, Weiss A, Aqeel A, Wu F, Lopatkin AJ, David LA, et al. Horizontal gene transfer enables programmable gene stability in synthetic microbiota. Nat Chem Biol. 2022 Nov;18(11):1245–52.
• Wang T, You L. Bringing cells to the edge. eLife. 2022 Nov;11:e83789.
• Lu J, Tsoi R, Luo N, Ha Y, Wang S, Kwak M, et al. Distributed information encoding and decoding using self-organized spatial patterns. Patterns (New York, NY). 2022 Oct;3(10):100590.
• Roden CA, Dai Y, Giannetti CA, Seim I, Lee M, Sealfon R, et al. Double-stranded RNA drives SARS-CoV-2 nucleocapsid protein to undergo phase separation at specific temperatures. Nucleic Acids Res. 2022 Aug 12;50(14):8168–92.
• Jin G, Hong S, Rich J, Xia J, Kim K, You L, et al. Intelligent nanoscope for rapid nanomaterial identification and classification. Lab on a chip. 2022 Aug;22(16):2978–85.
• Wang L, Zhang X, Tang C, Li P, Zhu R, Sun J, et al. Engineering consortia by polymeric microbial swarmbots. Nature communications. 2022 Jul;13(1):3879.
• Lu J, Şimşek E, Silver A, You L. Advances and challenges in programming pattern formation using living cells. Current opinion in chemical biology. 2022 Jun;68:102147.
• Yao Y, Maddamsetti R, Weiss A, Ha Y, Wang T, Wang S, et al. Intra- and interpopulation transposition of mobile genetic elements driven by antibiotic selection. Nature ecology & evolution. 2022 May;6(5):555–64.
• Wu F, Ha Y, Weiss A, Wang M, Letourneau J, Wang S, et al. Modulation of microbial community dynamics by spatial partitioning. Nat Chem Biol. 2022 Apr;18(4):394–402.
• Chen B, Kang W, Sun J, Zhu R, Yu Y, Xia A, et al. Programmable living assembly of materials by bacterial adhesion. Nature chemical biology. 2022 Mar;18(3):289–94.
• Gore J, You L. Editorial overview: All microbial systems go`. Current opinion in microbiology. 2022 Feb;65:iii–iv.
• Duncker KE, Holmes ZA, You L. Engineered microbial consortia: strategies and applications. Microbial cell factories. 2021 Nov;20(1):211.
• Son H-I, Weiss A, You L. Design patterns for engineering genetic stability. Current opinion in biomedical engineering. 2021 Sep;19:100297.
• Wang T, Weiss A, Ha Y, You L. Predicting plasmid persistence in microbial communities by coarse-grained modeling. BioEssays : news and reviews in molecular, cellular and developmental biology. 2021 Sep;43(9):e2100084.
• Dai Z, Yang X, Wu F, Wang L, Xiang K, Li P, et al. Living fabrication of functional semi-interpenetrating polymeric materials. Nature communications. 2021 Jun;12(1):3422.
• Luo N, Wang S, Lu J, Ouyang X, You L. Collective colony growth is optimized by branching pattern formation in Pseudomonas aeruginosa. Molecular systems biology. 2021 Apr;17(4):e10089.
• Cao Y, Neu J, Blanchard AE, Lu T, You L. Repulsive expansion dynamics in colony growth and gene expression. PLoS computational biology. 2021 Mar;17(3):e1008168.
• Lee ED, Aurand ER, Friedman DC, Engineering Biology Research Consortium Microbiomes Roadmapping Working Group. Engineering Microbiomes-Looking Ahead. ACS synthetic biology. 2020 Dec;9(12):3181–3.
• Wang T, You L. The persistence potential of transferable plasmids. Nature communications. 2020 Nov;11(1):5589.
• Zhang C, Song W, Ma HR, Peng X, Anderson DJ, Fowler VG, et al. Temporal encoding of bacterial identity and traits in growth dynamics. Proc Natl Acad Sci U S A. 2020 Aug 18;117(33):20202–10.
