Eugene Berezikov

Summary

Affiliation: Netherlands Institute of Ecology
Country: The Netherlands

Publications

  1. pmc Mammalian mirtron genes
    Eugene Berezikov
    Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
    Mol Cell 28:328-36. 2007
  2. pmc CASCAD: a database of annotated candidate single nucleotide polymorphisms associated with expressed sequences
    Victor Guryev
    Hubrecht Laboratory, Netherlands Institute for Developmental Biology, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands
    BMC Genomics 6:10. 2005
  3. pmc Cloning and expression of new microRNAs from zebrafish
    Wigard P Kloosterman
    Hubrecht Laboratory, Centre for Biomedical Genetics, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
    Nucleic Acids Res 34:2558-69. 2006
  4. ncbi request reprint Diversity of microRNAs in human and chimpanzee brain
    Eugene Berezikov
    Hubrecht Laboratory KNAW, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
    Nat Genet 38:1375-7. 2006
  5. pmc MicroRNA-directed siRNA biogenesis in Caenorhabditis elegans
    Régis L Corrêa
    Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Centre Utrecht, Utrecht, The Netherlands
    PLoS Genet 6:e1000903. 2010
  6. pmc Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis
    Eugene Berezikov
    Hubrecht Laboratory, 3584 CT Utrecht, The Netherlands
    Genome Res 16:1289-98. 2006
  7. ncbi request reprint Camels and zebrafish, viruses and cancer: a microRNA update
    Eugene Berezikov
    Hubrecht Laboratory, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
    Hum Mol Genet 14:R183-90. 2005
  8. pmc CONREAL web server: identification and visualization of conserved transcription factor binding sites
    Eugene Berezikov
    Hubrecht Laboratory, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
    Nucleic Acids Res 33:W447-50. 2005
  9. pmc Differences in vertebrate microRNA expression
    Brandon Ason
    Hubrecht Laboratory, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
    Proc Natl Acad Sci U S A 103:14385-9. 2006
  10. pmc Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence
    Eugene Berezikov
    Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
    Genome Res 21:203-15. 2011

