Publications
2026
Short, N. E., Warren, E. C., Porter, I. E., Pinto, Y., Rodriguez, J., Sarkisyan, K., Bhatt, A. S., Brown, A., Riglar, D. T., & Riglar, D. T. (2026). A whole organism screening platform identifies gut microbiome microproteins that modulate host metabolism. https://doi.org/10.64898/2026.02.11.705328
2025
Finkelstein, S., Frishman, S., Turjeman, S., Shtossel, O., Tikhonov, E., Ohayon, M. N., Pinto, Y., Popova, P., Tkachuk, A., Vasukova, E., Anopova, A., Pustozerov, E., Pervunina, T., Grineva, E., Hod, M., Schwartz, B., Hadar, E., Koren, O., Louzoun, Y., ... Nuriel-Ohayon, M. (2025). Early Pregnancy Marks Significant Shifts in the Oral Microbiome. https://doi.org/10.1101/2025.09.29.679276
Pinto, Y. (2025). Beyond bacteria: Phanta adds flavour to microbiome profiling with a focus on phages. Nature Reviews Immunology, 25(3), 159. https://doi.org/10.1038/s41577-025-01138-5
Finkelstein, S., Frishman, S., Turjeman, S., Shtossel, O., Riumin, A., Tikhonov, E., Ohayon, M. N., Pinto, Y., Popova, P., Tkachuk, A., Vasukova, E., Anopova, A., Pustozerov, E., Pervunina, T., Grineva, E., Hod, M., Schwartz, B., Hadar, E., Koren, O., ... Louzoun, Y. (2025). Nutrition-dependent development of the Oral Microbiome in Early Pregnancy. https://doi.org/10.1101/2025.09.29.679276
Camargo, A. P., Baltoumas, F. A., Ndela, E. O., Fiamenghi, M. B., Merrill, B. D., Carter, M. M., Pinto, Y., Chakraborty, M., Andreeva, A., Ghiotto, G., Shaw, J., Proal, A. D., Sonnenburg, J. L., Bhatt, A. S., Roux, S., Pavlopoulos, G. A., Nayfach, S., Kyrpides, N. C., & Camargo, A. P. (2025). A genomic atlas of the human gut virome elucidates genetic factors shaping host interactions. https://doi.org/10.1101/2025.11.01.686033
2024
Zlitni, S., Bowden, S., Sberro, H., Torres, M. D. T., Vaughan, J. M., Pinto, A. F. M., Pinto, Y., Fernandez, D., Rost, H., Saghatelian, A., de la Fuente-Nunez, C., Bhatt, A. S., & Bhatt, A. S. (2024). Dual quorum-sensing control of purine biosynthesis drives pathogenic fitness of Enterococcus faecalis. https://doi.org/10.1101/2024.08.13.607696
Pinto, Y., & Bhatt, A. S. (2024). Sequencing-based analysis of microbiomes. Nature Reviews Genetics, 25(12), 829-845. https://doi.org/10.1038/s41576-024-00746-6
Pinto, Y., Chakraborty, M., Jain, N., & Bhatt, A. S. (2024). Phage-inclusive profiling of human gut microbiomes with Phanta. Nature Biotechnology, 42(4), 651-662. https://doi.org/10.1038/s41587-023-01799-4
Frishman, S., Nuriel-Ohayon, M., Turjeman, S., Pinto, Y., Yariv, O., Tenenbaum-Gavish, K., Peled, Y., Poran, E., Pardo, J., Chen, R., Muller, E., Borenstein, E., Hod, M., Louzoun, Y., Schwartz, B., Hadar, E., Collado, M. C., & Koren, O. (2024). Positive effects of diet-induced microbiome modification on GDM in mice following human faecal transfer. Gut, 73(10), e17. https://doi.org/10.1136/gutjnl-2023-331456
2023
