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32. Kociemba, J., Joergensen, A.C.S., Tadic, N., Harris, A., Sideri, T., Chan, W.Y., Ibrahim, F., Unal, E., Skehel, M., Shahrezaei, V., FJ van Werven (2024). Multi-signal regulation of the GSK-3β homolog Rim11 governs meiosis entry in yeast. EMBO Journal, doi: 10.1038/s44318-024-00149-7.

31. Albihlal, W.S., W.Y. Chan, and F.J. van Werven. 2024. “Budding Yeast as an Ideal Model for Elucidating the Role of N6-Methyladenosine in Regulating Gene Expression.” Yeast  41 (4): 148–57.

30. Ensinck, I., Maman, A., Albihlal, W.S., Lassandro, M., Salzano, G., Sideri, T., Howell, S.A., Calvani, E., Patel, H., Bushkin, G., et al. FJ van Werven (2023). The yeast RNA methylation complex consists of conserved yet reconfigured components with m6A-dependent and independent roles. Elife 12. 10.7554/eLife.87860.

29. Ensinck I, T Sideri, M Modic, C Capitanchik, C Vivori, P Toolan-Kerr, FJ van Werven.
m6A-ELISA, a simple method for quantifying N6-methyladenosine from mRNA populations. 2023. RNA. May;29(5):705-712

28. Varier RA, T. Sideri, C. Capitanchik, Z. Manova, E. Calvani, A. Rossi, R.R. Edupuganti, I. Ensinck, V.W.C. Chan, H. Patel, J. Kirkpatrick, P. Faull, A.P. Snijders, M. Vermeulen, M. Ralser, J. Ule, N. M. Luscombe, F.J. van Werven. N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast. 2022. Elife Nov 24, doi: 10.7554/eLife.84034

27. Wu A.C.K., C. Vivori, H. Patel, T. Sideri, F.J. van Werven. RSC-mediated nucleosome positioning and GRFs form barriers in promoters to limit divergent noncoding transcription. 2022. Life Sci Alliance. Sep 16;5(12):e202201394. doi: 10.26508/lsa.202201394.

26. Tresenrider A, M. Chia, F.J. van Werven, E. Ünal. 2022. Long undecoded transcript isoform (LUTI) detection in meiotic budding yeast by direct RNA and transcript leader sequencing.
STAR Protoc. 2022 Feb 4;3(1):101145. doi: 10.1016/j.xpro.2022.101145.

25. Leger A, P.P. Amaral, L. Pandolfini, C. Capitanchik, F. Capraro, V. Miano, V. Migliori, P. Toolan-Kerr, T. Sideri, A.J. Enright, K. Tzelepis, F.J. van Werven, N.M. Luscombe, I. Barbieri, Jernej Ule, T. Fitzgerald, E. Birney, T. Leonardi, T. Kouzarides. 2021. RNA modifications detection by comparative Nanopore direct RNA sequencing. Nature communications. Dec 10;12(1):7198. doi: 10.1038/s41467-021-27393-3.

24. Dierks D., M. Garcia-Campos, A. Uzonyi, M. Safra, S. Edelheit, A. Rossi, T. Sideri, R.A. Varier, A. Brandis, Y. Stelzer, F.J. van Werven, R. Scherz-Shouval & S. Schwartz. Multiplexed profiling facilitates robust m6A quantification at site, gene and sample resolution. Nature Methods. Sep;18(9):1060-1067. doi: 10.1038/s41592-021-01242-z.

23. Tresenrider A, K. Morse, V. Jorgensen, M. Chia, H. Liao, F.J. van Werven, E. Ünal. 2021. Integrated genomic analysis reveals key features of long undecoded transcript isoform-based gene repression. Molecular Cell. 2021 May 20;81(10):2231-2245.e11. doi: 10.1016/j.molcel.2021.03.013.

22. Chia, M., Li, C., Marques, S., Pelechano, V., Luscombe, N.M., and van Werven, F.J. (2021). Author Correction: High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts. Genome Biol. 22, 46. 

21. Chia M.*, C. Li*, S. Marques, V. Pelechano, N.M. Luscombe and F.J. van Werven. 2021. Cell-state transitions feature widespread transcriptional control by alternative starts. Genome biology. 22(1):34. doi: 10.1186/s13059-020-02245-3.*equal contributions

20. Moretto F., N.E. Wood, M. Chia, C. Li, N.M. Luscombe, F.J. van Werven. Transcription levels of a long noncoding RNA orchestrate opposing regulatory and cell fate outcomes in yeast. Cell reports (in print)

19. Tam J., and F.J. van Werven. Regulated repression, and not activation, governs the cell fate promoter controlling yeast meiosis. Nature Communications. 10.1038/s41467-020-16107-w.

18. Neurohr G.E., R.L. Terry, J. Lengefeld, M. Bonney, G.P. Brittingham, F. Moretto, T.P. Miettinen, L. Pontano Vaites, L.M. Soares, J. Paulo, W. Harper, S. Buratowski, S. Manalis, F.J. van Werven, L.J. Holt, B. A. Amon. Excessive cell growth causes cytoplasm dilution. Cell. 2019;176(5):1083-1097.e18.

