Selected Publications
(Lab members are in bald)
Danov A*, Pollin I*, Moon E, Ho M, Wilson BA, Papathanos PA, Kaplan T, and Levy A Identification of novel toxins associated with the extracellular contractile injection system using machine learning.
Molecular Systems Biology 2024 (Cover page!)
https://www.embopress.org/doi/full/10.1038/s44320-024-00053-6
Haimlich S, Fridman Y, Khandal H, Savaldi-Goldstein S, and Levy A Widespread horizontal gene transfer between plants and bacteria
ISME Communications 2024
https://academic.oup.com/ismecommun/article/4/1/ycae073/7671050?login=false
Geller AM, Shalom M, Zlotkin D, Blum N, and Levy A Identification of type VI secretion system effector-immunity pairs using structural bioinformatics.
Molecular Systems Biology 2024
https://www.embopress.org/doi/full/10.1038/s44320-024-00035-8
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.
https://journals.asm.org/doi/10.1128/mbio.01911-23
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 2023. Volume 72, 2023.4.102283.
https://www.sciencedirect.com/science/article/pii/S1369527423000206
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 2021.10.19.465003v2
https://www.biorxiv.org/content/10.1101/2021.10.19.465003v2
Geller AM, Zlotkin D, Levy A. Large-scale discovery of candidate type VI secretion effectors with antibacterial activity.
bioRxiv 2021 2021.10.07.463556.
https://www.biorxiv.org/content/10.1101/2021.10.07.463556v1
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).
https://www.nature.com/articles/s41467-021-23777-7
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.
https://academic.oup.com/nar/article/50/3/e17/6454267
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.
https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2020.589416/full
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
https://journals.asm.org/doi/full/10.1128/aem.00622-20
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 Interactions. 2020 Feb;33(2):349-363. doi: 10.1094/MPMI-09-19-0256-R. Epub 2019 Dec 18.
https://apsjournals.apsnet.org/doi/10.1094/MPMI-09-19-0256-R
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.
https://www.microbiologyresearch.org/content/journal/micro/10.1099/mic.0.000865
Levy A, Conway JM, Dangl JL, Woyke T. Elucidating Bacterial Gene Functions in the Plant Microbiome.
(Levy A - corresponding author)
Cell Host Microbe. 2018 Oct 10;24(4):475-485. doi: 10.1016/j.chom.2018.09.005. Review. PubMed PMID: 30308154.https://www.sciencedirect.com/science/article/pii/S193131281830489X
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.
https://www.nature.com/articles/s41588-017-0012-9
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
https://enviromicro-journals.onlinelibrary.wiley.com/doi/full/10.1111/1462-2920.13471
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.
https://www.nature.com/articles/nature14302
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”,
Molecular Cell. 2013 Jun 27;50(6):869- 81https://www.sciencedirect.com/science/article/pii/S1097276513003705
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):802-9https://genome.cshlp.org/content/early/2012/02/01/gr.133850.111
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
