List of works - Markus Hafner

6mer seed toxicity in tumor suppressive microRNAs

scientific article published in Nature Communications

6mer seed toxicity in tumor suppressive microRNAs

article

A census of human RNA-binding proteins

A non-radioactive, improved PAR-CLIP and small RNA cDNA library preparation protocol

scientific article published on 01 May 2021

AUF1 promotes let-7b loading on Argonaute 2.

scientific article

Absolute quantification of microRNAs by using a universal reference

scientific article published on 27 October 2009

Analysis of the miRNA targetome in EBV-infected B cells

scientific article published on 19 April 2012

Barcoded cDNA Libraries for miRNA Profiling by Next-Generation Sequencing

Barcoded cDNA library preparation for small RNA profiling by next-generation sequencing

scientific article

Biochemical isolation of Argonaute protein complexes by Ago-APP

scientific article

Bioinformatic analysis of barcoded cDNA libraries for small RNA profiling by next-generation sequencing

scientific article

CD95/Fas ligand mRNA is toxic to cells

scientific article published on 16 October 2018

CD95/Fas ligand mRNA is toxic to cells

Characterizing Expression and Processing of Precursor and Mature Human tRNAs by Hydro-tRNAseq and PAR-CLIP.

scientific article published in August 2017

Combined characterization of microRNA and mRNA profiles delineates early differentiation pathways of CD133+ and CD34+ hematopoietic stem and progenitor cells

scientific article

DGCR8-dependent microRNA biogenesis is essential for skin development

scholarly article

DHX36 prevents the accumulation of translationally inactive mRNAs with G4-structures in untranslated regions

scientific article published on 03 June 2019

DND1 maintains germline stem cells via recruitment of the CCR4-NOT complex to target mRNAs

scientific article published on 15 March 2017

Deep sequencing of small RNAs specifically associated with Arabidopsis AGO1 and AGO4 uncovers new AGO functions

scientific article

Displacement of protein-bound aptamers with small molecules screened by fluorescence polarization

scientific article

Dysregulation of Lipid Metabolism in Mkp-1 Deficient Mice during Gram-Negative Sepsis

article

ELAVL1 modulates transcriptome-wide miRNA binding in murine macrophages

scientific article

Evolutionary conservation and expression of human RNA-binding proteins and their role in human genetic disease

scientific article

Evolving specificity of tRNA 3-methyl-cytidine-32 (m3C32) modification: a subset of tRNAsSer requires N6-isopentenylation of A37.

scientific article published on 27 June 2016

FMRP targets distinct mRNA sequence elements to regulate protein expression

scientific journal article

Genome-wide annotation and analysis of zebra finch microRNA repertoire reveal sex-biased expression

scientific article (publication date: 26 December 2012)

Genome-wide identification of miRNA targets by PAR-CLIP.

scientific article published on 19 August 2012

Genome-wide identification of microRNA targets in human ES cells reveals a role for miR-302 in modulating BMP response

scientific article

Global target mRNA specification and regulation by the RNA-binding protein ZFP36.

scientific article

Human CLP1 mutations alter tRNA biogenesis, affecting both peripheral and central nervous system function

scientific article

Identification of RNA-protein interaction networks using PAR-CLIP

scientific article

Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition

scientific article published on 12 March 2013

Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing

scientific article

Inhibition of cytohesins by SecinH3 leads to hepatic insulin resistance

scientific article published on December 2006

Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability

scientific article published on 30 June 2011

Keratin 19 regulates cell cycle pathway and sensitivity of breast cancer cells to CDK inhibitors

scientific article published on 10 October 2019

LARP4 mRNA codon-tRNA match contributes to LARP4 activity for ribosomal protein mRNA poly(A) tail length protection

scientific article published on 12 September 2017

Laboratory mice born to wild mice have natural microbiota and model human immune responses

scientific article published on 01 August 2019

Laser capture microdissection followed by next-generation sequencing identifies disease-related microRNAs in psoriatic skin that reflect systemic microRNA changes in psoriasis.

scientific article

Learning the language of post-transcriptional gene regulation

scientific article

Mammalian miRNA curation through next-generation sequencing

scientific article

Many si/shRNAs can kill cancer cells by targeting multiple survival genes through an off-target mechanism

scientific article published on 24 October 2017

Many si/shRNAs can kill cancer cells by targeting multiple survival genes through an off-target mechanism

article

MicroRNA sequence and expression analysis in breast tumors by deep sequencing

scientific article

MicroRNAs MiR-17, MiR-20a, and MiR-106b act in concert to modulate E2F activity on cell cycle arrest during neuronal lineage differentiation of USSC.

