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Eugene Berezikov

Research Profile

Chemicals & Drugs

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Physiology

Gene Expression Regulation

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Publications

TOP 3
Lucas J T Kaaij; Eugene Berezikov; Suzanne W Hoogstrate; René F Ketting
piRNA dynamics in divergent zebrafish strains reveal long-lasting maternal influence on zygotic piRNA profiles.
Stefanos Leptidis; Sjoukje I Lok; Serv Olieslagers; Gustavo J Silva; Roel de Weger; Leon J De Windt; Hamid El Azzouzi; Stephane Heymans; Natasja Kisters; Eugene Berezikov; Edwin Cuppen; Paula da Costa Martins
A deep sequencing approach to uncover the miRNOME in the human heart.
Marta Chiodin; Eugene Berezikov; Aina Børve; Peter Ladurner; Pedro Martinez; Andreas Hejnol
Mesodermal gene expression in the acoel Isodiametra pulchra indicates a low number of mesodermal cell types and the endomesodermal origin of the gonads.

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All Publications

2013: Lucas J T Kaaij; Eugene Berezikov; Suzanne W Hoogstrate; René F Ketting
piRNA dynamics in divergent zebrafish strains reveal long-lasting maternal influence on zygotic piRNA profiles.
RNA (New York, N.Y.) 2013;19(3):345-56.
2013: Stefanos Leptidis; Sjoukje I Lok; Serv Olieslagers; Gustavo J Silva; Roel de Weger; Leon J De Windt; Hamid El Azzouzi; Stephane Heymans; Natasja Kisters; Eugene Berezikov; Edwin Cuppen; Paula da Costa Martins
A deep sequencing approach to uncover the miRNOME in the human heart.
PloS one 2013;8(2):e57800.
2013: Marta Chiodin; Eugene Berezikov; Aina Børve; Peter Ladurner; Pedro Martinez; Andreas Hejnol
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 2013;8(2):e55499.
2013: Meltem Isik; Eugene Berezikov
Biolistic transformation of Caenorhabditis elegans.
Methods in molecular biology (Clifton, N.J.) 2013;940():77-86.
2013: Meltem Isik; Eugene Berezikov
Expression pattern analysis of microRNAs in Caenorhabditis elegans.
Methods in molecular biology (Clifton, N.J.) 2013;936():129-41.
2012: Anne Dueck; Alexander Eichner; Eugene Berezikov; Christian Ziegler; Gunter Meister
microRNAs associated with the different human Argonaute proteins.
Nucleic acids research 2012;40(19):9850-62.
2012: Maartje J Luteijn; Elke F Roovers; Petra van Bergeijk; Miguel Vasconcelos Almeida; Eugene Berezikov; Lucas J T Kaaij; René F Ketting
Extremely stable Piwi-induced gene silencing in Caenorhabditis elegans.
The EMBO journal 2012;31(16):3422-30.
2012: Daniil Simanov; Irina Sormacheva; Imre Mellaart-Straver; Eugene Berezikov
The Flatworm Macrostomum lignano Is a Powerful Model Organism for Ion Channel and Stem Cell Research.
Stem cells international 2012;2012():167265.
2012: Leonie Marjan Kamminga; Marloes P Bagijn; Eugene Berezikov; Lucas J T Kaaij; Maartje J Luteijn; Eric A Miska; Alexandra Sapetschnig; Josien C van Wolfswinkel; René F Ketting
Differential impact of the HEN1 homolog HENN-1 on 21U and 26G RNAs in the germline of Caenorhabditis elegans.
PLoS genetics 2012;8(7):e1002702.
2012: Willemijn M Gommans; Eugene Berezikov
Controlling miRNA regulation in disease.
Methods in molecular biology (Clifton, N.J.) 2012;822():1-18.
2012: Willemijn M Gommans; Eugene Berezikov
Sample preparation for small RNA massive parallel sequencing.
Methods in molecular biology (Clifton, N.J.) 2012;786():167-78.
2011: Eugene Berezikov
Evolution of microRNA diversity and regulation in animals.
Nature reviews. Genetics 2011;12(12):846-60.
2011: Georg Kuales; Willi Salvenmoser; Walter Salzburger; Shigeo Takashima; Eugene Berezikov; Katrien De Mulder; Jade Glashauser; Volker Hartenstein; Peter Ladurner
Boule-like genes regulate male and female gametogenesis in the flatworm Macrostomum lignano.
