Publications

Preprints

C. M. Blassick, J. B. Lugagne, M. J. Dunlop. "Dynamic Heterogeneity in an E. coli Stress Response Regulon Mediates Gene Activation and Antimicrobial Peptide Tolerance."
[bioRxiv]

R. N. Alnahhas, V. Andreani, M. J. Dunlop. "Evaluating the Predictive Power of Combined Gene Expression Dynamics from Single Cells on Antibiotic Survival."
[bioRxiv]

O. M. O'Connor, M. J. Dunlop. "Cell-TRACTR: A Transformer-based Model for End-to-end Segmentation and Tracking of Cells."
[bioRxiv]

J. W. Ribis, C. A. Nieto-Acuña, Q. Dong, N. V. DiBenedetto, A. Mehra, I. Nagawa, I. El Meouche, B. B. Aldridge, M. J. Dunlop, R. Tamayo, A. Singh, A. Shen. "Unique Growth and Morphology Properties of Clade 5 Clostridioides difficile Strains Revealed by Single-cell Time-lapse Microscopy."
[bioRxiv]

2024

F. Jafarbeglou, M. J. Dunlop. "Red Light Responsive Cre Recombinase for Bacterial Optogenetics."
ACS Synthetic Biology, DOI: 10.1021/acssynbio.4c00388, 2024.
[PDF]

H. Lin, S. Seitz, Y. Tan, J. B. Lugagne, L. Wang, G. Ding, H. He, M. J. Dunlop, J. Connor, J. A. Porco, L. Tian, J.-X. Cheng. "Label-free Nanoscopy of Cell Metabolism by Ultrasensitive Reweighted Visible Stimulated Raman Scattering." Nature Methods (in press), 2024.

R. N. Alnahhas, M. J. Dunlop. "Evaluation of Choudhary et al.: Single-cell gene expression dynamics in the E. coli oxidative stress response network." Cell Systems, DOI: 10.1016/j.cels.2024.10.011, 2024.
[Published peer review]

K. A. Haynes, L. B. Andrews, C. L. Beisel, J. Chappell, C. E. Cuba Samaniego, J. E. Dueber, M. J. Dunlop, E. Franco, J. B. Lucks, V. Noireaux, D. F. Savage, P. A. Silver, M. Smanski, E. Young. "Ten Years of the Synthetic Biology Summer Course at Cold Spring Harbor Laboratory." ACS Synthetic Biology, DOI: 10.1021/acssynbio.4c00276, 2024.
[PDF]

V. Andreani*, E. J. South*, M. J. Dunlop. (*Equal contribution) "Generating Information-dense Promoter Sequences with Optimal String Packing." PLOS Computational Biology, DOI: 10.1371/journal.pcbi.1012276, 2024.
[PDF]

J. B. Lugagne, C. M. Blassick, M. J. Dunlop. "Deep Model Predictive Control of Gene Expression in Thousands of Single Cells." Nature Communications, https://doi.org/10.1038/s41467-024-46361-1, 2024.
[PDF]

N. Tague, C. Coriano-Ortiz, M. B. Sheets, M. J. Dunlop. "Light Inducible Protein Degradation in E. coli with the LOVdeg tag." eLife, https://doi.org/10.7554/eLife.87303.3, 2024.
[PDF]

2023

N. Tague, V. Andreani, Y. Fan, W. Timp, M. J. Dunlop. "Comprehensive Screening of a Light-Inducible Split Cre Recombinase with Domain Insertion Profiling." ACS Synthetic Biology, https://doi.org/10.1021/acssynbio.3c00328, 2023.
[PDF]

H. E. Klumpe*, J. B. Lugagne*+, A. S. Khalil, M. J. Dunlop+. (*Equal contribution, +Co-corresponding) "Deep Neural Networks for Predicting Single Cell Responses and Probability Landscapes." ACS Synthetic Biology, https://doi.org/10.1021/acssynbio.3c00203, 2023.
[PDF]

