Lopatkin Lab

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Lab Publications

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  2. Publications
See all of our work on Google Scholar
  • Disturbing the Spatial Organization of Biofilm Communities Affects Expression of agr-Regulated Virulence Factors in Staphylococcus aureus

    • Ivana Barraza, Camryn Pajon, Gabriela Diaz-Tang, Estefania Marin Meneses,a Fatima Abu-Rumman, Laura García-Diéguez, Victor Castro, AJ Lopatkin, Robert P. Smith
    • 2022
    • Environmental Microbiology
  • Growth productivity as a determinant of the inoculum effect for bactericidal antibiotics.

    • Gabriela Diaz-Tang, Estefania Marin Menses, Kavish Patel, Sophia Mirkin, Laura Garcia-Dieguez, Camryn Pajon, Ivana Barrara, Vijay Patel, Helana Ghali, Angelica P. Tracey, Christopher A. Blanar, AJ Lopatkin, and Robert P. Smith
    • 2022
    • Science Advances
  • Metabolic genes on conjugative plasmids are highly prevalent in Escherichia coli and can protect against antibiotic treatment.

    • Alana Palomino, Danya Gewurz, Lela DeVine, Ujana Zajmi, Jenifer Moralez, Fatima Abu-Rumman, Robert P. Smith & AJ Lopatkin
    • 2022
    • ISME
  • Horizontal gene transfer enables programmable gene stability in synthetic microbiota.

    • T Wang, A Weiss, A aqeel, F Wu, AJ Lopatkin, LA David, L You
    • 2022
    • Nature Chemical Biology
  • Population structure of blaKPC-harbouring IncN plasmids at a New York City medical centre and evidence for multi-species horizontal transmission.

    • A Gomez-Simmonds, MK Annavajhala, N Tang, FD Rozenberg, M Ahmad, H Park, AJ Lopatkin, and AC Uhlemann
    • 2022
    • Antimicrobial Chemotherapy
  • Phylogenetic analysis of two antibiotic susceptible non-clinical Acinetobacter baumannii strains belonging to global clone 1 reveals close relationship with multiply-antibiotic resistant clinical strains.

    • J Koong, C Johnson, R Rafei, M Hamze, GSA Myers, AJ Lopatkin, and M Hamidian
    • 2021
    • Microbial Genomics
  • Thermal stress induces tissue damage and a broad shift in regenerative signaling pathways in the honey bee digestive tract.

    • DM Bach, MA Holzman, F Wague, JJ Miranda, AJ Lopatkin, JH Mansfield, and JW Snow
    • 2021
    • Journal of Experimental Biology
  • Honey bee sHSP are responsive to diverse proteostatic stresses and potentially promising biomarkers of honey bee stress.

    • SR Shih, D Bach, N Rondeau, J Sam, NL Lovinger, AJ Lopatkin, and JW Snow
    • 2021
    • Scientific Reports
  • Honey bee sHSP are responsive to diverse proteostatic stresses and potentially promising biomarkers of honey bee stress.

    • ME Shoen, MA Jahne, J Garland, L Ramirez, AJ Lopatkin, and K Hamilton
    • 2021
    • Environmental Science & Technology
  • Quantitative analysis of horizontal gene transfer in complex systems.

    • J Moralez, K Szenkiel, K Hamilton, A Pruden, AJ Lopatkin
    • 2021
    • Current Opinion in Microbiology
  • Investigation of the prevalence and catalytic activity of rubredoxin-fused alkane monooxygenases (AlkBs).

    • SC Williams, AP Forsberg, J Lee, C Vizcarra, AJ Lopatkin, RN Austin
    • 2021
    • Journal of Inorganic Biochemistry
  • Conjugation dynamics depend on both the plasmid acquisition cost and the fitness cost.

    • H Prensky, A Gomez-Simmons, AC Uhlemann, AJ Lopatkin
    • 2021
    • Molecular Systems Biology
  • Clinically relevant mutations in core metabolic genes confer antibiotic resistance.

    • AJ Lopatkin, SC Bening, AL Manson, JM Stokes, MA Kohanski, AH Badran, AM Earl, NJ Cheney, JH Yang, JJ Collins
    • 2021
    • Science
  • Nucleotide metabolism and antibiotic treatment failure.

    • AJ Lopatkin, JH Yang
    • 2021
    • Frontiers in Digital Health
  • Predictive biology: modelling, understanding and harnessing microbial complexity.

    • AJ Lopatkin and J Collins
    • 2020
    • Nature Microbiology Reviews
  • Environmental and genetic determinants of plasmid mobility in pathogenic Escherichia coli.

