Caroline C Friedel

Summary

Country: Germany

Publications

  1. ncbi 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
  2. ncbi 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
  3. ncbi 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
  4. ncbi 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
  5. ncbi 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
  6. ncbi 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
  7. ncbi 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. ncbi 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. ncbi 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. ncbi 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

Collaborators

Detail Information

Publications19

  1. ncbi 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...
  2. ncbi 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...
  3. ncbi 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...
  4. ncbi 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...
  5. ncbi 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...
  6. ncbi 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
    ..AVAILABILITY: Source code, executables and documentation are available at http://www.bio.ifi.lmu.de/software/halo...
  7. ncbi 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. ncbi 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. ncbi 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. ncbi 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...
  11. ncbi 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
    ..AVAILABILITY: Source code and executables are available at http://www.bio.ifi.lmu.de/Complexes/ProCope/...
  12. ncbi 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...
  13. ncbi 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
    ....
  14. ncbi 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...
  15. ncbi 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...
  16. ncbi 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...
  17. ncbi Reliable gene signatures for microarray classification: assessment of stability and performance
    Chad A Davis
    Institute of Informatics, , Amalienstrasse 17 80333 Munich, Germany
    Bioinformatics 22:2356-63. 2006
    ..We compared our approach to others based on a publicly available dataset on breast cancer. AVAILABILITY: R package at http://www.bio.ifi.lmu.de/~davis/edaprakt..
  18. ncbi Toward the complete interactome
    Caroline C Friedel
    Nat Biotechnol 24:614-5; author reply 615. 2006
  19. ncbi 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...