Mihaela Zavolan

Computational and Systems Biology, University of Basel

Research Area

Biography

Mihaela Zavolan has not added Biography.
If you are Mihaela Zavolan and would like to personalize this page please email our Author Liaison for assistance.

JoVE Journal Publications

ArticleTotal : 2	Year
Publication title Cited by 267	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