Publications
De novo mutations mediate phenotypic switching in an opportunistic human lung pathogen
AJ. Poret, M. Schaefers, C. Merakou, KE. Mansour, CD. Ahern, GK. Lagoudas, A. Haynes, AR. Cross, JB. Goldberg, R. Kishony, AZ. Uluer, AJ. McAdam, PC. Blainey, SO. Vargas, TD. Lieberman, GP. Priebe
Nature Communications (2025)
Autonomous LLM-Driven Research — from Data to Human-Verifiable Research Papers
T. Ifargan*, L. Hafner*, M. Kern, O. Alcalay, R. Kishony
NEJM AI (2024)
Beta-lactamase dependent and independent evolutionary paths to high-level ampicillin resistance
R. Gross*, I, Yelin*, V. Lazar, M.S. Datta, R. Kishony
Nature Communications (2024)
Systematic identification of gene-altering programmed inversions across the bacterial domain
O. Milman, I. Yelin, R. Kishony
Nucleic Acids Research (2023)
Multistep diversification in spatiotemporal bacterial-phage coevolution
E. Shaer-Tamar, R. Kishony
Nature Communications (2022), 13(1), p.7971.
Antibiotic combinations reduce Staphylococcus aureus clearance
V. Lázár, O. Snitser, D. Barkan, R. Kishony
Nature (2022), 610(7932), pp.540-546.
Minimizing treatment-induced emergence of antibiotic resistance in bacterial infections
M. Stracy, O. Snitser, I. Yelin, Y. Amer, M. Parizade, R. Katz, G. Rimler, T. Wolf, E. Herzel, G. Koren, J. Kuint, B. Foxman, G. Chodick, V. Shalev, R. Kishony
Science (2022), 375(6583), pp.889-894.
Host-parasite coevolution promotes innovation through deformations in fitness landscapes
A. Gupta, L. Zaman, H.M. Strobel, J. Gallie, A.R. Burmeister, B. Kerr, E. Shaer-Tamar, R.Kishony†, J.R. Meyer†
eLife (2022)
Rapid expansion and extinction of antibiotic resistance mutations during treatment of acute bacterial respiratory infections
H. Chung, C. Merakou, M. M. Schaefers, K. B. Flett, S. Martini, R. Lu, J. A. Blumenthal, S. S. Webster, A. R. Cross, R. Al Ahmar, E. Halpin, M. Anderson, N. S. Moore, E. C. Snesrud, H. D. Yu, J. B. Goldberg, G. A. O’Toole, P. McGann, J. A. Stam, M. Hinkle, A. J. McAdam, R. Kishony†, G. P. Priebe†
Nature Communications (2022) 13:1231
Waning of SARS-CoV-2 booster viral-load reduction effectiveness
M. Levine-Tiefenbrun, I. Yelin, H. Alapi, E. Herzel, J. Kuint, G. Chodick, S. Gazit, T. Patalon†, R. Kishony†
Nature Communications (2022), 13:1237
SARS-CoV-2 RT-qPCR Test Detection Rates Are Associated with Patient Age, Sex, and Time since Diagnosis
M. Levine-Tiefenbrun*, I. Yelin*, H. Uriel*, J. Kuint, L. Schreiber, E. Herzel, R. Katz, A. Ben-Tov, S. Gazit, T. Patalon, G. Chodick, R. Kishony
Journal of Molecular Diagnostics (2022)
Viral loads of Delta-variant SARS-CoV2 breakthrough infections following vaccination and booster with the BNT162b2 vaccine
M. Levine-Tiefenbrun, I. Yelin, H. Alapi, R. Katz, E. Herzel, J. Kuint, G. Chodick, S. Gazit, T. Patalon†, R. Kishony†
Nature Medicine (2021), 1-3.
Rapid methicillin resistance diversification in Staphylococcus epidermidis colonizing human neonates
M.S. Datta*, I. Yelin*, O. Hochwald, I. Kassis, L. Borenstein-Levin, A. Kugelman & R. Kishony.
Nature Communications (2021), 12, 6062
Community-level evidence for SARS-CoV-2 vaccine protection of unvaccinated individuals
O. Milman*, I. Yelin*, N. Aharony, R. Katz, E. Herzel, A. Ben-Tov, J. Kuint, S. Gazit, G. Chodick, T. Patalon†, R. Kishony†
Nature Medicine (2021), 1-3.
