Ola Söderberg

Summary

Affiliation: Uppsala University
Country: Sweden

Publications

  1. ncbi Characterizing proteins and their interactions in cells and tissues using the in situ proximity ligation assay
    Ola Söderberg
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE 75185 Uppsala, Sweden
    Methods 45:227-32. 2008
  2. ncbi High content screening for inhibitors of protein interactions and post-translational modifications in primary cells by proximity ligation
    Karl Johan Leuchowius
    Molecular Medicine, Department of Genetics and Pathology, Uppsala University, Rudbeck Laboratory, Dag Hammarskjölds väg 20, S 751 85 Uppsala, Sweden
    Mol Cell Proteomics 9:178-83. 2010
  3. ncbi Direct observation of individual endogenous protein complexes in situ by proximity ligation
    Ola Söderberg
    Department of Genetics and Pathology, Rudbeck Laboratory, University of Uppsala, SE 75185 Uppsala, Sweden
    Nat Methods 3:995-1000. 2006
  4. ncbi Visualising individual sequence-specific protein-DNA interactions in situ
    Irene Weibrecht
    Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, SE 75185 Uppsala, Sweden
    N Biotechnol 29:589-98. 2012
  5. ncbi In situ proximity ligation assay for microscopy and flow cytometry
    Karl Johan Leuchowius
    Department of Immunology, Uppsala University, Uppsala, Sweden
    Curr Protoc Cytom . 2011
  6. ncbi Flow cytometric in situ proximity ligation analyses of protein interactions and post-translational modification of the epidermal growth factor receptor family
    Karl Johan Leuchowius
    Department of Genetics and Pathology, Rudbeck Laboratory, University of Uppsala, Uppsala SE 75185, Sweden
    Cytometry A 75:833-9. 2009
  7. ncbi Western blotting via proximity ligation for high performance protein analysis
    Yanling Liu
    Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, SE 751 85 Uppsala, Sweden
    Mol Cell Proteomics 10:O111.011031. 2011
  8. ncbi Proximity ligation assays: a recent addition to the proteomics toolbox
    Irene Weibrecht
    Department of Genetics and Pathology, Rudbeck Laboratory, University of Uppsala, Uppsala, Sweden
    Expert Rev Proteomics 7:401-9. 2010
  9. ncbi Proximity ligation: a specific and versatile tool for the proteomic era
    Ola Söderberg
    University of Uppsala, Department of Genetics and Pathology, Rudbeck Laboratory, SE 751 85 Uppsala, Sweden
    Genet Eng (N Y) 28:85-93. 2007
  10. ncbi Analysis of genes, transcripts, and proteins via DNA ligation
    Tim Conze
    Department of Genetics and Pathology, The Rudbeck Lab, Uppsala University, Uppsala, Sweden
    Annu Rev Anal Chem (Palo Alto Calif) 2:215-39. 2009