N. Tague*, H. Lin*, J. B. Lugagne, O. M. O’Connor, D. Burman, W. W. Wong, J.-X. Cheng+, M. J. Dunlop+ (*Equal contribution, +Co-corresponding). "Longitudinal Single‐Cell Imaging of Engineered Strains with Stimulated Raman Scattering to Characterize Heterogeneity in Fatty Acid Production." Advanced Science, https://doi.org/10.1002/advs.202206519, 2023.
[PDF]

E. Tague, J. McMahan, N. Tague, M. J. Dunlop, J. Ngo. "Controlled Protein Activities with Viral Proteases, Antiviral Peptides, and Antiviral Drugs." ACS Chemical Biology, https://doi.org/10.1021/acschembio.3c00138, 2023.
[PDF]

M. B. Sheets, N. Tague, M. J. Dunlop. "An Optogenetic Toolkit for Light-Inducible Antibiotic Resistance." Nature Communications, https://doi.org/10.1038/s41467-023-36670-2, 2023.
[PDF]

R. N. Alnahhas, M. J. Dunlop. "Advances in Linking Single Cell Bacterial Stress Response to Population Level Survival." Current Opinion in Biotechnology, https://doi.org/10.1016/j.copbio.2022.102885, 2023.
[PDF]

2022

J. Zhang, J. Shin, N. Tague, H. Lin, M. Zhang, X. Ge, W. Wong, M. J. Dunlop+, J.-X. Cheng+ (+Co-corresponding). "Visualization of a Limonene Synthesis Metabolon Inside Living Bacteria by Hyperspectral SRS Microscopy." Advanced Science, https://doi.org/10.1002/advs.202203887, 2022.
(PDF)

W. A. V. Beardall, G.-B. Stan+, M. J. Dunlop+ (+Co-corresponding). "Deep Learning Concepts and Applications for Synthetic Biology." GEN Biotechnology, https://doi.org/10.1089/genbio.2022.0017, 2022.
(PDF)

J. Shin*, E. J. South*, M. J. Dunlop (*Equal contribution). "Transcriptional Tuning of Mevalonate Pathway Enzymes to Identify Impact on Limonene Production in E. coli." ACS Omega, https://doi.org/10.1021/acsomega.2c00483, 2022. (PDF)

N. M. V. Sampaio*, C. M. Blassick*, V. Andreani, J. B. Lugagne, M. J. Dunlop (*Equal contribution). "Dynamic Gene Expression and Growth Underlie Cell-to-Cell Heterogeneity in Escherichia coli Stress Response." Proceedings of the National Academy of Sciences (PNAS), https://doi.org/10.1073/pnas.2115032119, 2022.
(PDF)

J. B. Lugagne, M. J. Dunlop. "Anticipating Antibiotic Resistance." Science, DOI: 10.1126/science.a bo0498, 2022.
(PDF)
[Perspective]

O. M. O’Connor, R. N. Alnahhas, J. B. Lugagne+, M. J. Dunlop+ (+Co-Corresponding). “DeLTA 2.0: A Deep Learning Pipeline for Quantifying Single-cell Spatial and Temporal Dynamics.” PLOS Computational Biology, https://doi.org/10.1371/journal.pcbi.1009797, 2022.
(PDF)

2021

H. Lin, H. J. Lee, N. Tague, J. B. Lugagne, C. Zong, F. Deng, J. Shin, L. Tian, W. Wong, M. J. Dunlop, and J. X. Cheng. "Microsecond Fingerprint Stimulated Raman Spectroscopic Imaging by Ultrafast Tuning and Spatial-Spectral Learning." Nature Communications, https://doi.org/10.1038/s41467-021-23202-z, 2021.
(PDF)

