C. Friedel

发表

Evolutionarily Conserved Herpesviral Protein Interaction Networks

Sourav Bandyopadhyay, Yu-An Dong, Christine Zeretzke, 2009, PLoS pathogens.

p53-Regulated Networks of Protein, mRNA, miRNA, and lncRNA Expression Revealed by Integrated Pulsed Stable Isotope Labeling With Amino Acids in Cell Culture (pSILAC) and Next Generation Sequencing (NGS) Analyses*

Thomas Bonfert, Caroline C. Friedel, Ralf Zimmer, 2015, Molecular & Cellular Proteomics.

Metabolic tagging and purification of nascent RNA: implications for transcriptomics.

L. Dölken, C. Friedel, 2009, Molecular bioSystems.

High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay.

R. Zimmer, P. Ghazal, L. Dölken, 2008, RNA.

Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution

S. Kaufmann, S. Schreiber, R. Zimmer, 2012, Genome research.

Widespread disruption of host transcription termination in HSV-1 infection

Thomas Bonfert, Caroline C. Friedel, Ralf Zimmer, 2015, Nature Communications.

Virus-host interactomes and global models of virus-infected cells.

Caroline C Friedel, J. Haas, C. Friedel, 2011, Trends in microbiology.

Explorer Evolutionarily Conserved Herpesviral Protein Interaction Networks

Sourav Bandyopadhyay, Yu-An Dong, Christine Zeretzke, 2017 .

A Systematic Analysis of Host Factors Reveals a Med23-Interferon-λ Regulatory Axis against Herpes Simplex Virus Type 1 Replication

Orland R. Gonzalez, Even Fossum, J. Haas, 2013, PLoS pathogens.

Analysis of Intraviral Protein-Protein Interactions of the SARS Coronavirus ORFeome

Caroline C. Friedel, Ralph Baric, Ralf Zimmer, 2007, PloS one.

Quantitative proteomics of the integrin adhesome show a myosin II‐dependent recruitment of LIM domain proteins

H. Schiller, C. Friedel, R. Fässler, 2011, EMBO reports.

Integrative functional genomics decodes herpes simplex virus 1

M. Landthaler, R. Zimmer, T. Dandekar, 2020, Nature Communications.

Integrative functional genomics decodes herpes simplex virus 1

M. Landthaler, R. Zimmer, T. Dandekar, 2019, bioRxiv.

Immunostimulatory RNA leads to functional reprogramming of myeloid-derived suppressor cells in pancreatic cancer

C. Friedel, S. Endres, J. Ahlfeld, 2019, Journal of Immunotherapy for Cancer.

P-TEFb controls cell fate upon p53 activation by modulating intrinsic apoptosis pathway

Tina Lenasi, C. Friedel, M. Barborič, 2022, bioRxiv.

Dissecting HSV-1-induced host shut-off at RNA level

P. Lehner, S. Sauer, Florian Erhard, 2020, bioRxiv.

RC 3 H 1 post-transcriptionally regulates A 20 mRNA and modulates the activity of the IKK / NFk B pathway

M. Landthaler, R. Backofen, J. Wolf, 2015 .

Women in the European Virus Bioinformatics Center

Irmtraud M. Meyer, I. Meyer, K. Metzner, 2022, Viruses.

Metabolic labeling of newly transcribed RNA for high resolution gene expression profiling of RNA synthesis, processing and decay in cell culture.

L. Dölken, C. Friedel, U. Koszinowski, 2013, Journal of visualized experiments : JoVE.

Herpes simplex virus 1 (HSV-1) is one of nine herpesviruses known to infect humans

T. Hennig, L. Dölken, C. Friedel, 2022 .

Virus-Host Transcriptomics

C. Friedel, 2021 .

Edinburgh Research Explorer P-TEFb activation by RBM7 shapes a pro-survival transcriptional response to genotoxic stress

Christopher R. Sibley, J. Ule, T. Hennig, 2019 .