• Villa MM, Bloom RJ, Silverman JD, Durand HK, Jiang S, Wu A, et al. Interindividual Variation in Dietary Carbohydrate Metabolism by Gut Bacteria Revealed with Droplet Microfluidic Culture. mSystems. 2020 Jun 30;5(3).
• Kim K, You L. Bacterial Aggregation Leads to Collective Elimination. Trends in microbiology. 2020 Apr;28(4):243–4.
• Sysoeva TA, Kim Y, Rodriguez J, Lopatkin AJ, You L. Growth-stage-dependent regulation of conjugation. AIChE Journal. 2020 Mar 1;66(3).
• Mathey-Prevot B, Parker B-T, Im C, Hong C, Dong P, Yao G, et al. Quantifying E2F1 protein dynamics in single cells. Quantitative biology (Beijing, China). 2020 Mar;8(1):20–30.
• Bethke JH, Davidovich A, Cheng L, Lopatkin AJ, Song W, Thaden JT, et al. Environmental and genetic determinants of plasmid mobility in pathogenic Escherichia coli. Sci Adv. 2020 Jan;6(4):eaax3173.
• Zhu K, Chen S, Sysoeva TA, You L. Universal antibiotic tolerance arising from antibiotic-triggered accumulation of pyocyanin in Pseudomonas aeruginosa. PLoS biology. 2019 Dec;17(12):e3000573.
• Lopatkin AJ, Stokes JM, Zheng EJ, Yang JH, Takahashi MK, You L, et al. Bacterial metabolic state more accurately predicts antibiotic lethality than growth rate. Nature microbiology. 2019 Dec;4(12):2109–17.
• Tsoi R, Dai Z, You L. Emerging strategies for engineering microbial communities. Biotechnology advances. 2019 Nov;37(6):107372.
• Dai Z, Lee AJ, Roberts S, Sysoeva TA, Huang S, Dzuricky M, et al. Versatile biomanufacturing through stimulus-responsive cell-material feedback. Nature chemical biology. 2019 Oct;15(10):1017–24.
• Shi X, You L, Luo R-Y. Glycolytic reprogramming in cancer cells: PKM2 dimer predominance induced by pulsatile PFK-1 activity. Physical biology. 2019 Sep;16(6):066007.
• Ma HR, You L. Polar-opposite fates. Nature chemical biology. 2019 Sep;15(9):850–2.
• Wang S, Fan K, Luo N, Cao Y, Wu F, Zhang C, et al. Massive computational acceleration by using neural networks to emulate mechanism-based biological models. Nature communications. 2019 Sep;10(1):4354.
• Song W, Sun H-X, Zhang C, Cheng L, Peng Y, Deng Z, et al. Prophage Hunter: an integrative hunting tool for active prophages. Nucleic acids research. 2019 Jul;47(W1):W74–80.
• Simon JR, Eghtesadi SA, Dzuricky M, You L, Chilkoti A. Engineered Ribonucleoprotein Granules Inhibit Translation in Protocells. Molecular cell. 2019 Jul;75(1):66-75.e5.
• Luo N, Wang S, You L. Synthetic Pattern Formation. Biochemistry. 2019 Mar;58(11):1478–83.
• Wu F, Lopatkin AJ, Needs DA, Lee CT, Mukherjee S, You L. A unifying framework for interpreting and predicting mutualistic systems. Nature communications. 2019 Jan;10(1):242.
• Meredith HR, Andreani V, Ma HR, Lopatkin AJ, Lee AJ, Anderson DJ, et al. Applying ecological resistance and resilience to dissect bacterial antibiotic responses. Sci Adv. 2018 Dec;4(12):eaau1873.
• Dong P, Maddali MV, Srimani JK, Thélot F, Nevins JR, Mathey-Prevot B, et al. Author Correction: Division of labour between Myc and G1 cyclins in cell cycle commitment and pace control. Nature communications. 2018 Nov;9(1):4766.
• Feng Y, Marusak KE, You L, Zauscher S. Biosynthetic transition metal chalcogenide semiconductor nanoparticles: Progress in synthesis, property control and applications. Current Opinion in Colloid and Interface Science. 2018 Nov 1;38:190–203.
