Peer-reviewed Publications

Click here for a full list of all publications,

below are articles we've published since 2015.

Articles since 2020 (Names of Gophna lab members are highlighted)

Research Articles

2026

Choudhary, D.K., Turgeman-Grott, I., Robinzon S., Gophna, U (2026) CRISPR-Cas targeting in Haloferax volcanii promotes within-species gene exchange by triggering homologous recombination. microLife 7, uqaf047

Navok, S., Singla, H., Cohen, L., Ron, E.Z., Gophna, U. (2026) Detecting chronically infecting viruses of haloarchaea. FEMS Microbiology Letters 373: fnag005

2025

Meir, M., Kahn, A., Farage, C., Maoz, Y., Harel, N., Ben-Zvi , A. Segev, S., M., Volkov, M., , Yahud, R., Gophna, U., and Stern, A. (2025) Navigating a fine balance: point-mutant cheater viruses disrupt the viral replication cycle. Molecular Biology and Evolution 1(42): msae258

Godny L, Elial-Fatal S, Arrouasse J, Sharar Fischler T, Reshef L, Kutukov Y, Cohen S, Pfeffer-Gik T, Barkan R, Shakhman S, Friedenberg A, Pauker MH, Rabinowitz KM, Shaham-Barda E, Goren I, Gophna U, Banai Eran H, Ollech JE, Snir Y, Broitman Y, Avni-Biron I, Yanai H, Dotan I. (2025) Mechanistic Implications of the Mediterranean Diet in Patients With Newly Diagnosed Crohn's Disease: Multiomic Results From a Prospective Cohort. Gastroenterology. 168(5):952-964.

Sharar-Fischler, T., Reshef L,, Godny L, Goren, I., Ollech J.E., Avni-Biron I, Cohen S, Barkan R, Brotiman, Y, Pfeffer-Gik T,, Friedenberg A., Pauker M.H., Rabinowitz K.M., Gophna U., Banai-Eran H., Snir Y., Broitman Y., Dotan I., Yanai H, (2025) Microbial Shift Over 1 Year Among Patients With Newly Diagnosed Crohn's Disease Reflects Clinical Trajectory and Exposure to Biologic Treatment: A Prospective Real-World Inception Cohort. Clinical and Translational Gastroenterology 16 (9), e00902

Naki D, Gophna U. (2025) Evolutionary insights into provirus-encoded CRISPR-Cas systems in halophilic archaea. Microlife. Oct 22;6:uqaf033

Turgeman-Grott, I., Golan, N. Neri, U., Naki, D., Altman-Price, N., Eizenstein, K., Choudhary, D.K., Levy, R., Shalev, Singla, H., Reshef, L., Gophna, U (2025) A previously undescribed archaeal virus that suppresses the transcription of host immunity genes EMBO Reports 2025 26(24):6159-6178.

Shakhman, S., Pfeffer-Gik T,, Elial-Fatal, S., Broitman Y., Yanai H, Gophna U., Dotan I. Godny L, (2025) Industrial Bread Composition: Potential Implications for Patients with Inflammatory Bowel Disease Nutrients 17 (13), 2120

2024

Turgeman-Grott, I., Shalev, N. Shemesh, Y., Levy, R. Eini, I., Pasmanik-Chor, M , Gophna, U. (2024) A Haloarchaeal Transcriptional Regulator That Represses the Expression of CRISPR-Associated Genes. Microorganisms 12 (9), 1772

Feng, Y.., Arsenault, D., Louyakis, A.S.., Altman-Price, N. Papke, R.T., Gophna, U., Gogarten, J.P, (2024) Using the pan-genomic framework for the discovery of genomic islands in the haloarchaeon Halorubrum ezzemoulense. mBio 15(5), e00408-24

Reshef N, Gophna U, Reshef L, Konikoff F, Gabay G, Zornitzki T, Knobler H, Maor Y. (2024) Prebiotic Treatment in Patients with Nonalcoholic Fatty Liver Disease (NAFLD)-A Randomized Pilot Trial. Nutrients. 22;16(11):1571.

