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Berezikov group

Demircan, T. and Berezikov, E. (2013) The hippo pathway regulates stem cells during homeostasis and regeneration of the flatworm Macrostomum lignano. Stem Cells Dev. 22, 2174-2185.

Leptidis, S., El Azzouzi, H., Lok, S.I., de Weger, R., Olieslagers, S., Kisters, N., Silva, G.J., Heymans, S., Cuppen, E., Berezikov, E., De Windt, L.J., and da Costa Martins, P. (2013) A deep sequencing approach to uncover the miRNOME in the human heart. PLoS One 8, e57800.

Chiodin, M., Børve, A., Berezikov, E., Ladurner, P., Martinez, P., and Hejnol, A. (2013) Mesodermal gene expression in the acoel Isodiametra pulchra indicates a low number of mesodermal cell types and the endomesodermal origin of the gonads. PLoS One 8, e55499.

Kaaij, L.J., Hoogstrate, S.W., Berezikov, E., and Ketting, R.F. (2013) piRNA dynamics in divergent zebrafish strains reveal long-lasting maternal influence on zygotic piRNA profiles. RNA 19, 345-356.

Isik, M., and Berezikov, E. (2013) Biolistic transformation of Caenorhabditis elegans. Methods Mol Biol. 940, 77-86.

Isik, M., and Berezikov, E. (2013) Expression pattern analysis of microRNAs in Caenorhabditis elegans. Methods Mol Biol. 936, 129-141.

Simanov, D., Mellaart-Straver, I., Sormacheva, I., and Berezikov, E. (2012) The Flatworm Macrostomum lignano Is a Powerful Model Organism for Ion Channel and Stem Cell Research. Stem Cells Int. 2012, 167265.

Luteijn, M.J., van Bergeijk, P., Kaaij, L.J., Almeida, M.V., Roovers, E.F., Berezikov, E., and Ketting, R.F. (2012) Extremely stable Piwi-induced gene silencing in Caenorhabditis elegansEMBO J. 31, 3422-3430.

Dueck, A., Ziegler, C., Eichner, A., Berezikov, E., and Meister, G. (2012) microRNAs associated with the different human Argonaute proteins. Nucleic Acids Res. 40, 9850-9862.

Kamminga, L.M., van Wolfswinkel, J.C., Luteijn, M.J., Kaaij, L.J., Bagijn, M.P., Sapetschnig, A., Miska, E.A., Berezikov, E., and Ketting, R.F. (2012). Differential impact of the HEN1 homolog HENN-1 on 21U and 26G RNAs in the germline of Caenorhabditis elegans. PLoS Genet. 8, e1002702.

Gommans, W.M., and Berezikov, E. (2012) Controlling miRNA regulation in disease. Methods Mol Biol. 822, 1-18.

Gommans, W.M., and Berezikov, E. (2012) Sample preparation for small RNA massive parallel sequencing. Methods Mol Biol. 786, 167-178.

Berezikov, E. (2011) Evolution of microRNA diversity and regulation in animals. Nat Rev Genet. 12, 846-860.

Poell, J.B., van Haastert, R.J., Cerisoli, F, Bolijn, A.S., Timmer, L.M., Diosdado-Calvo, B., Meijer, G.A., van Puijenbroek, A.A., Berezikov, E., Schaapveld, R.Q., and Cuppen, E. (2011) Functional microRNA screening using a comprehensive lentiviral human microRNA expression library. BMC Genomics. 12, 546.

Eacker, S.M., Keuss, M.J., Berezikov, E., Dawson, V.L., and Dawson, T.M. (2011) Neuronal activity regulates hippocampal miRNA expression. PLoS One 6, e25068.

Ryazansky, S.S., Gvozdev, V.A., and Berezikov, E. (2011) Evidence for post-transcriptional regulation of clustered microRNAs in Drosophila. BMC Genomics 12, 371.