17. Wu, A.C.K., and F.J. Van Werven. 2019. “Transcribe This Way: Rap1 Confers Promoter Directionality by Repressing Divergent Transcription.” Transcription 10 (3): 164–70.

16.  Wu, A.C.K., H. Patel, M. Chia, F. Moretto, D. Frith, A.P. Snijders, F.J. van Werven. 2018. Repression of Divergent Noncoding Transcription by a Sequence-Specific Transcription Factor. Molecular Cell. 20;72(6):942-954. 10.1016/j.molcel.2018.10.018.

15. Moretto, F., N.E. Wood, G. Kelly, A. Doncic and F.J. van Werven. 2018. A regulatory circuit of two lncRNAs and a master regulator directs cell fate in yeast. Nature Communications. 10.1038/s41467-018-03213-z.

14. Chia M., A. Tresenrider, J. Chen, G. Spedale, V. Jorgensen, E. Ünal* and F.J. van Werven*. 2017. Transcription of a 5’ extended mRNA isoform directs dynamic chromatin changes and interference of a downstream promoter. Elife. 10.7554/eLife.27420. *co-corresponding authors.

12. Chen, J., A. Tresenrider, M. Chia, D.T. McSwiggen, G. Spedale, H. Liao, F.J. Van Werven* and E. Ünal*. 2017. Kinetochore inactivation by expression of a repressive mRNA. Elife. 10.7554/eLife.27417. *co-corresponding authors.

12. Chia, M., and van Werven, F.J. 2016. Temporal Expression of a Master Regulator Drives Synchronous Sporulation in Budding Yeast. G3 6, 3553–3560.

11. Moretto, F. and F.J. van Werven. 2016. Transcription of the mating-type-regulated lncRNA IRT1 is governed by TORC1 and PKA. Current Genetics. 10.1007/s00294-016-0639-6

10. Weidberg, H., F. Moretto, G. Spedale, A. Amon, F.J. van Werven. 2016. Nutrient control of yeast gametogenesis is mediated by TORC1, PKA and energy availability. PLOS Genetics. 12 (6): e1006075

9. Berchowitz, L.E., A.S. Gajadhar, F.J. van Werven, A.A. De Rosa, M.L. Samoylova, G.A. Brar, Y. Xu , C Xiao, B. Futcher, J.S. Weissman, F.M. White, A. Amon. 2013. A developmentally regulated translational control pathway establishes the meiotic chromosome segregation pattern. Genes & Development. 27:2147-2163.

8. van Werven, F.J., G. Neuert, N. Hendrick, A. Lardenois, S. Buratowski,  A. van Oudenaarden, M. Primig and A. Amon. 2012. Transcription of two long non-coding RNAs mediates mating type control of gametogenesis in budding yeast. Cell. 50: 1170-81  

7. van Werven, F.J., and A. Amon. 2011. Regulation of entry into gametogenesis. Philos Trans R Soc Lond B Biol Sci. 366, 3521-3531

6. van Werven, F.J. H.A. van Teeffelen, F.C. Holstege and H.T. Timmers. 2009. Distinct promoter dynamics of the basal transcription factor TBP across the yeast genome. Nature Structural & Molecular Biology. 16: 1043 - 1048

5. van Werven, F.J., H. van Bakel, H.A. van Teeffelen, A.F. Altelaar, M. Groot Koerkamp, A.J. Heck, F.C. Holstege and H.T. Timmers. 2008. Cooperative action of NC2 and Mot1p to regulate TATA-binding protein function across the genome. Genes & Development. 22: 2359-2369

4. van Bakel, H.*, F.J. van Werven*, M. Radonjic, M.O. Brok, D. van Leenen, F.C. Holstege, and H.T. Timmers. 2008. Improved genome-wide localization by ChIP-chip using double-round T7 RNA polymerase-based amplification. Nucleic Acids Res. 36: e21. * These authors contributed equally.

3. van Werven, F.J. and H.T. Timmers. 2006. The use of biotin tagging in Saccharomyces cerevisiae improves the sensitivity of chromatin immunoprecipitation. Nucleic Acids Res. 34: e33.

2. van Oevelen, C.J., H.A. van Teeffelen, F.J. van Werven, and H.T. Timmers. 2006. Snf1p-dependent Spt-Ada-Gcn5-acetyltransferase (SAGA) recruitment and chromatin remodeling activities on the HXT2 and HXT4 promoters. J Biol Chem. 281: 4523-4531.

1. Goto, D.B., M. Ogi, F. Kijima, T. Kumagai, F. van Werven, H. Onouchi, and S. Naito. 2002. A single-nucleotide mutation in a gene encoding S-adenosylmethionine synthetase is associated with methionine over-accumulation phenotype in Arabidopsis thaliana. Genes Genet Syst. 77: 89-95.