Publications

2024

Autonomous LLM-Driven Research — from Data to Human-Verifiable Research Papers

T. Ifargan*, L. Hafner*, M. Kern, O. Alcalay, R. Kishony

NEJM AI (2024)

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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)

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2023

Systematic identification of gene-altering programmed inversions across the bacterial domain

O. Milman, I. Yelin, R. Kishony

Nucleic Acids Research (2023)

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2022

Multistep diversiﬁcation in spatiotemporal bacterial-phage coevolution

E. Shaer-Tamar, R. Kishony

Nature Communications (2022), 13(1), p.7971.

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Antibiotic combinations reduce Staphylococcus aureus clearance

V. Lázár, O. Snitser, D. Barkan, R. Kishony

Nature (2022), 610(7932), pp.540-546.

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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.

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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)

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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

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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

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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

2024

Autonomous LLM-Driven Research — from Data to Human-Verifiable Research Papers

Beta-lactamase dependent and independent evolutionary paths to high-level ampicillin resistance

2023

Systematic identification of gene-altering programmed inversions across the bacterial domain

2022

Multistep diversiﬁcation in spatiotemporal bacterial-phage coevolution

Antibiotic combinations reduce Staphylococcus aureus clearance

Minimizing treatment-induced emergence of antibiotic resistance in bacterial infections

Host-parasite coevolution promotes innovation through deformations in fitness landscapes

Rapid expansion and extinction of antibiotic resistance mutations during treatment of acute bacterial respiratory infections

Waning of SARS-CoV-2 booster viral-load reduction effectiveness

SARS-CoV-2 RT-qPCR Test Detection Rates Are Associated with Patient Age, Sex, and Time since Diagnosis

2021

Viral loads of Delta-variant SARS-CoV2 breakthrough infections following vaccination and booster with the BNT162b2 vaccine

Rapid methicillin resistance diversification in Staphylococcus epidermidis colonizing human neonates

Community-level evidence for SARS-CoV-2 vaccine protection of unvaccinated individuals

Initial report of decreased SARS-CoV-2 viral load after inoculation with the BNT162b2 vaccine

Associations of the BNT162b2 COVID-19 vaccine effectiveness with patient age and comorbidities

2020

Antibiotic resistance: turning evolutionary principles into clinical reality

Ubiquitous selection for mecA in community-associated MRSA across diverse chemical environments

Evaluation of COVID-19 RT-qPCR test in multi-sample pools

Escape mutations circumvent a tradeoff between resistance to a beta-lactam and resistance to a beta-lactamase inhibitor

2019

Genomic and epidemiological evidence of bacterial transmission from probiotic capsule to blood in ICU patients.

Personal clinical history predicts antibiotic resistance of urinary tract infections

Transient antibiotic resistance calls for attention

2018

SnapShot: Antibiotic Resistance

Additivity of inhibitory effects in multi-drug combinations

Non-optimal gene expression creates latent potential for antibiotic resistance

A spotlight on bacterial mutations for 75 years

2017

RNA Structural Determinants of Optimal Codons Revealed by MAGE-Seq

Global and local selection acting on the pathogen Stenotrophomonas maltophilia in the human lung

Regulatory Dynamics Determine Cell Fate Following Abrupt Antibiotic Exposure

2016

Evolutionary stability of microbial communities with antibiotic degrading species

High-order species interactions shape ecosystem diversity

Compounds that select against the tetracycline resistance efflux pump

Spatiotemporal microbial evolution on antibiotic landscapes

A competitive trade-off limits the selective advantage of increased antibiotic production

Genomic diversity in autopsy samples reveals within-host dissemination of HIV-associated M. tuberculosis

Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments

Multidrug evolutionary strategies to reverse antibiotic resistance

A hybrid drug limits resistance by evading the action of the multiple antibiotic resistance pathway

2015

Polyploidy can drive rapid adaptation in yeast

Delayed commitment to evolutionary fate in antibiotic resistance fitness landscapes

Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes

Counteraction of antibiotic production and degradation generates stability in microbial communities

2014

Genetic variation of a bacterial pathogen within individuals with cystic fibrosis provides a record of selective pressures

Opposing effects of target overexpression reveal drug mechanisms

Alternating antibiotic treatments constrain evolutionary paths to multidrug resistance

Editorial overview: Antimicrobials: grappling with the complexities of antibiotics and resistance

2013

Evolution of Antibiotic Resistance through a Multi-Peaked Adaptive Landscape

Building a morbidostat: an automated continuous-culture device for studying bacterial drug resistance under dynamically sustained drug inhibition

Understanding, predicting and manipulating the genotypic evolution of antibiotic resistance

Optimization and control in bacterial Lag phase

2012

What counters antibiotic resistance in nature?

Evolutionary paths to antibiotic resistance under dynamically sustained drug selection

Distinct Growth Strategies of Soil Bacteria as Revealed by Large-Scale Colony Tracking

Targeting pan-resistant bacteria with antibodies to a broadly conserved surface polysaccharide expressed during infection

Regulation of cell size in response to nutrient availability by fatty acid biosynthesis in Escherichia coli

Distinct single-cell morphological dynamics under beta-lactam antibiotics

2011

Dynamic Phenotypic Clustering in Noisy Ecosystems

Resolution of gene regulatory conflicts caused by combinations of antibiotics

Systems Biology: Editorial Review

Structure and evolution of Streptomyces interaction networks in soil and in silico

Tackling antibiotic resistance

Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes

2010

Chemical decay of an antibiotic inverts selection for resistance

Need-based upregulation of protein levels in response to deletion of their duplicate genes