CDK11 regulates pre-mRNA splicing by phosphorylation of SF3B1

J. Ule, S. Knapp, C. Friedel, 2022, Nature.

HSV-1 infection induces a downstream shift of promoter-1 proximal pausing linked to H 2 A . Z-containing + 1 nucleosomes 2 3

Florian Erhard, T. Hennig, L. Dölken, 2022 .

Time-resolved single-cell RNA-seq using metabolic RNA labelling

I. Amit, A. Saliba, E. Miska, 2022, Nature Reviews Methods Primers.

The Drosophila neurogenic locus mastermind encodes a nuclear protein unusually rich in amino acid homopolymers.

D. Smoller, C. Friedel, B. Yedvobnick, 1990, Genes & development.

The SARS-coronavirus-host interactome

R. Zimmer, F. Weber, R. Hilgenfeld, 2011 .

Decoding murine cytomegalovirus

S. Jonjić, Florian Erhard, T. Hennig, 2022, bioRxiv.

Quantitative proteomics of the integrin adhesome reveals a myosin II-dependent recruitment of LIM do

H. Schiller, C. Friedel, C. Boulègue, 2011 .

HSV-1 infection induces a downstream shift of promoter-proximal pausing for most host genes

Florian Erhard, T. Hennig, L. Dölken, 2022, bioRxiv.

β1- and αv-class integrins cooperate to regulate myosin II during rigidity sensing of fibronectin-based microenvironments

M. Mann, H. Schiller, K. Gottschalk, 2013, Nature Cell Biology.

Microglia and macrophages promote corralling, wound compaction and recovery after spinal cord injury via Plexin-B2

Hongyan Zou, C. Friedel, R. Friedel, 2020, Nature Neuroscience.

Self-deleting retrovirus vectors for gene therapy

H. von Melchner, C. Friedel, M. Grez, 1996, Journal of virology.

ProCope - protein complex prediction and evaluation

Caroline C. Friedel, Ralf Zimmer, Jan Krumsiek, 2008, Bioinform..

The SARS-Coronavirus-Host Interactome: Identification of Cyclophilins as Target for Pan-Coronavirus Inhibitors

Christian Drosten, Caroline C. Friedel, Ralf Zimmer, 2011, PLoS pathogens.

4-thiouridine inhibits rRNA synthesis and causes a nucleolar stress response

L. Dölken, C. Friedel, D. Eick, 2013, RNA biology.

Calpain-mediated cleavage of collapsin response mediator protein-2 drives acute axonal degeneration

C. Lenz, H. Urlaub, C. Friedel, 2016, Scientific Reports.

Systematic analysis of viral and cellular microRNA targets in cells latently infected with human gamma-herpesviruses by RISC immunoprecipitation assay.

J. Haas, S. Pfeffer, R. Zimmer, 2010, Cell host & microbe.

RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-κB pathway

Nils Blüthgen, Rolf Backofen, Caroline C. Friedel, 2015, Nature Communications.

Gene signatures of quiescent glioblastoma cells reveal mesenchymal shift and interactions with niche microenvironment

Bin Zhang, Hongyan Zou, C. Friedel, 2019, EBioMedicine.

Plexin-B2 facilitates glioblastoma infiltration by modulating cell biomechanics

V. Lee, G. Dai, Hongyan Zou, 2021, Communications biology.

ContextMap 2: fast and accurate context-based RNA-seq mapping

Thomas Bonfert, Caroline C. Friedel, Ralf Zimmer, 2015, BMC Bioinformatics.

CDK12 controls G1/S progression by regulating RNAPII processivity at core DNA replication genes

C. Friedel, K. Paruch, J. Oppelt, 2019, EMBO reports.

Real-time Transcriptional Profiling of Cellular and Viral Gene Expression during Lytic Cytomegalovirus Infection

Thomas Bonfert, Caroline C. Friedel, Ralf Zimmer, 2012, PLoS pathogens.

