Naama Wagner
I am a Ph.D. graduate, in the lab of Prof. Tal Pupko in the Shmunis School of Biomedicine and Cancer Research, Tel Aviv University.
Research
My research interests include bacterial pathogenicity and bacterial genomics, where I use Machine-learning techniques for Bacterial protein annotation.
Education
- Ph.D. in Bioinformatics (2023)
- M.Sc. in Theoretical and Mathematical Biology (2019)
- B.Sc. in Biology (2017)
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Publications
- Geraffi, N.^, Gupta, P.^,Wagner, N., Barash, I., Pupko, T., Sessa, G. 2023. Comparative sequence analysis of pPATH pathogenicity plasmids in Pantoea agglomerans gall-forming bacteria. Frontiers in Plant Science. 14:1198160 [pdf] [abs]
- Wagner, N., Ben-Meir, D., Teper, D., Pupko, T. 2023. Complete genome sequence of an Israeli isolate of Xanthomonas hortorum pv. pelargonii strain 305 and novel type III effectors identified in Xanthomonas. Frontiers in Plant Science. 14:1817 [pdf] [abs]
- Wagner, N.^, Alburquerque, M.^, Ecker, N., Dotan, E., Zerah, B., Pena, M., Potnis, N., Pupko, T. 2022. Natural language processing approach to model the secretion signal of type III effectors. Frontiers in Plant Science. 13:4339 [pdf] [abs]
- Wagner, N., Teper, D., Pupko, T. 2022. Predicting Type III Effector Proteins Using the Effectidor Web Server. Methods in Molecular Biology. 2427:25–36 [abs]
- Liyanapathiranage, P.^, Wagner, N.^, Avram, O., Pupko, T., & Potnis, N. 2022. Phylogenetic Distribution and Evolution of Type VI Secretion System in the Genus Xanthomonas. Frontiers in Microbiology. 13:591 [pdf] [abs]
- Labes, S., Stupp, D.^, Wagner, N.^, Bloch, I., Lotem, M., Lahad, E. L., Polak, P., Pupko, T., & Tabach, Y. 2022. Machine-learning of complex evolutionary signals improves classification of SNVs. NAR Genomics and Bioinformatics. 4(2) [pdf] [abs]
- Wagner, N., Avram, O., Gold-Binshtok, D., Zerah, B., Teper, D., Pupko, T. 2022. Effectidor: an automated machine-learning based web server for the prediction of type-III secretion system effectors. Bioinformatics. 38(8):2341-2343 [pdf] [abs]
- Ruano-Gallego, D.^, Sánchez-Garrido, J.^, Kozik, Z., Núñez-Berrueco, E., Cepeda-Molero, M., Mullineaux-Sanders, C., Clark, J.B., Slater, S., Wagner, N., Glegola-Madejska, I., Roumeliotis, T.I., Pupko, T., Fernández, L.A, Rodríguez-Patón, A., Choudhary, J.S., Frankel, G. 2021. Type III secretion system effectors form robust and flexible intracellular virulence networks. Science. 371(6534):eabc9531 [pdf] [abs]
- Hada-Neeman, S.^, Weiss-Ottolenghi, Y.^, Wagner, N.^, Avram, O., Maor, Y., Sklan, E., Shcherbakov, D., Pupko, T. and Gershoni, J.M. 2021. Domain-Scan libraries as a tool for the diagnosis of infectious diseases. Frontiers Immunology. 11:3898 [pdf] [abs]
- Guerrero, IJ, Perez-Montano, F., Mateus da Silva, G., Wagner, N., Shkedy, D., Zhao, M., Pizarro, L.,Bar, M., Walcott, R., Sessa, G., Pupko, T., Burdman, S. 2020. Show me your secret(ed) weapons: a multifaceted approach reveals a wide arsenal of type III-secreted effectors in the cucurbit pathogenic bacterium Acidovorax citrulli and novel effectors in the Acidovorax genus. Molecular Plant Pathology. 21(1):17–37 [pdf] [abs]
Teaching
- General Genetics (04552526) fall semester 2022/23
- General Genetics (04552526) fall semester 2021/22
- General Genetics (04552526) fall semester 2020/21
- Introduction to Python (04553095) fall semester 2019/20
- Introduction to Python (04553095) fall semester 2018/19
Lab members
Prof. Tal Pupko
Noa Ecker
Elya Wygoda
Edo Dotan
Ksenia Polonsky
Shachar Barak
Yair Shimony
Noam Bracha
Noa Ecker
Elya Wygoda
Edo Dotan
Ksenia Polonsky
Shachar Barak
Yair Shimony
Noam Bracha
Contact me
The Shmunis School of Biomedicine and Cancer Research,
George S. Wise Faculty of Life Sciences,
Tel-Aviv University 69978, Israel.
Tel-Aviv University 69978, Israel.