Caroline C. Friedel

Publications

• Clonal Expansion Analysis of Transposon Insertions by High-Throughput Sequencing Identifies Candidate Cancer Genes in a PiggyBac Mutagenesis Screen
  PloS One. 2013  |   Pubmed ID: 23940809
• Deciphering the Modulation of Gene Expression by Type I and II Interferons Combining 4sU-tagging, Translational Arrest and in Silico Promoter Analysis
  Nucleic Acids Research. Jul, 2013  |   Pubmed ID: 23832230
• β1- and αv-class Integrins Cooperate to Regulate Myosin II During Rigidity Sensing of Fibronectin-based Microenvironments
  Nature Cell Biology. Jun, 2013  |   Pubmed ID: 23708002
• A Comprehensive Evaluation of Alignment Algorithms in the Context of RNA-seq
  PloS One. 2012  |   Pubmed ID: 23300661
• Real-time Transcriptional Profiling of Cellular and Viral Gene Expression During Lytic Cytomegalovirus Infection
  PLoS Pathogens. Sep, 2012  |   Pubmed ID: 22969428
• Detection and Correction of Probe-level Artefacts on Microarrays
  BMC Bioinformatics. 2012  |   Pubmed ID: 22647057
• Ultrashort and Progressive 4sU-tagging Reveals Key Characteristics of RNA Processing at Nucleotide Resolution
  Genome Research. Oct, 2012  |   Pubmed ID: 22539649
• A Context-based Approach to Identify the Most Likely Mapping for RNA-seq Experiments
  BMC Bioinformatics. 2012  |   Pubmed ID: 22537048
• Genome-wide Assessment of AU-rich Elements by the AREScore Algorithm
  PLoS Genetics. Jan, 2012  |   Pubmed ID: 22242014
• The SARS-coronavirus-host Interactome: Identification of Cyclophilins As Target for Pan-coronavirus Inhibitors
  PLoS Pathogens. Oct, 2011  |   Pubmed ID: 22046132
• Virus-host Interactomes and Global Models of Virus-infected Cells
  Trends in Microbiology. Oct, 2011  |   Pubmed ID: 21855347
• Quantitative Proteomics of the Integrin Adhesome Show a Myosin II-dependent Recruitment of LIM Domain Proteins
  EMBO Reports. Mar, 2011  |   Pubmed ID: 21311561
• Systematic Analysis of Viral and Cellular MicroRNA Targets in Cells Latently Infected with Human Gamma-herpesviruses by RISC Immunoprecipitation Assay
  Cell Host & Microbe. Apr, 2010  |   Pubmed ID: 20413099
• HALO--a Java Framework for Precise Transcript Half-life Determination
  Bioinformatics (Oxford, England). May, 2010  |   Pubmed ID: 20299326
• Metabolic Tagging and Purification of Nascent RNA: Implications for Transcriptomics
  Molecular BioSystems. Nov, 2009  |   Pubmed ID: 19823741
• Evolutionarily Conserved Herpesviral Protein Interaction Networks
  PLoS Pathogens. Sep, 2009  |   Pubmed ID: 19730696
• Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast
  Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. Aug, 2009  |   Pubmed ID: 19630542
• Conserved Principles of Mammalian Transcriptional Regulation Revealed by RNA Half-life
  Nucleic Acids Research. Sep, 2009  |   Pubmed ID: 19561200
• Identifying the Topology of Protein Complexes from Affinity Purification Assays
  Bioinformatics (Oxford, England). Aug, 2009  |   Pubmed ID: 19505940
• FERN - a Java Framework for Stochastic Simulation and Evaluation of Reaction Networks
  BMC Bioinformatics. 2008  |   Pubmed ID: 18755046
• High-resolution Gene Expression Profiling for Simultaneous Kinetic Parameter Analysis of RNA Synthesis and Decay
  RNA (New York, N.Y.). Sep, 2008  |   Pubmed ID: 18658122
• ProCope--protein Complex Prediction and Evaluation
  Bioinformatics (Oxford, England). Sep, 2008  |   Pubmed ID: 18635566
• Influence of Degree Correlations on Network Structure and Stability in Protein-protein Interaction Networks
  BMC Bioinformatics. 2007  |   Pubmed ID: 17688687
• Analysis of Intraviral Protein-protein Interactions of the SARS Coronavirus ORFeome
  PloS One. 2007  |   Pubmed ID: 17520018
• Inferring Topology from Clustering Coefficients in Protein-protein Interaction Networks
  BMC Bioinformatics. 2006  |   Pubmed ID: 17137490
• Reliable Gene Signatures for Microarray Classification: Assessment of Stability and Performance
  Bioinformatics (Oxford, England). Oct, 2006  |   Pubmed ID: 16882647
• Toward the Complete Interactome
  Nature Biotechnology. Jun, 2006  |   Pubmed ID: 16763580
• Support Vector Machines for Separation of Mixed Plant-pathogen EST Collections Based on Codon Usage
  Bioinformatics (Oxford, England). Apr, 2005  |   Pubmed ID: 15585526