Diversified transcriptional responses of myeloid and glial cells in spinal cord injury shaped by HDAC3 activity

Bin Zhang, Hongyan Zou, C. Friedel, 2021, Science Advances.

1 p 53-regulated networks of protein , mRNA , miRNA and lncRNA expression revealed by integrated p SILAC and NGS analyses

Ralf, G. Meister, H. Hermeking, 2015 .

Mechanism and consequences of herpes simplex virus 1-mediated regulation of host mRNA alternative polyadenylation

Florian Erhard, T. Hennig, L. Dölken, 2020, bioRxiv.

Herpes simplex virus blocks host transcription termination via the bimodal activities of ICP27

Florian Erhard, T. Hennig, L. Dölken, 2020, Nature Communications.

Plexin-B2 facilitates glioblastoma infiltration by modulating cell biomechanics

V. Lee, G. Dai, Hongyan Zou, 2021, Communications Biology.

OAS1/RNase L executes RIG-I ligand–dependent tumor cell apoptosis

C. Friedel, S. Endres, S. Lichtenthaler, 2021, Science Immunology.

Rapid Genome-wide Recruitment of RNA Polymerase II Drives Transcription, Splicing, and Translation Events during T Cell Responses.

C. Friedel, M. Heinig, N. H. Uhlenhaut, 2017, Cell reports.

Identification of genes induced by factor deprivation in hematopoietic cells undergoing apoptosis using gene-trap mutagenesis and site-specific recombination.

H. V. Melchner, H. von Melchner, C. Friedel, 1996, Proceedings of the National Academy of Sciences of the United States of America.

Reliable gene signatures for microarray classification: assessment of stability and performance

Caroline C. Friedel, Ralf Zimmer, Robert Küffner, 2006, Bioinform..

HSV-1-induced disruption of transcription termination resembles a cellular stress response but selectively increases chromatin accessibility downstream of genes

Florian Erhard, Marisa A. P. Baptista, T. Hennig, 2018, PLoS pathogens.

Immune homeostasis and regulation of the interferon pathway require myeloid-derived Regnase-3

A. Feuchtinger, W. Wurst, V. Hornung, 2019, The Journal of experimental medicine.

Selective disruption of genes expressed in totipotent embryonal stem cells.

H. V. Melchner, H. von Melchner, S. Reddy, 1992, Genes & development.

Analysis of high throughput data - protein protein interactions, protein complexes and RNA half life

Caroline C. Friedel, C. Friedel, 2009, Ausgezeichnete Informatikdissertationen.

A Comprehensive Evaluation of Alignment Algorithms in the Context of RNA-Seq

Caroline C. Friedel, Robert Lindner, C. Friedel, 2012, PloS one.

P-TEFb Activation by RBM7 Shapes a Pro-survival Transcriptional Response to Genotoxic Stress

Christopher R. Sibley, J. Ule, T. Hennig, 2018, bioRxiv.

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

C. Friedel, E. Glasmacher, Kathrin Davari, 2018, Journal of visualized experiments : JoVE.

Mining RNA–Seq Data for Infections and Contaminations

Thomas Bonfert, Caroline C. Friedel, Ralf Zimmer, 2013, PloS one.

Bioinformatics advances biology and medicine by turning big data troves into knowledge

Volker Heun, Burkhard Rost, Caroline C. Friedel, 2017, Informatik-Spektrum.

Widespread activation of antisense transcription of the host genome during herpes simplex virus 1 infection

Lars Dölken, Nikolaus Rajewsky, Carmelo Ferrai, 2017, Genome Biology.

Conserved principles of mammalian transcriptional regulation revealed by RNA half-life

Caroline C. Friedel, Ralf Zimmer, Lars Dölken, 2009, Nucleic acids research.

Prediction of Poly(A) Sites by Poly(A) Read Mapping

Thomas Bonfert, Caroline C. Friedel, C. Friedel, 2017, PloS one.

