Lingchong You
Professor of Biomedical Engineering
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.
Current Research Interests
Quantitative biology, synthetic biology, machine learning, antibiotic resistance, microbiome
Current Appointments & Affiliations
- Professor of Biomedical Engineering, Biomedical Engineering, Pratt School of Engineering 2019
- Associate Professor in Molecular Genetics and Microbiology, Molecular Genetics and Microbiology, Basic Science Departments 2016
- Professor in Molecular Genetics and Microbiology, Molecular Genetics and Microbiology, Basic Science Departments 2021
Contact Information
- 2355 CIEMAS, 101 Science Drive, Durham, NC 27708
- Box 90281, Durham, NC 27708-0281
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(919) 660-8408
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Google Scholar
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Youlab homepage
- Background
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Education, Training, & Certifications
- Ph.D., University of Wisconsin - Madison 2002
- M.S., University of Science and Technology of China (China) 1997
- B.S.E., Chengdu University of Science and Technology (China) 1994
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Previous Appointments & Affiliations
- Associate Professor of Biomedical Engineering, Biomedical Engineering, Pratt School of Engineering 2012 - 2018
- Paul Ruffin Scarborough Distinguished Associate Professor of Engineering, Biomedical Engineering, Pratt School of Engineering 2014 - 2018
- Assistant Professor of Biomedical Engineering, Biomedical Engineering, Pratt School of Engineering 2005 - 2011
- Recognition
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In the News
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JAN 29, 2020 Pratt School of Engineering -
OCT 3, 2019 Pratt School of Engineering -
DEC 5, 2018 Pratt School of Engineering -
FEB 21, 2018 Pratt School of Engineering -
DEC 7, 2017 Center for Genomic and Computational Biology -
MAY 2, 2016 WFDD-Winston-Salem’s “SciWorks Radio” -
APR 22, 2016 Pratt School of Engineering -
APR 11, 2016 Pratt School of Engineering -
MAR 2, 2016 Gizmodo -
FEB 29, 2016 Pratt School of Engineering -
JUN 4, 2015 Pratt School of Engineering -
OCT 27, 2014 BBC News -
JAN 21, 2014 Pratt School of Engineering -
NOV 11, 2013 The News & Observer -
OCT 8, 2013
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Awards & Honors
- Research
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Selected Grants
- Uncovering and applying the design principles of multiphasic natural and synthetic organelles awarded by Princeton University 2020 - 2025
- Targeted control of self-transmissible plasmids by using engineered interfering plasmids awarded by National Institutes of Health 2021 - 2025
- Predictable Engineering of Self-organized Spatial Patterns in Bacteria awarded by Office of Naval Research 2020 - 2024
- RoL: Modulation of microbial community dynamics by spatial partitioning awarded by National Science Foundation 2019 - 2023
- Inductive repair of human kidney tissues by cell type-specific sensing and reprogramming awarded by University of Michigan 2021 - 2023
- Testing the need to personalize prebiotic therapies targeting human gut microbiota awarded by National Institutes of Health 2017 - 2022
- A comprehensive research resource to define mechanisms underlying microbial regulation of host metabolism in pediatric obesity and obesity-targeted therapeutics awarded by National Institutes of Health 2016 - 2022
- Preparing Genetic Counselors for Genomic Medicine Research awarded by National Institutes of Health 2017 - 2022
- University Training Program in Biomolecular and Tissue Engineering awarded by National Institutes of Health 1994 - 2022
- Bioinformatics and Computational Biology Training Program awarded by National Institutes of Health 2005 - 2021
- Dynamics of horizontal gene transfer in response to antibiotic treatment awarded by National Institutes of Health 2017 - 2021
- Post-antibiotic effect and design of optimal antibiotic dosing protocols awarded by National Institutes of Health 2011 - 2021
- A synthetic-biology approach to study scaling properties of self-organized patterns awarded by National Science Foundation 2014 - 2020
- Understanding the Skin Microbiome through the Integration of Metagenomics, Bioinformatics, Spatial Ecology, and Synthetic Biology awarded by Johns Hopkins University Applied Physics Laboratory 2014 - 2019
- Programming bacteria for materials fabrication awarded by Office of Naval Research 2015 - 2019
- Temporal E2F Dynamics and Cell-Fate Decisions in Single Mammalian Cells awarded by National Institutes of Health 2014 - 2019
- Enhancing imaging capability for quantitative and synthetic biology research and education awarded by Office of Naval Research 2018 - 2019
- Reprogramming cellular behavior with synthetic gene circuits awarded by E.I. duPont de Nemours and Company, Inc. 2008 - 2018
- Supplement - Understanding the Skin Microbiome through the Integration of Metagenomics, Bioinformatics, Spatial Ecology, and Synthetic Biology awarded by Johns Hopkins University Applied Physics Laboratory 2018
- A synthetic biology approach to analyze evolution of programmed bacterial death awarded by National Institutes of Health 2014 - 2018
- DURIP: Enhancing capability of quantitative biology research and education awarded by Office of Naval Research 2015 - 2016
- Programming bacteria for materials fabrication awarded by Office of Naval Research 2012 - 2015
- Development of a Microfluidic Platform to Analyze Evolution of Programmed Bacterial Death awarded by Army Research Office 2014 - 2015
- Engineering Microbial Swarmbots awarded by National Science Foundation 2010 - 2015
- Delivery of Bacterial Therapeutics to Solid Tumors awarded by National Science Foundation 2009 - 2013
- Coordinating Cell Killing by Communication: Biological Control and Cancer Therapy awarded by National Institutes of Health 2006 - 2012
