פרופ' תמר יובן-גרשון

1. Adato, O.*, Sloutskin, A.*, Komemi, H., Brabb, I., Duttke, S., Bucher, P., Unger, R. ^‡, and Juven-Gershon, T. ^‡ (2024) ElemeNT 2023: an enhanced tool for detection and curation of core promoter elements. Bioinformatics, btae110

*The first two authors contributed equally to this paper

^‡ co-corresponding authors

2. Critical Assessment of Genome Interpretation Consortium (2024) CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods. Genome Biology, 25(1):53

3. Roth, S., Ideses, D., Juven-Gershon, T. and Danielli A. (2022) Rapid Biosensing Method for Detecting Protein-DNA Interactions. ACS Sensors, 7(1):60-70

4. Maybury-Lewis, S.Y., Brown, A.K., Yeary, M., Sloutskin, A., Dhakal, S, Juven-Gershon, T. and Webb, A.E. (2021) Changing and stable chromatin accessibility supports transcriptional overhaul during neural stem cell activation and is altered with age. Aging Cell, 20(11):e13499

5. Sloutskin, A., Shir-Shapira, H., Freiman, R. and Juven-Gershon, T. (2021) The core promoter is a regulatory hub for developmental gene expression. Frontiers in Cell and Developmental Biology, 9:666508

6. Dreos, R.*, Sloutskin, A.*, Malachi, N.*, Ideses, D., Bucher, P.^‡ and Juven-Gershon, T.^‡ (2021) Computational identification and experimental characterization of preferred downstream positions in human core promoters. PLOS Computational Biology, 17(8):e1009256

*The first three authors contributed equally to this paper

^‡ co-corresponding authors

7. Adato, O., Orenstein, Y., Kopolovic, J., Juven-Gershon, T.^‡ and Unger, R.^‡ (2020) Quantitative analysis of differential expression of HOX genes in multiple cancers. Cancers (Basel), 12(6):1572

^‡ co-corresponding authors

8. Levi, T.*, Sloutskin, A.*^‡, Kalifa, R., Juven-Gershon, T.^‡ and Gerlitz, O.^‡ (2020) Efficient in vivo introduction of point mutations using ssODN and a Co-CRISPR approach. Biological Procedures Online, 22:14

*The first two authors contributed equally to this paper

^‡ co-corresponding authors

9. Shigaki, D., Adato, O., Adhikari, A.N., Dong, S., Hawkins-Hooker, A., Inoue, F., Juven-Gershon, T., Kenlay, H., Martin, B., Patra, A., Penzar, D.D., Schubach, M., Xiong, C., Yan, Z., Boyle, A.P., Kreimer, A., Kulakovskiy, I.V., Reid, J., Unger, R., Yosef, N., Shendure, J., Ahituv, N., Kircher, M. and Beer, M.A. (2019) Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay. Human Mutation, 40(9): 1280-1291

10. Shir-Shapira, H.*, Sloutskin, A.*, Adato, O., Ovadia-Shochat, A., Ideses, D., Zehavi, Y., Kassavetis, G., Kadonaga, J.T., Unger, R. and Juven-Gershon, T. (2019) Identification of evolutionarily conserved downstream core promoter elements required for the transcriptional regulation of Fushi tarazu target genes. PLoS ONE. 14(4): e0215695

*The first two authors contributed equally to this paper

11. Even D.Y., Kedmi A., Ideses D. and Juven-Gershon T. (2017) Functional screening of core promoter activity. Methods Mol Biol. 1651, 77-91

12. Sameach, H., Narunsky, A., Azoulay-Ginsburg, S., Gevorkyan-Aiapetov, L., Zehavi, Y., Moskovitz, Y., Juven-Gershon, T., Ben-Tal, N. and Ruthstein, S. (2017) Structural and dynamics characterization of the MerR family metalloregulator CueR in its repression and activation states. Structure, 25, 1-9