Genome-Wide Assessment of AU-Rich Elements by the AREScore Algorithm

C. Friedel, Johanna Schott, G. Stoecklin, 2012, PLoS genetics.

Transcriptome analysis of dominant-negative Brd4 mutants identifies Brd4-specific target genes of small molecule inhibitor JQ1

H. Blum, C. Friedel, D. Eick, 2017, Scientific Reports.

HALO - a Java framework for precise transcript half-life determination

Caroline C. Friedel, Ralf Zimmer, Lars Dölken, 2010, Bioinform..

HSV-1 and influenza infection induce linear and circular splicing of the long NEAT1 isoform

T. Hennig, L. Dölken, C. Friedel, 2021, bioRxiv.

The Hepatitis E virus intraviral interactome

P. Uetz, A. Baiker, C. Friedel, 2015, Scientific Reports.

Deciphering the modulation of gene expression by type I and II interferons combining 4sU-tagging, translational arrest and in silico promoter analysis

Kevin A. Robertson, P. Ghazal, M. Albà, 2013, Nucleic acids research.

Watchdog 2.0: New developments for reusability, reproducibility, and workflow execution

Michael Kluge, Marie-Sophie Friedl, Amrei L Menzel, 2020, GigaScience.

Watchdog – a workflow management system for the distributed analysis of large-scale experimental data

Caroline C. Friedel, Michael Kluge, Michael Kluge, 2018, BMC Bioinformatics.

Computational Analysis of Virus–Host Interactomes

Caroline C Friedel, C. Friedel, 2013, Methods in molecular biology.

A context-based approach to identify the most likely mapping for RNA-seq experiments

Thomas Bonfert, Caroline C. Friedel, Ralf Zimmer, 2012, BMC Bioinformatics.

Dissecting Herpes Simplex Virus 1-Induced Host Shutoff at the RNA Level

P. Lehner, S. Sauer, Florian Erhard, 2020, Journal of Virology.

Inhibition of CDK12 induces cancer cell dependence on activated P-TEFb via the ATM-stimulated p53 and NF-κB transcriptional programs

C. Friedel, M. Barborič, Zhijia Wang, 2023, bioRxiv.

Support vector machines for separation of mixed plant?Cpathogen EST collections based on codon usage

Igor V. Tetko, Caroline C. Friedel, Katharina Jahn, 2005, Bioinform..

Microglia and macrophages promote corralling, wound compaction and recovery after spinal cord injury via Plexin-B2

Bin Zhang, Hongyan Zou, C. Friedel, 2020, Nature Neuroscience.

Comprehensive analysis of nuclear export of herpes simplex virus type 1 tegument proteins and their Epstein‐Barr virus orthologs

Caroline C Friedel, Susanne M Bailer, C. Friedel, 2019, Traffic.

FERN – Stochastic Simulation and Evaluation of Reaction Networks

Caroline C. Friedel, Ralf Zimmer, Florian Erhard, 2010 .

Herpes simplex virus blocks host transcription termination via the bimodal activities of ICP27

Florian Erhard, T. Hennig, L. Dölken, 2020, Nature Communications.

Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast

Caroline C. Friedel, Ralf Zimmer, Jan Krumsiek, 2008, J. Comput. Biol..

Widespread activation of antisense transcription of the host genome during herpes simplex virus 1 infection

C. Kocks, N. Rajewsky, M. Landthaler, 2017, Genome Biology.

Inferring topology from clustering coefficients in protein-protein interaction networks

Caroline C. Friedel, Ralf Zimmer, R. Zimmer, 2006, BMC Bioinformatics.

The Cytomegalovirus M35 Protein Directly Binds to the Interferon-β Enhancer and Modulates Transcription of Ifnb1 and Other IRF3-Driven Genes

M. Landthaler, K. Büssow, Florian Erhard, 2023, Journal of virology.

The Cytomegalovirus M35 Protein Modulates Transcription of Ifnb1 and Other IRF3-Driven Genes by Direct Promoter Binding

M. Landthaler, K. Büssow, Florian Erhard, 2023, bioRxiv.

iBRET Screen of the ABCD1 Peroxisomal Network and Mutation-Induced Network Perturbations.