- High-performance Computing System for Bioinformatics awarded by National Institutes of Health 2009 - 2010
- Modeling, Predicting, and Reprogramming Dynamic Cellular Networks awarded by National Science Foundation 2006 - 2008
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External Relationships
- BGI Genomics, Shenzhen, China
- Shenzhen Institute of Advanced Technologies, Shenzhen, China
- The Hebrew University of Jerusalem
- Publications & Artistic Works
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Selected Publications
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Academic Articles
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Chen, Baizhu, Wei Kang, Jing Sun, Runtao Zhu, Yue Yu, Aiguo Xia, Mei Yu, et al. “Programmable living assembly of materials by bacterial adhesion.” Nature Chemical Biology, December 21, 2021. https://doi.org/10.1038/s41589-021-00934-z.Full Text
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Duncker, Katherine E., Zachary A. Holmes, and Lingchong You. “Engineered microbial consortia: strategies and applications.” Microbial Cell Factories 20, no. 1 (November 16, 2021): 211. https://doi.org/10.1186/s12934-021-01699-9.Full Text
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Son, Hye-In, Andrea Weiss, and Lingchong You. “Design patterns for engineering genetic stability.” Current Opinion in Biomedical Engineering 19 (September 2021). https://doi.org/10.1016/j.cobme.2021.100297.Full Text
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Wang, Teng, Andrea Weiss, Yuanchi Ha, and Lingchong You. “Predicting plasmid persistence in microbial communities by coarse-grained modeling.” Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology 43, no. 9 (September 2021): e2100084. https://doi.org/10.1002/bies.202100084.Full Text
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Dai, Zhuojun, Xiaoyu Yang, Feilun Wu, Lihua Wang, Kun Xiang, Pengcheng Li, Qingqing Lv, et al. “Living fabrication of functional semi-interpenetrating polymeric materials.” Nature Communications 12, no. 1 (June 8, 2021): 3422. https://doi.org/10.1038/s41467-021-23812-7.Full Text
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Luo, Nan, Shangying Wang, Jia Lu, Xiaoyi Ouyang, and Lingchong You. “Collective colony growth is optimized by branching pattern formation in Pseudomonas aeruginosa.” Molecular Systems Biology 17, no. 4 (April 2021): e10089. https://doi.org/10.15252/msb.202010089.Full Text
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Cao, Yangxiaolu, John Neu, Andrew E. Blanchard, Ting Lu, and Lingchong You. “Repulsive expansion dynamics in colony growth and gene expression.” Plos Computational Biology 17, no. 3 (March 18, 2021): e1008168. https://doi.org/10.1371/journal.pcbi.1008168.Full Text
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Lee, Eric D., Emily R. Aurand, Douglas C. Friedman, and Douglas C. Engineering Biology Research Consortium Microbiomes Roadmapping Working Group. “Engineering Microbiomes-Looking Ahead.” Acs Synthetic Biology 9, no. 12 (December 2020): 3181–83. https://doi.org/10.1021/acssynbio.0c00558.Full Text
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Wang, Teng, and Lingchong You. “The persistence potential of transferable plasmids.” Nature Communications 11, no. 1 (November 4, 2020): 5589. https://doi.org/10.1038/s41467-020-19368-7.Full Text
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Zhang, Carolyn, Wenchen Song, Helena R. Ma, Xiao Peng, Deverick J. Anderson, Vance G. Fowler, Joshua T. Thaden, Minfeng Xiao, and Lingchong You. “Temporal encoding of bacterial identity and traits in growth dynamics.” Proc Natl Acad Sci U S A 117, no. 33 (August 18, 2020): 20202–10. https://doi.org/10.1073/pnas.2008807117.Full Text Link to Item
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Villa, Max M., Rachael J. Bloom, Justin D. Silverman, Heather K. Durand, Sharon Jiang, Anchi Wu, Eric P. Dallow, Shuqiang Huang, Lingchong You, and Lawrence A. David. “Interindividual Variation in Dietary Carbohydrate Metabolism by Gut Bacteria Revealed with Droplet Microfluidic Culture.” Msystems 5, no. 3 (June 30, 2020). https://doi.org/10.1128/mSystems.00864-19.Full Text Link to Item
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Kim, Kyeri, and Lingchong You. “Bacterial Aggregation Leads to Collective Elimination.” Trends in Microbiology 28, no. 4 (April 2020): 243–44. https://doi.org/10.1016/j.tim.2019.12.001.Full Text
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Mathey-Prevot, Bernard, Bao-Tran Parker, Carolyn Im, Cierra Hong, Peng Dong, Guang Yao, and Lingchong You. “Quantifying E2F1 protein dynamics in single cells.” Quant Biol 8, no. 1 (March 2020): 20–30. https://doi.org/10.1007/s40484-019-0193-6.Full Text Link to Item
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Sysoeva, T. A., Y. Kim, J. Rodriguez, A. J. Lopatkin, and L. You. “Growth-stage-dependent regulation of conjugation.” Aiche Journal 66, no. 3 (March 1, 2020). https://doi.org/10.1002/aic.16848.Full Text
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Bethke, Jonathan H., Adam Davidovich, Li Cheng, Allison J. Lopatkin, Wenchen Song, Joshua T. Thaden, Vance G. Fowler, Minfeng Xiao, and Lingchong You. “Environmental and genetic determinants of plasmid mobility in pathogenic Escherichia coli.” Sci Adv 6, no. 4 (January 2020): eaax3173. https://doi.org/10.1126/sciadv.aax3173.Full Text Link to Item
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Zhu, Kui, Shang Chen, Tatyana A. Sysoeva, and Lingchong You. “Universal antibiotic tolerance arising from antibiotic-triggered accumulation of pyocyanin in Pseudomonas aeruginosa.” Plos Biology 17, no. 12 (December 16, 2019): e3000573. https://doi.org/10.1371/journal.pbio.3000573.Full Text
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Lopatkin, Allison J., Jonathan M. Stokes, Erica J. Zheng, Jason H. Yang, Melissa K. Takahashi, Lingchong You, and James J. Collins. “Bacterial metabolic state more accurately predicts antibiotic lethality than growth rate.” Nature Microbiology 4, no. 12 (December 2019): 2109–17. https://doi.org/10.1038/s41564-019-0536-0.Full Text