Developmental biology 2011;357(1):117-32.
2011: Hsin-Yi Huang; Lucas J T Kaaij; Eugene Berezikov; Boudewijn M Burgering; Bruce W Draper; Sharon Gauci; Saskia Houwing; Jeroen Krijgsveld; Peter Ladurner; Amanda Meppelink; Cecilia B Moens; Stefan Redl; Harmjan Vos; René F Ketting
Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish.
The EMBO journal 2011;30(16):3298-308.
2011: Eugene Berezikov; Nicolas Robine; Anastasia Samsonova; Jakub O Westholm; Ammar Naqvi; Jui-Hung Hung; Katsutomo Okamura; Qi Dai; Diane Bortolamiol-Becet; Raquel Martin; Yongjun Zhao; Phillip D Zamore; Gregory J Hannon; Marco A Marra; Zhiping Weng; Norbert Perrimon; Eric C Lai
Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence.
Genome research 2011;21(2):203-15.
2011: Jos B Poell; Roel Q J Schaapveld; Lisette M Timmer; Rick J van Haastert; Andre A F L van Puijenbroek; Eugene Berezikov; Anne S Bolijn; Francesco Cerisoli; Begoña Diosdado-Calvo; Gerrit A Meijer; Edwin Cuppen
Functional microRNA screening using a comprehensive lentiviral human microRNA expression library.
BMC genomics 2011;12():546.
2011: Stephen M Eacker; Matthew J Keuss; Eugene Berezikov; Valina Dawson; Ted M Dawson
Neuronal activity regulates hippocampal miRNA expression.
PloS one 2011;6(10):e25068.
2011: Sergei S Ryazansky; Vladimir A Gvozdev; Eugene Berezikov
Evidence for post-transcriptional regulation of clustered microRNAs in Drosophila.
BMC genomics 2011;12():371.
2010: Leonie Marjan Kamminga; Maartje J Luteijn; Marjo J den Broeder; Stefan Redl; Lucas J T Kaaij; Elke F Roovers; Peter Ladurner; Eugene Berezikov; René F Ketting
Hen1 is required for oocyte development and piRNA stability in zebrafish.
The EMBO journal 2010;29(21):3688-700.
2010: Regis Correa; Florian A Steiner; Eugene Berezikov; René F Ketting
MicroRNA-directed siRNA biogenesis in Caenorhabditis elegans.
PLoS genetics 2010;6(4):e1000903.
2010: Erno Vreugdenhil; Eugene Berezikov
Fine-tuning the brain: MicroRNAs.
Frontiers in neuroendocrinology 2010;31(2):128-33.
2010: Katrien De Mulder; Eugene Berezikov
Tracing the evolution of tissue identity with microRNAs.
Genome biology 2010;11(3):111.
2010: Meltem Isik; Hendrik C Korswagen; Eugene Berezikov
Expression patterns of intronic microRNAs in Caenorhabditis elegans.
Silence 2010;1(1):5.
2010: Eugene Berezikov; Na Liu; Alex S Flynt; Emily Hodges; Michelle Rooks; Gregory J Hannon; Eric C Lai
Evolutionary flux of canonical microRNAs and mirtrons in Drosophila.
Nature genetics 2010;42(1):6-9; author reply 9-10.
2009: Elzo de Wit; Sam E V Linsen; Edwin Cuppen; Eugene Berezikov
Repertoire and evolution of miRNA genes in four divergent nematode species.
Genome research 2009;19(11):2064-74.
2009: Josien C van Wolfswinkel; Julie M Claycomb; Pedro J Batista; Craig C Mello; Eugene Berezikov; René F Ketting
CDE-1 affects chromosome segregation through uridylation of CSR-1-bound siRNAs.
Cell 2009;139(1):135-48.
2009: Nelson C Lau; Nicolas Robine; Raquel Martin; Wei-Jen Chung; Yuzo Niki; Eugene Berezikov; Eric C Lai
Abundant primary piRNAs, endo-siRNAs, and microRNAs in a Drosophila ovary cell line.
Genome research 2009;19(10):1776-85.
2009: Shuji Takada; Eugene Berezikov; Young Lim Choi; Yoshihiro Yamashita; Hiroyuki Mano
Potential role of miR-29b in modulation of Dnmt3a and Dnmt3b expression in primordial germ cells of female mouse embryos.
RNA (New York, N.Y.) 2009;15(8):1507-14.
2009: Ronald P van Rij; Eugene Berezikov
Small RNAs and the control of transposons and viruses in Drosophila.
Trends in microbiology 2009;17(4):163-71.
2009: Jens C Schwamborn; Eugene Berezikov; Juergen A Knoblich
The TRIM-NHL protein TRIM32 activates microRNAs and prevents self-renewal in mouse neural progenitors.
Cell 2009;136(5):913-25.
2008: Saskia Houwing; Eugene Berezikov; René F Ketting
