Mihaela Zavolan Computational and Systems Biology, Biozentrum University of Basel Biography Publications Institution JoVE Articles Mihaela Zavolan has not added a biography. If you are Mihaela Zavolan and would like to personalize this page please email our Author Liaison for assistance. Publications The Gcn4 Transcription Factor Reduces Protein Synthesis Capacity and Extends Yeast Lifespan Nature Communications. Sep, 2017 | Pubmed ID: 28878244 Automated Incorporation of Pairwise Dependency in Transcription Factor Binding Site Prediction Using Dinucleotide Weight Tensors PLoS Computational Biology. Jul, 2017 | Pubmed ID: 28753602 TFAP2A is a Component of the ZEB1/2 Network That Regulates TGFB1-induced Epithelial to Mesenchymal Transition Biology Direct. Apr, 2017 | Pubmed ID: 28412966 Explicit Modeling of SiRNA-Dependent On- and Off-Target Repression Improves the Interpretation of Screening Results Cell Systems. Feb, 2017 | Pubmed ID: 28215525 High-throughput Identification of C/D Box SnoRNA Targets with CLIP and RiboMeth-seq Nucleic Acids Research. Mar, 2017 | Pubmed ID: 28031372 Patterns of Ribosomal Protein Expression Specify Normal and Malignant Human Cells Genome Biology. Nov, 2016 | Pubmed ID: 27884178 TUT-DIS3L2 is a Mammalian Surveillance Pathway for Aberrant Structured Non-coding RNAs The EMBO Journal. Oct, 2016 | Pubmed ID: 27647875 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. 08, 2016 | Pubmed ID: 27382025 Corrigendum to "Quantifying the Strength of MiRNA-target Interactions" [Methods (2015) 90-99] Methods (San Diego, Calif.). Jul, 2016 | Pubmed ID: 27372217 Redesigning CLIP for Efficiency, Accuracy and Speed Nature Methods. May, 2016 | Pubmed ID: 27243472 An Updated Human SnoRNAome Nucleic Acids Research. Jun, 2016 | Pubmed ID: 27174936 Roquin Recognizes a Non-canonical Hexaloop Structure in the 3'-UTR of Ox40 Nature Communications. Mar, 2016 | Pubmed ID: 27010430 Accurate Transcriptome-wide Prediction of MicroRNA Targets and Small Interfering RNA Off-targets with MIRZA-G Nucleic Acids Research. Oct, 2015 | Pubmed ID: 26365243 Cooperative Target MRNA Destabilization and Translation Inhibition by MiR-58 MicroRNA Family in C. Elegans Genome Research. Nov, 2015 | Pubmed ID: 26232411 Comparative Assessment of Methods for the Computational Inference of Transcript Isoform Abundance from RNA-seq Data Genome Biology. Jul, 2015 | Pubmed ID: 26201343 Inferring Gene Expression Regulatory Networks from High-throughput Measurements Methods (San Diego, Calif.). Sep, 2015 | Pubmed ID: 26188125 MiR-184 Regulates Pancreatic β-Cell Function According to Glucose Metabolism The Journal of Biological Chemistry. Aug, 2015 | Pubmed ID: 26152724 Quantifying the Strength of MiRNA-target Interactions Methods (San Diego, Calif.). Sep, 2015 | Pubmed ID: 25892562 Reflections on the RNA World RNA (New York, N.Y.). Apr, 2015 | Pubmed ID: 25780126 Accurate Transcriptome-wide Prediction of MicroRNA Targets and Small Interfering RNA Off-targets with MIRZA-G Nucleic Acids Research. Feb, 2015 | Pubmed ID: 25628353 MiR-CLIP Capture of a MiRNA Targetome Uncovers a LincRNA H19-miR-106a Interaction Nature Chemical Biology. Feb, 2015 | Pubmed ID: 25531890 Global 3' UTR Shortening Has a Limited Effect on Protein Abundance in Proliferating T Cells Nature Communications. 