20022019
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Research Output 2002 2019

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2019

Synthetic, Context-Dependent Microbial Consortium of Predator and Prey

Lu, T., Liu, F., Mao, J. & Hua, Q., Jan 1 2019, In : ACS synthetic biology.

Research output: Contribution to journalArticle

Microbial Consortia
Ecosystems
Ecosystem
Microbial Interactions
Synthetic Biology
2018

Bacterial Consortium-Based Sensing System for Detecting Organophosphorus Pesticides

Khatun, M. A., Hoque, M. A., Zhang, Y., Lu, T., Cui, L., Zhou, N. Y. & Feng, Y., Sep 4 2018, In : Analytical chemistry. 90, 17, p. 10577-10584 8 p.

Research output: Contribution to journalArticle

Pesticides
Galactosidases
Impurities
Ecosystems
Agriculture

Designing microbial consortia with defined social interactions

Kong, W., Meldgin, D. R., Collins, J. J. & Lu, T., Aug 1 2018, In : Nature chemical biology. 14, 8, p. 821-829 9 p.

Research output: Contribution to journalArticle

Microbial Consortia
Interpersonal Relations
Ecosystem
Synthetic Biology
Symbiosis

Developing a Synthetic Biology Toolkit for Comamonas testosteroni, an Emerging Cellular Chassis for Bioremediation

Tang, Q., Lu, T. & Liu, S. J., Jul 20 2018, In : ACS synthetic biology. 7, 7, p. 1753-1762 10 p.

Research output: Contribution to journalArticle

Comamonas testosteroni
Synthetic Biology
Environmental Biodegradation
Bioremediation
Chassis
Clostridium beijerinckii
Flavin Mononucleotide
Clostridium
Fluorescence
Oxygen

Engineering the bacterium Comamonas testosteroni CNB-1: Plasmid curing and genetic manipulation

Tang, Q., Lu, T. & Liu, S. J., May 15 2018, In : Biochemical Engineering Journal. 133, p. 74-82 9 p.

Research output: Contribution to journalArticle

Comamonas testosteroni
Chassis
Curing
Bacteria
Plasmids

Spatial interference scale as a determinant of microbial range expansion

Ozgen, V. C., Kong, W., Blanchard, A. E., Liu, F. & Lu, T., Nov 21 2018, In : Science Advances. 4, 11, eaau0695.

Research output: Contribution to journalArticle

Ecosystem
Interpersonal Relations
Noise
Population
Psychological Extinction

Stochastic Turing patterns in a synthetic bacterial population

Karig, D., Michael Martini, K., Lu, T., DeLateur, N. A., Goldenfeld, N. D. & Weiss, R., Jun 26 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 26, p. 6572-6577 6 p.

Research output: Contribution to journalArticle

Morphogenesis
Gene Regulatory Networks
Population
Parturition
Bacteria
2017

An integrative circuit-host modelling framework for predicting synthetic gene network behaviours /631/553/552 /631/553/2695 article

Liao, C., Blanchard, A. E. & Lu, T., Dec 1 2017, In : Nature Microbiology. 2, 12, p. 1658-1666 9 p.

Research output: Contribution to journalArticle

Synthetic Genes
Gene Regulatory Networks
Synthetic Biology
Population Dynamics
Ecology

Characterization of a Clostridium beijerinckii spo0A mutant and its application for butyl butyrate production

Seo, S. O., Wang, Y., Lu, T., Jin, Y-S. & Blaschek, H-P. M., Jan 1 2017, In : Biotechnology and bioengineering. 114, 1, p. 106-112 7 p.

Research output: Contribution to journalArticle

Clostridium beijerinckii
Clostridium
Butenes
Fermentation
Butyrates

Engineering robust and tunable spatial structures with synthetic gene circuits

Kong, W., Blanchard, A. E., Liao, C. & Lu, T., Jan 1 2017, In : Nucleic acids research. 45, 2, p. 1005-1014 10 p.

Research output: Contribution to journalArticle

Nisin
Synthetic Genes
Gene Regulatory Networks
Synthetic Biology
Bioengineering

Genomic, Transcriptional, and Phenotypic Analysis of the Glucose Derepressed Clostridium beijerinckii Mutant Exhibiting Acid Crash Phenotype

Seo, S. O., Janssen, H., Magis, A., Wang, Y., Lu, T., Price, N. D., Jin, Y-S. & Blaschek, H-P. M., Nov 2017, In : Biotechnology Journal. 12, 11, 1700182.