2020

T. Wang*, N. Tague*, S. A. Whelan, M. J. Dunlop. (*Equal contribution) "Programmable Gene Regulation for Metabolic Engineering Using Decoy Transcription Factor Binding Sites." Nucleic Acids Research, https://doi.org/10.1093/nar/gkaa1234, 2020.
(PDF)

A. M. Langevin, I. El Meouche, M. J. Dunlop. "Mapping the Role of AcrAB-TolC Efflux Pumps in the Evolution of Antibiotic Resistance Reveals Near-MIC Treatments Facilitate Resistance Acquisition." mSphere, DOI: 10.1128/mSphere.01056-20, 2020.
(PDF)

N. M. V. Sampaio, M. J. Dunlop. "Functional Roles of Microbial Cell-to-Cell Heterogeneity and Emerging Technologies for Analysis and Control." Current Opinion in Microbiology, https://doi.org/10.1016/j.mib.2020.08.002, 2020.
(PDF)

J. B. Lugagne, H. Lin, M. J. Dunlop. "DeLTA: Automated Cell Segmentation, Tracking, and Lineage Reconstruction using Deep Learning." PLOS Computational Biology, https://doi.org/10.1371/journal.pcbi.1007673, 2020.
(PDF)

J. A. White, et al. "Core Competencies for Undergraduates in Bioengineering and Biomedical Engineering: Findings, Consequences, and Recommendations." Annals of Biomedical Engineering, 48, 905–912, 2020.
(PDF)

M. B. Sheets, W. W. Wong, M. J. Dunlop. "Light-Inducible Recombinases for Bacterial Optogenetics." ACS Synthetic Biology. https://doi.org/10.1021/acssynbio.9b00395, 2020.
(PDF) (Correction)

2019

T. Wang, C. Kunze, M. J. Dunlop. "Salicylate Increases Fitness Cost Associated with MarA-mediated Antibiotic Resistance." Biophysical Journal, 17, 563–571, 2019.
(PDF)

N. A. Rossi, I. El Meouche, M. J. Dunlop. "Forecasting Cell Fate During Antibiotic Exposure Using Stochastic Gene Expression." Communications Biology. https://doi.org/10.1038/s42003-019-0509-0, 2019.
(PDF)

J. B. Lugagne, M. J. Dunlop. "Cell-Machine Interfaces for Characterizing Gene Regulatory Network Dynamics." Current Opinion in Systems Biology. https://doi.org/10.1016/j.coisb.2019.01.001, 2019.
(PDF)

A. Westbrook, X. Tang, R. Marshall, C. Maxwell, J. Chappell, D. Agrawal, M. J. Dunlop, V. Noireaux, C. Beisel, J. B. Lucks, E. Franco. "Distinct Timescales of RNA Regulators Enable the Construction of a Genetic Pulse Generator." Biotechnology and Bioengineering. https://doi.org/10.1002/bit.26918, 2019.
(PDF)

2018

N. A. Rossi, T. Mora, A. Walczak, M. J. Dunlop. "Active Degradation of MarA Controls Coordination of its Downstream Targets." PLOS Computational Biology. 14(12): e1006634. https://doi.org/10.1371/journal.pcbi.1006634, 2018.
(PDF)

I. El Meouche, M. J. Dunlop. "Heterogeneity in Efflux Pump Expression Predisposes Antibiotic Resistant Cells to Mutation." Science. DOI: 10.1126/science.aar7981, 2018.
(PDF)
* Nature Reviews Microbiology: Research Highlight

X. Wen, A. M. Langevin, M. J. Dunlop. "Antibiotic Export by Efflux Pumps Affects Growth of Neighboring Bacteria." Scientific Reports. DOI:10.1038/s41598-018-33275-4, 2018.
(PDF)

T. Wang, M. J. Dunlop. "Controlling and Exploiting Cell-to-Cell Variation in Metabolic Engineering." Current Opinion in Biotechnology. DOI:10.1016/j.copbio.2018.08.013, 2018.
(PDF)