Zili is required for germ cell differentiation and meiosis in zebrafish.
The EMBO journal 2008;27(20):2702-11.
2008: Partha P Das; Marloes P Bagijn; Leonard D Goldstein; Julie R Woolford; Nicolas J Lehrbach; Alexandra Sapetschnig; Heeran R Buhecha; Michael J Gilchrist; Kevin L Howe; Rory Stark; Nik Matthews; Eugene Berezikov; René F Ketting; Simon Tavaré; Eric A Miska
Piwi and piRNAs act upstream of an endogenous siRNA pathway to suppress Tc3 transposon mobility in the Caenorhabditis elegans germline.
Molecular cell 2008;31(1):79-90.
2008: S Takada; Y Yamashita; Eugene Berezikov; H Hatanaka; S-i Fujiwara; K Kurashina; H Watanabe; M Enomoto; M Soda; Y L Choi; H Mano
MicroRNA expression profiles of human leukemias.
Leukemia 2008;22(6):1274-8.
2008: David M Tyler; Katsutomo Okamura; Wei-Jen Chung; Joshua W Hagen; Eugene Berezikov; Gregory J Hannon; Eric C Lai
Functionally distinct regulatory RNAs generated by bidirectional transcription and processing of microRNA loci.
Genes & development 2008;22(1):26-36.
2007: Yurii Aulchenko; Jan Pullen; Wigard P Kloosterman; Mojgan Yazdanpanah; Albert Hofman; Norbert Vaessen; Pieter J L M Snijders; Dmitry Zubakov; Ian Mackay; Mark Olavesen; Balbinder Sidhu; Vicki E Smith; Alisoun Carey; Eugene Berezikov; André G Uitterlinden; Ronald H Plasterk; Ben A Oostra; C.M. Duijn
LPIN2 is associated with type 2 diabetes, glucose metabolism, and body composition.
Diabetes 2007;56(12):3020-6.
2007: Eugene Berezikov; Wei-Jen Chung; Jason Willis; Edwin Cuppen; Eric C Lai
Mammalian mirtron genes.
Molecular cell 2007;28(2):328-36.
2007: Saskia Houwing; Leonie Marjan Kamminga; Eugene Berezikov; Daniela Cronembold; Angélique Girard; Hans van den Elst; Dmitri V Filippov; Heiko Blaser; erez raz; Cecilia B Moens; Ronald H Plasterk; Gregory J Hannon; Bruce W Draper; René F Ketting
A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in Zebrafish.
Cell 2007;129(1):69-82.
2007: Eugene Berezikov; Victor Guryev; Edwin Cuppen
Exploring conservation of transcription factor binding sites with CONREAL.
Methods in molecular biology (Clifton, N.J.) 2007;395():437-48.
2007: Asli N Silahtaroglu; Dorrit Nolting; Lars Dyrskjøt; Eugene Berezikov; Morten Møller; Niels Tommerup; Sakari Kauppinen
Detection of microRNAs in frozen tissue sections by fluorescence in situ hybridization using locked nucleic acid probes and tyramide signal amplification.
Nature protocols 2007;2(10):2520-8.
2006: Eugene Berezikov; Fritz Thuemmler; Linda W van Laake; Ivanela Kondova; Ronald E Bontrop; Edwin Cuppen; Ronald H Plasterk
Diversity of microRNAs in human and chimpanzee brain.
Nature genetics 2006;38(12):1375-7.
2006: Eugene Berezikov; Geert van Tetering; Mark Verheul; Jose van de Belt; Linda W van Laake; Joost Vos; Robert E Verloop; Marc van de Wetering; Victor Guryev; Shuji Takada; Anton-Jan van Zonneveld; Hiroyuki Mano; Ronald H Plasterk; Edwin Cuppen
Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis.
Genome research 2006;16(10):1289-98.
2006: Brandon Ason; Diana Darnell; Beate Wittbrodt; Eugene Berezikov; Wigard P Kloosterman; Joachim Wittbrodt; Parker B Antin; Ronald H Plasterk
Differences in vertebrate microRNA expression.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(39):14385-9.
2006: Eugene Berezikov; Edwin Cuppen; Ronald H Plasterk
Approaches to microRNA discovery.
Nature genetics 2006;38 Suppl():S2-7.
2006: Victor Guryev; Marco J Koudijs; Eugene Berezikov; Stephen L Johnson; Ronald H Plasterk; Fredericus J M van Eeden; Edwin Cuppen
Genetic variation in the zebrafish.
Genome research 2006;16(4):491-7.
2006: Shuji Takada; Eugene Berezikov; Yoshihiro Yamashita; Mariana Lagos-Quintana; Wigard P Kloosterman; Munehiro Enomoto; Hisashi Hatanaka; Shin-ichiro Fujiwara; Hideki Watanabe; Manabu Soda; Young Lim Choi; Ronald H Plasterk; Edwin Cuppen; Hiroyuki Mano