Collaborators

Detail Information

Publications34

  1. pmc Mammalian mirtron genes
    Eugene Berezikov
    Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
    Mol Cell 28:328-36. 2007
    ..This notion is supported by our observation of several clade-specific features of mammalian and invertebrate mirtrons...
  2. pmc CASCAD: a database of annotated candidate single nucleotide polymorphisms associated with expressed sequences
    Victor Guryev
    Hubrecht Laboratory, Netherlands Institute for Developmental Biology, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands
    BMC Genomics 6:10. 2005
    ..However, such information is very important for selecting the most promising and useful candidate polymorphisms for use in experimental setups...
  3. pmc Cloning and expression of new microRNAs from zebrafish
    Wigard P Kloosterman
    Hubrecht Laboratory, Centre for Biomedical Genetics, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
    Nucleic Acids Res 34:2558-69. 2006
    ..Most newly discovered miRNAs have low expression levels and are less conserved in other vertebrate species. Our cloning and expression analysis indicates that most abundant and conserved miRNAs in zebrafish are now known...
  4. ncbi request reprint Diversity of microRNAs in human and chimpanzee brain
    Eugene Berezikov
    Hubrecht Laboratory KNAW, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
    Nat Genet 38:1375-7. 2006
    ..These data suggest that evolution of miRNAs is an ongoing process and that along with ancient, highly conserved miRNAs, there are a number of emerging miRNAs...
  5. pmc MicroRNA-directed siRNA biogenesis in Caenorhabditis elegans
    Régis L Corrêa
    Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Centre Utrecht, Utrecht, The Netherlands
    PLoS Genet 6:e1000903. 2010
    ....
  6. pmc Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis
    Eugene Berezikov
    Hubrecht Laboratory, 3584 CT Utrecht, The Netherlands
    Genome Res 16:1289-98. 2006
    ..Most novel microRNAs candidates are not conserved beyond mammals, and ~10% are taxon-specific. Our analyses indicate that the entire microRNA repertoire is not remotely exhausted...
  7. ncbi request reprint Camels and zebrafish, viruses and cancer: a microRNA update
    Eugene Berezikov
    Hubrecht Laboratory, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
    Hum Mol Genet 14:R183-90. 2005
    ....
  8. pmc CONREAL web server: identification and visualization of conserved transcription factor binding sites
    Eugene Berezikov
    Hubrecht Laboratory, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
    Nucleic Acids Res 33:W447-50. 2005
    ..Comparative analysis using different algorithms can be started by keyword without any prior sequence retrieval. The interface is available at http://conreal.niob.knaw.nl...
  9. pmc Differences in vertebrate microRNA expression
    Brandon Ason
    Hubrecht Laboratory, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
    Proc Natl Acad Sci U S A 103:14385-9. 2006
    ....
  10. pmc Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence
    Eugene Berezikov
    Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
    Genome Res 21:203-15. 2011
    ..Altogether, this study lays a comprehensive foundation for the study of miRNA diversity and evolution in a complex animal model...
  11. doi request reprint CDE-1 affects chromosome segregation through uridylation of CSR-1-bound siRNAs
    Josien C Van Wolfswinkel
    Hubrecht Institute KNAW and University Medical Centre Utrecht, Uppsalalaan 8, Utrecht, The Netherlands
    Cell 139:135-48. 2009
    ..The conserved nature of CDE-1 suggests that similar sorting mechanisms may operate in other animals, including mammals...
  12. ncbi request reprint Approaches to microRNA discovery
    Eugene Berezikov
    Hubrecht Laboratory, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
    Nat Genet 38:S2-7. 2006
    ..How can new miRNAs be discovered and distinguished from other types of small RNA? Here we summarize current methods for identifying and validating miRNAs and discuss criteria used to define an miRNA...
  13. ncbi request reprint Expression pattern analysis of microRNAs in Caenorhabditis elegans
    Meltem Isik
    Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, University Medical Center Utrecht, Utrecht, The Netherlands
    Methods Mol Biol 936:129-41. 2013
    ..In this chapter, we describe a detailed protocol for the analysis of miRNA expression patterns in Caenorhabditis elegans...
  14. pmc Single nucleotide polymorphisms associated with rat expressed sequences
    Victor Guryev
    Hubrecht Laboratory, Netherlands Institute for Developmental Biology, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands
    Genome Res 14:1438-43. 2004
    ..Two of these "in silico-identified knockouts" reside in interesting QTL regions. Data are publicly available via a Web interface (http://cascad.niob.knaw.nl), allowing simple and advanced search queries...
  15. pmc CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting
    Eugene Berezikov
    Hubrecht Laboratory, Netherlands Institute for Developmental Biology, 3584 CT, Utrecht, The Netherlands
    Genome Res 14:170-8. 2004
    ..CONREAL is accessible via a Web interface at http://conreal.niob.knaw.nl/...
  16. pmc piRNA dynamics in divergent zebrafish strains reveal long-lasting maternal influence on zygotic piRNA profiles
    Lucas J T Kaaij
    Hubrecht Institute KNAW and University Medical Centre Utrecht, 3584 CT Utrecht, The Netherlands
    RNA 19:345-56. 2013
    ..These differences can be detected at least two generations later. Our data illustrate, for the first time, the fluidity of piRNA populations in vertebrates and how the established diversity is transmitted to future generations...
  17. doi request reprint Evolution of microRNA diversity and regulation in animals
    Eugene Berezikov
    Hubrecht Institute, KNAW, University Medical Center Utrecht, The Netherlands
    Nat Rev Genet 12:846-60. 2011
