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List of works by Mihaela Zavolan

3' End Sequencing Library Preparation with A-seq2.

scientific article

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

scientific article published on 24 October 2013

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

article

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

scientific article

A mammalian microRNA expression atlas based on small RNA library sequencing

scientific article

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

scientific journal article

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

scientific article published on 15 May 2011

A rare codon-based translational program of cell proliferation

scientific article published on 27 February 2020

A simple physical model predicts small exon length variations

scientific article published on 28 April 2006

Aberrant interaction of FUS with the U1 snRNA provides a molecular mechanism of FUS induced amyotrophic lateral sclerosis

scientific article published on 11 December 2020

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

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

scientific article

Alternative cleavage and polyadenylation in health and disease

scientific article published on 02 July 2019

An updated human snoRNAome

scientific article published on 12 May 2016

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

scientific article published on 18 January 2013

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

scientific article

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

scientific article

Analysis of the genetic variability of virulence-related loci in epidemic clones of methicillin-resistant Staphylococcus aureus.

scientific article

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

scientific article (publication date: 5 December 2002)

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

scientific article published on 27 September 2012

Argonaute2 mediates compensatory expansion of the pancreatic β cell

scientific article

Authors' Reply

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

scientific article

CFIm-mediated alternative polyadenylation remodels cellular signaling and miRNA biogenesis

scientific article published on 01 April 2022

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

scientific article

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

scholarly article

Cellular cofactors affecting hepatitis C virus infection and replication

scientific article

Characterization and Prediction of miRNA Targets

Cleavage factor Im is a key regulator of 3' UTR length

scientific article published on 27 November 2012

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

scientific article

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

scientific article

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

scientific article published on 14 February 2008

Computational analysis of small RNA cloning data

scientific article

Conserved generation of short products at piRNA loci

scientific article

Conserved regulation of RNA processing in somatic cell reprogramming

scientific article published on 31 January 2019

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

scientific article

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

scientific article

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

scientific article

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

scientific article

Dicer partners expand the repertoire of miRNA targets

scientific article published on 29 November 2012

Discovery of physiological and cancer-related regulators of 3' UTR processing with KAPAC.

scientific article published on 28 March 2018

Distinct and additive effects of calorie restriction and rapamycin in aging skeletal muscle

scientific article published on 19 April 2022

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

scientific article

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

scientific article

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

scientific article published on 16 July 2014

Erratum: Identification and consequences of miRNA–target interactions — beyond repression of gene expression

article

Ewing sarcoma breakpoint region 1 prevents transcription-associated genome instability

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

scientific article published on 14 February 2017

Exploiting variability of single cells to uncover the in vivo hierarchy of miRNA targets

article

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

scientific article published on 14 August 2009

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

scientific article

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

scientific article

Gene Expression Signatures of a Preclinical Mouse Model during Colorectal Cancer Progression under Low-Dose Metronomic Chemotherapy

scientific article published on 26 December 2020

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.

scientific article

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

scientific article

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

scientific article published on 27 December 2016

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

scientific article

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

scientific article published on 15 July 2014

Identification of clustered microRNAs using an ab initio prediction method

scientific article

Identification of microRNAs of the herpesvirus family

scientific article (publication date: April 2005)

Identification of virus-encoded microRNAs

scientific article

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

scientific article

In memoriam: Francisc Schneider (1933‐2017)

Inference of miRNA targets using evolutionary conservation and pathway analysis

scientific article published in March 2007

Inference of miRNA targets using evolutionary conservation and pathway analysis

article

Inferring gene expression regulatory networks from high-throughput measurements

article

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

scientific article

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

scientific article

Loss of TSC complex enhances gluconeogenesis via upregulation of Dlk1-Dio3 locus miRNAs

scientific article published on 09 January 2020

MINA-1 and WAGO-4 are part of regulatory network coordinating germ cell death and RNAi in C. elegans

scientific article published on 06 February 2019

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

scientific article

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

scientific article

MicroRNA activity is suppressed in mouse oocytes

scientific article

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

scientific article

MicroRNA-7a regulates pancreatic β cell function

scientific article

MicroRNAs 103 and 107 regulate insulin sensitivity

scientific article (publication date: 8 June 2011)