R. Zimmer, C. Friedel, S. Gersting, 2021, Journal of proteome research.

FERN – a Java framework for stochastic simulation and evaluation of reaction networks

Caroline C. Friedel, Ralf Zimmer, Florian Erhard, 2008, BMC Bioinformatics.

Enrichment of insertional mutants following retrovirus gene trap selection.

H. Ruley, C. Friedel, W. Chang, 1993, Virology.

Influence of degree correlations on network structure and stability in protein-protein interaction networks

Caroline C. Friedel, Ralf Zimmer, R. Zimmer, 2007, BMC Bioinformatics.

Reliable gene signatures for microarray classification: assessment of stability and performance

Chad A. Davis, R. Küffner, R. Zimmer, 2006, Bioinform..

A context-based approach to identify the most likely mapping for RNA-seq experiments

R. Zimmer, C. Friedel, Thomas Bonfert, 2012, BMC Bioinformatics.

Transcriptome analysis of dominant-negative Brd4 mutants identifies Brd4-specific target genes of small molecule inhibitor JQ1

H. Blum, C. Friedel, D. Eick, 2017, Scientific Reports.

Inhibition of CDK12 elevates cancer cell dependence on P-TEFb by stimulation of RNA polymerase II pause release

Heidi M. Haikala, C. Friedel, M. Barborič, 2023, bioRxiv.

P-TEFb promotes cell survival upon p53 activation by suppressing intrinsic apoptosis pathway

Tina Lenasi, C. Friedel, M. Barborič, 2023, Nucleic acids research.

Clonal Expansion Analysis of Transposon Insertions by High-Throughput Sequencing Identifies Candidate Cancer Genes in a PiggyBac Mutagenesis Screen

R. Rad, Philippe Soriano, C. Friedel, 2013, PloS one.

β1- and αv-class integrins cooperate to regulate myosin II during rigidity sensing of fibronectin-based microenvironments

M. Mann, H. Schiller, K. Gottschalk, 2013, Nature Cell Biology.

Quantitative proteomics of the integrin adhesome show a myosin II‐dependent recruitment of LIM domain proteins

H. Schiller, C. Friedel, R. Fässler, 2011, EMBO reports.

High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay.

R. Zimmer, P. Ghazal, L. Dölken, 2008, RNA.

RegCFinder: targeted discovery of genomic subregions with differential read density

C. Friedel, E. Weiß, 2023, Bioinformatics Advances.

Watchdog – a workflow management system for the distributed analysis of large-scale experimental data

C. Friedel, Michael Kluge, 2018, BMC Bioinformatics.

mRNA N1-2’O-methylation by CMTR1 affects NVL2 mRNA splicing

C. Friedel, M. Schlee, Steven Wolter, 2023, bioRxiv.

HSV-1 Infection Induces a Downstream Shift of Promoter-Proximal Pausing for Host Genes

Florian Erhard, L. Dölken, C. Friedel, 2023, Journal of virology.

Cost Curves for Abstaining Classifiers

Ulrich Rückert, Caroline C. Friedel, U. Rückert, 2006 .

HSV-1 infection induces a downstream-shift of the +1 nucleosome

C. Friedel, Adam W. Whisnant, Lara Djakovic, 2024, bioRxiv.

Sustainable data analysis with Snakemake [version 1; peer review: 1 approved, 1 approved with reservations]

A. Wilm, S. Nahnsen, M. Holtgrewe, 2022 .

MIR sequences recruit zinc finger protein ZNF768 to expressed genes

H. Blum, C. Friedel, D. Eick, 2018, Nucleic acids research.

The HSV-1 ICP22 protein selectively impairs histone repositioning upon Pol II transcription downstream of genes

Florian Erhard, L. Dölken, C. Friedel, 2021, Nature communications.