2014 | Pubmed ID: 25413384 Reconstitution of CPSF Active in Polyadenylation: Recognition of the Polyadenylation Signal by WDR33 Genes & Development. Nov, 2014 | Pubmed ID: 25301781 Embryonic Stem Cell-specific MicroRNAs Contribute to Pluripotency by Inhibiting Regulators of Multiple Differentiation Pathways Nucleic Acids Research. Aug, 2014 | Pubmed ID: 25030899 Identification and Consequences of MiRNA-target Interactions--beyond Repression of Gene Expression Nature Reviews. Genetics. Sep, 2014 | Pubmed ID: 25022902 Structural and Functional Implications of the QUA2 Domain on RNA Recognition by GLD-1 Nucleic Acids Research. Jul, 2014 | Pubmed ID: 24838563 Fifteen Years SIB Swiss Institute of Bioinformatics: Life Science Databases, Tools and Support Nucleic Acids Research. Jul, 2014 | Pubmed ID: 24792157 MicroRNA-7a Regulates Pancreatic β Cell Function The Journal of Clinical Investigation. Jun, 2014 | Pubmed ID: 24789908 Widespread Context Dependency of MicroRNA-mediated Regulation Genome Research. Jun, 2014 | Pubmed ID: 24668909 PAR-CLIP (Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation): a Step-by-step Protocol to the Transcriptome-wide Identification of Binding Sites of RNA-binding Proteins Methods in Enzymology. 2014 | Pubmed ID: 24581442 ISMARA: Automated Modeling of Genomic Signals As a Democracy of Regulatory Motifs Genome Research. May, 2014 | Pubmed ID: 24515121 Seq and CLIP Through the MiRNA World Genome Biology. Jan, 2014 | Pubmed ID: 24460822 TSSer: an Automated Method to Identify Transcription Start Sites in Prokaryotic Genomes from Differential RNA Sequencing Data Bioinformatics (Oxford, England). Apr, 2014 | Pubmed ID: 24371151 Argonaute2 Mediates Compensatory Expansion of the Pancreatic β Cell Cell Metabolism. Jan, 2014 | Pubmed ID: 24361012 Means to an End: Mechanisms of Alternative Polyadenylation of Messenger RNA Precursors Wiley Interdisciplinary Reviews. RNA. Mar-Apr, 2014 | Pubmed ID: 24243805 3'-UTR Poly(T/U) Tract Deletions and Altered Expression of EWSR1 Are a Hallmark of Mismatch Repair-deficient Cancers Cancer Research. Jan, 2014 | Pubmed ID: 24158095 Timescales and Bottlenecks in MiRNA-dependent Gene Regulation Molecular Systems Biology. Dec, 2013 | Pubmed ID: 24301800 Modulation of Epigenetic Regulators and Cell Fate Decisions by MiRNAs Epigenomics. Dec, 2013 | Pubmed ID: 24283881 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.). Oct, 2013 | Pubmed ID: 23974436 Translation-dependent Displacement of UPF1 from Coding Sequences Causes Its Enrichment in 3' UTRs Nature Structural & Molecular Biology. Aug, 2013 | Pubmed ID: 23832275 Insights into SnoRNA Biogenesis and Processing from PAR-CLIP of SnoRNA Core Proteins and Small RNA Sequencing Genome Biology. May, 2013 | Pubmed ID: 23706177 Analysis of CDS-located MiRNA Target Sites Suggests That They Can Effectively Inhibit Translation Genome Research. Apr, 2013 | Pubmed ID: 23335364 A Biophysical MiRNA-mRNA Interaction Model Infers Canonical and Noncanonical Targets Nature Methods. Mar, 2013 | Pubmed ID: 23334102 Dicer Partners Expand the Repertoire of MiRNA Targets Genome Biology. Nov, 2012 | Pubmed ID: 23194401 Argonaute CLIP--a Method to Identify in Vivo Targets of MiRNAs Methods (San Diego, Calif.). Oct, 2012 | Pubmed ID: 23022257 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. Jun, 2012 | Pubmed ID: 22813749 MicroRNA-194 is a Target of Transcription Factor 1 (Tcf1, HNF1α) in Adult Liver and Controls Expression of Frizzled-6 Hepatology (Baltimore, Md.). Jan, 2012 | Pubmed ID: 21887698 Kaposi's Sarcoma Herpesvirus MicroRNAs Target Caspase 3 and Regulate Apoptosis PLoS Pathogens. Dec, 2011 | Pubmed ID: 22174674 PAPD5, a Noncanonical Poly(A) Polymerase with an Unusual RNA-binding Motif RNA (New York, N.Y.). Sep, 2011 | Pubmed ID: 21788334 MicroRNAs 103 and 107 Regulate Insulin Sensitivity Nature. Jun, 2011 | Pubmed ID: 21654750 A Quantitative Analysis of CLIP Methods for Identifying Binding Sites of RNA-binding Proteins Nature Methods. Jul, 2011 | Pubmed ID: 21572407 Conserved Generation of Short Products at PiRNA Loci BMC Genomics. 