D. K. Agrawal, X. Tang, A. Westbrook, R. Marshall, C. S. Maxwell, J. B. Lucks, V. Noireaux, C. L. Beisel, M. J. Dunlop+, and E. Franco+ (+Co-Corresponding). “Mathematical Modeling of RNA-based Architectures for Closed Loop Control of Gene Expression.” ACS Synthetic Biology. DOI: 10.1021/acssynbio.8b00040, 2018.
(PDF)

N. A. Rossi, M. J. Dunlop. "Making Waves with Synthetic Oscillators." Cell Systems, DOI: 10.1016/j.cels.2018.04.001, 2018.
(PDF)
[Preview]

A. M. Langevin, M. J. Dunlop. "Stress Introduction Rate Alters Benefit of AcrAB-TolC Efflux Pumps." Journal of Bacteriology, doi: 10.1128/JB.00525-17, 2018.
(PDF)

2017

Y. Siu, J. Fenno, J. Lindle, M. J. Dunlop. "Design and Selection of a Synthetic Feedback Loop for Optimizing Biofuel Tolerance." ACS Synthetic Biology, DOI: 10.1021/acssynbio.7b00260, 2017.
(PDF)

T. Tomko, M. J. Dunlop. "Expression of Heterologous Sigma Factor Expands the Searchable Space for Biofuel Tolerance Mechanisms." ACS Synthetic Biology, DOI: 10.1021/acssynbio.6b00375, 2017.
(PDF)

T. Wang, I. El Meouche, M. J. Dunlop. "Bacterial Persistence Induced by Salicylate via Reactive Oxygen Species." Scientific Reports, doi:10.1038/srep43839, 2017.
(PDF)

N. A. Rossi, M. J. Dunlop. "Customized Regulation of Diverse Stress Response Genes by the Multiple Antibiotic Resistance Activator MarA." PLOS Computational Biology, DOI:10.1371/journal.pcbi.1005310, 2017.
(PDF)

2016

J. Garcia-Bernardo, M. J. Dunlop. "Phenotypic Diversity using Bimodal and Unimodal Expression of Stress Response Proteins in Fluctuating Environments." Biophysical Journal, 110:2278–2287, 2016.
(PDF)

I. El Meouche, Y. Siu, M. J. Dunlop. "Stochastic Expression of a Multiple Antibiotic Resistance Activator Confers Transient Resistance in Single Cells." Scientific Reports, 6:19538, 2016.
(PDF)

J. M. Lindle, M. J. Dunlop. "Performing Selections Under Dynamic Conditions for Synthetic Biology Applications." Integrative Biology, DOI: 10.1039/c5ib00286a, 2016.
(PDF)

2015

T. Tomko, M. J. Dunlop. "Engineering Improved Bio-jet Fuel Tolerance in Escherichia coli using a Transgenic Library from the Hydrocarbon-degrader Marinobacter aquaeolei." Biotechnology for Biofuels. 8:165, 2015.
(PDF)

J. Garcia-Bernardo, M. J. Dunlop. "Noise and Low-Level Dynamics Can Coordinate Multicomponent Bet Hedging Mechanisms." Biophysical Journal, 108:184-193, 2015.
(PDF)

2014

W. J. Turner, M. J. Dunlop. "Trade-offs in Improving Biofuel Tolerance Using Combinations of Efflux Pumps." ACS Synthetic Biology, DOI: 10.1021/sb500307w, 2014.
(PDF)

M. Frederix, K. Hutter, J. Leu, T. S. Batth, W. J. Turner, T. L. Ruegg, H. Blanch, B. A. Simmons, P. D. Adams, J. D. Keasling, M. P. Thelen, M. J. Dunlop, C. J. Petzold, A. Mukhopadhyay. "Development of a Native Escherichia coli Induction System for Ionic Liquid Tolerance." PLOS One, 2014.
(PDF)

