Publications

Wragg, J., Louise White, P., Hadzhiev, Y., Wanigasooriya, K., Stodolna, A., Tee, L., Barros-Silva J., Beggs A. and Müller F. (2023) Intra-promoter switch of transcription initiation sites in proliferation signalling-dependent RNA metabolism Nat. Struct. Mol. Biol. (12):1970-1984.

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Hadzhiev Y, Wheatley L, Cooper L, Ansaloni F, Whalley C, Chen Z, Finaurini S, Gustincich S, Sanges R, Burgess S, Beggs A, Müller F. (2023) The miR-430 locus with extreme promoter density forms a transcription body during the minor wave of zygotic genome activation. Dev. Cell, Jan 23;58(2):155-170.e8. 3. Jimenez Gonzalez A, Baranasic D, Müller F. (2023) Zebrafish regulatory genomic resources for disease modelling and regeneration. Dis. Model Mech. Aug 1;16(8):dmm050280. doi: 10.1242/dmm.050280.

 

Baranasic D, Hörtenhuber M, Balwierz PJ, Zehnder T, Mukarram AK, Nepal C, Várnai C, Hadzhiev Y, Jimenez-Gonzalez A, Li N, Wragg J, D'Orazio FM, Relic D,Pachkov M, Díaz N, Hernández-Rodríguez B, Chen Z, Stoiber M, Dong M, Stevens I,Ross SE, Eagle A, Martin R, Obasaju O, Rastegar S, McGarvey AC, Kopp W, Chambers E, Wang D, Kim HR, Acemel RD, Naranjo S, Łapiński M, Chong V, Mathavan S, Peers B, Sauka-Spengler T, Vingron M, Carninci P, Ohler U, Lacadie SA, Burgess SM, Winata C, van Eeden F, Vaquerizas JM, Gómez-Skarmeta JL, Onichtchouk D, Brown BJ, Bogdanovic O, van Nimwegen E, Westerfield M, Wardle FC, Daub CO, Lenhard B, Müller F. (2022) Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements. Nat. Genet. 54(7):1037-1050. doi: 10.1038/s41588-022-01089-w.

 

D'Orazio FM, Balwierz PJ, González AJ, Guo Y, Hernández-Rodríguez B, Wheatley L, Jasiulewicz A, Hadzhiev Y, Vaquerizas JM, Cairns B, Lenhard B, Müller F. Germ cell differentiation requires Tdrd7-dependent chromatin and transcriptome reprogramming marked by germ plasm relocalization. (2021) Dev. Cell. 56(5):641-656.e5. doi: 10.1016/j.devcel.2021.02.007.

 

Nepal, C., Hadzhiev, Y., Tarifeño-Saldivia, E., Carninci, P., Andersen, J.B., Peers, B., Lenhard B., and Müller F. (2020) Intertwined canonical and non-canonical initiation in dual promoters are pervasive and differentially regulate Polymerase II transcription Nat. Commun. 2020, Jan 11; 168. doi:10.1038/s41467-019-13687-0

 

Andersson, R., Gebhard, C., Miguel-Escalada, I., Hoof, I., Zhao, X., Schmidl, C., Valen, E., Li, K., Schwarzfischer, L., Glatz, D., Raithel, J., Chen, Y., Lilje, B., Rapin, N., Otzen Bagger, F., Jørgensen, M., Boyd, M., Bornholdt Lange, J., Baillie, K., Mungall, C., Lassman, T., Kawaji, H., Lennartsson, A., Daub, C., Hume, D., Heutink, P., Krogh, A., Hayashizaki, Y., Müller, F., Forrest, F., Carninci, P., Rehli, M., Sandelin A., (2014) Systematic in-vivo characterization of active enhancers across the human body. Nature, 507(7493):455-61.

 

Haberle, V., Li, N., Hadzhiev, Y., Plessy, C., Previti, C., Nepal, C., Gehrig, J., Dong, X., Akalin, A., Suzuki, A-M., van IJcken, W., Armant, O., Ferg, M., Strähle, U., Carninci, P., Müller F.*, Lenhard B. Two independent transcription initiation codes overlap on vertebrate core promoters. Nature, 507(7492):381-5.

 

Nepal C, Hadzhiev, Y., Previti, C., Haberle V., Li, N., Takahashi, H., Suzuki, A-M. S., Sheng, Y., Abdelhamid, R.A., Anand, S., Gehrig, J., Akalin, A., Kockx, C.E.M. van der Sloot, A.A.J., van IJcken, W.F.J., Armant, O., Rastegar, S., Watson, C., Strähle, U., Stupka, E., Carninci, P., Lenhard B. and Müller F. (2013) Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis. Genome Res, 23(11):1938-50. (IF13.6)

 

Gehrig J, Reischl M, Kalmár E, Ferg M, Hadzhiev Y, Zaucker A, Song C, Schindler S, Liebel U. and Müller F. Automated high-throughput mapping of promoter-enhancer interactions in zebrafish embryos (2009). Nat. Methods, 6(12):911-6.