MirZ: an integrated microRNA expression atlas and target prediction resource (2009)
Hausser, Jean, Berninger, Philipp, Rodak, Christoph, Jantscher, Yvonne, Wirth, Stefan, Zavolan, Mihaela
MicroRNAs (miRNAs) are short RNAs that act as guides for the degradation and translational repression of protein-coding mRNAs. A large body of work showed that miRNAs are involved in the regulation...
Hausser, Jean, Landthaler, Markus, Jaskiewicz, Lukasz, Gaidatzis, Dimos, Zavolan, Mihaela
How miRNAs recognize their target sites is a puzzle that many experimental and computational studies aimed to solve. Several features, such as perfect pairing of the miRNA seed, additional pairing in...
Chern, Tzu-Ming, Paul, Nicodeme, Van Nimwegen, Erik, Zavolan, Mihaela
High-throughput sequencing studies revealed that the majority of human and mouse multi-exon genes have multiple splice forms. High-density oligonucleotide array-based measurements have further...
Chen, Po Yu, Weinmann, Lasse, Gaidatzis, Dimos, Pei, Yi, Zavolan, Mihaela, Tuschl, Thomas, ...
Small interfering RNAs (siRNAs) and microRNAs (miRNAs) guide catalytic sequence-specific cleavage of fully or nearly fully complementary target mRNAs or control translation and/or stability of many...
Landthaler, Markus, Gaidatzis, Dimos, Rothballer, Andrea, Chen, Po Yu, Soll, Steven Joseph, Dinic, Lana, ...
microRNAs (miRNAs) regulate the expression of mRNAs in animals and plants through miRNA-containing ribonucleoprotein particles (RNPs). At the core of these miRNA silencing effector complexes are the...
Correction: Inference of miRNA targets using evolutionary conservation and pathway analysis (2007)
Gaidatzis, Dimos, Van Nimwegen, Erik, Hausser, Jean, Zavolan, Mihaela
No abstract available.
Inference of miRNA targets using evolutionary conservation and pathway analysis (2007)
Gaidatzis, Dimos, Van Nimwegen, Erik, Hausser, Jean, Zavolan, Mihaela
Abstract Background MicroRNAs have emerged as important regulatory genes in a variety of cellular processes and, in recent years, hundreds of such genes have been discovered in animals. In contrast,...
Bmc Bioinformatics, Dimos Gaidatzis, Erik Van Nimwegen, Jean Hausser, Mihaela Zavolan
Inference of miRNA targets using evolutionary conservation and
A Simple Physical Model Predicts Small Exon Length Variations (2006)
Tzu-Ming Chern, Erik Van Nimwegen, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, ...
One of the most common splice variations are small exon length variations caused by the use of alternative donor or acceptor splice sites that are in very close proximity on the pre-mRNA. Among...
SPA: A Probabilistic Algorithm for Spliced Alignment (2006)
Erik Van Nimwegen, Nicodeme Paul, Robert Sheridan, Mihaela Zavolan
Recent large-scale cDNA sequencing efforts show that elaborate patterns of splice variation are responsible for much of the proteome diversity in higher eukaryotes. To obtain an accurate account of...
Effects of Dicer and Argonaute down-regulation on mRNA levels in human HEK293 cells (2006)
Schmitter, Daniela, Filkowski, Jody, Sewer, Alain, Pillai, Ramesh S., Oakeley, Edward J., Zavolan, Mihaela, ...
RNA interference and the microRNA (miRNA) pathway can induce sequence-specific mRNA degradation and/or translational repression. The human genome encodes hundreds of miRNAs that can...
Effects of Dicer and Argonaute down-regulation on mRNA levels in human HEK293 cells (2006)
Schmitter, Daniela, Filkowski, Jody, Sewer, Alain, Pillai, Ramesh S., Oakeley, Edward J., Zavolan, Mihaela, ...
RNA interference and the microRNA (miRNA) pathway can induce sequence-specific mRNA degradation and/or translational repression. The human genome encodes hundreds of miRNAs that can...
Effects of Dicer and Argonaute down-regulation on mRNA levels in human HEK293 cells (2006)
Schmitter, Daniela, Filkowski, Jody, Sewer, Alain, Pillai, Ramesh S., Oakeley, Edward J., Zavolan, Mihaela, ...
