Mihaela Zavolan

Probabilistic clustering of sequences: inferring new bacterial regulons by comparative genomics.

Splice variation in mouse full-length cDNAs identified by mapping to the mouse genome.

Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome.

Systematic characterization of the zinc-finger-containing proteins in the mouse transcriptome.

Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes.

The small RNA profile during Drosophila melanogaster development.

Identification of virus-encoded microRNAs.

Analysis of human immunodeficiency virus cytopathicity by using a new method for quantitating viral dynamics in cell culture.

Identification of microRNAs of the herpesvirus family.

The developmental miRNA profiles of zebrafish as determined by small RNA cloning.

Identification of clustered microRNAs using an ab initio prediction method.

SMASHing regulatory sites in DNA by human-mouse sequence comparisons.

Cell-type-specific signatures of microRNAs on target mRNA expression.

Virus-encoded microRNAs: novel regulators of gene expression.

SPA: a probabilistic algorithm for spliced alignment.

A simple physical model predicts small exon length variations.

The types and prevalence of alternative splice forms.

A novel class of small RNAs bind to MILI protein in mouse testes.

Effects of Dicer and Argonaute down-regulation on mRNA levels in human HEK293 cells.

Quantitative technologies establish a novel microRNA profile of chronic lymphocytic leukemia.

Inference of miRNA targets using evolutionary conservation and pathway analysis.

Marek's disease virus type 2 (MDV-2)-encoded microRNAs show no sequence conservation with those encoded by MDV-1.

A mammalian microRNA expression atlas based on small RNA library sequencing.

Cellular cofactors affecting hepatitis C virus infection and replication.

Regulation of human liver delta-aminolevulinic acid synthase by bile acids.

Strand-specific 5'-O-methylation of siRNA duplexes controls guide strand selection and targeting specificity.

Computational analysis of small RNA cloning data.

Computational analysis of full-length cDNAs reveals frequent coupling between transcriptional and splicing programs.

MicroRNAs control de novo DNA methylation through regulation of transcriptional repressors in mouse embryonic stem cells.

Elevated expression of the miR-17-92 polycistron and miR-21 in hepadnavirus-associated hepatocellular carcinoma contributes to the malignant phenotype.

Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system.

Molecular characterization of human Argonaute-containing ribonucleoprotein complexes and their bound target mRNAs.

miRNA in situ hybridization in formaldehyde and EDC-fixed tissues.

miR-375 maintains normal pancreatic alpha- and beta-cell mass.

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

MirZ: an integrated microRNA expression atlas and target prediction resource.

Expression and processing of a small nucleolar RNA from the Epstein-Barr virus genome.

Relative contribution of sequence and structure features to the mRNA binding of Argonaute/EIF2C-miRNA complexes and the degradation of miRNA targets.

The snoRNA MBII-52 (SNORD 115) is processed into smaller RNAs and regulates alternative splicing.

MicroRNA activity is suppressed in mouse oocytes.

Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP.

Expression proteomics of UPF1 knockdown in HeLa cells reveals autoregulation of hnRNP A2/B1 mediated by alternative splicing resulting in nonsense-mediated mRNA decay.

Analysis of in situ pre-mRNA targets of human splicing factor SF1 reveals a function in alternative splicing.

CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins.

Deciphering the role of RNA-binding proteins in the post-transcriptional control of gene expression.

Conserved generation of short products at piRNA loci.

A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins.

MicroRNAs 103 and 107 regulate insulin sensitivity.

PAPD5, a noncanonical poly(A) polymerase with an unusual RNA-binding motif.

MicroRNA-194 is a target of transcription factor 1 (Tcf1, HNF1α) in adult liver and controls expression of frizzled-6.

Kaposi's sarcoma herpesvirus microRNAs target caspase 3 and regulate apoptosis.

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.

Argonaute CLIP--a method to identify in vivo targets of miRNAs.

Dicer partners expand the repertoire of miRNA targets.

A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets.

Analysis of CDS-located miRNA target sites suggests that they can effectively inhibit translation.

Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing.

Translation-dependent displacement of UPF1 from coding sequences causes its enrichment in 3' UTRs.

Modeling the binding specificity of the RNA-binding protein GLD-1 suggests a function of coding region-located sites in translational repression.

3'-UTR poly(T/U) tract deletions and altered expression of EWSR1 are a hallmark of mismatch repair-deficient cancers.

Means to an end: mechanisms of alternative polyadenylation of messenger RNA precursors.

Modulation of epigenetic regulators and cell fate decisions by miRNAs.

Timescales and bottlenecks in miRNA-dependent gene regulation.

Argonaute2 mediates compensatory expansion of the pancreatic β cell.

TSSer: an automated method to identify transcription start sites in prokaryotic genomes from differential RNA sequencing data.

Seq and CLIP through the miRNA world.

ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs.

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.

Widespread context dependency of microRNA-mediated regulation.

MicroRNA-7a regulates pancreatic β cell function.

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support.

Structural and functional implications of the QUA2 domain on RNA recognition by GLD-1.

Identification and consequences of miRNA-target interactions--beyond repression of gene expression.

Embryonic stem cell-specific microRNAs contribute to pluripotency by inhibiting regulators of multiple differentiation pathways.

Reconstitution of CPSF active in polyadenylation: recognition of the polyadenylation signal by WDR33.

Global 3' UTR shortening has a limited effect on protein abundance in proliferating T cells.

miR-CLIP capture of a miRNA targetome uncovers a lincRNA H19-miR-106a interaction.

Accurate transcriptome-wide prediction of microRNA targets and small interfering RNA off-targets with MIRZA-G.

Reflections on the RNA world.

Quantifying the strength of miRNA-target interactions.

miR-184 Regulates Pancreatic β-Cell Function According to Glucose Metabolism.

Inferring gene expression regulatory networks from high-throughput measurements.

Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data.

Cooperative target mRNA destabilization and translation inhibition by miR-58 microRNA family in C. elegans.

Accurate transcriptome-wide prediction of microRNA targets and small interfering RNA off-targets with MIRZA-G.

Roquin recognizes a non-canonical hexaloop structure in the 3'-UTR of Ox40.

An updated human snoRNAome.

Redesigning CLIP for efficiency, accuracy and speed.

Corrigendum to "Quantifying the strength of miRNA-target interactions" [Methods (2015) 90-99].

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.

TUT-DIS3L2 is a mammalian surveillance pathway for aberrant structured non-coding RNAs.

Patterns of ribosomal protein expression specify normal and malignant human cells.

High-throughput identification of C/D box snoRNA targets with CLIP and RiboMeth-seq.

Explicit Modeling of siRNA-Dependent On- and Off-Target Repression Improves the Interpretation of Screening Results.

TFAP2A is a component of the ZEB1/2 network that regulates TGFB1-induced epithelial to mesenchymal transition.

Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors.

The Gcn4 transcription factor reduces protein synthesis capacity and extends yeast lifespan.