Initial report of decreased SARS-CoV-2 viral load after inoculation with the BNT162b2 vaccine
M. Levine-Tiefenbrun*, I. Yelin*, R. Katz, E. Herzel, Z. Golan, L. Schreiber, T. Wolf, V. Nadler, A. Ben-Tov, J. Kuint, S. Gazit, T. Patalon, G. Chodick, R. Kishony
Nature Medicine (2021), 27(5), pp.790-792.
Associations of the BNT162b2 COVID-19 vaccine effectiveness with patient age and comorbidities
I. Yelin, R. Katz, E. Herzel, T. Berman-Zilberstein, A. Ben-Tov, J. Kuint, S. Gazit, T. Patalon, G. Chodick, R. Kishony
medRxiv (2021).
Antibiotic resistance: turning evolutionary principles into clinical reality
D.I. Andersson, N.Q. Balaban, F. Baquero, P. Courvalin, , P. Glaser, U. Gophna, R. Kishony, S. Molin, T. Tønjum
FEMS microbiology reviews (2020), 44(2), pp.171-188. {Review}
Ubiquitous selection for mecA in community-associated MRSA across diverse chemical environments
O. Snitser, D. Russ, L.K Stone, K.K Wang, H. Sharir, N. Kozer, G. Cohen, H.M Barr, R. Kishony
Nature Communications (2020), 11(1), pp.1-9.
Evaluation of COVID-19 RT-qPCR test in multi-sample pools
I. Yelin*, N. Aharony*, E. Shaer-Tamar*, A. Argoetti*, E. Messer, D. Berenbaum, E. Shafran, A. Kuzli, N. Gandali, O. Shkedi, T. Hashimshony, Y. Mandel-Gutfreund, M. Halberthal†, Y. Geffen†, M. Szwarcwort-Cohen†, R. Kishony†
Clinical Infectious Diseases (2020).
Escape mutations circumvent a tradeoff between resistance to a beta-lactam and resistance to a beta-lactamase inhibitor
D. Russ, F. Glaser, E. Shaer-Tamar, I. Yelin, M. Baym, E.D. Kelsic, C. Zampaloni, A. Haldimann, R. Kishony
Nature Communications (2020), 11(1), pp.1-9.
Genomic and epidemiological evidence of bacterial transmission from probiotic capsule to blood in ICU patients.
I. Yelin*, K.B. Flett*, C. Merakou*, P. Mehrotra, J. Stam, E. Snesrud, M. Hikle, E. Lesho, P. McGann, A.J. McAdam, T.J. Sandora†, R. Kishony† & G.P. Priebe†
Nature Medicine (2019), 25(11), pp.1728-1732.
Personal clinical history predicts antibiotic resistance of urinary tract infections
I. Yelin, O. Snitser, G. Novich, R. Katz, O. Tal, M. Parizade, G. Chodick, G. Koren, V. Shalev, R. Kishony
Nature Medicine (2019), 25(7), pp.1143-1152.
Transient antibiotic resistance calls for attention
V. Lázár & R. Kishony
Nature Microbiology (2019), 4(10), pp.1606-1607. {News&Views}
SnapShot: Antibiotic Resistance
I. Yelin & R. Kishony
Cell (2018), 172(5), pp.1136-1136 {Review}
Additivity of inhibitory effects in multi-drug combinations
D. Russ & R. Kishony
Nature Microbiology (2018), 3(12), pp.1339-1345.
Non-optimal gene expression creates latent potential for antibiotic resistance
A. C. Palmer, R. Chait, R. Kishony
Molecular Biology and Evolution (2018), 35(11), pp.2669-2684.
A spotlight on bacterial mutations for 75 years
M. S. Datta & R. Kishony
Nature (2018). {In retrospect}
RNA Structural Determinants of Optimal Codons Revealed by MAGE-Seq
E. D. Kelsic*, H. Chung*, N. Cohen, J. Park, H. H. Wang, R. Kishony
Cell Systems (2017), 3(6), pp.563-571.
Global and local selection acting on the pathogen Stenotrophomonas maltophilia in the human lung
H. Chung, T. D. Lieberman, S. O. Vargas, K. B. Flett, A. J. McAdam*, G.y P. Priebe*, R. Kishony*
Nature Communications (2017), 8, p.14078.
Regulatory Dynamics Determine Cell Fate Following Abrupt Antibiotic Exposure
D. Schultz, A. C. Palmer, R. Kishony
Cell Systems (2017) 5(5), 509-517.