RNA interference and the microRNA (miRNA) pathway can induce sequence-specific mRNA degradation and/or translational repression. The human genome encodes hundreds of miRNAs that can...
Identification of clustered microRNAs using an ab initioprediction method (2005)
Sewer, Alain, Paul, Nicodème, Landgraf, Pablo, Aravin, Alexei, Pfeffer, Sébastien, Brownstein, Michael J, ...
Abstract Background MicroRNAs (miRNAs) are endogenous 21 to 23-nucleotide RNA molecules that regulate protein-coding gene expression in plants and animals via the RNA interference pathway. Hundreds...
The developmental miRNA profiles of zebrafish as determined by small RNA cloning (2005)
Chen, Po Yu, Manninga, Heiko, Slanchev, Krasimir, Chien, Minchen, Russo, James J., Ju, Jingyue, ...
MicroRNAs (miRNAs) represent a family of small, regulatory, noncoding RNAs that are found in plants and animals. Here, we describe the miRNA profile of the zebrafish Danio rerio resolved in a...
Systematic characterization of the zinc-finger-containing proteins in the mouse transcriptome (2003)
Ravasi, Timothy, Huber, Thomas, Zavolan, Mihaela, Forrest, Alistair Raymond Russell, Gaasterland, Terry, Grimmond, Sean M, ...
Zinc-finger-containing proteins can be classified into evolutionary and functionally divergent protein families that share one or more domains in which a zinc ion is tetrahedrally coordinated by...
Edward Yang, Erik Van Nimwegen, Mihaela Zavolan, Nikolaus Rajewsky, Mark Schroeder, James E. Darnell, ...
Access the most recent version at doi: 10.1101/gr.1272403
Systematic characterization of the zinc-finger-containing proteins in the mouse transcriptome (2003)
Ravasi, Timothy, Huber, Thomas, Zavolan, Mihaela, Forrest, Alistair Raymond Russell, Gaasterland, Terry, Grimmond, Sean M, ...
Zinc-finger-containing proteins can be classified into evolutionary and functionally divergent protein families that share one or more domains in which a zinc ion is tetrahedrally coordinated by...
Systematic characterization of the zinc-finger-containing proteins in the mouse transcriptome (2003)
Ravasi, Timothy, Huber, Thomas, Zavolan, Mihaela, Forrest, Alistair Raymond Russell, Gaasterland, Terry, Grimmond, Sean M, ...
Zinc-finger-containing proteins can be classified into evolutionary and functionally divergent protein families that share one or more domains in which a zinc ion is tetrahedrally coordinated by...
Zavolan, Mihaela, Kondo, Shinji, Schönbach, Christian, Adachi, Jun, Hume, David A., ...
We analyzed the FANTOM2 clone set of 60,770 RIKEN full-length mouse cDNA sequences and 44,122 public mRNA sequences. We developed a new computational procedure to identify and classify the forms of...
Systematic Characterization of the Zinc-Finger-Containing Proteins in the Mouse Transcriptome (2003)
Ravasi, Timothy, Huber, Thomas, Zavolan, Mihaela, Forrest, Alistair, Gaasterland, Terry, Grimmond, Sean, ...
Zinc-finger-containing proteins can be classified into evolutionary and functionally divergent protein families that share one or more domains in which a zinc ion is tetrahedrally coordinated by...
Yang, Edward, Van Nimwegen, Erik, Zavolan, Mihaela, Rajewsky, Nikolaus, Schroeder, Mark, Magnasco, Marcelo, ...
Although mRNA decay rates are a key determinant of the steady-state concentration for any given mRNA species, relatively little is known, on a population level, about what factors influence turnover...
Van Nimwegen, Erik, Zavolan, Mihaela, Rajewsky, Nikolaus, Siggia, Eric D.
Genome wide comparisons between enteric bacteria yield large sets of conserved putative regulatory sites on a gene by gene basis that need to be clustered into regulons. Using the assumption that...
Probabilistic clustering of sequences: Inferring new bacterial regulons by comparative genomics
Van Nimwegen, Erik, Zavolan, Mihaela, Rajewsky, Nikolaus, Siggia, Eric D.