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Tsoi, Ryan, Zhuojun Dai, and Lingchong You. “Emerging strategies for engineering microbial communities.” Biotechnology Advances 37, no. 6 (November 2019): 107372. https://doi.org/10.1016/j.biotechadv.2019.03.011.Full Text
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Dai, Zhuojun, Anna J. Lee, Stefan Roberts, Tatyana A. Sysoeva, Shuqiang Huang, Michael Dzuricky, Xiaoyu Yang, et al. “Versatile biomanufacturing through stimulus-responsive cell-material feedback.” Nature Chemical Biology 15, no. 10 (October 2019): 1017–24. https://doi.org/10.1038/s41589-019-0357-8.Full Text
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Wang, Shangying, Kai Fan, Nan Luo, Yangxiaolu Cao, Feilun Wu, Carolyn Zhang, Katherine A. Heller, and Lingchong You. “Massive computational acceleration by using neural networks to emulate mechanism-based biological models.” Nature Communications 10, no. 1 (September 25, 2019): 4354. https://doi.org/10.1038/s41467-019-12342-y.Full Text
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Shi, Xiangguang, Lingchong You, and Ruo-Yu Luo. “Glycolytic reprogramming in cancer cells: PKM2 dimer predominance induced by pulsatile PFK-1 activity.” Physical Biology 16, no. 6 (September 18, 2019): 066007. https://doi.org/10.1088/1478-3975/ab3f5a.Full Text
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Ma, Helena R., and Lingchong You. “Polar-opposite fates.” Nature Chemical Biology 15, no. 9 (September 2019): 850–52. https://doi.org/10.1038/s41589-019-0337-z.Full Text
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Simon, Joseph R., Seyed Ali Eghtesadi, Michael Dzuricky, Lingchong You, and Ashutosh Chilkoti. “Engineered Ribonucleoprotein Granules Inhibit Translation in Protocells.” Molecular Cell 75, no. 1 (July 2019): 66-75.e5. https://doi.org/10.1016/j.molcel.2019.05.010.Full Text
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Song, Wenchen, Hai-Xi Sun, Carolyn Zhang, Li Cheng, Ye Peng, Ziqing Deng, Dan Wang, et al. “Prophage Hunter: an integrative hunting tool for active prophages.” Nucleic Acids Research 47, no. W1 (July 2019): W74–80. https://doi.org/10.1093/nar/gkz380.Full Text
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Luo, Nan, Shangying Wang, and Lingchong You. “Synthetic Pattern Formation.” Biochemistry 58, no. 11 (March 2019): 1478–83. https://doi.org/10.1021/acs.biochem.8b01242.Full Text
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Wu, Feilun, Allison J. Lopatkin, Daniel A. Needs, Charlotte T. Lee, Sayan Mukherjee, and Lingchong You. “A unifying framework for interpreting and predicting mutualistic systems.” Nature Communications 10, no. 1 (January 16, 2019): 242. https://doi.org/10.1038/s41467-018-08188-5.Full Text
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Meredith, Hannah R., Virgile Andreani, Helena R. Ma, Allison J. Lopatkin, Anna J. Lee, Deverick J. Anderson, Gregory Batt, and Lingchong You. “Applying ecological resistance and resilience to dissect bacterial antibiotic responses.” Sci Adv 4, no. 12 (December 2018): eaau1873. https://doi.org/10.1126/sciadv.aau1873.Full Text Link to Item
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Dong, Peng, Manoj V. Maddali, Jaydeep K. Srimani, François Thélot, Joseph R. Nevins, Bernard Mathey-Prevot, and Lingchong You. “Author Correction: Division of labour between Myc and G1 cyclins in cell cycle commitment and pace control.” Nat Commun 9, no. 1 (November 13, 2018): 4766. https://doi.org/10.1038/s41467-018-07169-y.Full Text Link to Item
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Feng, Y., K. E. Marusak, L. You, and S. Zauscher. “Biosynthetic transition metal chalcogenide semiconductor nanoparticles: Progress in synthesis, property control and applications.” Current Opinion in Colloid and Interface Science 38 (November 1, 2018): 190–203. https://doi.org/10.1016/j.cocis.2018.11.002.Full Text
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You, Lingchong, and Eriko Takano. “Synthetic Biology: Reports from CSHA 2016 and More.” Biotechnology Journal 13, no. 5 (May 2018): e1800160. https://doi.org/10.1002/biot.201800160.Full Text
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Lee, Anna J., Shangying Wang, Hannah R. Meredith, Bihan Zhuang, Zhuojun Dai, and Lingchong You. “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 115, no. 16 (April 2, 2018): 4069–74. https://doi.org/10.1073/pnas.1719504115.Full Text
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Tsoi, Ryan, Feilun Wu, Carolyn Zhang, Sharon Bewick, David Karig, and Lingchong You. “Metabolic division of labor in microbial systems.” Proceedings of the National Academy of Sciences of the United States of America 115, no. 10 (March 2018): 2526–31. https://doi.org/10.1073/pnas.1716888115.Full Text
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Marusak, Katherine E., Julia R. Krug, Yaying Feng, Yangxiaolu Cao, Lingchong You, and Stefan Zauscher. “Bacterially driven cadmium sulfide precipitation on porous membranes: Toward platforms for photocatalytic applications.” Biointerphases 13, no. 1 (February 9, 2018): 011006. https://doi.org/10.1116/1.5008393.Full Text
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Dong, Peng, Carolyn Zhang, Bao-Tran Parker, Lingchong You, and Bernard Mathey-Prevot. “Cyclin D/CDK4/6 activity controls G1 length in mammalian cells.” Plos One 13, no. 1 (2018): e0185637. https://doi.org/10.1371/journal.pone.0185637.Full Text Link to Item
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Wu, Feilun, Jonathan H. Bethke, Meidi Wang, and Lingchong You. “Quantitative and synthetic biology approaches to combat bacterial pathogens.” Current Opinion in Biomedical Engineering 4 (December 2017): 116–26. https://doi.org/10.1016/j.cobme.2017.10.007.Full Text