    ..Insights are also emerging into how the evolution of miRNA-containing regulatory networks has contributed to organismal complexity...
  18. ncbi request reprint MicroRNA expression in zebrafish embryonic development
    Erno Wienholds
    Hubrecht Laboratory, Centre for Biomedical Genetics, 3584 CT Utrecht, The Netherlands
    Science 309:310-1. 2005
    ....
  19. doi request reprint Controlling miRNA regulation in disease
    Willemijn M Gommans
    Hubrecht Institute, Utrecht, The Netherlands
    Methods Mol Biol 822:1-18. 2012
    ..The interplay between these two processes defines the final protein output in a cell, and thus the normal or pathological cellular phenotype...
  20. pmc Zili is required for germ cell differentiation and meiosis in zebrafish
    Saskia Houwing
    Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, University Medical Centre Utrecht, Utrecht, The Netherlands
    EMBO J 27:2702-11. 2008
    ....
  21. pmc Tracing the evolution of tissue identity with microRNAs
    Katrien De Mulder
    Hubrecht Institute and University Medical Center Utrecht, Uppsalalaan 8, Utrecht, The Netherlands
    Genome Biol 11:111. 2010
    ..Comparison of microRNA expression identified tissues present in the last common ancestor of Bilaterians and put evolution of microRNAs in the context of tissue evolution...
  22. ncbi request reprint A position-dependent organisation of retinoid response elements is conserved in the vertebrate Hox clusters
    Gaell Mainguy
    Hubrecht Laboratory, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
    Trends Genet 19:476-9. 2003
  23. pmc Functional microRNA screening using a comprehensive lentiviral human microRNA expression library
    Jos B Poell
    Hubrecht Institute, Cancer Genomics Center, and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
    BMC Genomics 12:546. 2011
    ..Dissecting the complexities of miRNA function continues to prove challenging as miRNAs are predicted to have thousands of targets, and mRNAs can be targeted by dozens of miRNAs...
  24. pmc Homologous gene targeting in Caenorhabditis elegans by biolistic transformation
    Eugene Berezikov
    Hubrecht Laboratory, Netherlands Institute for Developmental Biology, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
    Nucleic Acids Res 32:e40. 2004
    ..We describe a scaled up version of biolistic transformation that can be used as a method for homologous gene targeting in the worm...
  25. ncbi request reprint GENOTRACE: cDNA-based local GENOme assembly from TRACE archives
    Eugene Berezikov
    Hubrecht Laboratory, Netherlands Institute for Developmental Biology, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
    Bioinformatics 18:1396-7. 2002
    ..Local genomic contigs are generated, allowing for example the design of PCR primers in intronic sequences to amplify coding regions of a gene, needed for example for mutation or SNP detection...
  26. ncbi request reprint The Evolution of SINEs and LINEs in the genus Chironomus (Diptera)
    Ekaterina Papusheva
    Physiologisches Institut, Universität Goettingen, Goettingen, Germany
    J Mol Evol 58:269-79. 2004
    ....
  27. ncbi request reprint Phylogenetic shadowing and computational identification of human microRNA genes
    Eugene Berezikov
    Cell 120:21-4. 2005
    ..Taken together, these results suggest the presence of significantly higher numbers of miRNAs in the human genome than previously estimated...
  28. pmc Functionally distinct regulatory RNAs generated by bidirectional transcription and processing of microRNA loci
    David M Tyler
    Department of Developmental Biology, Sloan Kettering Institute, New York, New York 10021, USA
    Genes Dev 22:26-36. 2008
    ..These findings demonstrate that antisense transcription and processing contributes to the functional diversification of miRNA genes...
  29. ncbi request reprint Exploring conservation of transcription factor binding sites with CONREAL
    Eugene Berezikov
    Hubrecht Laboratory
    Methods Mol Biol 395:437-48. 2007
    ..The web tool is particularly suited for the analysis of individual genes or genomic regions, although the underlying algorithm can also be used in high-throughput promoter analysis...
  30. pmc Genetic variation in the zebrafish
    Victor Guryev
    Hubrecht Laboratory, Netherlands Institute for Developmental Biology, 3584CT, Utrecht, The Netherlands
    Genome Res 16:491-7. 2006
    ..Overall, the levels and organization of genetic variation between and within commonly used zebrafish strains are markedly different from other laboratory model organisms, which may affect experimental design and interpretation...
  31. ncbi request reprint Detection of microRNAs in frozen tissue sections by fluorescence in situ hybridization using locked nucleic acid probes and tyramide signal amplification
    Asli N Silahtaroglu
    Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK 2200 Copenhagen N, Denmark
    Nat Protoc 2:2520-8. 2007
    ....
  32. ncbi request reprint LPIN2 is associated with type 2 diabetes, glucose metabolism, and body composition
    Yurii S Aulchenko
    Department of Epidemiology and Biostatistics, Erasmus Medical Centre Rotterdam, Postbus 2040, 3000 CA Rotterdam, Netherlands
    Diabetes 56:3020-6. 2007
    ..To identify the type 2 diabetes gene located at chromosome 18p11...
  33. ncbi request reprint A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in Zebrafish
    Saskia Houwing
    Hubrecht Laboratory, Uppsalalaan 8, Utrecht, Netherlands
    Cell 129:69-82. 2007
    ..Furthermore, we show that piRNAs are Dicer independent and that their 3' end likely carries a 2'O-Methyl modification...
  34. pmc Mouse microRNA profiles determined with a new and sensitive cloning method
    Shuji Takada
    Division of Functional Genomics, Jichi Medical University, 3311 1 Yakushiji, Shimotsukeshi, Tochigi 329 0498, Japan
    Nucleic Acids Res 34:e115. 2006
    ..Our data thus indicate that the total number of miRNAs in vertebrates is larger than previously appreciated and that the expression of these molecules is tightly controlled in a tissue- and developmental stage-specific manner...