Publications

28 publications, 2010–2026

2026

1. A comprehensive catalogue of receptor-binding domains in extracellular contractile injection systems

   Nimrod Nachmias, Zhiren Wang, Xiao Feng, Feng Jiang, Asaf Levy

   Nature Communications doi:10.1038/s41467-026-68710-y

2. Discovery of novel antimicrobials within microbiomes

   Erez Weisberg, Aya Friedman, Cesar de la Fuente-Nunez, Asaf Levy

   Current Opinion in Microbiology doi:10.1016/j.mib.2026.102781

2025

1. Deciphering bacterial protein functions with innovative computational methods

   Shani Cheskis, Avital Akerman, Asaf Levy (* co-first authors)

   Trends in Microbiology doi:10.1016/j.tim.2024.11.013

2. Crop root bacterial and viral genomes reveal unexplored species and microbiome patterns

   Rui Dai, Jingying Zhang, Fang Liu, Haoran Xu, Jing-Mei Qian, Shani Cheskis, Weidong Liu, Binglei Wang, Honghui Zhu, Lotte J.U. Pronk, Marnix H. Medema, Ronnie de Jonge, Corné M.J. Pieterse, Asaf Levy, Klaus Schlaeppi, Yang Bai

   Cell doi:10.1016/j.cell.2025.02.013

3. Plasmids, prophages, and defense systems are depleted from plant microbiota genomes

   Avi Bograd, Yaara Oppenheimer-Shaanan, Asaf Levy

   Genome Biology doi:10.1186/s13059-025-03641-3

2024

1. Toxinome—the bacterial protein toxin database

   Aleks Danov, Ofir Segev, Avi Bograd, Yedidya Ben Eliyahu, Noam Dotan, Tommy Kaplan, Asaf Levy (* co-first authors)

   mBio doi:10.1128/mbio.01911-23

2. Identification of type VI secretion system effector-immunity pairs using structural bioinformatics

   Alexander M Geller, Maor Shalom, David Zlotkin, Noam Blum, Asaf Levy

   Molecular Systems Biology doi:10.1038/s44320-024-00035-8

3. Widespread horizontal gene transfer between plants and bacteria

   Shelly Haimlich, Yulia Fridman, Hitaishi Khandal, Sigal Savaldi-Goldstein, Asaf Levy

   ISME Communications doi:10.1093/ismeco/ycae073

4. Identification of novel toxins associated with the extracellular contractile injection system using machine learning

   Aleks Danov, Inbal Pollin, Eric Moon, Mengfei Ho, Brenda A Wilson, Philippos A Papathanos, Tommy Kaplan, Asaf Levy (* co-first authors)

   Molecular Systems Biology doi:10.1038/s44320-024-00053-6

5. Systematic discovery of antibacterial and antifungal bacterial toxins

   Nimrod Nachmias, Noam Dotan, Marina Campos Rocha, Rina Fraenkel, Katharina Detert, Monika Kluzek, Maor Shalom, Shani Cheskis, Sonu Peedikayil-Kurien, Gilad Meitav, Arbel Rivitz, Naama Shamash-Halevy, Inbar Cahana, Noam Deouell, Jacob Klein, Meital Oren-Suissa, Herbert Schmidt, Neta Shlezinger, Netanel Tzarum, Yaara Oppenheimer-Shaanan, Asaf Levy (* co-first authors)

   Nature Microbiology doi:10.1038/s41564-024-01820-9

2023

1. “What I cannot create, I do not understand": elucidating microbe–microbe interactions to facilitate plant microbiome engineering

   Alexander M Geller, Asaf Levy

   Current Opinion in Microbiology doi:10.1016/j.mib.2023.102283

2022

1. Deeplasmid: deep learning accurately separates plasmids from bacterial chromosomes

   William B Andreopoulos, Alexander M Geller, Miriam Lucke, Jan Balewski, Alicia Clum, Natalia N Ivanova, Asaf Levy (* co-first authors)

   Nucleic Acids Research doi:10.1093/nar/gkab1115

2021

1. The extracellular contractile injection system is enriched in environmental microbes and associates with numerous toxins

   Alexander Martin Geller, Inbal Pollin, David Zlotkin, Aleks Danov, Nimrod Nachmias, William B. Andreopoulos, Keren Shemesh, Asaf Levy

   Nature Communications doi:10.1038/s41467-021-23777-7

2. Large-scale discovery of candidate type VI secretion effectors with antibacterial activity preprint

   Alexander Martin Geller, David Zlotkin, Asaf Levy

   bioRxiv doi:10.1101/2021.10.07.463556

3. Systematic Discovery of Antibacterial and Antifungal Bacterial Toxins preprint

   Nimrod Nachmias, Noam Dotan, Rina Fraenkel, Marina Campos Rocha, Monika Kluzek, Maor Shalom, Arbel Rivitz, Naama Shamash-Halevy, Inbar Cahana, Noam Deouell, Jacob Klein, Neta Schlezinger, Netanel Tzarum, Yaara Oppenheimer-Shaanan, Asaf Levy (* co-first authors)

   bioRxiv doi:10.1101/2021.10.19.465003

2020

1. AzeR, a transcriptional regulator that responds to azelaic acid in Pseudomonas nitroreducens

   Cristina Bez, Sree Gowrinadh Javvadi, Iris Bertani, Giulia Devescovi, Corrado Guarnaccia, David J. Studholme, Alexander M. Geller, Asaf Levy, Vittorio Venturi