Evolutionary stability of microbial communities with antibiotic degrading species
E. D. Kelsic, K. Vetsigian*, R. Kishony*
bioRxiv doi:10.1101/045732 (2016).
High-order species interactions shape ecosystem diversity
E. Bairey, E. D. Kelsic, R. Kishony
Nature Communications (2016), 7(1), pp.1-7.
Compounds that select against the tetracycline resistance efflux pump
L. K. Stone, M. Baym, T. D. Lieberman, R. Chait, J. Clardy, R. Kishony
Nature Chemical Biology (2016), 12(11), p.902.
Spatiotemporal microbial evolution on antibiotic landscapes
M. Baym, T. D. Lieberman, E. D. Kelsic, R. Chait, R. Gross, I. Yelin, R. Kishony
Science (2016), 353(6304), pp.1147-1151.
A competitive trade-off limits the selective advantage of increased antibiotic production
Y. Gerardin, M. Springer* & R. Kishony*
Nature Microbiology (2016), 1(12), pp.1-7.
Genomic diversity in autopsy samples reveals within-host dissemination of HIV-associated M. tuberculosis
T. D. Lieberman, D. Wilson, R. Misra, L. L. Xiong, P. Moodley, T. Cohen*, R. Kishony*
Nature Medicine (2016), 22(12), p.1470.
Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments
R. Chait, A. C. Palmer, I. Yelin, R. Kishony
Nature Communications (2016), 7(1), pp.1-8.
Multidrug evolutionary strategies to reverse antibiotic resistance
M. Baym*, L.K. Stone*, R. Kishony
Science (2016), 351(6268), p.aad3292. {Review}
A hybrid drug limits resistance by evading the action of the multiple antibiotic resistance pathway
K. K. Wang, L. K. Stone, T. D Lieberman, M. Shavit, T. Baasov*, R. Kishony*
Molecular Biology and Evolution (2016), 33(2), pp.492-500.
Polyploidy can drive rapid adaptation in yeast
A. M Selmecki, Y.E Maruvka, P.A Richmond, M. Guillet, N. Shoresh, A.L Sorenson, S. De, R. Kishony, F. Michor, R. Dowell, D. Pellman
Nature (2015), 519(7543), pp.349-352.
Delayed commitment to evolutionary fate in antibiotic resistance fitness landscapes
A. C. Palmer, E. Toprak, M. H. Baym, S. Kim, A. Veres, S. Bershtein, R. Kishony
Nature Communications (2015), 6(1), pp.1-8.
Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes
M. Baym*, S. Kryazhimskiy*, T. D. Lieberman*, H. Chung*, M. M. Desai#, and R. Kishony#
PLoS ONE(2015), 10(5), p.e0128036.
Counteraction of antibiotic production and degradation generates stability in microbial communities
E. D. Kelsic, J. Zhao, K. Vetsigian*, R. Kishony*
Nature (2015), 521(7553), pp.516-519.
Genetic variation of a bacterial pathogen within individuals with cystic fibrosis provides a record of selective pressures
T. D. Lieberman, K. B. Flett, I. Yelin, T. R. Martin, A. J. McAdam*, G. P. Priebe*, R. Kishony*
Nature Genetics (2014), 46(1), p.82.
Opposing effects of target overexpression reveal drug mechanisms
A. C. Palmer & R. Kishony
Nature Communications (2014), 5(1), pp.1-8.
Alternating antibiotic treatments constrain evolutionary paths to multidrug resistance
S. Kim, T.D. Lieberman, R. Kishony
PNAS (2014), 111(40), pp.14494-14499.
Editorial overview: Antimicrobials: grappling with the complexities of antibiotics and resistance
R. Kishony & J.J. Collins
Current Opinion Microbiology 21, v-vi. (2014).
Evolution of Antibiotic Resistance through a Multi-Peaked Adaptive Landscape
E. Toprak, A. C. Palmer, S. Kim, A. Veres, S. Bershtein, R. Kishony
Biophysical Journal (2013), 104(2), p.660a.
Building a morbidostat: an automated continuous-culture device for studying bacterial drug resistance under dynamically sustained drug inhibition
E. Toprak, A. Veres, S. Yildiz, J. M. Pedraza, R. Chait, J. Paulsson, R. Kishony
Nature Protocols (2013), 8(3), p.555.
Understanding, predicting and manipulating the genotypic evolution of antibiotic resistance
A. C. Palmer & R. Kishony
Nature Reviews Genetics (2013), 14(4), pp.243-248. {Review}
Optimization and control in bacterial Lag phase
D. Schultz & R. Kishony
BMC Biology (2013), 11(1), p.120. {Commentary}
What counters antibiotic resistance in nature?