• You L, Takano E. Synthetic Biology: Reports from CSHA 2016 and More. Biotechnology journal. 2018 May;13(5):e1800160.
• Sysoeva TA, Kim Y, You L. REGULATION OF CONJUGATIVE TRANSFER OF beta-LACTAM RESISTANCE FROM UROPATHOGENIC STRAINS OF ESCHERICHIA COLI. In: JOURNAL OF UROLOGY. ELSEVIER SCIENCE INC; 2018. p. E285–E285.
• Lee AJ, Wang S, Meredith HR, Zhuang B, Dai Z, You L. Robust, linear correlations between growth rates and β-lactam-mediated lysis rates. Proceedings of the National Academy of Sciences of the United States of America. 2018 Apr;115(16):4069–74.
• Tsoi R, Wu F, Zhang C, Bewick S, Karig D, You L. Metabolic division of labor in microbial systems. Proceedings of the National Academy of Sciences of the United States of America. 2018 Mar;115(10):2526–31.
• Sysoeva T, You L. REGULATION OF CONJUGATIVE TRANSFER OF B-LACTAM RESISTANCE FROM UROPATHOGENIC STRAINS OF ESCHERICHIA COLI. In: NEUROUROLOGY AND URODYNAMICS. WILEY; 2018. p. S529–30.
• Marusak KE, Krug JR, Feng Y, Cao Y, You L, Zauscher S. Bacterially driven cadmium sulfide precipitation on porous membranes: Toward platforms for photocatalytic applications. Biointerphases. 2018 Feb;13(1):011006.
• Dong P, Zhang C, Parker B-T, You L, Mathey-Prevot B. Cyclin D/CDK4/6 activity controls G1 length in mammalian cells. PloS one. 2018 Jan;13(1):e0185637.
• Wu F, Bethke JH, Wang M, You L. Quantitative and synthetic biology approaches to combat bacterial pathogens. Current opinion in biomedical engineering. 2017 Dec;4:116–26.
• Lopatkin AJ, Meredith HR, Srimani JK, Pfeiffer C, Durrett R, You L. Persistence and reversal of plasmid-mediated antibiotic resistance. Nature communications. 2017 Nov;8(1):1689.
• Cao Y, Feng Y, Ryser MD, Zhu K, Herschlag G, Cao C, et al. Programmable assembly of pressure sensors using pattern-forming bacteria. Nat Biotechnol. 2017 Nov;35(11):1087–93.
• Srimani JK, Huang S, Lopatkin AJ, You L. Drug detoxification dynamics explain the postantibiotic effect. Molecular systems biology. 2017 Oct;13(10):948.
• Wu F, You L. Hacking DNA copy number for circuit engineering. Nature genetics. 2017 Jul;49(8):1164–5.
• Shats I, Deng M, Davidovich A, Zhang C, Kwon JS, Manandhar D, et al. Expression level is a key determinant of E2F1-mediated cell fate. Cell Death Differ. 2017 Apr;24(4):626–37.
• Tanouchi Y, Pai A, Park H, Huang S, Buchler NE, You L. Long-term growth data of Escherichia coli at a single-cell level. Scientific data. 2017 Mar;4:170036.
• Feng Y, Ngaboyamahina E, Marusak KE, Cao Y, You L, Glass JT, et al. Hybrid (Organic/Inorganic) Electrodes from Bacterially Precipitated CdS for PEC/Storage Applications. Journal of Physical Chemistry C. 2017 Feb 23;121(7):3734–43.
• Lopatkin AJ, Sysoeva TA, You L. Dissecting the effects of antibiotics on horizontal gene transfer: Analysis suggests a critical role of selection dynamics. BioEssays : news and reviews in molecular, cellular and developmental biology. 2016 Dec;38(12):1283–92.
• Cao Y, Lopatkin A, You L. Elements of biological oscillations in time and space. Nature structural & molecular biology. 2016 Dec;23(12):1030–4.
• Zhang C, Tsoi R, Wu F, You L. Processing Oscillatory Signals by Incoherent Feedforward Loops. PLoS computational biology. 2016 Sep;12(9):e1005101.