scientific article

MicroRNAs miR-26a, miR-26b, and miR-29b accelerate osteogenic differentiation of unrestricted somatic stem cells from human cord blood

scientific article

Mitochondrial Matrix Protease ClpP Agonists Inhibit Cancer Stem Cell Function in Breast Cancer Cells by Disrupting Mitochondrial Homeostasis

scientific article published in 2022

Mitogen-activated protein kinase phosphatase-1 controls PD-L1 expression by regulating type I interferon during systemic Escherichia coli infection

scientific article published in 2022

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

scientific article published on 31 October 2008

Multicolor microRNA FISH effectively differentiates tumor types

scientific article

Multiple capsid protein binding sites mediate selective packaging of the alphavirus genomic RNA

scientific article published on 17 September 2020

New insights in the mechanism of microRNA-mediated target repression

scientific article published on 4 November 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

scientific article

PAR-CLIP analysis uncovers AUF1 impact on target RNA fate and genome integrity

scientific article

PAR-CLIP and streamlined small RNA cDNA library preparation protocol for the identification of RNA binding protein target sites

scientific article

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

scientific article

Post-transcriptional Control of Tumor Cell Autonomous Metastatic Potential by CCR4-NOT Deadenylase CNOT7

scientific article

Posttranscriptional regulation of human endogenous retroviruses by RNA-binding motif protein 4, RBM4

scientific article published on 05 October 2020

Proximity-CLIP Provides a Snapshot of Protein-Occupied RNA Elements at Subcellular Resolution and Transcriptome-Wide Scale

scientific article published on 01 January 2020

Proximity-CLIP provides a snapshot of protein-occupied RNA elements in subcellular compartments

scientific article published on 26 November 2018

Quantitative mass spectrometry and PAR-CLIP to identify RNA-protein interactions

scientific article

RNA Polymerase III Output Is Functionally Linked to tRNA Dimethyl-G26 Modification.

scientific article published on 31 December 2015

RNA targets of wild-type and mutant FET family proteins

scientific article published on 13 November 2011

RNA-binding protein IGF2BP1 maintains leukemia stem cell properties by regulating HOXB4, MYB, and ALDH1A1

scientific article published on 25 November 2019

RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries

scientific article

Rapid image deconvolution and multiview fusion for optical microscopy

scientific article published on 29 June 2020

Small RNA sequencing and functional characterization reveals MicroRNA-143 tumor suppressor activity in liposarcoma

scientific article

Structure-function studies of STAR family Quaking proteins bound to their in vivo RNA target sites

scientific article

The miR-17-92 cluster and its target THBS1 are differentially expressed in angiosarcomas dependent on MYC amplification

scientific article

The p53-induced RNA-binding protein ZMAT3 is a splicing regulator that inhibits the splicing of oncogenic CD44 variants in colorectal carcinoma

scientific article published on 17 December 2020

The viral and cellular microRNA targetome in lymphoblastoid cell lines

scientific article published in January 2012

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

Viral microRNA targetome of KSHV-infected primary effusion lymphoma cell lines

scientific article

miR-450a Acts as a Tumor Suppressor in Ovarian Cancer by Regulating Energy Metabolism

scientific article published on 17 May 2019

miRNA in situ hybridization in formaldehyde and EDC-fixed tissues

scientific article published on 11 January 2009

microRNAs are biomarkers of oncogenic human papillomavirus infections

scientific article published on 03 March 2014

List of works by Markus Hafner

6mer seed toxicity in tumor suppressive microRNAs

6mer seed toxicity in tumor suppressive microRNAs

A census of human RNA-binding proteins

A non-radioactive, improved PAR-CLIP and small RNA cDNA library preparation protocol

AUF1 promotes let-7b loading on Argonaute 2.

Absolute quantification of microRNAs by using a universal reference

Analysis of the miRNA targetome in EBV-infected B cells

Barcoded cDNA Libraries for miRNA Profiling by Next-Generation Sequencing

Barcoded cDNA library preparation for small RNA profiling by next-generation sequencing

Biochemical isolation of Argonaute protein complexes by Ago-APP

Bioinformatic analysis of barcoded cDNA libraries for small RNA profiling by next-generation sequencing

CD95/Fas ligand mRNA is toxic to cells

CD95/Fas ligand mRNA is toxic to cells

Characterizing Expression and Processing of Precursor and Mature Human tRNAs by Hydro-tRNAseq and PAR-CLIP.

Combined characterization of microRNA and mRNA profiles delineates early differentiation pathways of CD133+ and CD34+ hematopoietic stem and progenitor cells

DGCR8-dependent microRNA biogenesis is essential for skin development

DHX36 prevents the accumulation of translationally inactive mRNAs with G4-structures in untranslated regions

DND1 maintains germline stem cells via recruitment of the CCR4-NOT complex to target mRNAs

Deep sequencing of small RNAs specifically associated with Arabidopsis AGO1 and AGO4 uncovers new AGO functions

Displacement of protein-bound aptamers with small molecules screened by fluorescence polarization

Dysregulation of Lipid Metabolism in Mkp-1 Deficient Mice during Gram-Negative Sepsis

ELAVL1 modulates transcriptome-wide miRNA binding in murine macrophages

Evolutionary conservation and expression of human RNA-binding proteins and their role in human genetic disease

Evolving specificity of tRNA 3-methyl-cytidine-32 (m3C32) modification: a subset of tRNAsSer requires N6-isopentenylation of A37.