Dor-Roterman, Y.R., Benayahu, Y., Reshef, L., Gophna, U. (2024) Host–Microbiome Interactions in a Changing Sea: The Gill Microbiome of an Invasive Oyster under Drastic Temperature Changes. Microorganisms 12 (1), 197

2023

Dubinsky V., Dotan I., Gophna U. (2023) Strains Colonizing Different Intestinal Sites within an Individual Are Derived from a Single Founder Population. mBio. 14(1):e0345622 Editor's Pick

Lee B.D., Neri U., Roux S., Wolf Y.I., Camargo A.P., Krupovic M.; RNA Virus Discovery Consortium; Simmonds P., Kyrpides N., Gophna U., Dolja V.V., Koonin E.V.. (2023) Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs. Cell 21:S0092-8674(22)01582-3.

Miezner G., Turgeman-Grott I., Zatopek K.M., Gardner A.F., Reshef L., Choudhary D.K., Alstetter M., Allers T., Marchfelder A., Gophna U. (2023) An archaeal Cas3 protein facilitates rapid recovery from DNA damage. Microlife. 9;4:uqad007

Harel N., Reshef L., Biran D., Ron E.Z., Gophna U. (2023) Skin microbiome of people living at the Dead Sea area - The lowest place on earth. Research in Microbiology. 174(5):104059.

Harel N., Ogen-Shtern N., Reshef L., Biran D, Ron EZ, Gophna U. (2023) Skin microbiome bacteria enriched following long sun exposure can reduce oxidative damage. Research in Microbiology. 174(8):104138.

Turgeman-Grott, I., Arsenault, D., Yahav, D., Feng, Y., Miezner, G., Naki, D., Peri, O., Papke, R.T., Gogarten, J.P., Gophna, U. (2023) Neighboring inteins interfere with one another's homing capacity. PNAS Nexus 2(11): pgad354.

2022

Lapidot, Y., Reshef, L., Mayan, M., Cohen, D., Gophna, U. Muhsen, K. (2022). Socioeconomic disparities and household crowding in association with the fecal microbiome of school-age children. NPJ Biofilms Microbiomes. 3;8(1):10.

Alarcón-Schumacher, T., Naor, A., Gophna, U., Erdmann, S. (2022) Isolation of a virus causing a chronic infection in the archaeal model organism Haloferax volcanii reveals antiviral activities of a provirus. PNAS 119 (35), e2205037119

Bar N., Avraham Y., Dubinsky V., Cohen N.A., Weiss G.A., Banon L., Tulchinsky H., Maharshak N., Gophna U., Dotan I. (2022). Long-term Antibiotic Treatment in Pouchitis-Patterns of Use and Safety. Inflammatory Bowel Diseases 1;28(7):1027-1033.

Lavy O., Lewin-Epstein O., Bendett Y., Gophna U., Gefen E., Hadany L., Ayali A. (2022) Microbiome-related aspects of locust density-dependent phase transition. Environmental Microbiology 24(1):507-516.

Dubinsky V., Reshef L., Rabinowitz K., Wasserberg N., Dotan I., Gophna U. (2022) Escherichia coli strains from patients with inflammatory bowel diseases have disease-specific genomic adaptations. Journal of Crohn's and Colitis. 16 (10), 1584-1597

Harel, N. Reshef, L., Biran, D., Brenner, S.. Ron, E.Z., Gophna U. (2022) Effect of Solar Radiation on Skin Microbiome: Study of Two Populations. Microorganisms 10 (8) 1523

Neri, U., Wolf, Y.I, Roux, S., Camargo, A.P., Lee, B., Kazlauskas, D., Min Chen, I., Ivanova, N. Zeigler Allen, L., Paez-Espino, D., Bryant, D.A., Bhaya, D., RNA Virus Discovery Consortium, Krupovic, M., Dolja, V.D., Kyrpides, N.C., Koonin, E.V., Gophna U*. (2022) Expansion of the global RNA virome reveals new clades of bacteriophages. Cell 185 (21), 4023-4037

