Pascal Braun

Summary

Affiliation: Technische Universitaet Muenchen (TUM)
Location: Munich, Germany
URL: http://www.wzw.tum.de/sysbiol/index.php?id=36&L=1
Summary:
The goal of my group is to map and functionally understand the principles underlying biological networks using Arabidopsis thaliana as a model. The long-term objective is to understand and predict how perturbation by natural genetic variation or experimental manipulation causes phenotypes.
We perform experimental network mapping on proteome- and module-scale, followed by bioinformatic and experimental functional analyses.

Publications

  1. pmc Genetic characterization of a mammalian protein-protein interaction domain by using a yeast reverse two-hybrid system
    M Vidal
    Massachusetts General Hospital Cancer Center, Charlestown 02129, USA
    Proc Natl Acad Sci U S A 93:10321-6. 1996
  2. doi request reprint High-quality binary interactome mapping
    Matija Dreze
    Center for Cancer Systems Biology CCSB, Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
    Methods Enzymol 470:281-315. 2010
  3. pmc Next-generation sequencing to generate interactome datasets
    Haiyuan Yu
    Center for Cancer Systems Biology, Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
    Nat Methods 8:478-80. 2011
  4. pmc Independently evolved virulence effectors converge onto hubs in a plant immune system network
    M Shahid Mukhtar
    Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    Science 333:596-601. 2011
  5. pmc A systematic screen for CDK4/6 substrates links FOXM1 phosphorylation to senescence suppression in cancer cells
    Lars Anders
    Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
    Cancer Cell 20:620-34. 2011
  6. doi request reprint Interactome mapping for analysis of complex phenotypes: insights from benchmarking binary interaction assays
    Pascal Braun
    Department of Plant Systems Biology, Center of Life and Food Sciences, Technische Universitat Munchen, Freising, Germany
    Proteomics 12:1499-518. 2012
  7. doi request reprint History of protein-protein interactions: from egg-white to complex networks
    Pascal Braun
    Department of Plant Systems Biology, Center for Life and Food Sciences Weihenstephan, Technical University Munich, Freising, Germany
    Proteomics 12:1478-98. 2012
  8. pmc Viral perturbations of host networks reflect disease etiology
    Natali Gulbahce
    Center for Complex Networks Research CCNR and Department of Physics, Northeastern University, Boston, Massachusetts, United States of America
    PLoS Comput Biol 8:e1002531. 2012
  9. pmc Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network
    Nicolas Simonis
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA
    Nat Methods 6:47-54. 2009
  10. pmc Literature-curated protein interaction datasets
    Michael E Cusick
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, 44 Binney Street, Boston, Massachusetts 02115, USA
    Nat Methods 6:39-46. 2009