• Cao Y, Ryser MD, Payne S, Li B, Rao CV, You L. Collective Space-Sensing Coordinates Pattern Scaling in Engineered Bacteria. Cell. 2016 Apr 21;165(3):620–30.
• Zhang C, Tsoi R, You L. Addressing biological uncertainties in engineering gene circuits. Integrative biology : quantitative biosciences from nano to macro. 2016 Apr;8(4):456–64.
• Lopatkin AJ, Huang S, Smith RP, Srimani JK, Sysoeva TA, Bewick S, et al. Antibiotics as a selective driver for conjugation dynamics. Nature microbiology. 2016 Apr;1(6):16044.
• Huang S, Lee AJ, Tsoi R, Wu F, Zhang Y, Leong KW, et al. Coupling spatial segregation with synthetic circuits to control bacterial survival. Molecular systems biology. 2016 Feb;12(2):859.
• Marusak KE, Feng Y, Eben CF, Payne ST, Cao Y, You L, et al. Cadmium sulphide quantum dots with tunable electronic properties by bacterial precipitation. RSC advances. 2016 Jan;6(80):76158–66.
• Huang S, Srimani JK, Lee AJ, Zhang Y, Lopatkin AJ, Leong KW, et al. Dynamic control and quantification of bacterial population dynamics in droplets. Biomaterials. 2015 Aug;61:239–45.
• Tanouchi Y, Pai A, Park H, Huang S, Stamatov R, Buchler NE, et al. A noisy linear map underlies oscillations in cell size and gene expression in bacteria. Nature. 2015 Jul;523(7560):357–60.
• Lee TJ, Wong J, Bae S, Lee AJ, Lopatkin A, Yuan F, et al. A power-law dependence of bacterial invasion on mammalian host receptors. PLoS computational biology. 2015 Apr;11(4):e1004203.
• Meredith HR, Lopatkin AJ, Anderson DJ, You L. Bacterial temporal dynamics enable optimal design of antibiotic treatment. PLoS Comput Biol. 2015 Apr;11(4):e1004201.
• Meredith HR, Srimani JK, Lee AJ, Lopatkin AJ, You L. Collective antibiotic tolerance: mechanisms, dynamics and intervention. Nature chemical biology. 2015 Mar;11(3):182–8.
• Srimani JK, You L. Emergent dynamics from quorum eavesdropping. Chemistry & biology. 2014 Dec;21(12):1601–2.
• Eidum D, Asthana K, Unni S, Deng M, You L. Construction, visualization, and analysis of biological network models in Dynetica. Quantitative Biology. 2014 Dec 1;2(4):142–50.
• Lopatkin AJ, You L. Synthetic biology looks good on paper. Cell. 2014 Nov;159(4):718–20.
• Li B, You L. Stochastic sensitivity analysis and kernel inference via distributional data. Biophysical journal. 2014 Sep;107(5):1247–55.
• Dong P, Maddali MV, Srimani JK, Thélot F, Nevins JR, Mathey-Prevot B, et al. Division of labour between Myc and G1 cyclins in cell cycle commitment and pace control. Nature communications. 2014 Sep;5:4750.
• Tan C, Smith RP, Tsai M-C, Schwartz R, You L. Phenotypic signatures arising from unbalanced bacterial growth. PLoS computational biology. 2014 Aug;10(8):e1003751.
• Pai A, Srimani JK, Tanouchi Y, You L. Generic metric to quantify quorum sensing activation dynamics. ACS synthetic biology. 2014 Apr;3(4):220–7.
• Smith R, Tan C, Srimani JK, Pai A, Riccione KA, Song H, et al. Programmed Allee effect in bacteria causes a tradeoff between population spread and survival. Proceedings of the National Academy of Sciences of the United States of America. 2014 Feb;111(5):1969–74.
• Lee AJ, You L. Cell biology. Cells listen to their inner voice. Science (New York, NY). 2014 Feb;343(6171):624–5.
• Payne S, You L. Engineered cell-cell communication and its applications. Advances in biochemical engineering/biotechnology. 2014 Jan;146:97–121.