2013

J. Garcia-Bernardo, M. J. Dunlop. "Tunable Stochastic Pulsing in the Escherichia coli Multiple Antibiotic Resistance Network from Interlinked Positive and Negative Feedback Loops." PLOS Computational Biology, 9(9), 2013.
(PDF)

2012

M. E. Harrison, M. J. Dunlop. "Synthetic Feedback Loop Model for Increasing Microbial Biofuel Production Using a Biosensor." Frontiers in Microbiology 3:360, 2012.
(PDF)

R. S. Koh, M. J. Dunlop. "Modeling Suggests that Gene Circuit Architecture Controls Phenotypic Variability in a Bacterial Persistence Network." BMC Systems Biology 6:47, 2012.
(PDF)

2011

M. J. Dunlop. "Engineering Microbes for Tolerance to Next-Generation Biofuels." Biotechnology for Biofuels 4:32, 2011.
(PDF)

M. J. Dunlop, Z. Y. Dossani, H. L. Szmidt, H. C. Chu, T. S. Lee, J. D. Keasling, M. Hadi, A. Mukhopadhyay. "Engineering Microbial Biofuel Tolerance and Export Using Efflux Pumps." Molecular Systems Biology 7:487, 2011.
(PDF)

2010 and earlier

M. J. Dunlop, J. D. Keasling, A. Mukhopadhyay. "A Model for Improving Microbial Biofuel Production Using a Synthetic Feedback Loop." Systems and Synthetic Biology DOI 10.1007/s11693-010-9052-5, 2010.
(PDF)

R. S. Cox, M. J. Dunlop, M. B. Elowitz. "A Synthetic Three-Color Reporter Framework for Monitoring Genetic Regulation and Noise." Journal of Biological Engineering 4:10, 2010.
(PDF)

M. J. Dunlop, R. S. Cox, J. H. Levine, R. M. Murray, M. B. Elowitz. "Regulation Revealed by Dynamic Correlations In Gene Expression Noise." Nature Genetics 40:1493-1498, 2008.
(PDF)

M. J. Dunlop, E. Franco, R. M. Murray. "A Multi-Model Approach to Identification of Biosynthetic Pathways." In Proceedings of the 26th American Control Conference 2007.
(PDF)

J. Ugander, M. J. Dunlop, R. M. Murray. "Analysis of a Digital Clock for Molecular Computing." In Proceedings of the 26th American Control Conference 2007.
(PDF)

M. E. Wall, M. J. Dunlop, W. S. Hlavacek. "Multiple Functions of a Feed-Forward Loop Gene Circuit." Journal of Molecular Biology 349:501-514, 2005.
(PDF)

M. J. Dunlop, M. E. Wall. "Robustness in Gene Circuits: Clustering of Functional Responses." Proceedings of the 24th American Control Conference, 2005.

M. B. Reiser, J. S. Humbert, M. J. Dunlop, D. Del Vecchio, R. M. Murray, M. H. Dickinson. "Vision as a Compensatory Mechanism for Disturbance Rejection in Upwind Flight." Proceedings of the 23rd American Control Conference, 2004.
(PDF)

T. Colonius, M. J. Dunlop, R. Reba, S. Narayanan. "A Study of the Role of Organized Structures in Jet Noise Generation." AIAA Paper 2003-3314, 2003.
(PDF)

Ph.D. Thesis

M. J. Dunlop. "Dynamics and Correlated Noise in Gene Regulation." California Institute of Technology, 2008.
(PDF)

Patents

E. Tague, N. Tague, A. Marzilli, M. J. Dunlop, J. T. Ngo. “Novel Drug-controlled Systems and Uses Thereof.” International Application No. PCT/US21/48338. Filed August 31, 2021.

M. J. Dunlop, J. D. Keasling, A. Mukhopadhyay. "Modified Host Cells with Efflux Pumps." U.S. Patent No. 9428726. Filed May 25, 2011.