Publications
Featured Publications
2025
Article
Beneath the surface: Unsolved questions in soil virus ecology
Christina Hazard, Karthik Anantharaman, Luke S. Hillary, Uri Neri, Simon Roux, Gareth Trubl, Kurt Williamson, Jennifer Pett-Ridge, Graeme W. Nicol, Joanne B. Emerson
Soil Biology and Biochemistry (2025)
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Article
The protein structurome of Orthornavirae and its dark matter
Pascal Mutz, Antonio Pedro Camargo, Harutyun Sahakyan, Uri Neri, Anamarija Butkovic, Yuri I. Wolf, Mart Krupovic, Valerian V. Dolja, Eugene V. Koonin
mBio (2025)
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Article
Meeting report: International soil virus conference 2024
María Touceda-Suárez, Matthew A. Perry, Riccardo Frizzo, John Henry Lotz-McMillen, Ruby Ann Gilmore, Shauna M. Bennett, Jonelle T.R. Basso, William Donovan, Jane D. Fudyma, Sara E. Geonczy, Marissa Gittrich, Grant Gogul, Christina Hazard, Luke S. Hillary, Ellie Jameson, Lucie Jiraska, Sarah Stewart Johnson, James C. Kosmopoulos, Ikaia Leleiwi, Bin Ma, Catherine M. Mageeney, Andrew Millard, Uri Neri, Josué Rodríguez-Ramos, Simon Roux, Di Tong, Yiling Wang, Kurt Williamson, Ruonan Wu, Paula Dalcin Martins, Rumakanta Sapkota, Joanne B. Emerson, Gareth Trubl
Virus Research (2025)
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2024
Article
Consensus statement from the first RdRp Summit: advancing RNA virus discovery at scale across communities
Justine Charon, Ingrida Olendraite, Marco Forgia, Li Chuin Chong, Luke S. Hillary, Simon Roux, Anne Kupczok, Humberto Debat, Shoichi Sakaguchi, Rachid Tahzima, So Nakagawa, Artem Babaian, Aare Abroi, Nicolas Bejerman, Karima Ben Mansour, Katherine Brown, Anamarija Butkovic, Amelia Cervera, Florian Charriat, Guowei Chen, Yuto Chiba, Lander De Coninck, Tatiana Demina, Guillermo Dominguez-Huerta, Jeremy Dubrulle, Serafin Gutierrez, Erin Harvey, Fhilmar Raj Jayaraj Mallika, Dimitris Karapliafis, Shen Jean Lim, Sunitha Manjari Kasibhatla, Jonathon C. O. Mifsud, Yosuke Nishimura, Ayda Susana Ortiz-Baez, Milica Raco, Ricardo Rivero, Sabrina Sadiq, Shahram Saghaei, James Emmanuel San, Hisham Mohammed Shaikh, Ella Tali Sieradzki, Matthew B. Sullivan, Yanni Sun, Michelle Wille, Yuri I. Wolf, Nikita Zrelovs, Uri Neri
Frontiers in Virology (2024)
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Article
Identification of diverse RNA viruses in Obscuromonas flagellates (Euglenozoa: Trypanosomatidae: Blastocrithidiinae)
Danyil Grybchuk, Arnau Galan, Donnamae Klocek, Diego H Macedo, Yuri I Wolf, Jan Votýpka, Anzhelika Butenko, Julius Lukeš, Uri Neri, Kristína Záhonová, Alexei Yu Kostygov, Eugene V Koonin, Vyacheslav Yurchenko
Virus Evolution (2024)
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Article
Identification of a novel mycovirus belonging to the “flexivirus”-related family with icosahedral virion
Chien-Fu Wu, Ryo Okada, Uri Neri, Yi-Cheng Chang, Takashi Ogawara, Kentaro Kitaura, Ken Komatsu, Hiromitsu Moriyama
Virus Evolution (2024)
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preprint
A new archaeal virus that suppresses the transcription of host immunity genes
Israela Turgeman-Grott, Noam Golan, Uri Neri, Doron Naki, Neta Altman-Price, Kim Eizenshtein, Deepak K. Choudhary, Rachel Levy, Yarden Shalev, Himani Himani, Leah Reshef, Uri Gophna
bioRxiv (2024)
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2023
Article
Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs
Benjamin D. Lee, Uri Neri, Simon Roux, Yuri I. Wolf, Antonio Pedro Camargo, Mart Krupovic, Peter Simmonds, Nikos Kyrpides, Uri Gophna, Valerian V. Dolja, Eugene V. Koonin