Mouse microRNA profiles determined with a new and sensitive cloning method.
Nucleic acids research 2006;34(17):e115.
2006: Wigard P Kloosterman; Florian A Steiner; Eugene Berezikov; Ewart de Bruijn; Jose van de Belt; Mark Verheul; Edwin Cuppen; Ronald H Plasterk
Cloning and expression of new microRNAs from zebrafish.
Nucleic acids research 2006;34(9):2558-69.
2005: Eugene Berezikov; Ronald H Plasterk
Camels and zebrafish, viruses and cancer: a microRNA update.
Human molecular genetics 2005;14 Spec No. 2():R183-90.
2005: Erno Wienholds; Wigard P Kloosterman; Eric A Miska; Ezequiel Alvarez-Saavedra; Eugene Berezikov; Ewart de Bruijn; H Robert Horvitz; Sakari Kauppinen; Ronald H Plasterk
MicroRNA expression in zebrafish embryonic development.
Science (New York, N.Y.) 2005;309(5732):310-1.
2005: Eugene Berezikov; Victor Guryev; Edwin Cuppen
CONREAL web server: identification and visualization of conserved transcription factor binding sites.
Nucleic acids research 2005;33(Web Server issue):W447-50.
2005: Eugene Berezikov; Victor Guryev; Jose van de Belt; Erno Wienholds; Ronald H Plasterk; Edwin Cuppen
Phylogenetic shadowing and computational identification of human microRNA genes.
Cell 2005;120(1):21-4.
2005: Victor Guryev; Eugene Berezikov; Edwin Cuppen
CASCAD: a database of annotated candidate single nucleotide polymorphisms associated with expressed sequences.
BMC genomics 2005;6():10.
2004: Victor Guryev; Eugene Berezikov; Rainer Malik; Ronald H Plasterk; Edwin Cuppen
Single nucleotide polymorphisms associated with rat expressed sequences.
Genome research 2004;14(7):1438-43.
2004: Bart M G Smits; Ursula M D'Souza; Eugene Berezikov; Edwin Cuppen; Frans Sluyter
Identifying polymorphisms in the Rattus norvegicus D3 dopamine receptor gene and regulatory region.
Genes, brain, and behavior 2004;3(3):138-48.
2004: Ekaterina Papusheva; Mary C Gruhl; Eugene Berezikov; Tatiana Groudieva; Svetlana V Scherbik; Jon Martin; Alexander Blinov; Gerald Bergtrom
The Evolution of SINEs and LINEs in the genus Chironomus (Diptera).
Journal of molecular evolution 2004;58(3):269-79.
2004: Eugene Berezikov; Cornelia I Bargmann; Ronald H Plasterk
Homologous gene targeting in Caenorhabditis elegans by biolistic transformation.
Nucleic acids research 2004;32(4):e40.
2004: Eugene Berezikov; Victor Guryev; Ronald H Plasterk; Edwin Cuppen
CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting.
Genome research 2004;14(1):170-8.
2003: Gaëll Mainguy; Paul M J In der Rieden; Eugene Berezikov; Joost Woltering; Ronald H Plasterk; Antony Durston
A position-dependent organisation of retinoid response elements is conserved in the vertebrate Hox clusters.
Trends in genetics : TIG 2003;19(9):476-9.
2002: Eugene Berezikov; Ronald H Plasterk; Edwin Cuppen
GENOTRACE: cDNA-based local GENOme assembly from TRACE archives.
Bioinformatics (Oxford, England) 2002;18(10):1396-7.
2001: Isabelle Busseau; Eugene Berezikov; Alain Bucheton
Identification of Waldo-A and Waldo-B, two closely related non-LTR retrotransposons in Drosophila.
Molecular biology and evolution 2001;18(2):196-205.
2000: I F Makarevich; Eugene Berezikov; VP Gur'ev; Alexander Blinov
[Molecular phylogeny of Chironomus genus based on nucleotide sequences analysis of two nuclear genes, ssp160 and globin 2b].
Molekuliarnaia biologiia 2000;34(4):701-7.
2000: Eugene Berezikov; Alain Bucheton; Isabelle Busseau
A search for reverse transcriptase-coding sequences reveals new non-LTR retrotransposons in the genome of Drosophila melanogaster.
Genome biology 2000;1(6):RESEARCH0012.
1998: Eugene Berezikov; Alexander Blinov; Svetlana V Scherbik; C K Cox; S T Case
Structure and polymorphism of the Chironomus thummi gene encoding special lobe-specific silk protein, ssp160.
Gene 1998;223(1-2):347-54.