13. Chen, D., Orenstein, Y., Golodnitsky, R., Pellach, M., Avrahami, D., Wachtel, C., Ovadia-Shochat, A., Shir-Shapira, H., Kedmi, A., Juven-Gershon, T., Shamir, R. and Gerber, D. (2016) SELMAP - SELEX affinity landscape MAPping of transcription factor binding sites using integrated microfluidics. Scientific Reports, 6, 33351

14. Even, D.Y. *, Kedmi, A. *, Basch-Barzilay, S. *, Ideses, D., Tikotzki, R., Shir-Shapira, H., Shefi, O. and Juven-Gershon, T. (2016) Engineered promoters for potent transient overexpression. PLoS ONE, 11(2): e0148918

*The first three authors contributed equally to this paper

15. Sloutskin, A., Danino, Y.M., Orenstein, Y., Zehavi, Y., Doniger, T., Shamir, R. and Juven-Gershon, T. (2015) ElemeNT: A computational tool for detecting core promoter elements. Transcription, 6(3), 41-50 


16. Shir-Shapira, H.*, Sharabany,J.*, Filderman, M., Ideses, D., Ovadia-Shochat, A., Mannervik, M. and Juven-Gershon, T. (2015) Structure-function analysis of the Drosophila melanogaster Caudal provides insights into core promoter-preferential activation. Journal of Biological Chemistry, 290(28), 17293-305


*The first two authors contributed equally to this paper

17. Danino,Y.M, Even, D., Ideses, D.  and Juven-Gershon,T. (2015) The core promoter: at the heart of gene expression.  BBA Gene Regulatory Mechanisms, 1849(8), 1116-31

18. Zehavi, Y*., Kedmi, A.*, Ideses, D. and Juven-Gershon, T. (2015) TRF2: TRansForming the view of general transcription factors. Transcription, 6:1, 1-6 


*The first two authors contributed equally to this paper

19. Safra, M., Fickentscher, R., Levi-Ferber, M., Danino, Y.M., Haviv-Chesner, A., Hansen, M., Juven-Gershon, T., Weiss, M. and Henis-Korenblit, S. (2014) The FOXO transcription factor DAF-16 bypasses ire-1 requirement to promote endoplasmic reticulum homeostasis. Cell Metabolism, 20, 870-881

20. Kedmi, A.*, Zehavi, Y*., Glick, Y., Orenstein, Y., Ideses, D., Wachtel, C., Doniger, T., Waldman Ben-Asher, H., Munster, N., Thompson, J., Anderson, S., Avrahami, D., Yates, JR 3rd, Shamir, R., Gerber, D. and Juven-Gershon, T.   (2014) TRF2 is a preferential core promoter regulator. Genes & Development, 28, 2163-2174 


*The first two authors contributed equally to this paper

21. Zehavi, Y., Sloutskin, A., Kuznetsov, O. and Juven-Gershon, T. (2014) The core promoter composition establishes a new dimension in developmental gene networks.  Nucleus, 5:4, 298–303

22. Zehavi, Y., Kuznetsov, O., Ovadia-Shochat, A. and Juven-Gershon, T. (2014) Core promoter functions in the regulation of gene expression of Drosophila Dorsal target genes. Journal of Biological Chemistry, 289, 11993-12004

23. Cianfrocco, M.A., Kassavetis, G.A., Grob, P., Fang, J., Juven-Gershon, T., Kadonaga, J.T. and Nogales, E. (2013) Human TFIID binds to core promoter DNA in a reorganized structural state. Cell, 152, 120-131

24. Juven-Gershon, T. and Kadonaga, J.T. (2010) Regulation of gene expression via the core promoter and the basal transcriptional machinery. Developmental Biology, 339, 225-229

- One of the top-five most cited articles published in the journal Developmental Biology during the period 1/1/2009-31/12/2011

25. Juven-Gershon, T., Hsu, J.-Y. and Kadonaga, J.T. (2008) Caudal, a key developmental regulator, is a DPE-specific transcriptional factor. Genes & Development, 22, 2823-2830