Avizemel, O., Frishman, S., Pinto, Y., Michael, Y., Turjeman, S., Tenenbaum-Gavish, K., Yariv, O., Peled, Y., Poran, E., Pardo, J., Chen, R., Hod, M., Schwartz, B., Hadar, E., Koren, O., & Agay-Shay, K. (2023). “Residential greenness, gestational diabetes mellitus (GDM) and microbiome diversity during pregnancy”. International Journal of Hygiene and Environmental Health, 251, Article 114191. https://doi.org/10.1016/j.ijheh.2023.114191
Pinto, Y., Frishman, S., Turjeman, S., Eshel, A., Nuriel-Ohayon, M., Shrossel, O., Ziv, O., Walters, W., Parsonnet, J., Ley, C., Johnson, E. L., Kumar, K., Schweitzer, R., Khatib, S., Magzal, F., Muller, E., Tamir, S., Tenenbaum-Gavish, K., Rautava, S., ... Koren, O. (2023). Gestational diabetes is driven by microbiota-induced inflammation months before diagnosis. Gut, 72(5), 918-928. https://doi.org/10.1136/gutjnl-2022-328406
2022
Babin, B. M., Keller, L. J., Pinto, Y., Li, V. L., Eneim, A. S., Vance, S. E., Terrell, S. M., Bhatt, A. S., Long, J. Z., & Bogyo, M. (2022). Identification of covalent inhibitors that disrupt M. tuberculosis growth by targeting multiple serine hydrolases involved in lipid metabolism. Cell Chemical Biology, 29(5), 897-909.e7. https://doi.org/10.1016/j.chembiol.2021.08.013
Pinto, Y., Chakraborty, M., Jain, N., Bhatt, A. S., & Bhatt, A. S. (2022). Phanta: Phage-inclusive profiling of human gut metagenomes. https://doi.org/10.1101/2022.08.05.502982
2021
Babin, B. M., Keller, L. J., Pinto, Y., Li, V. L., Eneim, A., Vance, S. E., Terrell, S. M., Bhatt, A. S., Long, J. Z., Bogyo, M., & Bogyo, M. (2021). A screen of covalent inhibitors in Mycobacterium tuberculosis identifies serine hydrolases involved in lipid metabolism as potential therapeutic targets. https://doi.org/10.1101/2021.06.07.447460
Pinto, Y., Frishman, S., Turjeman, S., Eshel, A., Nuriel-Ohayon, M., Ziv, O., Walters, W., Parsonnet, J., Ley, C., Johnson, E., Schweitzer, R., Khatib, S., Magzal, F., Tamir, S., Tenenbaum Gavish, K., Rautava, S., Salminen, S., Isolauri, E., Yariv, O., ... Koren, O. (2021). First trimester gut microbiome induces Inflammation-dependent gestational diabetes phenotype in mice. https://doi.org/10.1101/2021.09.17.21262268
Ben-Haim, M. S., Pinto, Y., Moshitch-Moshkovitz, S., Hershkovitz, V., Kol, N., Diamant-Levi, T., Beeri, M. S., Amariglio, N., Cohen, H. Y., & Rechavi, G. (2021). Dynamic regulation of N6,2′-O-dimethyladenosine (m6Am) in obesity. Nature Communications, 12(1), Article 7185. https://doi.org/10.1038/s41467-021-27421-2
Levin, D., Raab, N., Pinto, Y., Rothschild, D., Zanir, G., Godneva, A., Mellul, N., Futorian, D., Gal, D., Leviatan, S., Zeevi, D., Bachelet, I., & Segal, E. (2021). Diversity and functional landscapes in the microbiota of animals in the wild. Science, 372(6539), Article eabb5352. https://doi.org/10.1126/SCIENCE.ABB5352
Levin, D., Raab, N., Pinto, Y., Rothschild, D., Zanir, G., Godneva, A., Mellul, N., Futorian, D., Gal, D., Leviatan, S., Zeevi, D., Bachelet, I., & Segal, E. (2021). Diversity and functional landscapes in the microbiota of animals in the wild. Science, 372(6539), Article eabb5352. https://doi.org/10.1126/science.abb5352originally
2019