Genome-wide comparisons between enteric bacteria yield large sets of conserved putative regulatory sites on a gene-by-gene basis that need to be clustered into regulons. Using the assumption that...
Splice Variation in Mouse Full-Length cDNAs Identified by Mapping to the Mouse Genome
Zavolan, Mihaela, Van Nimwegen, Erik, Gaasterland, Terry
We mapped the collection of The Institute of Physical and Chemical Research (Japan) (RIKEN) 21,076 full-length mouse cDNA clone sequences and the mouse RefSeq sequences to the recently completed...
Systematic Characterization of the Zinc-Finger-Containing Proteins in the Mouse Transcriptome
Ravasi, Timothy, Huber, Thomas, Zavolan, Mihaela, Forrest, Alistair, Gaasterland, Terry, Grimmond, Sean, ...
Zinc-finger-containing proteins can be classified into evolutionary and functionally divergent protein families that share one or more domains in which a zinc ion is tetrahedrally coordinated by...
Zavolan, Mihaela, Kondo, Shinji, Schönbach, Christian, Adachi, Jun, Hume, David A., Hayashizaki, Yoshihide, ...
We analyzed the FANTOM2 clone set of 60,770 RIKEN full-length mouse cDNA sequences and 44,122 public mRNA sequences. We developed a new computational procedure to identify and classify the forms of...
Decay Rates of Human mRNAs: Correlation With Functional Characteristics and Sequence Attributes
Yang, Edward, Van Nimwegen, Erik, Zavolan, Mihaela, Rajewsky, Nikolaus, Schroeder, Mark, Magnasco, Marcelo, ...
Although mRNA decay rates are a key determinant of the steady-state concentration for any given mRNA species, relatively little is known, on a population level, about what factors influence turnover...
Speirs, Christina, Van Nimwegen, Erik, Bolton, Diane, Zavolan, Mihaela, Duvall, Melody, Angleman, Sara, ...
Human immunodeficiency virus (HIV) causes complex metabolic changes in infected CD4+ T cells that lead to cell cycle arrest and cell death by necrosis. To study the viral functions responsible for...
The developmental miRNA profiles of zebrafish as determined by small RNA cloning
Chen, Po Yu, Manninga, Heiko, Slanchev, Krasimir, Chien, Minchen, Russo, James J., Ju, Jingyue, ...
MicroRNAs (miRNAs) represent a family of small, regulatory, noncoding RNAs that are found in plants and animals. Here, we describe the miRNA profile of the zebrafish Danio rerio resolved in a...
Identification of clustered microRNAs using an ab initio prediction method
Sewer, Alain, Paul, Nicodème, Landgraf, Pablo, Aravin, Alexei, Pfeffer, Sébastien, Brownstein, Michael J, ...
SPA: A Probabilistic Algorithm for Spliced Alignment
Van Nimwegen, Erik, Paul, Nicodeme, Sheridan, Robert, Zavolan, Mihaela
Recent large-scale cDNA sequencing efforts show that elaborate patterns of splice variation are responsible for much of the proteome diversity in higher eukaryotes. To obtain an accurate account of...
A Simple Physical Model Predicts Small Exon Length Variations
Chern, Tzu-Ming, Van Nimwegen, Erik, Kai, Chikatoshi, Kawai, Jun, Carninci, Piero, Hayashizaki, Yoshihide, ...
One of the most common splice variations are small exon length variations caused by the use of alternative donor or acceptor splice sites that are in very close proximity on the pre-mRNA. Among...
Cell-type-specific signatures of microRNAs on target mRNA expression
Sood, Pranidhi, Krek, Azra, Zavolan, Mihaela, Macino, Giuseppe, Rajewsky, Nikolaus
Although it is known that the human genome contains hundreds of microRNA (miRNA) genes and that each miRNA can regulate a large number of mRNA targets, the overall effect of miRNAs on mRNA tissue...
Probabilistic clustering of sequences: Inferring new bacterial regulons by comparative genomics
Van Nimwegen, Erik, Zavolan, Mihaela, Rajewsky, Nikolaus, Siggia, Eric D.