• Srimani JK, Yao G, Neu J, Tanouchi Y, Lee TJ, You L. Linear population allocation by bistable switches in response to transient stimulation. PloS one. 2014 Jan;9(8):e105408.
• Payne S, Li B, Cao Y, Schaeffer D, Ryser MD, You L. Temporal control of self-organized pattern formation without morphogen gradients in bacteria. Mol Syst Biol. 2013 Oct 8;9:697.
• Shats I, Gatza ML, Liu B, Angus SP, You L, Nevins JR. FOXO transcription factors control E2F1 transcriptional specificity and apoptotic function. Cancer research. 2013 Oct;73(19):6056–67.
• Smith RP, Tanouchi Y, You L. Synthetic Microbial Consortia and their Applications. 2013 Aug 27;243–58.
• Li B, You L. Predictive power of cell-to-cell variability. Quantitative Biology. 2013 Jun 1;1(2):131–9.
• Tanouchi Y, Lee AJ, Meredith H, You L. Programmed cell death in bacteria and implications for antibiotic therapy. Trends in microbiology. 2013 Jun;21(6):265–70.
• Zhang Y, Ho Y-P, Chiu Y-L, Chan HF, Chlebina B, Schuhmann T, et al. A programmable microenvironment for cellular studies via microfluidics-generated double emulsions. Biomaterials. 2013 Jun;34(19):4564–72.
• Smith RP, Tanouchi Y, You L. Synthetic microbial consortia and their applications. In: Synthetic Biology: Tools and Applications. 2013. p. 243–58.
• Pai A, Tanouchi Y, You L. Optimality and robustness in quorum sensing (QS)-mediated regulation of a costly public good enzyme. Proceedings of the National Academy of Sciences of the United States of America. 2012 Nov;109(48):19810–5.
• Tanouchi Y, Smith RP, You L. Engineering microbial systems to explore ecological and evolutionary dynamics. Current opinion in biotechnology. 2012 Oct;23(5):791–7.
• Riccione KA, Smith RP, Lee AJ, You L. A synthetic biology approach to understanding cellular information processing. ACS synthetic biology. 2012 Sep;1(9):389–402.
• Chin JW, You L. A different life? Current opinion in chemical biology. 2012 Aug;16(3–4):243–4.
• Stone JE, Benfey PN, You L. Promoting collaborative interdisciplinary research at the Duke Center for Systems Biology. ACS synthetic biology. 2012 May;1(5):153–5.
• Song H, You L. Modeling spatiotemporal dynamics of bacterial populations. Methods in molecular biology (Clifton, NJ). 2012 Jan;880:243–54.
• Payne S, Smith RP, You L. Quantitative analysis of the spatiotemporal dynamics of a synthetic predator-prey ecosystem. Methods in molecular biology (Clifton, NJ). 2012 Jan;813:315–30.
• Tan C, Smith RP, Srimani JK, Riccione KA, Prasada S, Kuehn M, et al. The inoculum effect and band-pass bacterial response to periodic antibiotic treatment. Mol Syst Biol. 2012;8:617.
• Wong JV, Li B, You L. Tension and robustness in multitasking cellular networks. PLoS computational biology. 2012 Jan;8(4):e1002491.
• Tanouchi Y, Pai A, Buchler NE, You L. Programming stress-induced altruistic death in engineered bacteria. Molecular systems biology. 2012 Jan;8:626.
• Hallen M, Li B, Tanouchi Y, Tan C, West M, You L. Computation of steady-state probability distributions in stochastic models of cellular networks. PLoS computational biology. 2011 Oct;7(10):e1002209.
• Bonassi FV, You L, West M. Bayesian learning from marginal data in bionetwork models. Statistical applications in genetics and molecular biology. 2011 Oct;10(1):/j/sagmb.2011.10.issue-1/1544-6115.1684/1544-6115.
• Wong JV, Dong P, Nevins JR, Mathey-Prevot B, You L. Network calisthenics: control of E2F dynamics in cell cycle entry. Cell Cycle. 2011 Sep 15;10(18):3086–94.
• Song H, Payne S, Tan C, You L. Programming microbial population dynamics by engineered cell-cell communication. Biotechnology journal. 2011 Jul;6(7):837–49.