Huang, H.Y., Houwing, S., Kaaij, L.J., Meppelink, A., Redl, S., Gauci, S., Vos, H., Draper, B.W., Moens, C.B., Burgering, B.M., Ladurner, P., Krijgsveld, J., Berezikov, E., and Ketting, R.F. (2011) Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish. EMBO J. 30, 3298-3308.

Kuales, G., De Mulder, K., Glashauser, J., Salvenmoser, W., Takashima, S., Hartenstein, V., Berezikov, E., Salzburger, W., and Ladurner, P. (2011) Boule-like genes regulate male and female gametogenesis in the flatworm Macrostomum lignano. Dev Biol. 357, 117-132.

modENCODE consortium et al. (2011) Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330, 1787-1797.

Berezikov, E., Robine, N., Samsonova, A., Westholm, .JO., Naqvi, A., Hung, J.H., Okamura, K., Dai, Q., Bortolamiol-Becet, D., Martin, R., Zhao, Y., Zamore, P.D., Hannon, G.J., Marra, M.A., Weng, Z., Perrimon, N., and Lai, E.C. (2011) Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence. Genome Res. 21, 203-215.

Kamminga, L.M., Luteijn, M.J., den Broeder, M.J., Redl, S., Kaaij, L.J., Roovers, E.F., Ladurner, P., Berezikov, E., and Ketting, R.F. (2010) Hen1 is required for oocyte development and piRNA stability in zebrafish. EMBO J. 29, 3688-3700.

Corrêa, R.L., Steiner, F.A., Berezikov, E., and Ketting, R.F. (2010) MicroRNA-directed siRNA biogenesis in Caenorhabditis elegans. PLoS Genet. 6, e1000903.

De Mulder, K., AND Berezikov, E. (2010) Tracing the evolution of tissue identity with microRNAs. Genome Biol. 11, 111.

Isik, M., Korswagen, H.C., and Berezikov, E. (2010) Expression patterns of intronic microRNAs in Caenorhabditis elegans. Silence 1, 5.

Berezikov, E. Liu, N., Flynt, A.S., Hodges, E., Rooks, M. Hannon, G.J., and Lai, E.C. (2010) Evolutionary flux of canonical microRNAs and mirtrons in Drosophila. Nat. Genet. 42, 6-9.

van Wolfswinkel, J.C., Claycomb, J.M., Batista, P.J., Mello, C.C., Berezikov, E., and Ketting, R.F. (2009) CDE-1 affects chromosome segregation through uridylation of CSR-1-bound siRNAs. Cell 139, 135-148.

de Wit, E., Linsen, S.E., Cuppen, E., and Berezikov, E. (2009) Repertoire and evolution of miRNA genes in four divergent nematode species. Genome Res. 19, 2064-2074.

Lau, N.C., Robine, N., Martin, R., Chung, W.-J., Niki, Y., Berezikov, E., and Lai, E.C. (2009) Abundant primary piRNAs, endo-siRNAs and microRNAs in a Drosophila ovary cell line. Genome Res. 19, 1776-1785.

Vreugdenhil, E., Berezikov, E. (2009) Fine-tuning the brain: MicroRNAs. Front. Neuroendocrinol. In press.

Takada, S., Berezikov, E., Choi, Y.L., Yamashita, Y., and Mano, H. (2009) Potential role of miR-29b in modulation of Dnmt3a and Dnmt3b expression in primordial germ cells of female mouse embryos. RNA 15:1507-1514.

van Rij, R.P., and Berezikov, E. (2009) Small RNAs and the control of transposons and viruses in Drosophila. Trends Microbiol. 17, 163-171.

Schwamborn, J.C., Berezikov, E., and Knoblich, J.A. (2009) The TRIM-NHL protein TRIM32 activates microRNAs and prevents self-renewal in mouse neural progenitors. Cell 136, 913-925.

Houwing, S., Berezikov, E., and Ketting, R.F. (2008) Zili is required for germ cell differentiation and meiosis in zebrafish. EMBO J. 27, 2702-2711.