R. Chait, K. Vetsigian, R. Kishony
Nature Chemical Biology (2012), 8(1), pp.2-5. {Perspective}
Evolutionary paths to antibiotic resistance under dynamically sustained drug selection
E. Toprak*, A. Veres*, J-B Michel, R. Chait, D. L Hartl, R. Kishony
Nature Genetics (2012), 44(1), p.101.
Distinct Growth Strategies of Soil Bacteria as Revealed by Large-Scale Colony Tracking
M. Ernebjerg & R. Kishony
Applied and Environmental Microbiology (2012), 78(5), pp.1345-1352.
Targeting pan-resistant bacteria with antibodies to a broadly conserved surface polysaccharide expressed during infection
Skurnik D, Davis MR Jr, Benedetti D, Moravec KL, Cywes-Bentley C, Roux D, Traficante DC, Walsh RL, Maira-Litrà n T, Cassidy SK, Hermos CR, Martin TR, Thakkallapalli EL, Vargas SO, McAdam AJ, Lieberman TD, Kishony R, Lipuma JJ, Pier GB, Goldberg JB, Priebe GP
Journal of Infectious Diseases (2012), 205(11), pp.1709-1718.
Regulation of cell size in response to nutrient availability by fatty acid biosynthesis in Escherichia coli
Z. Yao, R. M. Davis, R. Kishony, D. Kahne, N. Ruiz
PNAS (2012), 109(38), pp.E2561-E2568.
Distinct single-cell morphological dynamics under beta-lactam antibiotics
Z. Yao, D. Kahne*, R. Kishony*
Molecular Cell (2012), 48(5), pp.705-712.
Dynamic Phenotypic Clustering in Noisy Ecosystems
M. Ernebjerg & R. Kishony
PLoS Computational Biology (2011), 7(3).
Resolution of gene regulatory conflicts caused by combinations of antibiotics
T. Bollenbach & R. Kishony
Molecular Cell 42 (2011), 42(4), pp.413-425.
Systems Biology: Editorial Review
R. Kishony & V. Hatzimanikatis
Current Opinion in Biotechnology (2011), 22, pp.1-3. {Editorial}
Structure and evolution of Streptomyces interaction networks in soil and in silico
K. Vetsigian, R. Jajoo, R. Kishony
PLoS Biology (2011), 9(10).
Tackling antibiotic resistance
K. Bush, P. Courvalin , G. Dantas, J. Davies, B. Eisenstein, P. Huovinen, G.A. Jacob, R. Kishony, B.N Kreiswirth, E. Kutter, S.A Lerner, S. Levy, Lewis K, O. Lomovskaya, J.H. Miller, S. Mobashery, L.J Piddock, S. Projan, C.M. Thomas, A. Tomasz, P.M. Tulkens, T.R. Walsh, J.D. Watson, J. Witkowski, W. Witte, G. Wright, P. Yeh, H.I Zgurskaya
Nature Reviews Microbiology (2011), 9(12), pp.894-896. {Perspective}
Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes
T. D. Lieberman, J-B Michel, M. Aingaran, G. Potter-Bynoe, D. Roux, M. R. Davis Jr, D. Skurnik, N. Leiby, J. J. LiPuma, J. B. Goldberg, A. J. McAdam*, G. P. Priebe*, R. Kishony*
Nature Genetics (2011), 43(12), p.1275. [Selected for F1000; N&Vs by R. Lenski; Nature Reviews Microbiology; Science; The Scientist; Wall Street Journal; Boston Globe]
Chemical decay of an antibiotic inverts selection for resistance
A. Palmer, E. Angelino, R. Kishony
Nature Chemical Biology 6, 105 (2010).
Need-based upregulation of protein levels in response to deletion of their duplicate genes
A. DeLuna, M. Springer, M. W. Kirschner, R. Kishony
PLoS Biology 8, e1000347 (2010).
Optimal drug synergy in antimicrobial treatments
J. P. Torella, R. Chait, R. Kishony
PLoS Computational Biology 6 (6), e1000796 (2010).
A differential drug screen for compounds that select against antibiotic resistance
R. Chait., S. Shrestha, A. Shah, J-B Michel, R. Kishony
PLoS ONE 5 (12): e15179 (2010).