Godny, L., Reshef, L., Sharar Fischler, T., Elial-Fatal, S., Pfeffer-Gik, T., Raykhel, B., Rabinowitz, K., Levi-Barda, A., Perets, T.T., Barkan, R., Goren, I., Ollech, J.E., Yanai, H., Gophna, U., Dotan, I. (2022) Increasing adherence to the Mediterranean diet and lifestyle is associated with reduced fecal calprotectin and intra-individual changes in microbial composition of healthy subjects. Gut Microbes 14 (1), 2120749.

2021

Dangoor I., Stanić D., Reshef L., Pešić V., Gophna U. (2021). Specific Changes in the Mammalian Gut Microbiome as a Biomarker for Oxytocin-Induced Behavioral Changes. Microorganisms. 12;(9):1938.

Yanuka-Golub, K., Dubinsky, V., Korenblum, E., Reshef, L., Ofek-Lalzar, M., Rishpon, J., and Gophna, U. (2021) Anode Surface Bioaugmentation Enhances Deterministic Biofilm Assembly in Microbial Fuel Cells. mBIO 12(2):e03629-20.

Dubinsky, V., Reshef, L., Rabinowitz, K., Yadgar, K., Godny, L., Zonensain, K., Wasserberg, N., Dotan, I. and Gophna, U., (2021). Dysbiosis in metabolic genes of the gut microbiomes of patients with an ileo-anal pouch resembles that observed in Crohn's Disease. mSystems 2(6):e00984-20.

Ryvchin, R., Dubinsky, V., Rabinowitz,K., Wasserberg, N., Dotan, I., and Gophna, U. (2021) Alteration in urease-producing bacteria in the gut microbiomes of patients with inflammatory bowel diseases. Journal of Crohn's and Colitis 18;15(12):2066-2077.

Lavy, O., Gophna, U., Ayali, A., Gihaz, S. Fishman, A., Gefen, E. (2021) The maternal foam plug constitutes a reservoir for the desert locust's bacterial symbionts Environmental Microbiology 23 (5), 2461-2472.

Feng, Y., Neri, U., Gosselin, S., Louyakis, A.S., Papke, R.T., Gophna, U., and Gogarten, J.P. (2021). The Evolutionary Origins of Extreme Halophilic Archaeal Lineages. Genome Biology and Evolution. 13(8):evab166.

Lapidot, Y., Reshef, L., Goldsmith, R., Na’amnih, W., Kassem, E., Ornoy, A., Gophna, U. Muhsen, K. (2021). The Associations between Diet and Socioeconomic Disparities and the Intestinal Microbiome in Preadolescence. Nutrients 13(8):2645.

2020

Meir, M., Harel, N., Miller, D. Gelbart, M., Eldar, A., Gophna, U.,* and Stern, A.* (2020) Competition between social cheater viruses is driven by mechanistically different cheating strategies. Science Advances 21;6(34) * Corresponding authors

Babakobi M.D., Reshef L., Gihaz S., Belgorodsky B., Fishman A., Bujanover Y., Gophna U. (2020) Effect of Maternal Diet and Milk Lipid Composition on the Infant Gut and Maternal Milk Microbiomes. Nutrients 21;12(9):E2539.

Robinzon S., Cawood A.R., Ruiz M.A., Gophna U., Altman-Price N., Mills K.V. (2020) Protein splicing activity of the Haloferax volcanii PolB-c intein is sensitive to homing endonuclease domain mutations. Biochemistry 59, 36, 3359–3367.

Stachler A.E., Wörtz J., Alkhnbashi O.S., Turgeman-Grott I., Smith R., Allers T., Backofen R., Gophna U., Marchfelder A. (2020) Adaptation induced by self-targeting in a type I-B CRISPR-Cas system. Journal of Biological Chemistry 25; 295(39): 13502–13515.

