Research and Publications


Microbial Evolution
Multiple stressors and their interactions affect the ecological and evolutionary trajectory of populations, but interactions in general remain poorly understood. We use antibiotics and bacteria systems to understanding how higher-order combination of stressors interact, how interactions in a network context can be used to understand mechanisms underlying change, and how multiple stressors affect the magnitude and direction of selection and rate of adaptation. In addition, we are using evolutionary principles and ideas to develop strategies to combat the evolution of multi-drug resistant pathogens.

Our research focuses on basic biological questions, yet is also relevant to clinical and public health issues. We develop strategies to combat the evolution and spread of multi-drug resistant pathogens.

Avian Urban Ecology and Evolution
Urban environments present a number of unique stressors to its inhabitants. We examine how birds respond and adapt to urban environments, focusing on two species: the house sparrow and the dark-eyed junco. Our house sparrow populations span multiple areas within Los Angeles county and is part of a larger study that includes Mexico and Spain. Our junco study focuses on urban juncos in southern California.

Selected Publications:

J. Pruitt, A. Berdahl, C. Riehl, N. Pinter-Wollman, H. Moeller, E. Pringle, L. Aplin, E. Robinson, J. Grilli, P. Yeh, V. Savage, M. Price, J. Garland, I. Gilby, M. Crofoot, G. Doering, E. Hobson. 2018. Social tipping points in animal societies.
Proceedings of the Royal Society B

M. Cruz-Loya, T. Kang, N. Lozano, R. Watanabe, E. Tekin, R. Damoiseaux, V. Savage, and P. J. Yeh. 2018. Stressor interaction networks suggest antibiotic resistance coopted from stress responses to temperature.
ISME journal

E. Tekin, C. White, T. M. Kang, N. Singh, M. Cruz-Loya, R. Damoiseaux, V. M. Savage, and P. J. Yeh. 2018. Prevalence and patterns of higher-order drug interactions in Escherichia coli.
npj Systems Biology and Applications

D. Chung, E. Ferree, D. M. Simon, and P. J. Yeh. 2018. Patterns of bird-bacteria associations.

L. Lee, V. Savage, and P. J. Yeh. 2018. Intermediate levels of antibiotics may increase diversity of colony size phenotype in bacteria.
Computational and Structural Biotechnology

I. Macgregor-Fors, J. Quesada Lara, J. Lee, and P. Yeh. 2017. Space invaders: House Sparrow densities along three urban-agricultural landscapes.
Avian Conservation and Ecology

N. Singh and P. Yeh. 2017. Suppressive drug combinations and their potential to combat antibiotic resistance.
Journal of Antibiotics 1-10

N. Singh, M. Sit, M. Schutte, G. Chan, J. Aldana, D. Cervantes, C. Himmelstein, and P. Yeh. 2017. A systematic review of differential rate of use of the word ‘‘evolve’’ across fields
Peer J

E. Tekin, V. Savage, and P. Yeh. 2017. Measuring higher-order drug interactions: A review of recent approaches.
Current Opinion in Systems Biology 4: 16-23

C. Beppler, E. Tekin, C. White, Z. Mao, J. H. Miller, R. Damoiseaux, V. Savage, and P. Yeh. 2017. When more is less: emergent suppressive interactions in three-drug combinations.
BMC Microbiology 17:107

J. Lee, I. MacGregor-Fors, and P. Yeh. 2017. Sunrise in the city: disentangling drivers of temporal shifts in the avian dawn chorus in urban greenspaces.
Journal of Avian Biology

C. Beppler, E. Tekin, Z. Mao, C. White, C. McDiarmid, E. Vargas, J. Miller, V. Savage, and P. Yeh. 2016. Uncovering emergent interactions in three-way combinations of stressors.
Royal Society Interface 13:20160800.

E. Tekin, C. Beppler, C. White, Z. Mao, V. Savage, and P. Yeh. 2016. Enhanced identification of synergistic and antagonistic emergent interactions among three or more drugs.
Royal Society Interface 13:20160332.

C. Nguyen, A. Zhou, A. Khan, J. H. Miller, and P. Yeh. 2016. Pairwise Antibiotic Interactions in Escherichia coli: Triclosan, Rifampicin, and Aztreonam with Nine Other Classes of Antibiotics.
Journal of Antibiotics.

L. Song, K. Nguyen, S. D’Sousa, Tina Manzhu Kang, P. Yeh*, and J. H. Miller*. 2016. Studies with mutagens as antibiotics: exploring synergy between classic mutagens and antibiotics to examine mechanisms of synergy and of antibiotic action.
Antimicrobial Agents and Chemotherapy 60:1515-1520.

N. Singh, M. Sit, D. Chung, A. Lopez, R. Weerackoon, and P. Yeh. 2016. How often do bacteria “evolve” resistance to antibiotics in general public news articles on drug resistance?
PLoS One 11 e0150396.

A. Zhou, T. Kang, J. Yuan, C. Beppler, C. Nguyen, Z. Mao, M. Nguyen, P. Yeh* and J. Miller*. 2015. Synergistic interaction of vancomycin with different antibiotics in Escherichia coli: trimethoprim and nitrofurantoin display strong synergies with vancomycin in wild-type E. coli.
Antimicrobial Agents and Chemotherapy 59:276-281. * co-senior and co-corresponding authors

T. Oz, A. Guvenek, S. Yildiz, E. Karaboga, N. Mumcuyan, V. B. Ozan, M. Cokol, P. Yeh, and E. Toprak. 2014. Strength of selection pressure is an important parameter contributing to the complexity of antibiotic resistance evolution.
Molecular Biology and Evolution 214: 2387-2401.

P. Yeh, D. Simon, J. Millar, F. Alexander, and D. Franklin, A diversity of antibiotic-resistant Staphylococcus spp. in a public transportation system, Public Health and Research Perspectives, 2: 202-209 (2011).

K. Bush, et al., Tackling Antibiotic Resistance, Nature Reviews Microbiology, 9: 894-896 (2011).

P. Yeh, M. Hegreness, A. Aiden, and R. Kishony, Drug interactions and the evolution of antibiotic resistance, Nature Reviews Microbiology, 7: 460-466 (2009).

J.-B. Michel*, P. Yeh*, R. Chait, R. Moellering, and R. Kishony, Drug interactions modulate the potential for evolution of resistance, Proceedings of the National Academy of Science, 105: 14918-14923 (2008).

T. Price, P. Yeh, and B. Harr, Phenotypic plasticity and the evolution of a socially selected trait following colonization of a novel environment, American Naturalist, 172 : S49-S62 (2008).

M. Newman, P. Yeh, and T. Price, Song variation in a recently founded population of the Dark-eyed Junco, Junco hyemalis, Ethology, 114: 164-173 (2008).

P. Yeh and R. Kishony, Networks from drug-drug surfaces, Molecular Systems Biology, 3 (85): 1-3 (2007).

P. Yeh, M. Hauber, and T. Price, Alternative nesting behaviours following colonisation of a novel environment by a passerine bird, Oikos, 116: 1473-1480 (2007).

H. Slabbekoorn, P. Yeh, and K. Hunt, Sound transmission and song divergence: a comparison of urban and forest acoustics, Condor, 109: 67-68 (2007).

P. Yeh, A. Tschumi, and R. Kishony, Functional classification of drugs by properties of their pair-wise interactions, Nature Genetics, 38: 489-494 (2006).