   Microbiology doi:10.1099/mic.0.000865

2. In Planta Colonization and Role of T6SS in Two Rice Kosakonia Endophytes

   Susan Mosquito, Iris Bertani, Danilo Licastro, Stéphane Compant, Michael P. Myers, Estefanía Hinarejos, Asaf Levy, Vittorio Venturi

   Molecular Plant-Microbe Interactions® doi:10.1094/mpmi-09-19-0256-r

3. LuxR Solos in the Plant Endophyte Kosakonia sp. Strain KO348

   Susan Mosquito, Xianfa Meng, Giulia Devescovi, Iris Bertani, Alexander M. Geller, Asaf Levy, Michael P. Myers, Cristina Bez, Sonia Covaceuszach, Vittorio Venturi

   Applied and Environmental Microbiology doi:10.1128/aem.00622-20

4. The Role of Secretion Systems, Effectors, and Secondary Metabolites of Beneficial Rhizobacteria in Interactions With Plants and Microbes

   Miriam Lucke, Mario Gabriel Correa, Asaf Levy

   Frontiers in Plant Science doi:10.3389/fpls.2020.589416

2018

1. Genomic features of bacterial adaptation to plants

   Asaf Levy, Isai Salas Gonzalez, Maximilian Mittelviefhaus, Scott Clingenpeel, Sur Herrera Paredes, Jiamin Miao, Kunru Wang, Giulia Devescovi, Kyra Stillman, Freddy Monteiro, Bryan Rangel Alvarez, Derek S. Lundberg, Tse-Yuan Lu, Sarah Lebeis, Zhao Jin, Meredith McDonald, Andrew P. Klein, Meghan E. Feltcher, Tijana Glavina Rio, Sarah R. Grant, Sharon L. Doty, Ruth E. Ley, Bingyu Zhao, Vittorio Venturi, Dale A. Pelletier, Julia A. Vorholt, Susannah G. Tringe, Tanja Woyke, Jeffery L. Dangl (* co-first authors)

   Nature Genetics doi:10.1038/s41588-017-0012-9

2. Elucidating Bacterial Gene Functions in the Plant Microbiome

   Asaf Levy, Jonathan M. Conway, Jeffery L. Dangl, Tanja Woyke

   Cell Host & Microbe doi:10.1016/j.chom.2018.09.005

2016

1. Toxin‐Antitoxin systems eliminate defective cells and preserve symmetry in B acillus subtilis biofilms

   Zohar Bloom‐Ackermann, Nitai Steinberg, Gili Rosenberg, Yaara Oppenheimer‐Shaanan, Dan Pollack, Shir Ely, Nimrod Storzi, Asaf Levy, Ilana Kolodkin‐Gal

   Environmental Microbiology doi:10.1111/1462-2920.13471

2015

1. CRISPR adaptation biases explain preference for acquisition of foreign DNA

   Asaf Levy, Moran G. Goren, Ido Yosef, Oren Auster, Miriam Manor, Gil Amitai, Rotem Edgar, Udi Qimron, Rotem Sorek (* co-first authors)

   Nature doi:10.1038/nature14302

2013

1. Alternative Splicing Regulates Biogenesis of miRNAs Located across Exon-Intron Junctions

   Ze’ev Melamed, Asaf Levy, Reut Ashwal-Fluss, Galit Lev-Maor, Keren Mekahel, Nir Atias, Shlomit Gilad, Roded Sharan, Carmit Levy, Sebastian Kadener, Gil Ast

   Molecular Cell doi:10.1016/j.molcel.2013.05.007

2012

1. A vast collection of microbial genes that are toxic to bacteria

   Aya Kimelman, Asaf Levy, Hila Sberro, Shahar Kidron, Azita Leavitt, Gil Amitai, Deborah R. Yoder-Himes, Omri Wurtzel, Yiwen Zhu, Edward M. Rubin, Rotem Sorek (* co-first authors)

   Genome Research doi:10.1101/gr.133850.111

2010

1. Single nucleotide polymorphisms in miRNA binding sites and miRNA genes as breast/ovarian cancer risk modifiers in Jewish high‐risk women

   Tair Kontorovich, Asaf Levy, Michael Korostishevsky, Uri Nir, Eitan Friedman (* co-first authors)

   International Journal of Cancer doi:10.1002/ijc.25065

2. Discovery of microRNAs and other small RNAs in solid tumors

   Eti Meiri, Asaf Levy, Hila Benjamin, Miriam Ben-David, Lahav Cohen, Avital Dov, Nir Dromi, Eran Elyakim, Noga Yerushalmi, Orit Zion, Gila Lithwick-Yanai, Einat Sitbon (* co-first authors)

   Nucleic Acids Research doi:10.1093/nar/gkq376

3. Large-scale discovery of insertion hotspots and preferential integration sites of human transposed elements

   Asaf Levy, Schraga Schwartz, Gil Ast

   Nucleic Acids Research doi:10.1093/nar/gkp1134