• Elliott N, Lee T, You L, Yuan F. Proliferation behavior of E. coli in a three-dimensional in vitro tumor model. Integrative biology : quantitative biosciences from nano to macro. 2011 Jun;3(6):696–705.
• Wong JV, Yao G, Nevins JR, You L. Using noisy gene expression mediated by engineered adenovirus to probe signaling dynamics in mammalian cells. Methods in Enzymology. 2011 May 30;497:221–37.
• Yao G, Tan C, West M, Nevins JR, You L. Origin of bistability underlying mammalian cell cycle entry. Molecular systems biology. 2011 Apr;7:485.
• Wong JV, Yao G, Nevins JR, You L. Viral-mediated noisy gene expression reveals biphasic E2f1 response to MYC. Molecular cell. 2011 Feb;41(3):275–85.
• Li B, You L. Synthetic biology: Division of logic labour. Nature. 2011 Jan;469(7329):171–2.
• Wong JV, Yao G, Nevins JR, You L. Using noisy gene expression mediated by engineered adenovirus to probe signaling dynamics in mammalian cells. Methods in enzymology. 2011 Jan;497:221–37.
• Lee TJ, Yao G, Bennett DC, Nevins JR, You L. Stochastic E2F activation and reconciliation of phenomenological cell-cycle models. PLoS biology. 2010 Sep;8(9):e1000488.
• Marguet P, Tanouchi Y, Spitz E, Smith C, You L. Oscillations by minimal bacterial suicide circuits reveal hidden facets of host-circuit physiology. PloS one. 2010 Jul;5(7):e11909.
• Wang Q, Niemi J, Tan C-M, You L, West M. Image segmentation and dynamic lineage analysis in single-cell fluorescence microscopy. Cytometry Part A : the journal of the International Society for Analytical Cytology. 2010 Jan;77(1):101–10.
• Song H, Payne S, Gray M, You L. Spatiotemporal modulation of biodiversity in a synthetic chemical-mediated ecosystem. Nature chemical biology. 2009 Dec;5(12):929–35.
• Tan C, Marguet P, You L. Emergent bistability by a growth-modulating positive feedback circuit. Nature chemical biology. 2009 Nov;5(11):842–8.
• Pai A, Tanouchi Y, Collins CH, You L. Engineering multicellular systems by cell-cell communication. Current opinion in biotechnology. 2009 Aug;20(4):461–70.
• Tanouchi Y, Pai A, You L. Decoding biological principles using gene circuits. Molecular bioSystems. 2009 Jul;5(7):695–703.
• Isaacs FJ, You L. A brave new synthetic world. A report of the first meeting on 'Frontiers in Synthetic Biology', Boston, USA, 1-2 December 2008. Genome biology. 2009 Feb;10(2):302.
• Pai A, You L. Optimal tuning of bacterial sensing potential. Molecular systems biology. 2009 Jan;5:286.
• Brenner K, You L, Arnold FH. Response to Goldman and Brown: Making sense of microbial consortia using ecology and evolution. Trends in Biotechnology. 2009 Jan 1;27(1):4.
• Song H, Gray M, You L. Spatiotemporal modulation of biodiversity in a synthetic predator-prey ecosystem. AIChE Annual Meeting, Conference Proceedings. 2008 Dec 1;
• Smith C, Song H, You L. Signal discrimination by differential regulation of protein stability in quorum sensing. Journal of molecular biology. 2008 Oct;382(5):1290–7.
• Brenner K, You L, Arnold FH. Engineering microbial consortia: a new frontier in synthetic biology. Trends in biotechnology. 2008 Sep;26(9):483–9.
• Tanouchi Y, Tu D, Kim J, You L. Noise reduction by diffusional dissipation in a minimal quorum sensing motif. PLoS Comput Biol. 2008 Aug 29;4(8):e1000167.
• Yao G, Lee TJ, Mori S, Nevins JR, You L. A bistable Rb-E2F switch underlies the restriction point. Nature cell biology. 2008 Apr;10(4):476–82.
• Lee T, Yao G, Nevins J, You L. Sensing and integration of Erk and PI3K signals by Myc. PLoS computational biology. 2008 Feb;4(2):e1000013.