Pinto, Y., & Levanon, E. Y. (2019). Computational approaches for detection and quantification of A-to-I RNA-editing. Methods, 156, 25-31. https://doi.org/10.1016/j.ymeth.2018.11.011
Stehlikova, Z., Kostovcik, M., Kostovcikova, K., Kverka, M., Juzlova, K., Rob, F., Hercogova, J., Bohac, P., Pinto, Y., Uzan, A., Koren, O., Tlaskalova-Hogenova, H., & Zakostelska, Z. J. (2019). Dysbiosis of skin microbiota in psoriatic patients: Co-occurrence of Fungal and Bacterial Communities. Frontiers in Microbiology, 10(MAR), Article 438. https://doi.org/10.3389/fmicb.2019.00438
2018
Pinto, Y., Buchumenski, I., Levanon, E. Y., & Eisenberg, E. (2018). Human cancer tissues exhibit reduced A-to-I editing of miRNAs coupled with elevated editing of their targets. Nucleic Acids Research, 46(1), 71-82. https://doi.org/10.1093/nar/gkx1176
2016
Levanon, E., Sapoznik, S., Bahar-Shany, K., Brand, H., Pinto, Y., Gabay, O., Glick-Saar, E., Dor, C., Zadok, O., Barshack, I., Zundelevich, A., Gal-Yam, E. N., Yung, Y., Hourvitz, A., Korach, J., Beiner, M., Jacob-Hirsch, J., Barak, M., Aviel-Ronen, S., & Levanon, K. (2016). Abstract A34: Activation-induced cytidine deaminase links ovulation-induced inflammation and serous carcinogenesis., Clinical Cancer Research, 22(2_Supplement), A34. https://doi.org/10.1158/1557-3265.ovca15-a34
Sapoznik, S., Bahar-Shany, K., Brand, H., Pinto, Y., Gabay, O., Glick-Saar, E., Dor, C., Zadok, O., Barshack, I., Zundelevich, A., Gal-Yam, E. N., Yung, Y., Hourvitz, A., Korach, J., Beiner, M., Jacob, J., Levanon, E. Y., Barak, M., Aviel-Ronen, S., & Levanon, K. (2016). Activation-Induced Cytidine Deaminase Links Ovulation-Induced Inflammation and Serous Carcinogenesis. Neoplasia (United States), 18(2), 90-99. https://doi.org/10.1016/j.neo.2015.12.003
Pinto, Y., Gabay, O., Arbiza, L., Sams, A. J., Keinan, A., & Levanon, E. Y. (2016). Clustered mutations in hominid genome evolution are consistent with APOBEC3G enzymatic activity. Genome Research, 26(5), 579-587. https://doi.org/10.1101/gr.199240.115
2015
Shamay-Ramot, A., Khermesh, K., Porath, H. T., Barak, M., Pinto, Y., Wachtel, C., Zilberberg, A., Lerer-Goldshtein, T., Efroni, S., Levanon, E. Y., & Appelbaum, L. (2015). Fmrp Interacts with Adar and Regulates RNA Editing, Synaptic Density and Locomotor Activity in Zebrafish. PLoS Genetics, 11(12), Article e1005702. https://doi.org/10.1371/journal.pgen.1005702
Geula, S., Moshitch-Moshkovitz, S., Dominissini, D., Mansour, A. A. F., Kol, N., Salmon-Divon, M., Hershkovitz, V., Peer, E., Mor, N., Manor, Y. S., Ben-Haim, M. S., Eyal, E., Yunger, S., Pinto, Y., Jaitin, D. A., Viukov, S., Rais, Y., Krupalnik, V., Chomsky, E., ... Hanna, J. H. (2015). m6A mRNA methylation facilitates resolution of naïve pluripotency toward differentiation. Science, 347(6225), 1002-1006. https://doi.org/10.1126/science.1261417
2014
Pinto, Y., Cohen, H. Y., & Levanon, E. Y. (2014). Mammalian conserved ADAR targets comprise only a small fragment of the human editosome. Genome Biology, 15(1), Article R5. https://doi.org/10.1186/gb-2014-15-1-r5