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Lopatkin, Allison J., Hannah R. Meredith, Jaydeep K. Srimani, Connor Pfeiffer, Rick Durrett, and Lingchong You. “Persistence and reversal of plasmid-mediated antibiotic resistance.” Nature Communications 8, no. 1 (November 22, 2017): 1689. https://doi.org/10.1038/s41467-017-01532-1.Full Text
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Cao, Yangxiaolu, Yaying Feng, Marc D. Ryser, Kui Zhu, Gregory Herschlag, Changyong Cao, Katherine Marusak, Stefan Zauscher, and Lingchong You. “Programmable assembly of pressure sensors using pattern-forming bacteria.” Nature Biotechnology 35, no. 11 (November 2017): 1087–93. https://doi.org/10.1038/nbt.3978.Full Text
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Srimani, Jaydeep K., Shuqiang Huang, Allison J. Lopatkin, and Lingchong You. “Drug detoxification dynamics explain the postantibiotic effect.” Molecular Systems Biology 13, no. 10 (October 23, 2017): 948. https://doi.org/10.15252/msb.20177723.Full Text
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Wu, Feilun, and Lingchong You. “Hacking DNA copy number for circuit engineering.” Nature Genetics 49, no. 8 (July 2017): 1164–65. https://doi.org/10.1038/ng.3923.Full Text
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Shats, Igor, Michael Deng, Adam Davidovich, Carolyn Zhang, Jungeun S. Kwon, Dinesh Manandhar, Raluca Gordân, Guang Yao, and Lingchong You. “Expression level is a key determinant of E2F1-mediated cell fate.” Cell Death Differ 24, no. 4 (April 2017): 626–37. https://doi.org/10.1038/cdd.2017.12.Full Text Link to Item
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Tanouchi, Yu, Anand Pai, Heungwon Park, Shuqiang Huang, Nicolas E. Buchler, and Lingchong You. “Long-term growth data of Escherichia coli at a single-cell level.” Scientific Data 4 (March 28, 2017): 170036. https://doi.org/10.1038/sdata.2017.36.Full Text
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Feng, Y., E. Ngaboyamahina, K. E. Marusak, Y. Cao, L. You, J. T. Glass, and S. Zauscher. “Hybrid (Organic/Inorganic) Electrodes from Bacterially Precipitated CdS for PEC/Storage Applications.” Journal of Physical Chemistry C 121, no. 7 (February 23, 2017): 3734–43. https://doi.org/10.1021/acs.jpcc.6b11387.Full Text
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Cao, Yangxiaolu, Allison Lopatkin, and Lingchong You. “Elements of biological oscillations in time and space.” Nature Structural & Molecular Biology 23, no. 12 (December 2016): 1030–34. https://doi.org/10.1038/nsmb.3320.Full Text
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Lopatkin, Allison J., Tatyana A. Sysoeva, and Lingchong You. “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 38, no. 12 (December 2016): 1283–92. https://doi.org/10.1002/bies.201600133.Full Text
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Zhang, Carolyn, Ryan Tsoi, Feilun Wu, and Lingchong You. “Processing Oscillatory Signals by Incoherent Feedforward Loops.” Plos Computational Biology 12, no. 9 (September 13, 2016): e1005101. https://doi.org/10.1371/journal.pcbi.1005101.Full Text
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Cao, Yangxiaolu, Marc D. Ryser, Stephen Payne, Bochong Li, Christopher V. Rao, and Lingchong You. “Collective Space-Sensing Coordinates Pattern Scaling in Engineered Bacteria.” Cell 165, no. 3 (April 21, 2016): 620–30. https://doi.org/10.1016/j.cell.2016.03.006.Full Text Link to Item
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Lopatkin, Allison J., Shuqiang Huang, Robert P. Smith, Jaydeep K. Srimani, Tatyana A. Sysoeva, Sharon Bewick, David K. Karig, and Lingchong You. “Antibiotics as a selective driver for conjugation dynamics.” Nature Microbiology 1, no. 6 (April 11, 2016): 16044. https://doi.org/10.1038/nmicrobiol.2016.44.Full Text
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Zhang, Carolyn, Ryan Tsoi, and Lingchong You. “Addressing biological uncertainties in engineering gene circuits.” Integrative Biology : Quantitative Biosciences From Nano to Macro 8, no. 4 (April 2016): 456–64. https://doi.org/10.1039/c5ib00275c.Full Text
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Huang, Shuqiang, Anna Jisu Lee, Ryan Tsoi, Feilun Wu, Ying Zhang, Kam W. Leong, and Lingchong You. “Coupling spatial segregation with synthetic circuits to control bacterial survival.” Molecular Systems Biology 12, no. 2 (February 29, 2016): 859. https://doi.org/10.15252/msb.20156567.Full Text
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Marusak, K. E., Y. Feng, C. F. Eben, S. T. Payne, Y. Cao, L. You, and S. Zauscher. “Cadmium sulphide quantum dots with tunable electronic properties by bacterial precipitation.” Rsc Advances 6, no. 80 (January 2016): 76158–66. https://doi.org/10.1039/c6ra13835g.Full Text
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Huang, Shuqiang, Jaydeep K. Srimani, Anna J. Lee, Ying Zhang, Allison J. Lopatkin, Kam W. Leong, and Lingchong You. “Dynamic control and quantification of bacterial population dynamics in droplets.” Biomaterials 61 (August 2015): 239–45. https://doi.org/10.1016/j.biomaterials.2015.05.038.Full Text
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Tanouchi, Yu, Anand Pai, Heungwon Park, Shuqiang Huang, Rumen Stamatov, Nicolas E. Buchler, and Lingchong You. “A noisy linear map underlies oscillations in cell size and gene expression in bacteria.” Nature 523, no. 7560 (July 2015): 357–60. https://doi.org/10.1038/nature14562.Full Text Open Access Copy
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Lee, Tae J., Jeffrey Wong, Sena Bae, Anna Jisu Lee, Allison Lopatkin, Fan Yuan, and Lingchong You. “A power-law dependence of bacterial invasion on mammalian host receptors.” Plos Computational Biology 11, no. 4 (April 16, 2015): e1004203. https://doi.org/10.1371/journal.pcbi.1004203.Full Text
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Meredith, Hannah R., Allison J. Lopatkin, Deverick J. Anderson, and Lingchong You. “Bacterial temporal dynamics enable optimal design of antibiotic treatment.” Plos Comput Biol 11, no. 4 (April 2015): e1004201. https://doi.org/10.1371/journal.pcbi.1004201.Full Text Link to Item