• Balagaddé FK, Song H, Ozaki J, Collins CH, Barnet M, Arnold FH, et al. A synthetic Escherichia coli predator-prey ecosystem. Molecular systems biology. 2008 Jan;4:187.
• Wong JV, Song H, You L. A whole more than the sum of its synthetic parts. ACS chemical biology. 2008 Jan;3(1):27–9.
• Tan C, Reza F, You L. Noise-limited frequency signal transmission in gene circuits. Biophysical journal. 2007 Dec;93(11):3753–61.
• You L. Engineering synthetic killer circuits in bacteria. Proceedings - Design Automation Conference. 2007 Aug 2;636–7.
• Marguet P, Balagadde F, Tan C, You L. Biology by design: reduction and synthesis of cellular components and behaviour. Journal of the Royal Society, Interface. 2007 Aug;4(15):607–23.
• Tan C, Song H, Niemi J, You L. A synthetic biology challenge: making cells compute. Molecular bioSystems. 2007 May;3(5):343–53.
• Reza F, Chandran K, Feltz M, Heinz A, Josephs E, O’Brien P, et al. Engineering novel synthetic biological systems. IET Synthetic Biology. 2007;1:48–52.
• Song H, You L. Evolving sensitivity. ACS chemical biology. 2006 Dec;1(11):681–2.
• You L, Yin J. Evolutionary design on a budget: robustness and optimality of bacteriophage T7. Systems biology. 2006 Mar;153(2):46–52.
• Ozaki J, Barnet M, Collins CH, Arnold FH, You L. A synthetic E.Coli predator-prey system. AIChE Annual Meeting, Conference Proceedings. 2005 Dec 1;11590.
• Balagaddé FK, You L, Hansen CL, Arnold FH, Quake SR. Long-term monitoring of bacteria undergoing programmed population control in a microchemostat. Science (New York, NY). 2005 Jul;309(5731):137–40.
• You L, Cox RS, Weiss R, Arnold FH. Programmed population control by cell-cell communication and regulated killing. Nature. 2004 Apr;428(6985):868–71.
• You L. Toward computational systems biology. Cell biochemistry and biophysics. 2004 Jan;40(2):167–84.
• You L, Hoonlor A, Yin J. Modeling biological systems using Dynetica--a simulator of dynamic networks. Bioinformatics (Oxford, England). 2003 Feb;19(3):435–6.
• Srivastava R, You L, Summers J, Yin J. Stochastic vs. deterministic modeling of intracellular viral kinetics. Journal of theoretical biology. 2002 Oct;218(3):309–21.
• You L, Yin J. Dependence of epistasis on environment and mutation severity as revealed by in silico mutagenesis of phage t7. Genetics. 2002 Apr;160(4):1273–81.
• You L, Suthers PF, Yin J. Effects of Escherichia coli physiology on growth of phage T7 in vivo and in silico. Journal of bacteriology. 2002 Apr;184(7):1888–94.
• You L, Yin J. Simulating the growth of viruses. Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing. 2001 Jan;532–43.
• You L, Yin J. Patterns of regulation from mRNA and protein time series. Metabolic engineering. 2000 Jul;2(3):210–7.
• Endy D, You L, Yin J, Molineux IJ. Computation, prediction, and experimental tests of fitness for bacteriophage T7 mutants with permuted genomes. Proceedings of the National Academy of Sciences of the United States of America. 2000 May;97(10):5375–80.
• You L, Yin J. Amplification and spread of viruses in a growing plaque. Journal of theoretical biology. 1999 Oct;200(4):365–73.
• Endy D, You L, Molineux IJ, Yin J. Prediction, design, and characterization of alternate genetic element orders for bacteriophage T7. Abstracts Of Papers Of The American Chemical Society. 1999 Mar;217:U205–U205.
• You L, Liu Q, Shi Y, Wang CX, Lahaye M, Tran V. The conformational study of β-D-GlcA-(1,4) -L-Rha in solution by NMR and molecular dynamics simulations. Chemical Physics. 1997 Nov 15;224(1):81–94.

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