    • JH Bethke, A Davidovich, L Cheng, AJ Lopatkin, W. Song, JT Thaden, VG Fowler Jr, M Xiao, L You
    • 2020
    • Science Advances
  • Growth‐Stage‐Dependent Regulation of Conjugation.

    • TA Sysoeva, YL Kim, J Rodriguez, AJ Lopatkin, L You
    • 2019
    • AlChE
  • Bacterial metabolic state more accurately predicts antibiotic lethality than growth rate.

    • AJ Lopatkin, JM Stokes, EJ Zheng, JH Yang, MK Takahashi, L You, JJ Collins
    • 2019
    • Nature Microbiology
  • Bacterial Metabolism and Antibiotic Efficacy.

    • JM Stokes, AJ Lopatkin, MA Lobritz, JJ Collins
    • 2019
    • Cell Metabolism
  • A white-box machine learning approach for revealing antibiotic mechanisms of action.

    • JH Yang, SN Wright, M Hamblin, D McCloskey, MA Alcantar, L Schrubbers, AJ Lopatkin, S Sateesh, A Nili, BO Palsson, GC Walker, JJ Collins
    • 2019
    • Cell
  • A multiplexable assay for screening antibiotic lethality against drug-tolerant bacteria.

    • JM Stokes, A Gutierrez, AJ Lopatkin, IW Andrews, S French, I Matic, ED Brown, JJ Collins
    • 2019
    • Nature Methods
  • A unifying framework for interpreting and predicting mutualistic systems.

    • F Wu, AJ Lopatkin, DA Needs, CT Lee, S Mukherjee, L You
    • 2019
    • Nature Communications
  • Applying ecological resistance and resilience to dissect bacterial antibiotic responses.

    • HR Meredith, V Andreani, HR Ma, AJ Lopatkin, AJ Lee, DJ Anderson, AJ Lee, DJ Anderson, G Batt, L You
    • 2018
    • Scientific Advances
  • Persistence and reversal of plasmid-mediated antibiotic resistance.

    • AJ Lopatkin, HR Meredith, JK Srimani, C Pfeiffer, R Durrett, L You
    • 2017
    • Nature Communications
  • Drug detoxification dynamics explain the postantibiotic effect.

    • JK Srimani, S Huang, AJ Lopatkin, L You
    • 2017
    • Molecular Systems Biology
  • Cooperation and competition shape ecological resistance during periodic spatial disturbance of engineered bacteria.

    • CE Wilson, AJ Lopatkin, TJA Craddock, WW Driscoll, OT Eldakar, JV Lopez, RP Smith
    • 2017
    • Scientific Reports
  • Antibiotics as a selective driver for conjugation dynamics.

    • AJ Lopatkin, S Huang, RP Smith, JK Srimani, TA Sysoeva, S Bewick, DK Karig, L You
    • 2016
    • Nature Microbiology
  • Elements of biological oscillations in time and space.

    • Y Cao, AJ Lopatkin, L You
    • 2016
    • Nature Structural & Molecular Biology
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  • Dissecting the effects of antibiotics on horizontal gene transfer: Analysis suggests a critical role of selection dynamics.

    • AJ Lopatkin, TA Sysoeva, L You
    • 2016
    • Bioessays
  • Collective antibiotic tolerance: mechanisms, dynamics and intervention.

    • HR Meredith, JK Srimani, AJ Lee, AJ Lopatkin, L You
    • 2015
    • Nature Chemical Biology
  • Dynamic control and quantification of bacterial population dynamics in droplets.

    • S Huang, JK Srimani, AJ Lee, Y Zhang, AJ Lopatkin, KW Leong, L You
    • 2015
    • Biomaterials
  • Dynamic control and quantification of bacterial population dynamics in droplets.

    • HR Meredith, AJ Lopatkin, DJ Anderson, L You
    • 2015
    • PLoS Computational Biology
  • A power-law dependence of bacterial invasion on mammalian host receptors.

    • TJ Lee, J Wong, S Bae, AJ Lee, AJ Lopatkin, F Yuan, L You
    • 2015
    • PLoS Computational Biology
  • Synthetic biology looks good on paper.

    • AJ Lopatkin, L You
    • 2014
    • Cell

Affiliations

  • Barnard College,
    Dept. of Biology
  • Columbia University,
    Data Science Institute
  • Columbia University,
    Evolutionary Genomics Group

Contact Us

1014 Altschul Hall
Barnard College
New York, NY 10027

Email: lopatkinlab@gmail.com

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