Das, P.P., Bagijn, M.P., Goldstein, L.D., Woolford, J.R., Lehrbach, N.J., Sapetschnig, A., Buhecha, H.R., Gilchrist, M.J., Howe, K.L., Stark, R., Matthews, N., Berezikov, E., Ketting, R.F., Tavare, S., and Miska, E.A. (2008) Piwi and piRNAs act upstream of an endogenous siRNA pathway to suppress Tc3 transposon mobility in the Caenorhabditis elegans germline. Mol. Cell 31, 79-90.

Tyler, D.M., Okamura, K., Chung, W.J., Hagen, J.W., Berezikov, E., Hannon, G.J., and Lai, E.C. (2008) Functionally distinct regulatory RNAs generated by bidirectional transcription and processing of microRNA loci. Genes Dev. 22, 26-36.

Takada, S., Yamashita, Y., Berezikov, E., Hatanaka, H., Fujiwara, S.I., Kurashina, K., Watanabe, H., Enomoto, M., Soda, M., Choi, Y.L., and Mano, H. (2007) MicroRNA expression profiles of human leukemias. Leukemia 22, 1274-1278.

Berezikov, E., Chung, W.-J., Willis, J., Cuppen, E., and Lai, E.C. (2007) Mammalian mirtron genes. Mol. Cell 28, 328-336.

Silahtaroglu, A.N., Nolting, D., Dyrskjot, L., Berezikov, E., Moller, M., Tommerup, N., and Kauppinen, S. (2007) Detection of microRNAs in frozen tissue sections by fluorescence in situ hybridization using locked nucleic acid probes and tyramide signal amplification. Nat. Protoc. 2, 2520-2528.

Aulchenko, Y.S., Pullen, J., Kloosterman, W.P., Yazdanpanah, M., Hofman, A., Vaessen, N., Snijders, P.J., Zubakov, D., Mackay, I., Olavesen, M., Sidhu, B., Smith, V.E., Carey, A., Berezikov, E., Uitterlinden, A.G., Plasterk, R.H., Oostra, B.A., and van Duijn, C.M. (2007) LPIN2 is associated with type 2 diabetes, glucose metabolism, and body composition. Diabetes 56, 3020-3026.

Houwing, S., Kamminga, L.M., Berezikov, E., Cronembold, D., Girard, A., van den Elst, H., Filippov, D.V., Blaser, H., Raz, E., Moens, C.B., Plasterk, R.H., Hannon, G.J., Draper, B.W., and Ketting, R.F. (2007) A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in Zebrafish. Cell 129, 69-82.

Berezikov, E., Thuemmler, F., van Laake, L., Kondova, I., Bontrop, R., Cuppen, E., and Plasterk, R.H.A. (2006) Diversity of microRNAs in human and chimpanzee brain. Nat. Genet. 38, 1375-1377.

Berezikov, E., Cuppen, E., and Plasterk, R. (2006) Approaches to microRNA discovery. Nat. Genet. 38, S2-S7.

Berezikov, E., van Tetering, G., Verheul, M., van de Belt, J., van Laake, L., Vos, J., Verloop, R., van de Wetering, M., Guryev, V., Takada, S., van Zonneveld, A.J., Mano, H., Plasterk, R.H.A., and Cuppen, E. (2006) Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis. Genome Res. 16, 1289-1298.

Takada, S., Berezikov, E., Yamashita, Y., Lagos-Quitana, M., Kloosterman, W., Enomoto, M., Hatanaka, H., Fujiwara, S., Watanabe, H., Soda, M., Choi, Y.L., Plasterk, R., Cuppen, E., and Mano, H. (2006) Mouse microRNA profilies determined with a new and sensitive cloning method. Nucleic Acids Res. 34, e115.

Ason, B., Darnell, D.K., Wittbrodt, B., Berezikov, E., Kloosterman, W.P., Wittbrodt, J., Antin, P.B., and Plasterk, R.H. (2006) Differences in vertebrate microRNA expression. Proc. Natl. Acad. Sci. U.S.A. 103, 14385-14389.