Genome-wide comparisons between enteric bacteria yield large sets of conserved putative regulatory sites on a gene-by-gene basis that need to be clustered into regulons. Using the assumption that...
Splice Variation in Mouse Full-Length cDNAs Identified by Mapping to the Mouse Genome
Zavolan, Mihaela, Van Nimwegen, Erik, Gaasterland, Terry
We mapped the collection of The Institute of Physical and Chemical Research (Japan) (RIKEN) 21,076 full-length mouse cDNA clone sequences and the mouse RefSeq sequences to the recently completed...
Systematic Characterization of the Zinc-Finger-Containing Proteins in the Mouse Transcriptome
Ravasi, Timothy, Huber, Thomas, Zavolan, Mihaela, Forrest, Alistair, Gaasterland, Terry, Grimmond, Sean, ...
Zinc-finger-containing proteins can be classified into evolutionary and functionally divergent protein families that share one or more domains in which a zinc ion is tetrahedrally coordinated by...
Zavolan, Mihaela, Kondo, Shinji, Schönbach, Christian, Adachi, Jun, Hume, David A., Hayashizaki, Yoshihide, ...
We analyzed the FANTOM2 clone set of 60,770 RIKEN full-length mouse cDNA sequences and 44,122 public mRNA sequences. We developed a new computational procedure to identify and classify the forms of...
Decay Rates of Human mRNAs: Correlation With Functional Characteristics and Sequence Attributes
Yang, Edward, Van Nimwegen, Erik, Zavolan, Mihaela, Rajewsky, Nikolaus, Schroeder, Mark, Magnasco, Marcelo, ...
Although mRNA decay rates are a key determinant of the steady-state concentration for any given mRNA species, relatively little is known, on a population level, about what factors influence turnover...
Speirs, Christina, Van Nimwegen, Erik, Bolton, Diane, Zavolan, Mihaela, Duvall, Melody, Angleman, Sara, ...
Human immunodeficiency virus (HIV) causes complex metabolic changes in infected CD4+ T cells that lead to cell cycle arrest and cell death by necrosis. To study the viral functions responsible for...
The developmental miRNA profiles of zebrafish as determined by small RNA cloning
Chen, Po Yu, Manninga, Heiko, Slanchev, Krasimir, Chien, Minchen, Russo, James J., Ju, Jingyue, ...
MicroRNAs (miRNAs) represent a family of small, regulatory, noncoding RNAs that are found in plants and animals. Here, we describe the miRNA profile of the zebrafish Danio rerio resolved in a...
Identification of clustered microRNAs using an ab initio prediction method
Sewer, Alain, Paul, Nicodème, Landgraf, Pablo, Aravin, Alexei, Pfeffer, Sébastien, Brownstein, Michael J, ...
Cell-type-specific signatures of microRNAs on target mRNA expression
Sood, Pranidhi, Krek, Azra, Zavolan, Mihaela, Macino, Giuseppe, Rajewsky, Nikolaus
Although it is known that the human genome contains hundreds of microRNA (miRNA) genes and that each miRNA can regulate a large number of mRNA targets, the overall effect of miRNAs on mRNA tissue...
SPA: A Probabilistic Algorithm for Spliced Alignment
Van Nimwegen, Erik, Paul, Nicodeme, Sheridan, Robert, Zavolan, Mihaela
Recent large-scale cDNA sequencing efforts show that elaborate patterns of splice variation are responsible for much of the proteome diversity in higher eukaryotes. To obtain an accurate account of...
A Simple Physical Model Predicts Small Exon Length Variations
Chern, Tzu-Ming, Van Nimwegen, Erik, Kai, Chikatoshi, Kawai, Jun, Carninci, Piero, Hayashizaki, Yoshihide, ...
One of the most common splice variations are small exon length variations caused by the use of alternative donor or acceptor splice sites that are in very close proximity on the pre-mRNA. Among...
Inference of miRNA targets using evolutionary conservation and pathway analysis
Gaidatzis, Dimos, Van Nimwegen, Erik, Hausser, Jean, Zavolan, Mihaela
Inference of miRNA targets using evolutionary conservation and pathway analysis
Gaidatzis, Dimos, Van Nimwegen, Erik, Hausser, Jean, Zavolan, Mihaela
Effects of Dicer and Argonaute down-regulation on mRNA levels in human HEK293 cells
Schmitter, Daniela, Filkowski, Jody, Sewer, Alain, Pillai, Ramesh S., Oakeley, Edward J., Zavolan, Mihaela, ...