Collaborators

Detail Information

Publications25

  1. pmc Genetic characterization of a mammalian protein-protein interaction domain by using a yeast reverse two-hybrid system
    M Vidal
    Massachusetts General Hospital Cancer Center, Charlestown 02129, USA
    Proc Natl Acad Sci U S A 93:10321-6. 1996
    ..This two-step selection procedure can be used to characterize any interaction domain that can be tested in the two-hybrid system...
  2. doi request reprint High-quality binary interactome mapping
    Matija Dreze
    Center for Cancer Systems Biology CCSB, Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
    Methods Enzymol 470:281-315. 2010
    ..This chapter describes a high-quality, high-throughput binary protein-protein interactome mapping pipeline that includes these features...
  3. pmc Next-generation sequencing to generate interactome datasets
    Haiyuan Yu
    Center for Cancer Systems Biology, Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
    Nat Methods 8:478-80. 2011
    ..Stitch-seq is applicable to various interaction assays and should help expand interactome network mapping...
  4. pmc Independently evolved virulence effectors converge onto hubs in a plant immune system network
    M Shahid Mukhtar
    Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
    Science 333:596-601. 2011
    ..Thus, pathogens from different kingdoms deploy independently evolved virulence proteins that interact with a limited set of highly connected cellular hubs to facilitate their diverse life-cycle strategies...
  5. pmc A systematic screen for CDK4/6 substrates links FOXM1 phosphorylation to senescence suppression in cancer cells
    Lars Anders
    Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
    Cancer Cell 20:620-34. 2011
    ..Melanoma cells, unlike melanocytes, are highly reliant on CDK4/6-mediated senescence suppression, which makes them particularly susceptible to CDK4/6 inhibition...
  6. doi request reprint Interactome mapping for analysis of complex phenotypes: insights from benchmarking binary interaction assays
    Pascal Braun
    Department of Plant Systems Biology, Center of Life and Food Sciences, Technische Universitat Munchen, Freising, Germany
    Proteomics 12:1499-518. 2012
    ..Here, I review the findings of assay benchmarking and discuss implications for quality control, and for strategies toward obtaining a near-complete map of the interactome of an organism...
  7. doi request reprint History of protein-protein interactions: from egg-white to complex networks
    Pascal Braun
    Department of Plant Systems Biology, Center for Life and Food Sciences Weihenstephan, Technical University Munich, Freising, Germany
    Proteomics 12:1478-98. 2012
    ....
  8. pmc Viral perturbations of host networks reflect disease etiology
    Natali Gulbahce
    Center for Complex Networks Research CCNR and Department of Physics, Northeastern University, Boston, Massachusetts, United States of America
    PLoS Comput Biol 8:e1002531. 2012
    ..The topological proximity found between cellular targets of viral proteins and disease genes was exploited to uncover a novel pathway linking HPV to Fanconi anemia...
  9. pmc Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network
    Nicolas Simonis
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA
    Nat Methods 6:47-54. 2009
    ..Comparison with other types of functional genomic data shows the complementarity of distinct experimental approaches in predicting different functional relationships between genes or proteins..
  10. pmc Literature-curated protein interaction datasets
    Michael E Cusick
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, 44 Binney Street, Boston, Massachusetts 02115, USA
    Nat Methods 6:39-46. 2009
    ..In an evaluation of existing curation of protein interaction experiments reported in the literature, we found that curation can be error-prone and possibly of lower quality than commonly assumed...
  11. pmc An empirical framework for binary interactome mapping
    Kavitha Venkatesan
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, 1 Jimmy Fund Way, Boston, MA 02115, USA
    Nat Methods 6:83-90. 2009
    ....
  12. pmc Combinatorial roles for pRB, p107, and p130 in E2F-mediated cell cycle control
    M Classon
    Massachusetts General Hospital Cancer Center, Building 149, 13th Street, Charlestown, MA 02129, USA
    Proc Natl Acad Sci U S A 97:10820-5. 2000
    ....
  13. ncbi request reprint Cloning of a catalytic subunit of cAMP-dependent protein kinase from the honeybee (Apis mellifera) and its localization in the brain
    D Eisenhardt
    Freie Universitaet Berlin, Institut für Biologie Neurobiologie, Koenigin Luise Strasse 28 30, 14195 Berlin, Germany
    Insect Mol Biol 10:173-81. 2001
    ..However, expression can also be found in the antennal and optic lobes. The level of expression varies within all three neuropiles...
  14. ncbi request reprint FLEXGene repository: from sequenced genomes to gene repositories for high-throughput functional biology and proteomics
    L Brizuela
    Department of Biological Chemistry and Molecular Pharmacology, Institute of Proteomics, Harvard Medical School, 250 Longwood Ave, Boston, MA 02115, USA
    Mol Biochem Parasitol 118:155-65. 2001
    ....
  15. pmc Proteome-scale purification of human proteins from bacteria
    Pascal Braun
    Institute of Proteomics, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 99:2654-9. 2002
    ..We observed that some domains in the Pfam database were found almost exclusively in proteins that were successfully purified and thus may have predictive character...
  16. pmc Molecular characterization of lymphatic endothelial cells
    Simona Podgrabinska
    Derald H Ruttenberg Cancer Center, Mount Sinai School of Medicine, New York, NY 10029, USA
    Proc Natl Acad Sci U S A 99:16069-74. 2002
    ....
  17. ncbi request reprint High throughput protein production for functional proteomics
    Pascal Braun
    Harvard University, Department for Chemistry and Chemical Biology, 12 Oxford Street, Cambridge, MA 02138, USA
    Trends Biotechnol 21:383-8. 2003
    ..This opportunity highlights the need for development of HT methods for protein isolation. This article describes the challenges faced and the approaches taken to develop proteome-scale protein expression systems...
  18. ncbi request reprint QUICKstep and GS-TAP: new moves for protein-interaction analysis
    Pascal Braun
    Nat Methods 3:975-6. 2006
  19. pmc Networking metabolites and diseases
    Pascal Braun
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 105:9849-50. 2008
  20. pmc High-quality binary protein interaction map of the yeast interactome network
    Haiyuan Yu
    Center for Cancer Systems Biology CCSB, Dana Farber Cancer Institute, Boston, MA 02115, USA
    Science 322:104-10. 2008
    ..Rather than correlating with essentiality, protein connectivity correlates with genetic pleiotropy...
  21. pmc An experimentally derived confidence score for binary protein-protein interactions
    Pascal Braun
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA
    Nat Methods 6:91-7. 2009
    ..This general approach will allow a systematic and empirical assignment of confidence scores to all individual protein-protein interactions in interactome networks...
  22. doi request reprint Plant protein interactomes
    Pascal Braun
    Department of Plant Systems Biology, Center for Life and Food Sciences Weihenstephan, Technische Universität München TUM, 85354 Freising Weihenstephan, Germany
    Annu Rev Plant Biol 64:161-87. 2013
    ....