Autonomous LLM-driven research from data to human-verifiable research papers

T. Ifargan, L. Hafner, M. Kern, O. Alcalay, R. Kishony
arXiv (2024)
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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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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
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.
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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
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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.
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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.
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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).
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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.