Quiet gene circuit more fragile than its noisy peer
T. Bollenbach & R. Kishony
Cell 139, 461 (2009). {N&V}
Non-optimal microbial response to antibiotics underlies suppressive drug interactions
T. Bollenbach, S. Quan, R. Chait, and R. Kishony
Cell 139, 707 (2009). [New England Journal of Medicine, Clinical implications of basic research, J. B. Xavier and C. Sander]
Hydroxyurea triggers cellular responses that actively cause bacterial cell death
T. Bollenbach & R. Kishony
Molecular Cell 36, 728 (2009).
Rapid β-lactam induced lysis requires successful assembly of the cell division machinery
H-S Chung*, Z. Yao*, N. W. Goehring*, R. Kishony, J. Beckwith , D. Kahne,
PNAS 106, 21872 (2009). [Selected for F1000]
Discovery of a small molecule that blocks wall teichoic acid biosynthesis in Staphylococcus aureus
J. G. Swoboda, T. C. Meredith, J. Campbell, S. Brown, T. Suzuki, T. Bollenbach, A. J. Malhowski, R. Kishony, M. S. Gilmore and S. Walker
ACS Chemical Biology 4, 875 (2009)
Drug interactions and the evolution of antibiotic resistance
P. Yeh, M. Hegreness, A. Presser, R. Kishony
Nature Reviews Microbiology 7, 460 (2009).
Drug interactions modulate the potential for evolution of resistance
J.-B. Michel, P. Yeh, R. Chait, R. Moellering, R. Kishony
PNAS 105, 14918 (2008). [Selected for F1000; PNAS “In this issue” Editorial]
The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication
A. Presser, M. B. Elowitz, M. Kellis, R. Kishony
PNAS 105, 950 (2008).
Nongenetic individuality in the host-phage interaction
S. Pearl, C. Gabay, R. Kishony, A. Oppenheim, N. Q. Balaban
PLoS Biology 6(5): e120 (2008).
Exposing the fitness contribution of duplicated genes
A. DeLuna, K. Vetsigian, N. Shoresh, M. Hegreness, M. Colón-González, S. Chao, R. Kishony
Nature Genetics 40, 676 (2008).
Evolution exacerbates the paradox of the plankton
N. Shoresh, M. Hegreness, R. Kishony
PNAS 105, 12365 (2008).
Accelerated evolution of resistance in multi-drug environments
M. Hegreness, N. Shoresh, D. Damian, D. Hartl, R. Kishony
PNAS 105, 13977 (2008). [“Editor Choice”, Science]
Analysis of genetic systems using experimental evolution and whole-genome sequencing
M. Hegreness & R. Kishony
Genome Biology 8:201 (2007). {Review}
Networks from drug-drug surfaces
P. Yeh & R. Kishony
Molecular Systems Biology 3:85 (2007).
Evolution and multilevel optimization of the genetic code
T. Bollenbach, K. Vetsigian, R. Kishony
Genome Research 17, 401 (2007).
Antibiotic interactions that select against resistance
R. Chait, A. Craney, R. Kishony
Nature 446, 668 (2007). [Nature News by J. Whitfield]
An equivalence principle for the incorporation of favorable mutations in asexual populations
M. Hegreness, N. Shoresh, D. Hartl, R. Kishony
Science 311, p. 1615 (2006). [Selected for F1000]
Functional classification of drugs by properties of their pair-wise interactions
P. Yeh, A. Tschumi, R. Kishony
Nature Genetics 38, 489 (2006).
Modular epistasis in yeast metabolism”, Nature Genetics 3, 77 (2005). [N&Vs by J. H. Moore; Editorial “From parts catalog to wiring diagram]
D. Segrè, A. DeLuna, G. M. Church, R. Kishony
Research Highlight, Nature Reviews Genetics; Selected for F1000]
Bacterial persistence: a model of survival in changing environments
E. Kussell, R. Kishony, N. Q. Balaban, S. Leibler
Genetics 169: 1807-1814 (2005). [Selected for F1000]
Environmental stresses can alleviate the average deleterious effect of mutations
R. Kishony & S. Leibler
Journal of Biology 2, p. 14 (2003). [Research news by P. Moore; Selected for F1000]
Ignition condition and gain prediction for perturbed ICF targets
R. Kishony & D. Shvarts
Physics of Plasmas 8, 4925 (2001).
Inertial confinement fusion ignition criteria, critical profiles and burn wave propagation using self-similar solutions
R. Kishony, E. Waxman, D. Shvarts
Physics of Plasmas 4, 1385 (1997).