Research output: Contribution to journalArticle

Clostridium beijerinckii
Phenotype
Glucose
Acids
Fermentation
2016

An Ecological Understanding of Quorum Sensing-Controlled Bacteriocin Synthesis

Blanchard, A. E., Liao, C. & Lu, T., Sep 1 2016, In : Cellular and Molecular Bioengineering. 9, 3, p. 443-454 12 p.

Research output: Contribution to journalArticle

Quorum Sensing
Bacteriocins
Synthesis
Costs
Trade-offs
Clostridium beijerinckii
Clustered Regularly Interspaced Short Palindromic Repeats
Bacterial Genomes
Clostridium
Nucleotides

Gene transcription repression in Clostridium beijerinckii using CRISPR-dCas9

Wang, Y., Zhang, Z. T., Seo, S. O., Lynn, P., Lu, T., Jin, Y-S. & Blaschek, H-P. M., Dec 1 2016, In : Biotechnology and bioengineering. 113, 12, p. 2739-2743 5 p.

Research output: Contribution to journalArticle

Clostridium beijerinckii
Clustered Regularly Interspaced Short Palindromic Repeats
Clostridium
Transcription
Genes

Population-Dynamic Modeling of Bacterial Horizontal Gene Transfer by Natural Transformation

Mao, J. & Lu, T., Jan 5 2016, In : Biophysical journal. 110, 1, p. 258-268 11 p.

Research output: Contribution to journalArticle

Bacterial Genes
Horizontal Gene Transfer
Population Dynamics
Neisseria gonorrhoeae
Noise
2015

A gene network engineering platform for lactic acid bacteria

Kong, W., Kapuganti, V. S. & Lu, T., Oct 9 2015, In : Nucleic acids research. 44, 4, e37.

Research output: Contribution to journalArticle

Gene Regulatory Networks
Nisin
Lactic Acid
Synthetic Biology
Bacteria

Autonomous production of 1,4-butanediol via a de novo biosynthesis pathway in engineered Escherichia coli

Liu, H. & Lu, T., May 1 2015, In : Metabolic Engineering. 29, p. 135-141 7 p.

Research output: Contribution to journalArticle

Biosynthesis
Escherichia coli
Production control
Metabolic engineering
Carbon

Bacterial social interactions drive the emergence of differential spatial colony structures

Blanchard, A. E. & Lu, T., Sep 16 2015, In : BMC Systems Biology. 9, 1, 59.

Research output: Contribution to journalArticle

Social Interaction
Interpersonal Relations
Mathematical models
Microbial Consortia
Mutualism

Integrated, systems metabolic picture of acetone-butanol-ethanol fermentation by Clostridium acetobutylicum

Liao, C., Seo, S. O., Celik, V., Liu, H., Kong, W., Wang, Y., Blaschek, H-P. M., Jin, Y-S. & Lu, T., Jul 7 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 27, p. 8505-8510 6 p.

Research output: Contribution to journalArticle

Clostridium acetobutylicum
Butanols
Acetone
Fermentation
Ethanol

Markerless chromosomal gene deletion in Clostridium beijerinckii using CRISPR/Cas9 system

Wang, Y., Zhang, Z. T., Seo, S. O., Choi, K., Lu, T., Jin, Y-S. & Blaschek, H-P. M., Apr 1 2015, In : Journal of Biotechnology. 200, p. 1-5 5 p.

Research output: Contribution to journalArticle

Clostridium beijerinckii
Clustered Regularly Interspaced Short Palindromic Repeats
Clostridium
Gene Deletion
Genes

Slow and steady wins the race: A bacterial exploitative competition strategy in fluctuating environments

Mao, J., Blanchard, A. E. & Lu, T., Mar 20 2015, In : ACS synthetic biology. 4, 3, p. 240-248 9 p.

Research output: Contribution to journalArticle

Synthetic Biology
Growth
Microbial Consortia
Population dynamics
Gene Regulatory Networks
2014

Cloning and optimization of a nisin biosynthesis pathway for bacteriocin harvest

Kong, W. & Lu, T., Jul 18 2014, In : ACS synthetic biology. 3, 7, p. 439-445 7 p.

Research output: Contribution to journalArticle

Nisin
Bacteriocins
Cloning
Biosynthesis
Organism Cloning

Extinction, coexistence, and localized patterns of a bacterial population with contact-dependent inhibition

Blanchard, A. E., Celik, V. & Lu, T., Feb 27 2014, In : BMC Systems Biology. 8, 1, 23.

