Selected Publications

Danov A, Segev O, Bograd A, Eliyahu Y, Dotan N, Kaplan T, Levy, A. Toxinome—the bacterial protein toxin database. mBio. Vol. 15, No. 1, 2024.1.

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Geller AM and Levy A. “What I cannot create, I do not understand": elucidating microbe–microbe interactions to facilitate plant microbiome engineering. Current Opinion in Microbiology. Volume 72, 2023.4.102283.

 

Nachmias N, Dotan N, Fraenkel R, Campos Rocha M, Kluzek M, Shalom M, Rivitz A, Shamash-Halevy N, Cahana I, Deouell N, Klein K, Schlezinger N, Tzarum N, Oppenheimer-Shaanan Y, Levy A. Systematic Discovery of Antibacterial and Antifungal Bacterial Toxins. bioRxiv 2021.10.19.465003.

 

Haimlich S, Fridman Y, Khandal H, Savaldi-Goldstein S, Levy A. Widespread horizontal gene transfer between plants and their microbiota. bioRxiv 2021.10.19.465003.

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Nachmias N, Dotan N, Fraenkel R, Campos Rocha M, Kluzek M, Shalom M, Rivitz A, Shamash-Halevy N, Cahana I, Deouell N, Klein K, Schlezinger N, Tzarum N, Oppenheimer-Shaanan Y, Levy A. Systematic Discovery of Antibacterial and Antifungal Bacterial Toxins. bioRxiv 2021.10.19.465003.

 

Geller AM, Zlotkin D, Levy A. Large-scale discovery of candidate type VI secretion effectors with antibacterial activity. bioRxiv 2021.10.07.463556.

 

Geller AM, Pollin I, Zlotkin D, Danov A, Nachmias N, Andreopoulos WB, Shemesh K & Levy A. The extracellular contractile injection system is enriched in environmental microbes and associates with numerous toxins. Nature Communications 12, 3743 (2021).

 

Andreopoulos WB, Geller AM, Lucke M, Balewski J, Clum A, Ivanova N, Levy A. Deeplasmid: Deep learning accurately separates plasmids from bacterial chromosomes. Nucleic Acids Research, Volume 50, Issue 3, 22 February 2022, Page e17.

 

Lucke M, Correa MG, Levy A. The Role of Secretion Systems, Effectors, and Secondary Metabolites of Beneficial Rhizobacteria in Interactions With Plants and Microbes. Frontiers in Plant Science. November 2020. 11, 1718.

 

Mosquito S, Meng X, Devescovi G, Bertani I, Geller AM, Levy A, Myers MP, Bez C, Covaceuszach S, Venturi V. LuxR Solos in the Plant Endophyte Kosakonia sp. Strain KO348. Applied and Environmental Microbiology. Jun 2020, 86 (13) e00622-20

 

Mosquito S, Bertani I, Licastro D, Compant S, Myers MP, Hinarejos E, Levy A, Venturi V. In Planta Colonization and Role of T6SS in Two Rice Kosakonia Endophytes. Mol Plant Microbe Interact. 2020 Feb;33(2):349-363. doi: 10.1094/MPMI-09-19-0256-R. Epub 2019 Dec 18.

 

Bez C, Javvadi SG, Bertani I, Devescovi G, Guarnaccia C, Studholme DJ, Geller AM, Levy A, Venturi V. AzeR, a transcriptional regulator that responds to azelaic acid in Pseudomonas nitroreducens. Microbiology. 2019 Oct 17. doi: 10.1099/mic.0.000865. [Epub ahead of print] PubMed PMID: 31621557.

 

Levy A, Conway JM, Dangl JL, Woyke T. Elucidating Bacterial Gene Functions in the Plant Microbiome. Cell Host Microbe. 2018 Oct 10;24(4):475-485. doi: 10.1016/j.chom.2018.09.005. Review. PubMed PMID: 30308154.

 

Levy A*, Gonzalez IS*, Mittelviefhaus M, Clingenpeel S, Paredes SH, Devescovi G, Stillman K, Monteiro F, Alvarez BR, Lundberg DS, Tse-Yuan L, Lebeis S, Jin Z, McDonald M, Klein AP, Feltcher ME, del Rio TG, Grant SR, Doty SL, Venturi V, Ley RE, Zhao B, Pelletier DA, Vorholt J, Tringe SG, Woyke T, Dangl JL. Genomic Features of Bacterial Adaptation to Plants. Nature Genetics. 2018. 50, 138-150.

 

Bloom-Ackermann Z, Steinberg N, Rosenberg G, Oppenheimer-Shaanan Y, Pollack D, Ely S, Storzi N, Levy A, Kolodkin-Gal I. Toxin-Antitoxin systems eliminate defective cells and preserve symmetry in Bacillus subtilis biofilms. Environ Microbiol. 2016 Dec;18(12):5032-5047

 

Levy A*, Goren M*, Yosef I, Auster O, Manor M, Amitai G, Edgar R, Qimron U, Sorek R, “CRISPR adaptation biases explain preference for acquisition of foreign DNA”. Nature. 2015 April 23, 520(7548):505-10.

 

Melamed Z, Levy A, Ashwal R., Lev-Maor G., Mekahel K., Atias N., Gilad S., Sharan R., Levy C., Kadener S., and Ast G., “Alternative splicing regulates biogenesis of miRNAs located across exon-intron junctions”, Mol Cell. 2013 Jun 27;50(6):869- 81

 

Kimelman A*, Levy A*, Sberro H*, Kidron S, Leavitt A, Amitai G, Yoder-Himes DR, Wurtzel O, Zhu Y, Rubin EM, Sorek R., “A vast collection of microbial genes that are toxic to bacteria”, Genome Research. 2012 Apr;22(4):802-9

 

Levy A, Schwartz S and Ast G., “Large-scale discovery of insertion hotspots and preferential integration sites of human transposed elements”, Nucleic Acids Research. 2010 Mar; 38(5):1515-30

 

Meiri E*, Levy A*, Benjamin H, Ben-David M, Cohen L, Dov A, Dromi N, Elyakim E, Yerushalmi N, Zion O, Lithwick-Yanai G, Sitbon E., “Discovery of microRNAs and other small RNAs in solid tumors”, Nucleic Acids Research. 2010 Oct;38(18):6234-46

 

Kontorovich T*, Levy A*, Korostishevsky M, Nir U, Friedman E. “SNPs in miRNA binding sites and miRNA genes as breast/ovarian cancer risk modifiers in Jewish high risk women”, Int J Cancer. 2010 Aug 1;127(3):589-97