Caroline C Friedel

Summary

Country: Germany

Publications

  1. doi request reprint Bootstrapping the interactome: unsupervised identification of protein complexes in yeast
    Caroline C Friedel
    Institut fur Informatik, Ludwig Maximilians Universitat Munchen, Munchen, Germany
    J Comput Biol 16:971-87. 2009
  2. doi request reprint HALO--a Java framework for precise transcript half-life determination
    Caroline C Friedel
    Institut fur Informatik, Ludwig Maximilians Universitat Munchen, Munchen, Germany
    Bioinformatics 26:1264-6. 2010
  3. pmc Conserved principles of mammalian transcriptional regulation revealed by RNA half-life
    Caroline C Friedel
    Institute for Informatics, Ludwig Maximilians Universitat Munchen, Munich 80333, Germany
    Nucleic Acids Res 37:e115. 2009
  4. pmc Identifying the topology of protein complexes from affinity purification assays
    Caroline C Friedel
    Institut fur Informatik, Ludwig Maximilians Universitat Munchen, Amalienstrasse 17, 80333 München, Germany
    Bioinformatics 25:2140-6. 2009
  5. ncbi request reprint Metabolic tagging and purification of nascent RNA: implications for transcriptomics
    Caroline C Friedel
    Institute for Informatics, Ludwig Maximilians University Munich, Amalienstr 17, 80333 München, Germany
    Mol Biosyst 5:1271-8. 2009
  6. pmc Influence of degree correlations on network structure and stability in protein-protein interaction networks
    Caroline C Friedel
    LFE Bioinformatik, Institut fur Informatik, Ludwig Maximilians Universitat Munchen, Amalienstrasse 17, 80333 München, Germany
    BMC Bioinformatics 8:297. 2007
  7. pmc Inferring topology from clustering coefficients in protein-protein interaction networks
    Caroline C Friedel
    LFE Bioinformatik, Institut fur Informatik, Ludwig Maximilians Universitat Munchen, Amalienstrasse 17, 80333 München, Germany
    BMC Bioinformatics 7:519. 2006
  8. pmc High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay
    Lars Dölken
    Max von Pettenkofer Institute, Ludwig Maximilians University Munich, Munich 80337, Germany
    RNA 14:1959-72. 2008
  9. pmc Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution
    Lukas Windhager
    Institute for Informatics, Ludwig Maximilians Universitat Munchen, Munich 80333, Germany
    Genome Res 22:2031-42. 2012
  10. pmc Deciphering the modulation of gene expression by type I and II interferons combining 4sU-tagging, translational arrest and in silico promoter analysis
    Mirko Trilling
    Institute for Virology, University Hospital in Essen, University of Duisburg Essen, Essen, D 45147, Germany, Computational Genomics Group, IMIM UPF Research Programme on Biomedical Informatics, Barcelona Biomedical Research Park PRBB, Barcelona 08003, Spain, Department of Medicine, University of Cambridge, Box 157, Addenbrooke s Hospital, Cambridge CB2 0QQ, UK, Division of Pathway Medicine, University of Edinburgh Medical School, Edinburgh, EH16 4SB, Scotland, UK, SynthSys, University of Edinburgh, Edinburgh, EH9 3JU Scotland, UK, Institute of Medical Microbiology, Technical University Munich, Munich 81675, Germany, Institute for Informatics, Ludwig Maximilians University Munich, Munich 80333, Germany and Catalan Institution for Research and Advanced Studies ICREA, Barcelona 08010, Spain
    Nucleic Acids Res 41:8107-25. 2013