Research output: Contribution to journalArticle

Contact Inhibition
Coexistence
Extinction
Contact
Dependent

MEP pathway-mediated isopentenol production in metabolically engineered Escherichia coli

Liu, H., Wang, Y., Tang, Q., Kong, W., Chung, W. J. & Lu, T., Sep 12 2014, In : Microbial cell factories. 13, 1, 135.

Research output: Contribution to journalArticle

Escherichia coli
Glycolysis
Phosphates
Pentoses
Pentose Phosphate Pathway
2013

A minimal transcriptional controlling network of regulatory T cell development

Liao, C. & Lu, T., Nov 4 2013, In : Journal of Physical Chemistry B. 117, 42, p. 12995-13004 10 p.

Research output: Contribution to journalArticle

T-cells
Gene Regulatory Networks
Regulatory T-Lymphocytes
T-Lymphocytes
Immune System
2012

A multiply redundant genetic switch 'locks in' the transcriptional signature of regulatory T cells

Fu, W., Ergun, A., Lu, T., Hill, J. A., Haxhinasto, S., Fassett, M. S., Gazit, R., Adoro, S., Glimcher, L., Chan, S., Kastner, P., Rossi, D., Collins, J. J., Mathis, D. & Benoist, C., Oct 1 2012, In : Nature Immunology. 13, 10, p. 972-980 9 p.

Research output: Contribution to journalArticle

Regulatory T-Lymphocytes
Transcription Factors
Cell Physiological Phenomena
Cell Differentiation
Phenotype
2011

Automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks

Beal, J., Lu, T. & Weiss, R., Aug 10 2011, In : PloS one. 6, 8, e22490.

Research output: Contribution to journalArticle

Programming Languages
Biological systems
Computer programming languages
Gene Regulatory Networks
Genes

Investigating the Impact of Uncertainty About Item Parameters on Ability Estimation

Zhang, J., Xie, M., Song, X. & Lu, T., Jan 1 2011, In : Psychometrika. 76, 1, p. 97-118 22 p.

Research output: Contribution to journalArticle

Maximum likelihood
Uncertainty
Estimator
Weighted Likelihood
Maximum Likelihood Estimator
2008

A molecular noise generator

Lu, T., Ferry, M., Weiss, R. & Hasty, J., Sep 1 2008, In : Physical Biology. 5, 3, 036006.

Research output: Contribution to journalArticle

Noise
Gene Expression
DNA
Genes
Proteins
2007

Phenotypic variability of growing cellular populations

Lu, T., Shen, T., Bennett, M. R., Wolynes, P. G. & Hasty, J., Nov 27 2007, In : Proceedings of the National Academy of Sciences of the United States of America. 104, 48, p. 18982-18987 6 p.

Research output: Contribution to journalArticle

Population
Population Growth
Phenotype
Growth
Epigenomics
2006

Effective temperature in stochastic kinetics and gene networks

Lu, T., Hasty, J. & Wolynes, P. G., Jan 1 2006, In : Biophysical journal. 91, 1, p. 84-94 11 p.

Research output: Contribution to journalArticle

Gene Regulatory Networks
Temperature
Language
Glass
Noise

Nonequilibrium self-assembly of linear fibers: Microscopic treatment of growth, decay, catastrophe and rescue

Zong, C., Lu, T., Shen, T. & Wolynes, P. G., Mar 1 2006, In : Physical Biology. 3, 1, p. 83-92 10 p.

Research output: Contribution to journalArticle

Microtubules
Growth
Cell Division
Cell Movement
Proteins

Statistics of cellular signal transduction as a race to the nucleus by multiple random walkers in compartment/phosphorylation space

Lu, T., Shen, T., Zong, C., Hasty, J. & Wolynes, P. G., Nov 7 2006, In : Proceedings of the National Academy of Sciences of the United States of America. 103, 45, p. 16752-16757 6 p.

Research output: Contribution to journalArticle

Walkers
Signal Transduction
Phosphorylation
Enzymes
Phosphates
2004

Cellular growth and division in the Gillespie algorithm.

Lu, T., Volfson, D., Tsimring, L. & Hasty, J., Jun 2004, In : Systems biology. 1, 1, p. 121-128 8 p.

Research output: Contribution to journalArticle

Division
Reaction Rate
Reaction rates
Growth
Hybrid Simulation