Guryev, Victor, Berezikov, Eugene, Cuppen, Edwin
Abstract Background With the recent progress made in large-scale genome sequencing projects a vast amount of novel data is becoming available. A comparative sequence analysis, exploiting sequence...
Berezikov, Eugene, Bucheton, Alain, Busseau, Isabelle
Abstract Background Non-long terminal repeat (non-LTR) retrotransposons are eukaryotic mobile genetic elements that transpose by reverse transcription of an RNA intermediate. We have performed a...
Berezikov, Eugene, Guryev, Victor, Plasterk, Ronald H.A., Cuppen, Edwin
Prediction of transcription-factor target sites in promoters remains difficult due to the short length and degeneracy of the target sequences. Although the use of orthologous sequences and...
Homologous gene targeting in Caenorhabditis elegans by biolistic transformation
Berezikov, Eugene, Bargmann, Cornelia I., Plasterk, Ronald H. A.
Targeted homologous recombination is a powerful approach for genome manipulation that is widely used for gene alteration and knockouts in mouse and yeast. In Caenorhabditis elegans, several methods...
Single Nucleotide Polymorphisms Associated With Rat Expressed Sequences
Guryev, Victor, Berezikov, Eugene, Malik, Rainer, Plasterk, Ronald H.A., Cuppen, Edwin
Single nucleotide polymorphisms (SNPs) are the most common source of genetic variation in populations and are thus most likely to account for the majority of phenotypic and behavioral differences...
CONREAL web server: identification and visualization of conserved transcription factor binding sites
Berezikov, Eugene, Guryev, Victor, Cuppen, Edwin
The use of orthologous sequences and phylogenetic footprinting approaches have become popular for the recognition of conserved and potentially functional sequences. Several algorithms have been...
Genetic variation in the zebrafish
Guryev, Victor, Koudijs, Marco J., Berezikov, Eugene, Johnson, Stephen L., Plasterk, Ronald H.A., ...
Although zebrafish was introduced as a laboratory model organism several decades ago and now serves as a primary model for developmental biology, there is only limited data on its genetic variation....
Berezikov, Eugene, Guryev, Victor, Plasterk, Ronald H.A., Cuppen, Edwin
Prediction of transcription-factor target sites in promoters remains difficult due to the short length and degeneracy of the target sequences. Although the use of orthologous sequences and...
Homologous gene targeting in Caenorhabditis elegans by biolistic transformation
Berezikov, Eugene, Bargmann, Cornelia I., Plasterk, Ronald H. A.
Targeted homologous recombination is a powerful approach for genome manipulation that is widely used for gene alteration and knockouts in mouse and yeast. In Caenorhabditis elegans, several methods...
Single Nucleotide Polymorphisms Associated With Rat Expressed Sequences
Guryev, Victor, Berezikov, Eugene, Malik, Rainer, Plasterk, Ronald H.A., Cuppen, Edwin
Single nucleotide polymorphisms (SNPs) are the most common source of genetic variation in populations and are thus most likely to account for the majority of phenotypic and behavioral differences...
CONREAL web server: identification and visualization of conserved transcription factor binding sites
Berezikov, Eugene, Guryev, Victor, Cuppen, Edwin
The use of orthologous sequences and phylogenetic footprinting approaches have become popular for the recognition of conserved and potentially functional sequences. Several algorithms have been...
Genetic variation in the zebrafish
Guryev, Victor, Koudijs, Marco J., Berezikov, Eugene, Johnson, Stephen L., Plasterk, Ronald H.A., ...
Although zebrafish was introduced as a laboratory model organism several decades ago and now serves as a primary model for developmental biology, there is only limited data on its genetic variation....
Differences in vertebrate microRNA expression
Ason, Brandon, Darnell, Diana K., Wittbrodt, Beate, Berezikov, Eugene, Kloosterman, Wigard P., Wittbrodt, Jochen, ...
MicroRNAs (miRNAs) attenuate gene expression by means of translational inhibition and mRNA degradation. They are abundant, highly conserved, and predicted to regulate a large number of transcripts....
Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis
Berezikov, Eugene, Van Tetering, Geert, Verheul, Mark, Van De Belt, Jose, Van Laake, Linda, Vos, Joost, ...
MicroRNAs are 20- to 23-nucleotide RNA molecules that can regulate gene expression. Currently >400 microRNAs have been experimentally identified in mammalian genomes, whereas estimates go up to 1000...
Mouse microRNA profiles determined with a new and sensitive cloning method
Takada, Shuji, Berezikov, Eugene, Yamashita, Yoshihiro, Lagos-Quintana, Mariana, Kloosterman, Wigard P., Enomoto, Munehiro, ...
MicroRNAs (miRNAs) are noncoding RNA molecules of 21 to 24 nt that regulate the expression of target genes in a post-transcriptional manner. Although evidence indicates that miRNAs play essential...
Tyler, David M., Okamura, Katsutomo, Chung, Wei-Jen, Hagen, Joshua W., Berezikov, Eugene, Hannon, Gregory J., ...
Many microRNA (miRNA) loci exhibit compelling hairpin structures on both sense and antisense strands; however, the possibility that a miRNA gene might produce functional species from its antisense...