Mihaela Zavolan

Biozentrum der Universität Basel and Swiss Institute of Bioinformatics (SIB)

Affiliated withBiozentrum der Universität Basel and Swiss Institute of Bioinformatics (SIB)University of Basel

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JoVE Journal Publications

ArticleTotal : 2	Year
Publication title Cited by 264	2010
Publication title Cited by 9	2017

Other Publications

Article	Year
Probabilistic clustering of sequences: inferring new bacterial regulons by comparative genomics. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 12032281	2002
Splice variation in mouse full-length cDNAs identified by mapping to the mouse genome. Genome research\| PubMed ID: 12213775	2002
Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome. Genome research\| PubMed ID: 12819126	2003
Systematic characterization of the zinc-finger-containing proteins in the mouse transcriptome. Genome research\| PubMed ID: 12819142	2003
Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes. Genome research\| PubMed ID: 12902380	2003
The small RNA profile during Drosophila melanogaster development. Developmental cell\| PubMed ID: 12919683	2003
Identification of virus-encoded microRNAs. Science (New York, N.Y.)\| PubMed ID: 15118162	2004
Analysis of human immunodeficiency virus cytopathicity by using a new method for quantitating viral dynamics in cell culture. Journal of virology\| PubMed ID: 15767404	2005
Identification of microRNAs of the herpesvirus family. Nature methods\| PubMed ID: 15782219	2005
The developmental miRNA profiles of zebrafish as determined by small RNA cloning. Genes & development\| PubMed ID: 15937218	2005
Identification of clustered microRNAs using an ab initio prediction method. BMC bioinformatics\| PubMed ID: 16274478	2005
SMASHing regulatory sites in DNA by human-mouse sequence comparisons. Proceedings / IEEE Computer Society Bioinformatics Conference. IEEE Computer Society Bioinformatics Conference\| PubMed ID: 16452803	2003
Cell-type-specific signatures of microRNAs on target mRNA expression. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 16477010	2006
Virus-encoded microRNAs: novel regulators of gene expression. Trends in microbiology\| PubMed ID: 16531046	2006
SPA: a probabilistic algorithm for spliced alignment. PLoS genetics\| PubMed ID: 16683023	2006
A simple physical model predicts small exon length variations. PLoS genetics\| PubMed ID: 16683028	2006
The types and prevalence of alternative splice forms. Current opinion in structural biology\| PubMed ID: 16713247	2006
A novel class of small RNAs bind to MILI protein in mouse testes. Nature\| PubMed ID: 16751777	2006
Effects of Dicer and Argonaute down-regulation on mRNA levels in human HEK293 cells. Nucleic acids research\| PubMed ID: 16971455	2006
Quantitative technologies establish a novel microRNA profile of chronic lymphocytic leukemia. Blood\| PubMed ID: 17327404	2007
Inference of miRNA targets using evolutionary conservation and pathway analysis. BMC bioinformatics\| PubMed ID: 17331257	2007
Marek's disease virus type 2 (MDV-2)-encoded microRNAs show no sequence conservation with those encoded by MDV-1. Journal of virology\| PubMed ID: 17459919	2007
A mammalian microRNA expression atlas based on small RNA library sequencing. Cell\| PubMed ID: 17604727	2007
Cellular cofactors affecting hepatitis C virus infection and replication. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 17616579	2007
Regulation of human liver delta-aminolevulinic acid synthase by bile acids. Hepatology (Baltimore, Md.)\| PubMed ID: 17975826	2007
Strand-specific 5'-O-methylation of siRNA duplexes controls guide strand selection and targeting specificity. RNA (New York, N.Y.)\| PubMed ID: 18094121	2008
Computational analysis of small RNA cloning data. Methods (San Diego, Calif.)\| PubMed ID: 18158128	2008
Computational analysis of full-length cDNAs reveals frequent coupling between transcriptional and splicing programs. DNA research : an international journal for rapid publication of reports on genes and genomes\| PubMed ID: 18276623	2008
MicroRNAs control de novo DNA methylation through regulation of transcriptional repressors in mouse embryonic stem cells. Nature structural & molecular biology\| PubMed ID: 18311153	2008
Elevated expression of the miR-17-92 polycistron and miR-21 in hepadnavirus-associated hepatocellular carcinoma contributes to the malignant phenotype. The American journal of pathology\| PubMed ID: 18688024	2008
Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system. PloS one\| PubMed ID: 18776931	2008
Molecular characterization of human Argonaute-containing ribonucleoprotein complexes and their bound target mRNAs. RNA (New York, N.Y.)\| PubMed ID: 18978028	2008
miRNA in situ hybridization in formaldehyde and EDC-fixed tissues. Nature methods\| PubMed ID: 19137005	2009
miR-375 maintains normal pancreatic alpha- and beta-cell mass. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 19289822	2009
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature genetics\| PubMed ID: 19377474	2009
MirZ: an integrated microRNA expression atlas and target prediction resource. Nucleic acids research\| PubMed ID: 19468042	2009
Expression and processing of a small nucleolar RNA from the Epstein-Barr virus genome. PLoS pathogens\| PubMed ID: 19680535	2009
Relative contribution of sequence and structure features to the mRNA binding of Argonaute/EIF2C-miRNA complexes and the degradation of miRNA targets. Genome research\| PubMed ID: 19767416	2009
The snoRNA MBII-52 (SNORD 115) is processed into smaller RNAs and regulates alternative splicing. Human molecular genetics\| PubMed ID: 20053671	2010
MicroRNA activity is suppressed in mouse oocytes. Current biology : CB\| PubMed ID: 20116252	2010
Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell\| PubMed ID: 20371350	2010
Expression proteomics of UPF1 knockdown in HeLa cells reveals autoregulation of hnRNP A2/B1 mediated by alternative splicing resulting in nonsense-mediated mRNA decay. BMC genomics\| PubMed ID: 20946641	2010
Analysis of in situ pre-mRNA targets of human splicing factor SF1 reveals a function in alternative splicing. Nucleic acids research\| PubMed ID: 21062807	2011
CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins. Nucleic acids research\| PubMed ID: 21087992	2011
Deciphering the role of RNA-binding proteins in the post-transcriptional control of gene expression. Briefings in functional genomics\| PubMed ID: 21127008	2010
Conserved generation of short products at piRNA loci. BMC genomics\| PubMed ID: 21247452	2011
A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins. Nature methods\| PubMed ID: 21572407	2011
MicroRNAs 103 and 107 regulate insulin sensitivity. Nature\| PubMed ID: 21654750	2011
PAPD5, a noncanonical poly(A) polymerase with an unusual RNA-binding motif. RNA (New York, N.Y.)\| PubMed ID: 21788334	2011
MicroRNA-194 is a target of transcription factor 1 (Tcf1, HNF1Î±) in adult liver and controls expression of frizzled-6. Hepatology (Baltimore, Md.)\| PubMed ID: 21887698	2012
Kaposi's sarcoma herpesvirus microRNAs target caspase 3 and regulate apoptosis. PLoS pathogens\| PubMed ID: 22174674	2011
Genome-wide analysis of pre-mRNA 3' end processing reveals a decisive role of human cleavage factor I in the regulation of 3' UTR length. Cell reports\| PubMed ID: 22813749	2012
Argonaute CLIP--a method to identify in vivo targets of miRNAs. Methods (San Diego, Calif.)\| PubMed ID: 23022257	2012
Dicer partners expand the repertoire of miRNA targets. Genome biology\| PubMed ID: 23194401	2012
A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets. Nature methods\| PubMed ID: 23334102	2013
Analysis of CDS-located miRNA target sites suggests that they can effectively inhibit translation. Genome research\| PubMed ID: 23335364	2013
Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing. Genome biology\| PubMed ID: 23706177	2013
Translation-dependent displacement of UPF1 from coding sequences causes its enrichment in 3' UTRs. Nature structural & molecular biology\| PubMed ID: 23832275	2013
Modeling the binding specificity of the RNA-binding protein GLD-1 suggests a function of coding region-located sites in translational repression. RNA (New York, N.Y.)\| PubMed ID: 23974436	2013
3'-UTR poly(T/U) tract deletions and altered expression of EWSR1 are a hallmark of mismatch repair-deficient cancers. Cancer research\| PubMed ID: 24158095	2014
Means to an end: mechanisms of alternative polyadenylation of messenger RNA precursors. Wiley interdisciplinary reviews. RNA\| PubMed ID: 24243805	2014
Modulation of epigenetic regulators and cell fate decisions by miRNAs. Epigenomics\| PubMed ID: 24283881	2013
Timescales and bottlenecks in miRNA-dependent gene regulation. Molecular systems biology\| PubMed ID: 24301800	2013
Argonaute2 mediates compensatory expansion of the pancreatic β cell. Cell metabolism\| PubMed ID: 24361012	2014