2011 | Pubmed ID: 21247452 CLIPZ: a Database and Analysis Environment for Experimentally Determined Binding Sites of RNA-binding Proteins Nucleic Acids Research. Jan, 2011 | Pubmed ID: 21087992 Analysis of in Situ Pre-mRNA Targets of Human Splicing Factor SF1 Reveals a Function in Alternative Splicing Nucleic Acids Research. Mar, 2011 | Pubmed ID: 21062807 Deciphering the Role of RNA-binding Proteins in the Post-transcriptional Control of Gene Expression Briefings in Functional Genomics. Dec, 2010 | Pubmed ID: 21127008 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. 2010 | Pubmed ID: 20946641 Transcriptome-wide Identification of RNA-binding Protein and MicroRNA Target Sites by PAR-CLIP Cell. Apr, 2010 | Pubmed ID: 20371350 MicroRNA Activity is Suppressed in Mouse Oocytes Current Biology : CB. Feb, 2010 | Pubmed ID: 20116252 The SnoRNA MBII-52 (SNORD 115) is Processed into Smaller RNAs and Regulates Alternative Splicing Human Molecular Genetics. Apr, 2010 | Pubmed ID: 20053671 Relative Contribution of Sequence and Structure Features to the MRNA Binding of Argonaute/EIF2C-miRNA Complexes and the Degradation of MiRNA Targets Genome Research. Nov, 2009 | Pubmed ID: 19767416 Expression and Processing of a Small Nucleolar RNA from the Epstein-Barr Virus Genome PLoS Pathogens. Aug, 2009 | Pubmed ID: 19680535 MirZ: an Integrated MicroRNA Expression Atlas and Target Prediction Resource Nucleic Acids Research. Jul, 2009 | Pubmed ID: 19468042 The Transcriptional Network That Controls Growth Arrest and Differentiation in a Human Myeloid Leukemia Cell Line Nature Genetics. May, 2009 | Pubmed ID: 19377474 MiR-375 Maintains Normal Pancreatic Alpha- and Beta-cell Mass Proceedings of the National Academy of Sciences of the United States of America. Apr, 2009 | Pubmed ID: 19289822 MiRNA in Situ Hybridization in Formaldehyde and EDC-fixed Tissues Nature Methods. Feb, 2009 | Pubmed ID: 19137005 Molecular Characterization of Human Argonaute-containing Ribonucleoprotein Complexes and Their Bound Target MRNAs RNA (New York, N.Y.). Dec, 2008 | Pubmed ID: 18978028 Comparative Analysis of MRNA Targets for Human PUF-family Proteins Suggests Extensive Interaction with the MiRNA Regulatory System PloS One. 2008 | Pubmed ID: 18776931 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. Sep, 2008 | Pubmed ID: 18688024 MicroRNAs Control De Novo DNA Methylation Through Regulation of Transcriptional Repressors in Mouse Embryonic Stem Cells Nature Structural & Molecular Biology. Mar, 2008 | Pubmed ID: 18311153 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. Apr, 2008 | Pubmed ID: 18276623 Computational Analysis of Small RNA Cloning Data Methods (San Diego, Calif.). Jan, 2008 | Pubmed ID: 18158128 Strand-specific 5'-O-methylation of SiRNA Duplexes Controls Guide Strand Selection and Targeting Specificity RNA (New York, N.Y.). Feb, 2008 | Pubmed ID: 18094121 Regulation of Human Liver Delta-aminolevulinic Acid Synthase by Bile Acids Hepatology (Baltimore, Md.). Dec, 2007 | Pubmed ID: 17975826 Cellular Cofactors Affecting Hepatitis C Virus Infection and Replication Proceedings of the National Academy of Sciences of the United States of America. Jul, 2007 | Pubmed ID: 17616579 A Mammalian MicroRNA Expression Atlas Based on Small RNA Library Sequencing Cell. Jun, 2007 | Pubmed ID: 17604727 Marek's Disease Virus Type 2 (MDV-2)-encoded MicroRNAs Show No Sequence Conservation with Those Encoded by MDV-1 Journal of Virology. Jul, 2007 | Pubmed ID: 17459919 Inference of MiRNA Targets Using Evolutionary Conservation and Pathway Analysis BMC Bioinformatics. 