RNA interference and the microRNA (miRNA) pathway can induce sequence-specific mRNA degradation and/or translational repression. The human genome encodes hundreds of miRNAs that can...
Yao, Yongxiu, Zhao, Yuguang, Xu, Hongtao, Smith, Lorraine P., Lawrie, Charles H., Sewer, Alain, ...
MicroRNAs (miRNAs) are increasingly being recognized as major regulators of gene expression in many organisms, including viruses. Among viruses, members of the family Herpesviridae account for the...
Cellular cofactors affecting hepatitis C virus infection and replication
Randall, Glenn, Panis, Maryline, Cooper, Jacob D., Tellinghuisen, Timothy L., Sukhodolets, Karen E., Pfeffer, Sebastien, ...
Recently identified hepatitis C virus (HCV) isolates that are infectious in cell culture provide a genetic system to evaluate the significance of virus–host interactions for HCV replication. We...
Chen, Po Yu, Weinmann, Lasse, Gaidatzis, Dimos, Pei, Yi, Zavolan, Mihaela, Tuschl, Thomas, ...
Small interfering RNAs (siRNAs) and microRNAs (miRNAs) guide catalytic sequence-specific cleavage of fully or nearly fully complementary target mRNAs or control translation and/or stability of many...
Galgano, Alessia, Forrer, Michael, Jaskiewicz, Lukasz, Kanitz, Alexander, Zavolan, Mihaela, Gerber, André P.
Genome-wide identification of mRNAs regulated by RNA-binding proteins is crucial to uncover post-transcriptional gene regulatory systems. The conserved PUF family RNA-binding proteins repress gene...
Connolly, Erin, Melegari, Margherita, Landgraf, Pablo, Tchaikovskaya, Tatyana, Tennant, Bud C., Slagle, Betty L., ...
Alterations in microRNA (miRNA) expression in both human and animal models have been linked to many forms of cancer. Such miRNAs, which act directly as repressors of gene expression, have been found...
Chern, Tzu-Ming, Paul, Nicodeme, Van Nimwegen, Erik, Zavolan, Mihaela
High-throughput sequencing studies revealed that the majority of human and mouse multi-exon genes have multiple splice forms. High-density oligonucleotide array-based measurements have further...
Landthaler, Markus, Gaidatzis, Dimos, Rothballer, Andrea, Chen, Po Yu, Soll, Steven Joseph, Dinic, Lana, ...
microRNAs (miRNAs) regulate the expression of mRNAs in animals and plants through miRNA-containing ribonucleoprotein particles (RNPs). At the core of these miRNA silencing effector complexes are the...
miR-375 maintains normal pancreatic α- and β-cell mass
Poy, Matthew N., Hausser, Jean, Trajkovski, Mirko, Braun, Matthias, Collins, Stephan, Rorsman, Patrik, ...
Altered growth and development of the endocrine pancreas is a frequent cause of the hyperglycemia associated with diabetes. Here we show that microRNA-375 (miR-375), which is highly expressed in...
MirZ: an integrated microRNA expression atlas and target prediction resource
Hausser, Jean, Berninger, Philipp, Rodak, Christoph, Jantscher, Yvonne, Wirth, Stefan, Zavolan, Mihaela
MicroRNAs (miRNAs) are short RNAs that act as guides for the degradation and translational repression of protein-coding mRNAs. A large body of work showed that miRNAs are involved in the regulation...
Expression and Processing of a Small Nucleolar RNA from the Epstein-Barr Virus Genome
Hutzinger, Roland, Feederle, Regina, Mrazek, Jan, Schiefermeier, Natalia, Balwierz, Piotr J., Zavolan, Mihaela, ...
Small nucleolar RNAs (snoRNAs) are localized within the nucleolus, a sub-nuclear compartment, in which they guide ribosomal or spliceosomal RNA modifications, respectively. Up until now, snoRNAs have...