Dubinsky, V., Reshef, L., Bar, N., Keizer, D., Golan, N., Rabinowitz, K., Godny, L., Yadgar, K., Zonensain, K., Tulchinsky, H., Gophna, U., and Dotan, I. (2020). Predominantly Antibiotic-resistant Intestinal Microbiome Persists in Patients With Pouchitis Who Respond to Antibiotic Therapy. Gastroenterology 158(3):610-624.

Turner D., Bishai J., Reshef L., Abitbol G., Focht G., Marcus D., Ledder O., Lev-Tzion R., Orlanski-Meyer E., Yerushalmi B., Aloi M., Griffiths AM., Albenberg L., Kolho KL., Assa A., Cohen S., Gophna U., Vlamakis H., Lurz E., Levine A. (2020) Antibiotic Cocktail for Pediatric Acute Severe Colitis and the Microbiome: The PRASCO Randomized Controlled Trial. Inflammatory Bowel Diseases. 26(11):1733-1742.

Yair Y., Borovok I., Mikula I., Falk R., Fox L.K., Gophna U., Lysnyansky I. (2020) Genomics-based epidemiology of bovine Mycoplasma bovis strains in Israel. BMC Genomics 21(1):70.

Lavy O., Gophna U., Gefen E., Ayali A. (2020) Dynamics of bacterial composition in the locust reproductive tract are affected by the density-dependent phase. FEMS Microbiology Ecology. 96(4).

Godny L., Reshef L., Pfeffer-Gik T., Goren I., Yanai H., Tulchinsky H., Gophna U., Dotan I. (2020) Adherence to the Mediterranean diet is associated with decreased fecal calprotectin in patients with ulcerative colitis after pouch surgery. European Journal of Nutrition. 59:3183–3190.

Reviews and commentaries

2022

Gophna, U. Et tu, Vibrio cholerae? Kin-cannibalism and a bacterial secretion system. Cell 185 (22), 4039-4040

Gophna U., Altman-Price, N. (2022). Horizontal Gene Transfer in Archaea - From Mechanisms to Genome Evolution. Annual Review of Microbiology 76:481-502

2020

Dubinsky V., Dotan I., Gophna U. Carriage of Colibactin-producing Bacteria and Colorectal Cancer Risk. (In press) Trends in Microbiology

Gophna U. (2020) Reviewing the right papers. FEMS Microbiol Lett. 1:367(1).

Andersson DI, Balaban NQ, Baquero F, Courvalin P, Glaser P, Gophna U, Kishony R, Molin S, Tønjum T. (in press) Antibiotic resistance: turning evolutionary principles into clinical reality. FEMS Microbiol Rev.

Peer-reviewed Publications

Articles since 2020 (Names of Gophna lab members are highlighted)

Research Articles

​​

2026

Choudhary, D.K., Turgeman-Grott, I., Robinzon S., Gophna, U (2026) CRISPR-Cas targeting in Haloferax volcanii promotes within-species gene exchange by triggering homologous recombination. microLife 7, uqaf047

​

Navok, S., Singla, H., Cohen, L., Ron, E.Z., Gophna, U. (2026) Detecting chronically infecting viruses of haloarchaea. FEMS Microbiology Letters 373: fnag005

2025

Meir, M., Kahn, A., Farage, C., Maoz, Y., Harel, N., Ben-Zvi , A. Segev, S., M., Volkov, M., , Yahud, R., Gophna, U., and Stern, A. (2025) Navigating a fine balance: point-mutant cheater viruses disrupt the viral replication cycle. Molecular Biology and Evolution 1(42): msae258

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Naki D, Gophna U. (2025) Evolutionary insights into provirus-encoded CRISPR-Cas systems in halophilic archaea. Microlife. Oct 22;6:uqaf033

​

Turgeman-Grott, I., Golan, N. Neri, U., Naki, D., Altman-Price, N., Eizenstein, K., Choudhary, D.K., Levy, R., Shalev, Singla, H., Reshef, L., Gophna, U (2025) A previously undescribed archaeal virus that suppresses the transcription of host immunity genes EMBO Reports 2025 26(24):6159-6178.