2007 | Pubmed ID: 17331257 Quantitative Technologies Establish a Novel MicroRNA Profile of Chronic Lymphocytic Leukemia Blood. Jun, 2007 | Pubmed ID: 17327404 Effects of Dicer and Argonaute Down-regulation on MRNA Levels in Human HEK293 Cells Nucleic Acids Research. 2006 | Pubmed ID: 16971455 A Novel Class of Small RNAs Bind to MILI Protein in Mouse Testes Nature. Jul, 2006 | Pubmed ID: 16751777 The Types and Prevalence of Alternative Splice Forms Current Opinion in Structural Biology. Jun, 2006 | Pubmed ID: 16713247 A Simple Physical Model Predicts Small Exon Length Variations PLoS Genetics. Apr, 2006 | Pubmed ID: 16683028 SPA: a Probabilistic Algorithm for Spliced Alignment PLoS Genetics. Apr, 2006 | Pubmed ID: 16683023 Virus-encoded MicroRNAs: Novel Regulators of Gene Expression Trends in Microbiology. Apr, 2006 | Pubmed ID: 16531046 Cell-type-specific Signatures of MicroRNAs on Target MRNA Expression Proceedings of the National Academy of Sciences of the United States of America. Feb, 2006 | Pubmed ID: 16477010 Identification of Clustered MicroRNAs Using an Ab Initio Prediction Method BMC Bioinformatics. 2005 | Pubmed ID: 16274478 The Developmental MiRNA Profiles of Zebrafish As Determined by Small RNA Cloning Genes & Development. Jun, 2005 | Pubmed ID: 15937218 Identification of MicroRNAs of the Herpesvirus Family Nature Methods. Apr, 2005 | Pubmed ID: 15782219 Analysis of Human Immunodeficiency Virus Cytopathicity by Using a New Method for Quantitating Viral Dynamics in Cell Culture Journal of Virology. Apr, 2005 | Pubmed ID: 15767404 Identification of Virus-encoded MicroRNAs Science (New York, N.Y.). Apr, 2004 | Pubmed ID: 15118162 SMASHing Regulatory Sites in DNA by Human-mouse Sequence Comparisons Proceedings / IEEE Computer Society Bioinformatics Conference. IEEE Computer Society Bioinformatics Conference. 2003 | Pubmed ID: 16452803 The Small RNA Profile During Drosophila Melanogaster Development Developmental Cell. Aug, 2003 | Pubmed ID: 12919683 Decay Rates of Human MRNAs: Correlation with Functional Characteristics and Sequence Attributes Genome Research. Aug, 2003 | Pubmed ID: 12902380 Systematic Characterization of the Zinc-finger-containing Proteins in the Mouse Transcriptome Genome Research. Jun, 2003 | Pubmed ID: 12819142 Impact of Alternative Initiation, Splicing, and Termination on the Diversity of the MRNA Transcripts Encoded by the Mouse Transcriptome Genome Research. Jun, 2003 | Pubmed ID: 12819126 Splice Variation in Mouse Full-length CDNAs Identified by Mapping to the Mouse Genome Genome Research. Sep, 2002 | Pubmed ID: 12213775 Probabilistic Clustering of Sequences: Inferring New Bacterial Regulons by Comparative Genomics Proceedings of the National Academy of Sciences of the United States of America. May, 2002 | Pubmed ID: 12032281 3' enden sekventering bibliotek forberedelse med A-seq2 Georges Martin1, Ralf Schmidt1, Andreas J. Gruber1, Souvik Ghosh1, Walter Keller1, Mihaela Zavolan1,2 1Computational and Systems Biology, Biozentrum, University of Basel, 2Swiss Institute of Bioinformatics, Biozentrum, University of Basel JoVE 56129 Biology PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins JoVE 2034 Biology
3' enden sekventering bibliotek forberedelse med A-seq2 Georges Martin1, Ralf Schmidt1, Andreas J. Gruber1, Souvik Ghosh1, Walter Keller1, Mihaela Zavolan1,2 1Computational and Systems Biology, Biozentrum, University of Basel, 2Swiss Institute of Bioinformatics, Biozentrum, University of Basel JoVE 56129 Biology
PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins JoVE 2034 Biology