TSSer: an automated method to identify transcription start sites in prokaryotic genomes from differential RNA sequencing data. Bioinformatics (Oxford, England)\| PubMed ID: 24371151	2014
Seq and CLIP through the miRNA world. Genome biology\| PubMed ID: 24460822	2014
ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs. Genome research\| PubMed ID: 24515121	2014
PAR-CLIP (Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation): a step-by-step protocol to the transcriptome-wide identification of binding sites of RNA-binding pro... Methods in enzymology\| PubMed ID: 24581442	2014
Widespread context dependency of microRNA-mediated regulation. Genome research\| PubMed ID: 24668909	2014
MicroRNA-7a regulates pancreatic β cell function. The Journal of clinical investigation\| PubMed ID: 24789908	2014
Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support. Nucleic acids research\| PubMed ID: 24792157	2014
Structural and functional implications of the QUA2 domain on RNA recognition by GLD-1. Nucleic acids research\| PubMed ID: 24838563	2014
Identification and consequences of miRNA-target interactions--beyond repression of gene expression. Nature reviews. Genetics\| PubMed ID: 25022902	2014
Embryonic stem cell-specific microRNAs contribute to pluripotency by inhibiting regulators of multiple differentiation pathways. Nucleic acids research\| PubMed ID: 25030899	2014
Reconstitution of CPSF active in polyadenylation: recognition of the polyadenylation signal by WDR33. Genes & development\| PubMed ID: 25301781	2014
Global 3' UTR shortening has a limited effect on protein abundance in proliferating T cells. Nature communications\| PubMed ID: 25413384	2014
miR-CLIP capture of a miRNA targetome uncovers a lincRNA H19-miR-106a interaction. Nature chemical biology\| PubMed ID: 25531890	2015
Accurate transcriptome-wide prediction of microRNA targets and small interfering RNA off-targets with MIRZA-G. Nucleic acids research\| PubMed ID: 25628353	2015
Reflections on the RNA world. RNA (New York, N.Y.)\| PubMed ID: 25780126	2015
Quantifying the strength of miRNA-target interactions. Methods (San Diego, Calif.)\| PubMed ID: 25892562	2015
miR-184 Regulates Pancreatic β-Cell Function According to Glucose Metabolism. The Journal of biological chemistry\| PubMed ID: 26152724	2015
Inferring gene expression regulatory networks from high-throughput measurements. Methods (San Diego, Calif.)\| PubMed ID: 26188125	2015
Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data. Genome biology\| PubMed ID: 26201343	2015
Cooperative target mRNA destabilization and translation inhibition by miR-58 microRNA family in C. elegans. Genome research\| PubMed ID: 26232411	2015
Accurate transcriptome-wide prediction of microRNA targets and small interfering RNA off-targets with MIRZA-G. Nucleic acids research\| PubMed ID: 26365243	2015
Roquin recognizes a non-canonical hexaloop structure in the 3'-UTR of Ox40. Nature communications\| PubMed ID: 27010430	2016
An updated human snoRNAome. Nucleic acids research\| PubMed ID: 27174936	2016
Redesigning CLIP for efficiency, accuracy and speed. Nature methods\| PubMed ID: 27243472	2016
Corrigendum to "Quantifying the strength of miRNA-target interactions" [Methods (2015) 90-99]. Methods (San Diego, Calif.)\| PubMed ID: 27372217	2016
A comprehensive analysis of 3' end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation. Genome research\| PubMed ID: 27382025	2016
TUT-DIS3L2 is a mammalian surveillance pathway for aberrant structured non-coding RNAs. The EMBO journal\| PubMed ID: 27647875	2016
Patterns of ribosomal protein expression specify normal and malignant human cells. Genome biology\| PubMed ID: 27884178	2016
High-throughput identification of C/D box snoRNA targets with CLIP and RiboMeth-seq. Nucleic acids research\| PubMed ID: 28031372	2017
Explicit Modeling of siRNA-Dependent On- and Off-Target Repression Improves the Interpretation of Screening Results. Cell systems\| PubMed ID: 28215525	2017
TFAP2A is a component of the ZEB1/2 network that regulates TGFB1-induced epithelial to mesenchymal transition. Biology direct\| PubMed ID: 28412966	2017
Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors. PLoS computational biology\| PubMed ID: 28753602	2017
The Gcn4 transcription factor reduces protein synthesis capacity and extends yeast lifespan. Nature communications\| PubMed ID: 28878244	2017