FMRP targets distinct mRNA sequence elements to regulate protein expression

Genome-wide annotation and analysis of zebra finch microRNA repertoire reveal sex-biased expression

Genome-wide identification of miRNA targets by PAR-CLIP.

Genome-wide identification of microRNA targets in human ES cells reveals a role for miR-302 in modulating BMP response

Global target mRNA specification and regulation by the RNA-binding protein ZFP36.

Human CLP1 mutations alter tRNA biogenesis, affecting both peripheral and central nervous system function

Identification of RNA-protein interaction networks using PAR-CLIP

Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition

Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing

Inhibition of cytohesins by SecinH3 leads to hepatic insulin resistance

Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability

Keratin 19 regulates cell cycle pathway and sensitivity of breast cancer cells to CDK inhibitors

LARP4 mRNA codon-tRNA match contributes to LARP4 activity for ribosomal protein mRNA poly(A) tail length protection

Laboratory mice born to wild mice have natural microbiota and model human immune responses

Laser capture microdissection followed by next-generation sequencing identifies disease-related microRNAs in psoriatic skin that reflect systemic microRNA changes in psoriasis.

Learning the language of post-transcriptional gene regulation

Mammalian miRNA curation through next-generation sequencing

Many si/shRNAs can kill cancer cells by targeting multiple survival genes through an off-target mechanism

Many si/shRNAs can kill cancer cells by targeting multiple survival genes through an off-target mechanism

MicroRNA sequence and expression analysis in breast tumors by deep sequencing

MicroRNAs MiR-17, MiR-20a, and MiR-106b act in concert to modulate E2F activity on cell cycle arrest during neuronal lineage differentiation of USSC.

MicroRNAs miR-26a, miR-26b, and miR-29b accelerate osteogenic differentiation of unrestricted somatic stem cells from human cord blood

Mitochondrial Matrix Protease ClpP Agonists Inhibit Cancer Stem Cell Function in Breast Cancer Cells by Disrupting Mitochondrial Homeostasis

Mitogen-activated protein kinase phosphatase-1 controls PD-L1 expression by regulating type I interferon during systemic Escherichia coli infection

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

Multicolor microRNA FISH effectively differentiates tumor types

Multiple capsid protein binding sites mediate selective packaging of the alphavirus genomic RNA

New insights in the mechanism of microRNA-mediated target repression

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

PAR-CLIP analysis uncovers AUF1 impact on target RNA fate and genome integrity

PAR-CLIP and streamlined small RNA cDNA library preparation protocol for the identification of RNA binding protein target sites

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

Post-transcriptional Control of Tumor Cell Autonomous Metastatic Potential by CCR4-NOT Deadenylase CNOT7

Posttranscriptional regulation of human endogenous retroviruses by RNA-binding motif protein 4, RBM4

Proximity-CLIP Provides a Snapshot of Protein-Occupied RNA Elements at Subcellular Resolution and Transcriptome-Wide Scale

Proximity-CLIP provides a snapshot of protein-occupied RNA elements in subcellular compartments

Quantitative mass spectrometry and PAR-CLIP to identify RNA-protein interactions

RNA Polymerase III Output Is Functionally Linked to tRNA Dimethyl-G26 Modification.

RNA targets of wild-type and mutant FET family proteins

RNA-binding protein IGF2BP1 maintains leukemia stem cell properties by regulating HOXB4, MYB, and ALDH1A1

RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries

Rapid image deconvolution and multiview fusion for optical microscopy

Small RNA sequencing and functional characterization reveals MicroRNA-143 tumor suppressor activity in liposarcoma

Structure-function studies of STAR family Quaking proteins bound to their in vivo RNA target sites

The miR-17-92 cluster and its target THBS1 are differentially expressed in angiosarcomas dependent on MYC amplification

The p53-induced RNA-binding protein ZMAT3 is a splicing regulator that inhibits the splicing of oncogenic CD44 variants in colorectal carcinoma

The viral and cellular microRNA targetome in lymphoblastoid cell lines

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

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

Viral microRNA targetome of KSHV-infected primary effusion lymphoma cell lines

miR-450a Acts as a Tumor Suppressor in Ovarian Cancer by Regulating Energy Metabolism

miRNA in situ hybridization in formaldehyde and EDC-fixed tissues

microRNAs are biomarkers of oncogenic human papillomavirus infections