​

Shakhman, S., Pfeffer-Gik T,, Elial-Fatal, S., Broitman Y., Yanai H, Gophna U., Dotan I. Godny L, (2025) Industrial Bread Composition: Potential Implications for Patients with Inflammatory Bowel Disease Nutrients 17 (13), 2120

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2024

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Turgeman-Grott, I., Shalev, N. Shemesh, Y., Levy, R. Eini, I., Pasmanik-Chor, M , Gophna, U. (2024) A Haloarchaeal Transcriptional Regulator That Represses the Expression of CRISPR-Associated Genes. Microorganisms 12 (9), 1772

​

Feng, Y.., Arsenault, D., Louyakis, A.S.., Altman-Price, N. Papke, R.T., Gophna, U., Gogarten, J.P, (2024) Using the pan-genomic framework for the discovery of genomic islands in the haloarchaeon Halorubrum ezzemoulense. mBio 15(5), e00408-24

​

Reshef N, Gophna U, Reshef L, Konikoff F, Gabay G, Zornitzki T, Knobler H, Maor Y. (2024) Prebiotic Treatment in Patients with Nonalcoholic Fatty Liver Disease (NAFLD)-A Randomized Pilot Trial. Nutrients. 22;16(11):1571.

​

Dor-Roterman, Y.R., Benayahu, Y., Reshef, L., Gophna, U. (2024) Host–Microbiome Interactions in a Changing Sea: The Gill Microbiome of an Invasive Oyster under Drastic Temperature Changes. Microorganisms 12 (1), 197

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2023

Dubinsky V., Dotan I., Gophna U. (2023) Strains Colonizing Different Intestinal Sites within an Individual Are Derived from a Single Founder Population. mBio. 14(1):e0345622 Editor's Pick

​

Lee B.D., Neri U., Roux S., Wolf Y.I., Camargo A.P., Krupovic M.; RNA Virus Discovery Consortium; Simmonds P., Kyrpides N., Gophna U., Dolja V.V., Koonin E.V.. (2023) Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs. Cell 21:S0092-8674(22)01582-3.

Miezner G., Turgeman-Grott I., Zatopek K.M., Gardner A.F., Reshef L., Choudhary D.K., Alstetter M., Allers T., Marchfelder A., Gophna U. (2023) An archaeal Cas3 protein facilitates rapid recovery from DNA damage. Microlife. 9;4:uqad007

Harel N., Reshef L., Biran D., Ron E.Z., Gophna U. (2023) Skin microbiome of people living at the Dead Sea area - The lowest place on earth. Research in Microbiology. 174(5):104059.

Harel N., Ogen-Shtern N., Reshef L., Biran D, Ron EZ, Gophna U. (2023) Skin microbiome bacteria enriched following long sun exposure can reduce oxidative damage. Research in Microbiology. 174(8):104138.

Turgeman-Grott, I., Arsenault, D., Yahav, D., Feng, Y., Miezner, G., Naki, D., Peri, O., Papke, R.T., Gogarten, J.P.*, Gophna, U.* (2023) Neighboring inteins interfere with one another's homing capacity. PNAS Nexus 2(11): pgad354.

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2022

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Lapidot, Y., Reshef, L., Mayan, M., Cohen, D., Gophna, U. Muhsen, K. (2022). Socioeconomic disparities and household crowding in association with the fecal microbiome of school-age children. NPJ Biofilms Microbiomes. 3;8(1):10.

​

Alarcón-Schumacher, T., Naor, A., Gophna, U., Erdmann, S. (2022) Isolation of a virus causing a chronic infection in the archaeal model organism Haloferax volcanii reveals antiviral activities of a provirus. PNAS 119 (35), e2205037119

​

Bar N., Avraham Y., Dubinsky V., Cohen N.A., Weiss G.A., Banon L., Tulchinsky H., Maharshak N., Gophna U., Dotan I. (2022). Long-term Antibiotic Treatment in Pouchitis-Patterns of Use and Safety. Inflammatory Bowel Diseases 1;28(7):1027-1033.