Collaborators

Detail Information

Publications23

  1. doi request reprint Bootstrapping the interactome: unsupervised identification of protein complexes in yeast
    Caroline C Friedel
    Institut fur Informatik, Ludwig Maximilians Universitat Munchen, Munchen, Germany
    J Comput Biol 16:971-87. 2009
    ..As a consequence, the approach presented in this article is easily applicable to large-scale TAP experiments for any species even if few complexes are already known...
  2. doi request reprint HALO--a Java framework for precise transcript half-life determination
    Caroline C Friedel
    Institut fur Informatik, Ludwig Maximilians Universitat Munchen, Munchen, Germany
    Bioinformatics 26:1264-6. 2010
    ....
  3. pmc Conserved principles of mammalian transcriptional regulation revealed by RNA half-life
    Caroline C Friedel
    Institute for Informatics, Ludwig Maximilians Universitat Munchen, Munich 80333, Germany
    Nucleic Acids Res 37:e115. 2009
    ..Therefore, this atlas of transcript half-lives provides new fundamental insights into many cellular processes...
  4. pmc Identifying the topology of protein complexes from affinity purification assays
    Caroline C Friedel
    Institut fur Informatik, Ludwig Maximilians Universitat Munchen, Amalienstrasse 17, 80333 München, Germany
    Bioinformatics 25:2140-6. 2009
    ..So far the focus has been on the prediction of complexes as sets of proteins from the experimental results. The modular substructure and the physical interactions within the protein complexes have been mostly ignored...
  5. ncbi request reprint Metabolic tagging and purification of nascent RNA: implications for transcriptomics
    Caroline C Friedel
    Institute for Informatics, Ludwig Maximilians University Munich, Amalienstr 17, 80333 München, Germany
    Mol Biosyst 5:1271-8. 2009
    ..In this article, we review these experimental procedures and discuss their implications for large-scale gene expression profiling...
  6. pmc Influence of degree correlations on network structure and stability in protein-protein interaction networks
    Caroline C Friedel
    LFE Bioinformatik, Institut fur Informatik, Ludwig Maximilians Universitat Munchen, Amalienstrasse 17, 80333 München, Germany
    BMC Bioinformatics 8:297. 2007
    ..We investigated how degree correlations influence the structure of networks and their tolerance against perturbations such as the targeted deletion of hubs...
  7. pmc Inferring topology from clustering coefficients in protein-protein interaction networks
    Caroline C Friedel
    LFE Bioinformatik, Institut fur Informatik, Ludwig Maximilians Universitat Munchen, Amalienstrasse 17, 80333 München, Germany
    BMC Bioinformatics 7:519. 2006
    ..Recently, the possibility was suggested that this scale-free nature may not actually reflect the topology of the complete interactome but could also be due to the error proneness and incompleteness of large-scale experiments...
  8. pmc High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay
    Lars Dölken
    Max von Pettenkofer Institute, Ludwig Maximilians University Munich, Munich 80337, Germany
    RNA 14:1959-72. 2008
    ....
  9. pmc Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution
    Lukas Windhager
    Institute for Informatics, Ludwig Maximilians Universitat Munchen, Munich 80333, Germany
    Genome Res 22:2031-42. 2012
    ..In summary, our study yields unparalleled insights into the kinetics of RNA processing and provides the tools to study molecular mechanisms of RNA processing and their contribution to the regulation of gene expression...
  10. pmc Deciphering the modulation of gene expression by type I and II interferons combining 4sU-tagging, translational arrest and in silico promoter analysis
    Mirko Trilling
    Institute for Virology, University Hospital in Essen, University of Duisburg Essen, Essen, D 45147, Germany, Computational Genomics Group, IMIM UPF Research Programme on Biomedical Informatics, Barcelona Biomedical Research Park PRBB, Barcelona 08003, Spain, Department of Medicine, University of Cambridge, Box 157, Addenbrooke s Hospital, Cambridge CB2 0QQ, UK, Division of Pathway Medicine, University of Edinburgh Medical School, Edinburgh, EH16 4SB, Scotland, UK, SynthSys, University of Edinburgh, Edinburgh, EH9 3JU Scotland, UK, Institute of Medical Microbiology, Technical University Munich, Munich 81675, Germany, Institute for Informatics, Ludwig Maximilians University Munich, Munich 80333, Germany and Catalan Institution for Research and Advanced Studies ICREA, Barcelona 08010, Spain
    Nucleic Acids Res 41:8107-25. 2013
    ..IFN-repressed genes include negative regulators of innate and stress response, and their decrease may thus aid the establishment of a signalling perceptive milieu. ..
  11. pmc FERN - a Java framework for stochastic simulation and evaluation of reaction networks