Kloosterman, W., Steiner, F., Berezikov, E., de Bruijn, E., van de Belt, J., Verheul, M., Cuppen, E., and Plasterk, R.H. (2006) Cloning and expression of new microRNAs from zebrafish. Nucleic Acids Res. 34, 2558-2569.

Berezikov, E., Guryev, V., Belt, J. v.d., Wienholds, E., Plasterk, R.H.A, and Cuppen, E. (2005) Phylogenetic Shadowing and Computational Identification of Human microRNA Genes. Cell 120, 21-24.

Berezikov, E., and Plasterk, R.H. (2005) Camels and zebrafish, viruses and cancer: a microRNA update. Hum. Mol. Genet. 14, R183-90.

Wienholds, E., Kloosterman, W. P., Miska, E., Alvarez-Saavedra, E., Berezikov, E., de Bruijn, E., Horvitz, H.R., Kauppinen, S., and Plasterk, R.H. (2005) MicroRNA expression in zebrafish embryonic development. Science 309, 310-311.

Berezikov, E., Guryev, V., and Cuppen, E. (2005) CONREAL Web Server: Identification and Visualization of Conserved Transcription Factor Binding Sites. Nucleic Acids Res. 33, W447-W450.

Guryev, V., Berezikov, E., and Cuppen, E. (2005) CASCAD: a database of annotated candidate single nucleotide polymorphisms associated with expressed sequences. BMC Genomics 6, 10.

Berezikov, E., Bargmann, C. I., and Plasterk, R.H. (2004) Homologous gene targeting in Caenorhabditis elegans by biolistic transformation. Nucleic Acids Res. 32, e40.

Berezikov, E., Guryev, V., Plasterk R.H.A., and Cuppen, E. (2004) CONREAL: Conserved Regulatory Elements Anchored Alignment Algorithm for Identification of Transcription Factor Binding Sites by Phylogenetic Footprinting. Genome Res. 14, 170-178.

Guryev, V., Berezikov, E., Malik, R., Plasterk, R.H.A., and Cuppen, E. (2004) Single Nucleotide Polymorphisms associated with rat expressed sequences. Genome Res. 14, 1438-1443.

Papusheva, E., Gruhl, M. C., Berezikov, E., Groudieva, T., Scherbik, S.V., Martin, J., Blinov, A., and Bergtrom, G. (2004) The Evolution of SINEs and LINEs in the genus Chironomus (Diptera). J. Mol. Evol. 58, 269-279.

Smits, B.M., D'Souza, U.M., Berezikov, E., Cuppen, E., and Sluyter, F. (2004) Identifying polymorphisms in the Rattus norvegicus D3 dopamine receptor gene and regulatory region. Genes Brain Behav. 3, 138-148.

Mainguy, G., In der, R.i.P., Berezikov, E., Woltering, J.M., Plasterk, R.H., and Durston, A.J. (2003) A position-dependent organisation of retinoid response elements is conserved in the vertebrate Hox clusters. Trends Genet. 19, 476-479.

Berezikov, E., Plasterk, R.H.A., and Cuppen, E. (2002) GENOTRACE: cDNA-based local GENOme assembly from TRACE archives. Bioinformatics 18, 1396-1397.

Busseau, I., Berezikov, E., and Bucheton, A. (2001) Identification of Waldo-A and Waldo-B, two closely related non-LTR retrotransposons in Drosophila. Mol. Biol. Evol. 18, 196-205.

Berezikov, E., Bucheton, A., and Busseau, I. (2000) A search for reverse transcriptase-coding sequences reveals new non-LTR retrotransposons in the genome of Drosophila melanogaster. Genome Biol. 1, RESEARCH0012.

Berezikov, E., Blinov, A.G., Scherbik, S., Cox, C. K., and Case, S.T. (1998) Structure and polymorphism of the Chironomus thummi gene encoding special lobe-specific silk protein, ssp160. Gene 223, 347-354.

Book chapters
Berezikov, E., Guryev, V., Cuppen, E. (2007) Exploring Conservation of Transcription Factor Binding Sites with CONREAL. Methods Mol. Biol. 395, 437-448.

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