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Meredith, Hannah R., Jaydeep K. Srimani, Anna J. Lee, Allison J. Lopatkin, and Lingchong You. “Collective antibiotic tolerance: mechanisms, dynamics and intervention.” Nature Chemical Biology 11, no. 3 (March 2015): 182–88. https://doi.org/10.1038/nchembio.1754.Full Text
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Eidum, D., K. Asthana, S. Unni, M. Deng, and L. You. “Construction, visualization, and analysis of biological network models in Dynetica.” Quantitative Biology 2, no. 4 (December 1, 2014): 142–50. https://doi.org/10.1007/s40484-014-0036-4.Full Text
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Srimani, Jaydeep K., and Lingchong You. “Emergent dynamics from quorum eavesdropping.” Chemistry & Biology 21, no. 12 (December 2014): 1601–2. https://doi.org/10.1016/j.chembiol.2014.12.002.Full Text
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Lopatkin, Allison J., and Lingchong You. “Synthetic biology looks good on paper.” Cell 159, no. 4 (November 2014): 718–20. https://doi.org/10.1016/j.cell.2014.10.003.Full Text
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Li, Bochong, and Lingchong You. “Stochastic sensitivity analysis and kernel inference via distributional data.” Biophysical Journal 107, no. 5 (September 2014): 1247–55. https://doi.org/10.1016/j.bpj.2014.07.025.Full Text
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Dong, Peng, Manoj V. Maddali, Jaydeep K. Srimani, François Thélot, Joseph R. Nevins, Bernard Mathey-Prevot, and Lingchong You. “Division of labour between Myc and G1 cyclins in cell cycle commitment and pace control.” Nat Commun 5 (September 1, 2014): 4750. https://doi.org/10.1038/ncomms5750.Full Text Link to Item
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Tan, Cheemeng, Robert Phillip Smith, Ming-Chi Tsai, Russell Schwartz, and Lingchong You. “Phenotypic signatures arising from unbalanced bacterial growth.” Plos Computational Biology 10, no. 8 (August 7, 2014): e1003751. https://doi.org/10.1371/journal.pcbi.1003751.Full Text
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Pai, Anand, Jaydeep K. Srimani, Yu Tanouchi, and Lingchong You. “Generic metric to quantify quorum sensing activation dynamics.” Acs Synthetic Biology 3, no. 4 (April 2014): 220–27. https://doi.org/10.1021/sb400069w.Full Text
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Lee, Anna Jisu, and Lingchong You. “Cell biology. Cells listen to their inner voice.” Science (New York, N.Y.) 343, no. 6171 (February 2014): 624–25. https://doi.org/10.1126/science.1250244.Full Text
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Smith, Robert, Cheemeng Tan, Jaydeep K. Srimani, Anand Pai, Katherine A. Riccione, Hao Song, and Lingchong You. “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 111, no. 5 (February 2014): 1969–74. https://doi.org/10.1073/pnas.1315954111.Full Text
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Payne, Stephen, and Lingchong You. “Engineered cell-cell communication and its applications.” Advances in Biochemical Engineering/Biotechnology 146 (January 2014): 97–121. https://doi.org/10.1007/10_2013_249.Full Text
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Srimani, Jaydeep K., Guang Yao, John Neu, Yu Tanouchi, Tae Jun Lee, and Lingchong You. “Linear population allocation by bistable switches in response to transient stimulation.” Plos One 9, no. 8 (January 2014): e105408. https://doi.org/10.1371/journal.pone.0105408.Full Text
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Payne, Stephen, Bochong Li, Yangxiaolu Cao, David Schaeffer, Marc D. Ryser, and Lingchong You. “Temporal control of self-organized pattern formation without morphogen gradients in bacteria.” Mol Syst Biol 9 (October 8, 2013): 697. https://doi.org/10.1038/msb.2013.55.Full Text Link to Item
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Shats, Igor, Michael L. Gatza, Beiyu Liu, Steven P. Angus, Lingchong You, and Joseph R. Nevins. “FOXO transcription factors control E2F1 transcriptional specificity and apoptotic function.” Cancer Research 73, no. 19 (October 2013): 6056–67. https://doi.org/10.1158/0008-5472.can-13-0453.Full Text
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Smith, R. P., Y. Tanouchi, and L. You. “Synthetic Microbial Consortia and their Applications,” August 27, 2013, 243–58. https://doi.org/10.1016/B978-0-12-394430-6.00013-3.Full Text
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Li, B., and L. You. “Predictive power of cell-to-cell variability.” Quantitative Biology 1, no. 2 (June 1, 2013): 131–39. https://doi.org/10.1007/s40484-013-0013-3.Full Text
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Tanouchi, Yu, Anna Jisu Lee, Hannah Meredith, and Lingchong You. “Programmed cell death in bacteria and implications for antibiotic therapy.” Trends in Microbiology 21, no. 6 (June 2013): 265–70. https://doi.org/10.1016/j.tim.2013.04.001.Full Text
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Zhang, Ying, Yi-Ping Ho, Ya-Ling Chiu, Hon Fai Chan, Ben Chlebina, Tom Schuhmann, Lingchong You, and Kam W. Leong. “A programmable microenvironment for cellular studies via microfluidics-generated double emulsions.” Biomaterials 34, no. 19 (June 2013): 4564–72. https://doi.org/10.1016/j.biomaterials.2013.03.002.Full Text
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Pai, Anand, Yu Tanouchi, and Lingchong You. “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 109, no. 48 (November 9, 2012): 19810–15. https://doi.org/10.1073/pnas.1211072109.Full Text
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Tanouchi, Yu, Robert P. Smith, and Lingchong You. “Engineering microbial systems to explore ecological and evolutionary dynamics.” Current Opinion in Biotechnology 23, no. 5 (October 2012): 791–97. https://doi.org/10.1016/j.copbio.2012.01.006.Full Text