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

scientific article published on 2 March 2008

MirZ: an integrated microRNA expression atlas and target prediction resource

scientific article published on 25 May 2009

Mirroring the multifaceted role of RNA and its partners in gene expression

scientific article published on 01 September 2018

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

scientific article published on 23 August 2013

Modulation of epigenetic regulators and cell fate decisions by miRNAs

scientific article published on December 2013

Molecular and phenotypic analysis of rodent models reveals conserved and species-specific modulators of human sarcopenia

scientific article published on 12 February 2021

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

scientific article published on 31 October 2008

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

scientific article

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

scientific article

PAR-CliP--a method to identify transcriptome-wide the binding sites of RNA binding proteins

scientific article

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

scientific article

PolyASite 2.0: a consolidated atlas of polyadenylation sites from 3' end sequencing

scientific article published on 01 January 2020

Prevention of dsRNA-induced interferon signaling by AGO1x is linked to breast cancer cell proliferation

scientific article published on 19 August 2020

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

scientific article

Protein synthesis rates and ribosome occupancies reveal determinants of translation elongation rates

scientific article published on 10 July 2019

Quantifying the strength of miRNA-target interactions

scientific article published on 16 April 2015

Quantitative technologies establish a novel microRNA profile of chronic lymphocytic leukemia

RNA splicing and its connection with other regulatory layers in somatic cell reprogramming.

scientific article

RNAs: dynamic and mutable

scientific article published on 29 November 2017

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

scientific article

Recruitment times, proliferation, and apoptosis rates during the CD8(+) T-cell response to lymphocytic choriomeningitis virus

scientific article

Redesigning CLIP for efficiency, accuracy and speed

Reflections on the RNA world

scientific article

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

scientific article published in December 2007

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

scientific article

Reply to 'A different perspective on alternative cleavage and polyadenylation'

scientific article published on 01 January 2020

Roquin Suppresses the PI3K-mTOR Signaling Pathway to Inhibit T Helper Cell Differentiation and Conversion of Treg to Tfr Cells

scientific article

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

scientific article

Roquin targets mRNAs in a 3'-UTR-specific manner by different modes of regulation

scientific article published in Nature Communications

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

scientific article published in January 2003

SPA: a probabilistic algorithm for spliced alignment

scientific article published on 28 April 2006

Seq and CLIP through the miRNA world

scientific article

Shortening of 3' UTRs in most cell types composing tumor tissues implicates alternative polyadenylation in protein metabolism

scientific article published on 14 September 2021

Single-cell mRNA profiling reveals the hierarchical response of miRNA targets to miRNA induction

scientific article published on 27 August 2018

Somatic mutation leads to efficient affinity maturation when centrocytes recycle back to centroblasts.

scientific article

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

scientific article published on September 2002

Statistical inference of sequence-dependent mutation rates.

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article published on 19 September 2016

Terminal exon characterization with TECtool reveals an abundance of cell-specific isoforms

scientific article published on 10 September 2018

The Alazami Syndrome-Associated Protein LARP7 Guides U6 Small Nuclear RNA Modification and Contributes to Splicing Robustness

scientific article published on 03 February 2020

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

scientific article published on 6 September 2017

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

scientific article

The neuromuscular junction is a focal point of mTORC1 signaling in sarcopenia

scientific article published on 09 September 2020

The small RNA profile during Drosophila melanogaster development

scientific article (publication date: August 2003)

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

scientific article

The transcriptional landscape of a hepatoma cell line grown on scaffolds of extracellular matrix proteins

scientific article published on 06 April 2021

The transcriptional landscape of the mammalian genome

scientific article

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

scientific article

The types and prevalence of alternative splice forms

scientific article

The types and prevalence of alternative splice forms [Current Opinion in Structural Biology 2006, 16:362–367]

Timescales and bottlenecks in miRNA-dependent gene regulation

scientific article published on 03 December 2013

Transcriptome-Wide Identification of Protein Binding Sites on RNA by PAR-CLIP (Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation)

scientific article

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

scientific article

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

scientific article published on 07 July 2013

Virus-encoded microRNAs: novel regulators of gene expression

scientific article

Whole-genome analysis: annotations and updates

scientific article

Widespread context dependency of microRNA-mediated regulation

scientific article published on 25 March 2014

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

scientific article

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

scientific article

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

scientific article published on 22 December 2014

miRNA in situ hybridization in formaldehyde and EDC-fixed tissues

scientific article published on 11 January 2009

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