    Florian Erhard
    LFE Bioinformatik, Institut fur Informatik, Ludwig Maximilians Universitat Munchen, Amalienstrasse 17, Munchen, Germany
    BMC Bioinformatics 9:356. 2008
    ..Thus, in order to use stochastic simulation in innovative high-level modeling and analysis approaches more flexible tools are necessary...
  12. doi request reprint ProCope--protein complex prediction and evaluation
    Jan Krumsiek
    Institut fur Informatik, Ludwig Maximilians Universitat Munchen, Amalienstrasse 17, 80333 München, Germany
    Bioinformatics 24:2115-6. 2008
    ....
  13. pmc Real-time transcriptional profiling of cellular and viral gene expression during lytic cytomegalovirus infection
    Lisa Marcinowski
    Max von Pettenkofer Institute, Ludwig Maximilians University, Munich, Germany
    PLoS Pathog 8:e1002908. 2012
    ..In summary, this study pioneers real-time transcriptional analysis during a lytic herpesvirus infection and highlights numerous novel regulatory aspects of virus-host-cell interaction...
  14. pmc Mining RNA-seq data for infections and contaminations
    Thomas Bonfert
    Institute for Informatics, Ludwig Maximilians Universitat Munchen, Munich, Germany
    PLoS ONE 8:e73071. 2013
    ..By using ContextMap, gene expression of infecting agents can be analyzed and novel insights in infection processes and tumorigenesis can be obtained. ..
  15. doi request reprint Systematic analysis of viral and cellular microRNA targets in cells latently infected with human gamma-herpesviruses by RISC immunoprecipitation assay
    Lars Dölken
    Max von Pettenkofer Institute, Ludwig Maximilians University Munich, 80336 Munich, Germany
    Cell Host Microbe 7:324-34. 2010
    ..Transcript half-life both of cellular and viral miRNA targets negatively correlated with recruitment to RISC complexes, indicating that RIP-Chip offers a quantitative estimate of miRNA function...
  16. ncbi request reprint Reliable gene signatures for microarray classification: assessment of stability and performance
    Chad A Davis
    Institute of Informatics, Ludwig Maximilians Universitat Munchen, Amalienstrasse 17 80333 Munich, Germany
    Bioinformatics 22:2356-63. 2006
    ..Both unstable gene signatures and overestimated classification accuracy can impair biological conclusions...
  17. pmc A context-based approach to identify the most likely mapping for RNA-seq experiments
    Thomas Bonfert
    Institute for Informatics, Ludwig Maximilians University Munich, Amalienstr, 17, 80333 Munich, Germany
    BMC Bioinformatics 13:S9. 2012
    ..e. information from other reads is not taken into account. Second, in case of multiple possible mappings, the mapping with the fewest mismatches is usually chosen which may lead to wrong assignments due to sequencing errors...
  18. doi request reprint Computational analysis of virus-host interactomes
    Caroline C Friedel
    Institute for Informatics, Ludwig Maximilians Universitat, Munchen, Germany
    Methods Mol Biol 1064:115-30. 2013
    ..Here, we describe the central steps of bioinformatics methods applied most commonly for this task and highlight important aspects that need to be considered and potential pitfalls that should be avoided. ..
  19. pmc Detection and correction of probe-level artefacts on microarrays
    Tobias Petri
    Institute for Informatics, Ludwig Maximilians Universitat Munchen, Munich, Germany
    BMC Bioinformatics 13:114. 2012
    ....
  20. pmc Analysis of intraviral protein-protein interactions of the SARS coronavirus ORFeome
    Albrecht von Brunn
    Genzentrum, Max von Pettenkofer Institut, Lehrstuhl Virologie, Ludwig Maximilians Universität LMU, Munchen, Germany
    PLoS ONE 2:e459. 2007
    ..The interactions identified provide valuable material for future studies...
  21. pmc Evolutionarily conserved herpesviral protein interaction networks
    Even Fossum
    Max von Pettenkofer Institut, Ludwig Maximilians Universitat, Munchen, Germany
    PLoS Pathog 5:e1000570. 2009
    ..By combining interactomes of different species we were able to systematically address the low coverage of the Y2H system and to extract biologically relevant interactions which were not evident from single species...
  22. ncbi request reprint Toward the complete interactome
    Caroline C Friedel
    Nat Biotechnol 24:614-5; author reply 615. 2006
  23. ncbi request reprint Support vector machines for separation of mixed plant-pathogen EST collections based on codon usage
    Caroline C Friedel
    Institut fuer Informatik, Ludwig Maximilians Universitaet Muenchen, Oettingenstrasse 67, 80538 Muenchen, Germany
    Bioinformatics 21:1383-8. 2005
    ..When using single-pass cDNA sequences difficulties arise from the short sequence length, the lack of sufficient taxonomically relevant sequence data in public databases and ambiguous sequence homology between plant and pathogen genes...