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Riccione, Katherine A., Robert P. Smith, Anna J. Lee, and Lingchong You. “A synthetic biology approach to understanding cellular information processing.” Acs Synthetic Biology 1, no. 9 (September 2012): 389–402. https://doi.org/10.1021/sb300044r.Full Text
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Chin, Jason W., and Lingchong You. “A different life?” Current Opinion in Chemical Biology 16, no. 3–4 (August 2012): 243–44. https://doi.org/10.1016/j.cbpa.2012.07.009.Full Text
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Stone, Jana E., Philip N. Benfey, and Lingchong You. “Promoting collaborative interdisciplinary research at the Duke Center for Systems Biology.” Acs Synthetic Biology 1, no. 5 (May 2012): 153–55. https://doi.org/10.1021/sb300036z.Full Text
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Payne, Stephen, Robert Phillip Smith, and Lingchong You. “Quantitative analysis of the spatiotemporal dynamics of a synthetic predator-prey ecosystem.” Methods in Molecular Biology (Clifton, N.J.) 813 (January 2012): 315–30. https://doi.org/10.1007/978-1-61779-412-4_19.Full Text
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Song, Hao, and Lingchong You. “Modeling spatiotemporal dynamics of bacterial populations.” Methods in Molecular Biology (Clifton, N.J.) 880 (January 2012): 243–54. https://doi.org/10.1007/978-1-61779-833-7_11.Full Text
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Tan, Cheemeng, Robert Phillip Smith, Jaydeep K. Srimani, Katherine A. Riccione, Sameer Prasada, Meta Kuehn, and Lingchong You. “The inoculum effect and band-pass bacterial response to periodic antibiotic treatment.” Mol Syst Biol 8 (2012): 617. https://doi.org/10.1038/msb.2012.49.Full Text Open Access Copy Link to Item
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Tanouchi, Yu, Anand Pai, Nicolas E. Buchler, and Lingchong You. “Programming stress-induced altruistic death in engineered bacteria.” Molecular Systems Biology 8 (January 2012): 626. https://doi.org/10.1038/msb.2012.57.Full Text Open Access Copy
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Wong, Jeffrey V., Bochong Li, and Lingchong You. “Tension and robustness in multitasking cellular networks.” Plos Computational Biology 8, no. 4 (January 2012): e1002491. https://doi.org/10.1371/journal.pcbi.1002491.Full Text
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Bonassi, Fernando V., Lingchong You, and Mike West. “Bayesian learning from marginal data in bionetwork models.” Statistical Applications in Genetics and Molecular Biology 10, no. 1 (October 27, 2011). https://doi.org/10.2202/1544-6115.1684.Full Text
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Hallen, Mark, Bochong Li, Yu Tanouchi, Cheemeng Tan, Mike West, and Lingchong You. “Computation of steady-state probability distributions in stochastic models of cellular networks.” Plos Computational Biology 7, no. 10 (October 13, 2011): e1002209. https://doi.org/10.1371/journal.pcbi.1002209.Full Text
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Wong, Jeffrey V., Peng Dong, Joseph R. Nevins, Bernard Mathey-Prevot, and Lingchong You. “Network calisthenics: control of E2F dynamics in cell cycle entry.” Cell Cycle 10, no. 18 (September 15, 2011): 3086–94. https://doi.org/10.4161/cc.10.18.17350.Full Text Link to Item
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Song, Hao, Stephen Payne, Cheemeng Tan, and Lingchong You. “Programming microbial population dynamics by engineered cell-cell communication.” Biotechnology Journal 6, no. 7 (July 2011): 837–49. https://doi.org/10.1002/biot.201100132.Full Text
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Elliott, Nelita, Tae Lee, Lingchong You, and Fan Yuan. “Proliferation behavior of E. coli in a three-dimensional in vitro tumor model.” Integrative Biology : Quantitative Biosciences From Nano to Macro 3, no. 6 (June 2011): 696–705. https://doi.org/10.1039/c0ib00137f.Full Text
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Wong, J. V., G. Yao, J. R. Nevins, and L. You. “Using noisy gene expression mediated by engineered adenovirus to probe signaling dynamics in mammalian cells.” Methods in Enzymology 497 (May 30, 2011): 221–37. https://doi.org/10.1016/B978-0-12-385075-100010-X.Full Text
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Yao, Guang, Cheemeng Tan, Mike West, Joseph R. Nevins, and Lingchong You. “Origin of bistability underlying mammalian cell cycle entry.” Molecular Systems Biology 7 (April 2011): 485. https://doi.org/10.1038/msb.2011.19.Full Text
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Wong, Jeffrey V., Guang Yao, Joseph R. Nevins, and Lingchong You. “Viral-mediated noisy gene expression reveals biphasic E2f1 response to MYC.” Molecular Cell 41, no. 3 (February 2011): 275–85. https://doi.org/10.1016/j.molcel.2011.01.014.Full Text
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Li, Bochong, and Lingchong You. “Synthetic biology: Division of logic labour.” Nature 469, no. 7329 (January 2011): 171–72. https://doi.org/10.1038/469171a.Full Text
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Wong, Jeffrey V., Guang Yao, Joseph R. Nevins, and Lingchong You. “Using noisy gene expression mediated by engineered adenovirus to probe signaling dynamics in mammalian cells.” Methods in Enzymology 497 (January 2011): 221–37. https://doi.org/10.1016/b978-0-12-385075-1.00010-x.Full Text
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Lee, Tae J., Guang Yao, Dorothy C. Bennett, Joseph R. Nevins, and Lingchong You. “Stochastic E2F activation and reconciliation of phenomenological cell-cycle models.” Plos Biology 8, no. 9 (September 21, 2010). https://doi.org/10.1371/journal.pbio.1000488.Full Text Open Access Copy
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Marguet, Philippe, Yu Tanouchi, Eric Spitz, Cameron Smith, and Lingchong You. “Oscillations by minimal bacterial suicide circuits reveal hidden facets of host-circuit physiology.” Plos One 5, no. 7 (July 30, 2010): e11909. https://doi.org/10.1371/journal.pone.0011909.Full Text Open Access Copy