26. Hsu, J.-Y, Juven-Gershon, T., Marr, M.T. 2nd, Wright, K.J., Tjian, R. and Kadonaga, J.T. (2008) TBP, Mot1, and NC2 establish a regulatory circuit that controls DPE-dependent versus TATA-dependent transcription. Genes & Development, 22, 2353-2358

27. Juven-Gershon, T., Hsu, J.-Y. Theisen J.W.M. and Kadonaga, J.T. (2008) The RNA polymerase II core promoter – the gateway to transcription. Current Opinion in Cell Biology, 20, 253-259

28. Juven-Gershon, T., Hsu, J.-Y. and Kadonaga, J.T. (2006) Perspectives on the RNA polymerase II core promoter. Biochemical Society Transactions 34, 1051-1054

29. Juven-Gershon, T., Cheng, S. and Kadonaga, J.T. (2006) Rational design of a super core promoter that enhances gene expression. Nature Methods, 3, 917 - 922

- Potential applications of this study were discussed in: Perkel, J.M. (2007) Studies you can use. The Scientist, 21,63

30. Susini, L.*, Passer, B.J.*, Amzallag-Elbaz, N.*, Juven-Gershon, T.*, Prieur, S., Privat, N., Tuynder, M, Gendron M., Israel, A., Amson, R., Oren, M. and Telerman, A. (2001) Siah-1 binds and regulates the function of Numb. Proc. Natl. Acad. Sci. USA, 98, 15067-15072

*The first four authors contributed equally to this paper

31. Unger, T.*, Juven-Gershon, T.*, Moallem, E.*, Berger, M., Vogt-Sionov, R., Lozano, G., Oren, M. and Haupt, Y. (1999) Critical role for Ser20 of human p53 in the negative regulation of p53 by Mdm2. EMBO J., 18, 1805-1814

*The first three authors contributed equally to this paper

32. Elkeles, A., Juven-Gershon, T., Israeli, D., Wilder, S., Zalcenstein, A. and Oren, M. (1999) The c-fos proto-oncogene is a target for transactivation by the p53 tumor suppressor. Molecular and Cellular Biology, 19, 2594-2600

33. Juven-Gershon, T. and Oren, M. (1999) Mdm2: the ups and the downs. Molecular Medicine, 5, 71-83

34. Juven-Gershon, T., Shifman, O., Unger, T., Elkeles, A., Haupt, Y. and Oren, M. (1998) The Mdm2 oncoprotein interacts with the cell fate regulator Numb. Molecular and Cellular Biology, 18, 3974-3982

35. Barak, Y., Gottlieb, E., Juven-Gershon, T. and Oren, M. (1994) Regulation of mdm2 expression by p53: alternative promoters produce transcripts with nonidentical translation potential. Genes & Development, 8, 1739-1749

36. Barak, Y., Lupo, A., Zauberman, A., Juven, T., Aloni-Grinstein, R., Gottlieb, E., Rotter, V. and Oren, M. (1994) Targets for transcriptional activation by wild-type p53: endogenous retroviral LTR, immunoglobulin-like promoter, and an internal promoter of the mdm2 gene. Cold Spring Harb Symp. Quant. Biol., 59, 225-235

37. Soussan, L., Tchernakov, K., Bachar-Lavi, O., Juven, T., Wertman, E. and Michaelson, D.M. (1994) Antibodies to different isoforms of the heavy neurofilament protein (NF- H) in normal aging and Alzheimer's disease. Molecular Neurobiology, 9, 83-91

38. Juven, T., Barak, Y., Zauberman, A., George, D.L. and Oren, M. (1993) Wild type p53 can mediate sequence-specific transactivation of an internal promoter within the mdm2 gene. Oncogene, 8, 3411-3416

39. Barak, Y., Juven, T., Haffner, R. and Oren, M. (1993) mdm2 expression is induced by wild type p53 activity. EMBO J., 12, 461-468

Patents

1. Optimized core promoters and uses thereof. Kadonaga and Gershon. Patent no. US 7,968,698 B2: 2006.