Cell (2023)
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2022
Article
Expansion of the global RNA virome reveals diverse clades of bacteriophages
Uri Neri, Yuri I. Wolf, Simon Roux, Antonio Pedro Camargo, Benjamin Lee, Darius Kazlauskas, I. Min Chen, Natalia Ivanova, Lisa Zeigler Allen, David Paez-Espino, Donald A. Bryant, Devaki Bhaya, Mart Krupovic, Valerian V. Dolja, Nikos C. Kyrpides, Eugene V. Koonin, Uri Gophna, Adrienne B. Narrowe, Alexander J. Probst, Alexander Sczyrba, Annegret Kohler, Armand Séguin, Ashley Shade, Barbara J. Campbell, Björn D. Lindahl, Brandi Kiel Reese, Breanna M. Roque, Chris DeRito, Colin Averill, Daniel Cullen, David A.C. Beck, David A. Walsh, David M. Ward, Dongying Wu, Emiley Eloe-Fadrosh, Eoin L. Brodie, Erica B. Young, Erik A. Lilleskov, Federico J. Castillo, Francis M. Martin, Gary R. LeCleir, Graeme T. Attwood, Hinsby Cadillo-Quiroz, Holly M. Simon, Ian Hewson, Igor V. Grigoriev, James M. Tiedje, Janet K. Jansson, Janey Lee, Jean S. VanderGheynst, Jeff Dangl, Jeff S. Bowman, Jeffrey L. Blanchard, Jennifer L. Bowen, Jiangbing Xu, Jillian F. Banfield, Jody W. Deming, Joel E. Kostka, John M. Gladden, Josephine Z. Rapp, Joshua Sharpe, Katherine D. McMahon, Kathleen K. Treseder, Kay D. Bidle, Kelly C. Wrighton, Kimberlee Thamatrakoln, Klaus Nusslein, Laura K. Meredith, Lucia Ramirez, Marc Buee, Marcel Huntemann, Marina G. Kalyuzhnaya, Mark P. Waldrop, Matthew B. Sullivan, Matthew O. Schrenk, Matthias Hess, Michael A. Vega, Michelle A. O’Malley, Monica Medina, Naomi E. Gilbert, Nathalie Delherbe, Olivia U. Mason, Paul Dijkstra, Peter F. Chuckran, Petr Baldrian, Philippe Constant, Ramunas Stepanauskas, Rebecca A. Daly, Regina Lamendella, Robert J. Gruninger, Robert M. McKay, Samuel Hylander, Sarah L. Lebeis, Sarah P. Esser, Silvia G. Acinas, Steven S. Wilhelm, Steven W. Singer, Susannah S. Tringe, Tanja Woyke, T.B.K. Reddy, Terrence H. Bell, Thomas Mock, Tim McAllister, Vera Thiel, Vincent J. Denef, Wen-Tso Liu, Willm Martens-Habbena, Xiao-Jun Allen Liu, Zachary S. Cooper, Zhong Wang
Cell (2022)
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preprint
A five-fold expansion of the global RNA virome reveals multiple new clades of RNA bacteriophages
Uri Neri, Yuri I. Wolf, Simon Roux, Antonio Pedro Camargo, Benjamin Lee, Darius Kazlauskas, I. Min Chen, Natalia Ivanova, Lisa Zeigler Allen, David Paez-Espino, Donald A. Bryant, Devaki Bhaya, Mart Krupovic, Valerian V. Dolja, Nikos C. Kyrpides, Eugene V. Koonin, Uri Gophna
bioRxiv (2022)
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preprint
A vast world of viroid-like circular RNAs revealed by mining metatranscriptomes
Benjamin D. Lee, Uri Neri, Simon Roux, Yuri I. Wolf, Antonio Pedro Camargo, Mart Krupovic, Peter Simmonds, Nikos Kyrpides, Uri Gophna, Valerian V. Dolja, Eugene V. Koonin
bioRxiv (2022)
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Article
ViroidDB: a database of viroids and viroid-like circular RNAs
Benjamin D Lee, Uri Neri, Caleb J Oh, Peter Simmonds, Eugene V Koonin
Nucleic Acids Research (2022)
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2021
Article
The evolutionary origins of extreme halophilic archaeal lineages
Yutian Feng, Uri Neri, Sophia Gosselin, Artemis S Louyakis, R Thane Papke, Uri Gophna, Johann Peter Gogarten
Genome biology and evolution (2021)
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2019
Article
Microbial interactions in the Dead Sea as reflected by enrichment cultures: the curious case of Nanohaloarchaea.
Studia Universitatis Babes-Bolyai, Biologia (2019)