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Wang, Quanli, Jarad Niemi, Chee-Meng Tan, Lingchong You, and Mike West. “Image segmentation and dynamic lineage analysis in single-cell fluorescence microscopy.” Cytometry. Part a : The Journal of the International Society for Analytical Cytology 77, no. 1 (January 2010): 101–10. https://doi.org/10.1002/cyto.a.20812.Full Text
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Song, Hao, Stephen Payne, Meagan Gray, and Lingchong You. “Spatiotemporal modulation of biodiversity in a synthetic chemical-mediated ecosystem.” Nature Chemical Biology 5, no. 12 (December 2009): 929–35. https://doi.org/10.1038/nchembio.244.Full Text
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Tan, Cheemeng, Philippe Marguet, and Lingchong You. “Emergent bistability by a growth-modulating positive feedback circuit.” Nature Chemical Biology 5, no. 11 (November 2009): 842–48. https://doi.org/10.1038/nchembio.218.Full Text
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Pai, Anand, Yu Tanouchi, Cynthia H. Collins, and Lingchong You. “Engineering multicellular systems by cell-cell communication.” Current Opinion in Biotechnology 20, no. 4 (August 2009): 461–70. https://doi.org/10.1016/j.copbio.2009.08.006.Full Text
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Tanouchi, Yu, Anand Pai, and Lingchong You. “Decoding biological principles using gene circuits.” Molecular Biosystems 5, no. 7 (July 2009): 695–703. https://doi.org/10.1039/b901584c.Full Text
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Isaacs, Farren J., and Lingchong You. “A brave new synthetic world. A report of the first meeting on 'Frontiers in Synthetic Biology', Boston, USA, 1-2 December 2008.” Genome Biology 10, no. 2 (February 3, 2009): 302. https://doi.org/10.1186/gb-2009-10-2-302.Full Text
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Brenner, K., L. You, and F. H. Arnold. “Response to Goldman and Brown: Making sense of microbial consortia using ecology and evolution.” Trends in Biotechnology 27, no. 1 (January 1, 2009): 4. https://doi.org/10.1016/j.tibtech.2008.10.004.Full Text
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Pai, Anand, and Lingchong You. “Optimal tuning of bacterial sensing potential.” Molecular Systems Biology 5 (January 2009): 286. https://doi.org/10.1038/msb.2009.43.Full Text
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Song, H., M. Gray, and L. You. “Spatiotemporal modulation of biodiversity in a synthetic predator-prey ecosystem.” Aiche Annual Meeting, Conference Proceedings, December 1, 2008.
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Smith, Cameron, Hao Song, and Lingchong You. “Signal discrimination by differential regulation of protein stability in quorum sensing.” Journal of Molecular Biology 382, no. 5 (October 2008): 1290–97. https://doi.org/10.1016/j.jmb.2008.08.009.Full Text
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Brenner, Katie, Lingchong You, and Frances H. Arnold. “Engineering microbial consortia: a new frontier in synthetic biology.” Trends in Biotechnology 26, no. 9 (September 2008): 483–89. https://doi.org/10.1016/j.tibtech.2008.05.004.Full Text
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Tanouchi, Yu, Dennis Tu, Jungsang Kim, and Lingchong You. “Noise reduction by diffusional dissipation in a minimal quorum sensing motif.” Plos Comput Biol 4, no. 8 (August 29, 2008): e1000167. https://doi.org/10.1371/journal.pcbi.1000167.Full Text Link to Item
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Yao, Guang, Tae Jun Lee, Seiichi Mori, Joseph R. Nevins, and Lingchong You. “A bistable Rb-E2F switch underlies the restriction point.” Nature Cell Biology 10, no. 4 (April 2008): 476–82. https://doi.org/10.1038/ncb1711.Full Text
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Lee, Tae, Guang Yao, Joseph Nevins, and Lingchong You. “Sensing and integration of Erk and PI3K signals by Myc.” Plos Computational Biology 4, no. 2 (February 29, 2008): e1000013. https://doi.org/10.1371/journal.pcbi.1000013.Full Text
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Balagaddé, Frederick K., Hao Song, Jun Ozaki, Cynthia H. Collins, Matthew Barnet, Frances H. Arnold, Stephen R. Quake, and Lingchong You. “A synthetic Escherichia coli predator-prey ecosystem.” Molecular Systems Biology 4 (January 2008): 187. https://doi.org/10.1038/msb.2008.24.Full Text
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Wong, Jeffrey V., Hao Song, and Lingchong You. “A whole more than the sum of its synthetic parts.” Acs Chemical Biology 3, no. 1 (January 2008): 27–29. https://doi.org/10.1021/cb700256w.Full Text
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Tan, Cheemeng, Faisal Reza, and Lingchong You. “Noise-limited frequency signal transmission in gene circuits.” Biophysical Journal 93, no. 11 (December 2007): 3753–61. https://doi.org/10.1529/biophysj.107.110403.Full Text
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You, L. “Engineering synthetic killer circuits in bacteria.” Proceedings Design Automation Conference, August 2, 2007, 636–37. https://doi.org/10.1109/DAC.2007.375242.Full Text
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Marguet, Philippe, Frederick Balagadde, Cheemeng Tan, and Lingchong You. “Biology by design: reduction and synthesis of cellular components and behaviour.” Journal of the Royal Society, Interface 4, no. 15 (August 2007): 607–23. https://doi.org/10.1098/rsif.2006.0206.Full Text
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Tan, Cheemeng, Hao Song, Jarad Niemi, and Lingchong You. “A synthetic biology challenge: making cells compute.” Molecular Biosystems 3, no. 5 (May 2007): 343–53. https://doi.org/10.1039/b618473c.Full Text
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Reza, F., K. Chandran, M. Feltz, A. Heinz, E. Josephs, P. O’Brien, B. Dyke, et al. “Engineering novel synthetic biological systems.” Iet Synthetic Biology 1 (2007): 48–52.