​

Lavy O., Lewin-Epstein O., Bendett Y., Gophna U., Gefen E., Hadany L., Ayali A. (2022) Microbiome-related aspects of locust density-dependent phase transition. Environmental Microbiology 24(1):507-516.

​

Dubinsky V., Reshef L., Rabinowitz K., Wasserberg N., Dotan I., Gophna U. (2022) Escherichia coli strains from patients with inflammatory bowel diseases have disease-specific genomic adaptations. Journal of Crohn's and Colitis. 16 (10), 1584-1597

​

Harel, N. Reshef, L., Biran, D., Brenner, S.. Ron, E.Z., Gophna U. (2022) Effect of Solar Radiation on Skin Microbiome: Study of Two Populations. Microorganisms 10 (8) 1523

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2021

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Dangoor I., Stanić D., Reshef L., Pešić V., Gophna U. (2021). Specific Changes in the Mammalian Gut Microbiome as a Biomarker for Oxytocin-Induced Behavioral Changes. Microorganisms. 12;(9):1938.

​

Yanuka-Golub, K., Dubinsky, V., Korenblum, E., Reshef, L., Ofek-Lalzar, M., Rishpon, J., and Gophna, U. (2021) Anode Surface Bioaugmentation Enhances Deterministic Biofilm Assembly in Microbial Fuel Cells. mBIO 12(2):e03629-20.

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Dubinsky, V., Reshef, L., Rabinowitz, K., Yadgar, K., Godny, L., Zonensain, K., Wasserberg, N., Dotan, I. and Gophna, U., (2021). Dysbiosis in metabolic genes of the gut microbiomes of patients with an ileo-anal pouch resembles that observed in Crohn's Disease. mSystems 2(6):e00984-20.

Ryvchin, R., Dubinsky, V., Rabinowitz,K., Wasserberg, N., Dotan, I., and Gophna, U. (2021) Alteration in urease-producing bacteria in the gut microbiomes of patients with inflammatory bowel diseases. Journal of Crohn's and Colitis 18;15(12):2066-2077.

Lavy, O., Gophna, U., Ayali, A., Gihaz, S. Fishman, A., Gefen, E. (2021) The maternal foam plug constitutes a reservoir for the desert locust's bacterial symbionts Environmental Microbiology 23 (5), 2461-2472.

​

Feng, Y., Neri, U., Gosselin, S., Louyakis, A.S., Papke, R.T., Gophna, U., and Gogarten, J.P. (2021). The Evolutionary Origins of Extreme Halophilic Archaeal Lineages. Genome Biology and Evolution. 13(8):evab166.

​

Lapidot, Y., Reshef, L., Goldsmith, R., Na’amnih, W., Kassem, E., Ornoy, A., Gophna, U. Muhsen, K. (2021). The Associations between Diet and Socioeconomic Disparities and the Intestinal Microbiome in Preadolescence. Nutrients 13(8):2645.

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2020

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Meir, M., Harel, N., Miller, D. Gelbart, M., Eldar, A., Gophna, U.,* and Stern, A.* (2020) Competition between social cheater viruses is driven by mechanistically different cheating strategies. Science Advances 21;6(34) * Corresponding authors

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Babakobi M.D., Reshef L., Gihaz S., Belgorodsky B., Fishman A., Bujanover Y., Gophna U. (2020) Effect of Maternal Diet and Milk Lipid Composition on the Infant Gut and Maternal Milk Microbiomes. Nutrients 21;12(9):E2539.

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Turgeman-Grott, I., Arsenault, D., Yahav, D., Feng, Y., Miezner, G., Naki, D., Peri, O., Papke, R.T., Gogarten, J.P., Gophna, U. (2023) Neighboring inteins interfere with one another's homing capacity. PNAS Nexus 2(11): pgad354.