Lista de obras - Mihaela Zavolan - Dominio Público Uruguay

3' End Sequencing Library Preparation with A-seq2.

artículo científico publicado en 2017

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

artículo científico publicado en 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

artículo científico publicado en 2016

A mammalian microRNA expression atlas based on small RNA library sequencing

artículo científico publicado en 2007

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

artículo científico publicado en 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

artículo científico publicado en 2006

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

artículo científico publicado en 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.

artículo científico publicado en 2015

Alternative cleavage and polyadenylation in health and disease

scientific article published on 02 July 2019

An updated human snoRNAome

artículo científico publicado en 2016

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

artículo científico publicado en 2013

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

artículo científico publicado en 2005

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

artículo científico publicado en 2010

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

artículo científico publicado en 2005

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

artículo científico publicado en 2002

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

artículo científico publicado en 2012

Argonaute2 mediates compensatory expansion of the pancreatic β cell

artículo científico publicado en 2013

Authors' Reply

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

artículo científico publicado en 2017

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

artículo científico publicado en 2011

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

artículo científico publicado en 2006

Cellular cofactors affecting hepatitis C virus infection and replication

artículo científico publicado en 2007

Characterization and Prediction of miRNA Targets

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

artículo científico publicado en 2012

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

artículo científico publicado en 2008

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

artículo científico publicado en 2015

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

artículo científico publicado en 2008

Computational analysis of small RNA cloning data

artículo científico publicado en 2008

Conserved generation of short products at piRNA loci

artículo científico publicado en 2011

Conserved regulation of RNA processing in somatic cell reprogramming

artículo científico publicado en 2019

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

artículo científico publicado en 2015

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

artículo científico publicado en 2016

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

artículo científico publicado en 2003

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

artículo científico publicado en 2010

Dicer partners expand the repertoire of miRNA targets

artículo científico publicado en 2012

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

artículo científico publicado en 2018

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

artículo científico publicado en 2022

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

artículo científico publicado en 2006

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

artículo científico publicado en 2008

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

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 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

artículo científico publicado en 2010

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

artículo científico publicado en 2014

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

artículo científico publicado en 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.

artículo científico publicado en 2012

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

artículo científico publicado en 2014

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

artículo científico publicado en 2016

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

artículo científico publicado en 2014

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

artículo científico

Identification of clustered microRNAs using an ab initio prediction method

artículo científico publicado en 2005

Identification of microRNAs of the herpesvirus family

artículo científico publicado en 2005

Identification of virus-encoded microRNAs

artículo científico publicado en 2004

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

artículo científico publicado en 2003

In memoriam: Francisc Schneider (1933‐2017)

Inference of miRNA targets using evolutionary conservation and pathway analysis

artículo científico publicado en 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

artículo científico publicado en 2013

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

artículo científico publicado en 2011

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.

artículo científico publicado en 2007

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

artículo científico publicado en 2014

MicroRNA activity is suppressed in mouse oocytes

artículo científico publicado en 2010

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

artículo científico publicado en 2012

MicroRNA-7a regulates pancreatic β cell function

artículo científico publicado en 2014

MicroRNAs 103 and 107 regulate insulin sensitivity

artículo científico publicado en 2011

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

artículo científico publicado en 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

artículo científico

Modulation of epigenetic regulators and cell fate decisions by miRNAs

artículo científico

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

artículo científico publicado en 2021

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

artículo científico publicado en 2008

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

artículo científico publicado en 2011

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

artículo científico publicado en 2014

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

artículo científico publicado en 2010

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

artículo científico publicado en 2016

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

artículo científico publicado en 2020

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

artículo científico publicado en 2020

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

artículo científico publicado en 2002

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

artículo científico publicado en 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.

artículo científico publicado en 2017

RNAs: dynamic and mutable

artículo científico publicado en 2017

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

artículo científico publicado en 2014

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

artículo científico publicado en 2001

Redesigning CLIP for efficiency, accuracy and speed

Reflections on the RNA world

artículo científico publicado en 2015

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

artículo científico publicado en 2007

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

artículo científico publicado en 2009

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

artículo científico publicado en 2020

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

artículo científico publicado en 2017

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

artículo científico publicado en 2016

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

artículo científico publicado en 2018

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

artículo científico publicado en 2003

SPA: a probabilistic algorithm for spliced alignment

artículo científico publicado en 2006

Seq and CLIP through the miRNA world

artículo científico publicado en 2014

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

artículo científico publicado en 2021

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

artículo científico publicado en 2018

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

artículo científico publicado en 1997

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

artículo científico publicado en 2002

Statistical inference of sequence-dependent mutation rates.

artículo científico publicado en 2001

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

artículo científico publicado en 2007

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

artículo científico publicado en 2014

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

artículo científico publicado en 2003

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

artículo científico publicado en 2017

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

artículo científico publicado en 2013

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

artículo científico publicado en 2016

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

artículo científico publicado en 2018

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

artículo científico publicado en 2020

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

artículo científico publicado en 2017

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

artículo científico publicado en 2005

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

artículo científico publicado en 2003

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

artículo científico publicado en 2010

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

artículo científico publicado en 2021

The transcriptional landscape of the mammalian genome

artículo científico publicado en 2005

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

artículo científico publicado en 2009

The types and prevalence of alternative splice forms

artículo científico publicado en 2006

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)

artículo científico publicado en 2014

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

artículo científico publicado en 2010

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

artículo científico

Virus-encoded microRNAs: novel regulators of gene expression

artículo científico publicado en 2006

Whole-genome analysis: annotations and updates

artículo científico publicado en 2001

Widespread context dependency of microRNA-mediated regulation

artículo científico publicado en 2014

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

artículo científico publicado en 2015

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

artículo científico publicado en 2009

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

artículo científico publicado en 2014

miRNA in situ hybridization in formaldehyde and EDC-fixed tissues

artículo científico publicado en 2009

Lista de obras de Mihaela Zavolan

3' End Sequencing Library Preparation with A-seq2.

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

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

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

A mammalian microRNA expression atlas based on small RNA library sequencing

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

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

A rare codon-based translational program of cell proliferation

A simple physical model predicts small exon length variations

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

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.

Alternative cleavage and polyadenylation in health and disease

An updated human snoRNAome

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

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

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

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

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

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

Argonaute2 mediates compensatory expansion of the pancreatic β cell

Authors' Reply

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

CFIm-mediated alternative polyadenylation remodels cellular signaling and miRNA biogenesis

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

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

Cellular cofactors affecting hepatitis C virus infection and replication

Characterization and Prediction of miRNA Targets

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

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

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

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

Computational analysis of small RNA cloning data

Conserved generation of short products at piRNA loci

Conserved regulation of RNA processing in somatic cell reprogramming

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

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

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

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

Dicer partners expand the repertoire of miRNA targets

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

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

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

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

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

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

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

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

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

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

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

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

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.

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

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

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

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

Identification of clustered microRNAs using an ab initio prediction method

Identification of microRNAs of the herpesvirus family

Identification of virus-encoded microRNAs

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

In memoriam: Francisc Schneider (1933‐2017)

Inference of miRNA targets using evolutionary conservation and pathway analysis

Inference of miRNA targets using evolutionary conservation and pathway analysis

Inferring gene expression regulatory networks from high-throughput measurements

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

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

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

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

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

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

MicroRNA activity is suppressed in mouse oocytes

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

MicroRNA-7a regulates pancreatic β cell function

MicroRNAs 103 and 107 regulate insulin sensitivity

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

MirZ: an integrated microRNA expression atlas and target prediction resource

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