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Song, Hao, and Lingchong You. “Evolving sensitivity.” Acs Chemical Biology 1, no. 11 (December 2006): 681–82. https://doi.org/10.1021/cb6004596.Full Text
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You, L., and J. Yin. “Evolutionary design on a budget: robustness and optimality of bacteriophage T7.” Systems Biology 153, no. 2 (March 2006): 46–52. https://doi.org/10.1049/ip-syb:20050026.Full Text
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Ozaki, J., M. Barnet, C. H. Collins, F. H. Arnold, and L. You. “A synthetic E.Coli predator-prey system.” Aiche Annual Meeting, Conference Proceedings, December 1, 2005, 11590.
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Balagaddé, Frederick K., Lingchong You, Carl L. Hansen, Frances H. Arnold, and Stephen R. Quake. “Long-term monitoring of bacteria undergoing programmed population control in a microchemostat.” Science (New York, N.Y.) 309, no. 5731 (July 2005): 137–40. https://doi.org/10.1126/science.1109173.Full Text
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You, Lingchong, Robert Sidney Cox, Ron Weiss, and Frances H. Arnold. “Programmed population control by cell-cell communication and regulated killing.” Nature 428, no. 6985 (April 4, 2004): 868–71. https://doi.org/10.1038/nature02491.Full Text
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You, Lingchong. “Toward computational systems biology.” Cell Biochemistry and Biophysics 40, no. 2 (January 2004): 167–84. https://doi.org/10.1385/cbb:40:2:167.Full Text
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You, Lingchong, Apirak Hoonlor, and John Yin. “Modeling biological systems using Dynetica--a simulator of dynamic networks.” Bioinformatics (Oxford, England) 19, no. 3 (February 2003): 435–36. https://doi.org/10.1093/bioinformatics/btg009.Full Text
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Srivastava, R., L. You, J. Summers, and J. Yin. “Stochastic vs. deterministic modeling of intracellular viral kinetics.” Journal of Theoretical Biology 218, no. 3 (October 2002): 309–21. https://doi.org/10.1006/jtbi.2002.3078.Full Text
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You, Lingchong, Patrick F. Suthers, and John Yin. “Effects of Escherichia coli physiology on growth of phage T7 in vivo and in silico.” Journal of Bacteriology 184, no. 7 (April 2002): 1888–94. https://doi.org/10.1128/jb.184.7.1888-1894.2002.Full Text
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You, Lingchong, and John Yin. “Dependence of epistasis on environment and mutation severity as revealed by in silico mutagenesis of phage t7.” Genetics 160, no. 4 (April 2002): 1273–81. https://doi.org/10.1093/genetics/160.4.1273.Full Text
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You, L., and J. Yin. “Simulating the growth of viruses.” Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, January 2001, 532–43. https://doi.org/10.1142/9789814447362_0051.Full Text
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You, L., and J. Yin. “Patterns of regulation from mRNA and protein time series.” Metabolic Engineering 2, no. 3 (July 2000): 210–17. https://doi.org/10.1006/mben.1999.0139.Full Text
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Endy, D., L. You, J. Yin, and I. J. Molineux. “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 97, no. 10 (May 2000): 5375–80. https://doi.org/10.1073/pnas.090101397.Full Text
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You, L., and J. Yin. “Amplification and spread of viruses in a growing plaque.” Journal of Theoretical Biology 200, no. 4 (October 1999): 365–73. https://doi.org/10.1006/jtbi.1999.1001.Full Text
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Endy, D., L. You, I. J. Molineux, and J. Yin. “Prediction, design, and characterization of alternate genetic element orders for bacteriophage T7.” Abstracts of Papers of the American Chemical Society 217 (March 1999): U205–U205.
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You, L., Q. Liu, Y. Shi, C. X. Wang, M. Lahaye, and V. Tran. “The conformational study of β-D-GlcA-(1,4) -L-Rha in solution by NMR and molecular dynamics simulations.” Chemical Physics 224, no. 1 (November 15, 1997): 81–94. https://doi.org/10.1016/S0301-0104(97)00246-2.Full Text
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Conference Papers
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Sysoeva, Tatyana A., Youlim Kim, and Lingchong You. “REGULATION OF CONJUGATIVE TRANSFER OF beta-LACTAM RESISTANCE FROM UROPATHOGENIC STRAINS OF ESCHERICHIA COLI.” In Journal of Urology, 199:E285–E285. ELSEVIER SCIENCE INC, 2018.Link to Item
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Sysoeva, Tatyana, and Lingchong You. “REGULATION OF CONJUGATIVE TRANSFER OF B-LACTAM RESISTANCE FROM UROPATHOGENIC STRAINS OF ESCHERICHIA COLI.” In Neurourology and Urodynamics, 37:S529–30. WILEY, 2018.Link to Item
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- Teaching & Mentoring
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Recent Courses
- BIOLOGY 293-1: Research Independent Study 2022
- BME 574: Modeling and Engineering Gene Circuits (GE, MC) 2022
- CBB 574: Modeling and Engineering Gene Circuits (GE, MC) 2022
- MGM 593: Research Independent Study 2022
- PHARM 394: Research Independent Study 2022
- BME 494: Projects in Biomedical Engineering (GE) 2021
- BME 574: Modeling and Engineering Gene Circuits (GE, MC) 2021
- BME 791: Graduate Independent Study 2021
- CBB 574: Modeling and Engineering Gene Circuits (GE, MC) 2021
- EGR 393: Research Projects in Engineering 2021
- MGM 293: Research Independent Study I 2021
- MGM 593: Research Independent Study 2021
- PHARM 394: Research Independent Study 2021
- BME 574: Modeling and Engineering Gene Circuits (GE, MC) 2020
- CBB 574: Modeling and Engineering Gene Circuits (GE, MC) 2020
- EGR 393: Research Projects in Engineering 2020
- MGM 293: Research Independent Study I 2020
- MGM 593: Research Independent Study 2020
- PHARM 394: Research Independent Study 2020
- PHARM 493: Research Independent Study 2020
- Scholarly, Clinical, & Service Activities
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Outreach & Engaged Scholarship
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