Collaborators

Detail Information

Publications23

  1. ncbi Characterizing proteins and their interactions in cells and tissues using the in situ proximity ligation assay
    Ola Söderberg
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE 75185 Uppsala, Sweden
    Methods 45:227-32. 2008
    ....
  2. ncbi High content screening for inhibitors of protein interactions and post-translational modifications in primary cells by proximity ligation
    Karl Johan Leuchowius
    Molecular Medicine, Department of Genetics and Pathology, Uppsala University, Rudbeck Laboratory, Dag Hammarskjölds väg 20, S 751 85 Uppsala, Sweden
    Mol Cell Proteomics 9:178-83. 2010
    ..In addition, inhibitor-induced perturbation of protein-protein interactions of the PDGF signaling pathway could be quantified, further demonstrating the usefulness of the assay in drug discovery...
  3. ncbi Direct observation of individual endogenous protein complexes in situ by proximity ligation
    Ola Söderberg
    Department of Genetics and Pathology, Rudbeck Laboratory, University of Uppsala, SE 75185 Uppsala, Sweden
    Nat Methods 3:995-1000. 2006
    ..We used this method to show specific regulation of protein-protein interactions between endogenous Myc and Max oncogenic transcription factors in response to interferon-gamma (IFN-gamma) signaling and low-molecular-weight inhibitors...
  4. ncbi Visualising individual sequence-specific protein-DNA interactions in situ
    Irene Weibrecht
    Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, SE 75185 Uppsala, Sweden
    N Biotechnol 29:589-98. 2012
    ..Although efficiency of detection currently is limiting, we conclude that in situ PLA can be used to achieve a highly selective analysis of PDIs in single cells...
  5. ncbi In situ proximity ligation assay for microscopy and flow cytometry
    Karl Johan Leuchowius
    Department of Immunology, Uppsala University, Uppsala, Sweden
    Curr Protoc Cytom . 2011
    ..It also includes information on expected results and information on how to troubleshoot the assay...
  6. ncbi Flow cytometric in situ proximity ligation analyses of protein interactions and post-translational modification of the epidermal growth factor receptor family
    Karl Johan Leuchowius
    Department of Genetics and Pathology, Rudbeck Laboratory, University of Uppsala, Uppsala SE 75185, Sweden
    Cytometry A 75:833-9. 2009
    ..The combination of in situ PLA and flow cytometry provided a statistically powerful way of analyzing protein-protein interactions and post-translational modifications on a single-cell basis...
  7. ncbi Western blotting via proximity ligation for high performance protein analysis
    Yanling Liu
    Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, SE 751 85 Uppsala, Sweden
    Mol Cell Proteomics 10:O111.011031. 2011
    ....
  8. ncbi Proximity ligation assays: a recent addition to the proteomics toolbox
    Irene Weibrecht
    Department of Genetics and Pathology, Rudbeck Laboratory, University of Uppsala, Uppsala, Sweden
    Expert Rev Proteomics 7:401-9. 2010
    ..Lastly, we apply the approach of recombining subcomponents to develop a few novel hypothetical methods hoping this might stimulate the readers to utilize this approach themselves...
  9. ncbi Proximity ligation: a specific and versatile tool for the proteomic era
    Ola Söderberg
    University of Uppsala, Department of Genetics and Pathology, Rudbeck Laboratory, SE 751 85 Uppsala, Sweden
    Genet Eng (N Y) 28:85-93. 2007
    ..In this review we discuss commonly used detection methods and compare these to the recently-developed proximity ligation technique...
  10. ncbi Analysis of genes, transcripts, and proteins via DNA ligation
    Tim Conze
    Department of Genetics and Pathology, The Rudbeck Lab, Uppsala University, Uppsala, Sweden
    Annu Rev Anal Chem (Palo Alto Calif) 2:215-39. 2009
    ....
  11. ncbi In situ detection and genotyping of individual mRNA molecules
    Chatarina Larsson
    Department of Genetics and Pathology, Uppsala University, Sweden
    Nat Methods 7:395-7. 2010
    ..We detect a somatic point mutation, differentiate between members of a gene family and perform multiplex detection of transcripts in human and mouse cells and tissue...
  12. ncbi In situ detection of phosphorylated platelet-derived growth factor receptor beta using a generalized proximity ligation method
    Malin Jarvius
    Department of Genetics and Pathology, Rudbeck Laboratory, University of Uppsala, SE 75185, Uppsala, Sweden
    Mol Cell Proteomics 6:1500-9. 2007
    ..The method should be of great value to study signal transduction, screen for effects of pharmacological agents, and enhance the diagnostic potential in histopathology...
  13. ncbi Methods for analysis of the cancer microenvironment and their potential for disease prediction, monitoring and personalized treatments
    Carl Magnus Clausson
    Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, University of Uppsala, S 751 85, Uppsala, Sweden
    EPMA J 3:7. 2012
    ..Herein we describe how padlock probes and in situ PLA can be used for visualization of nucleic acids and protein activity, respectively, directly in tissue sections, and their potential future role in personalized medicine...
  14. ncbi Ligation-based molecular tools for lab-on-a-chip devices
    Jonas Melin
    Department of Genetics and Pathology, Rudbeck Laboratory, University of Uppsala, SE 75185 Uppsala, Sweden
    N Biotechnol 25:42-8. 2008
    ..We discuss these problems and describe a series of molecular tools that may present new opportunities for lab-on-a-chip devices at the point-of-care...
  15. ncbi Simultaneous visualization of both signaling cascade activity and end-point gene expression in single cells
    Irene Weibrecht
    Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
    PLoS ONE 6:e20148. 2011
    ..g. pinpoint effector sites of drugs in a signaling pathway...
  16. ncbi Automated classification of multicolored rolling circle products in dual-channel wide-field fluorescence microscopy
    Milan Gavrilović
    Department of Information Technology, Centre for Image Analysis, Uppsala University, Uppsala, Sweden
    Cytometry A 79:518-27. 2011
    ..We also demonstrate how the methods can be used as tools to evaluate biochemical protocols by measuring detection probe quality and accuracy. Finally, the method is used to evaluate single-molecule detection events in situ...
  17. ncbi Molecular tools for companion diagnostics
    Agata Zieba
    Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, SE 75185 Uppsala, Sweden
    N Biotechnol 29:634-40. 2012
    ....
  18. ncbi Functional overlap between chondroitin and heparan sulfate proteoglycans during VEGF-induced sprouting angiogenesis
    Sebastien Le Jan
    Rudbeck Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
    Arterioscler Thromb Vasc Biol 32:1255-63. 2012
    ..The present study was undertaken to investigate if there is a functional overlap between heparan sulfate proteoglycans and chondroitin sulfate proteoglycans during sprouting angiogenesis...
  19. ncbi Molecular tools for a molecular medicine: analyzing genes, transcripts and proteins using padlock and proximity probes
    Ulf Landegren
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE 751 85 Uppsala, Sweden
    J Mol Recognit 17:194-7. 2004
    ..The procedures permit highly specific solution-phase or localized analyses of large sets of target molecules as required in future molecular analyses...
  20. ncbi VEGF receptor 2/-3 heterodimers detected in situ by proximity ligation on angiogenic sprouts
    Ingrid Nilsson
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
    EMBO J 29:1377-88. 2010
    ..We conclude that VEGFR2/-3 heterodimers on angiogenic sprouts induced by VEGFA or VEGFC may serve to positively regulate angiogenic sprouting...
  21. ncbi U-2973, a novel B-cell line established from a patient with a mature B-cell leukemia displaying concurrent t(14;18) and MYC translocation to a non-IG gene partner
    Hans Bostrom
    Department of Genetics and Pathology, Uppsala University, Uppsala, Sweden
    Eur J Haematol 81:218-25. 2008
    ..1...
  22. ncbi Transcriptional profiling of human glioblastoma vessels indicates a key role of VEGF-A and TGFβ2 in vascular abnormalization
    Lothar C Dieterich
    Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Sweden
    J Pathol 228:378-90. 2012
    ..Copyright © 2012 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd...
  23. ncbi MUC2 mucin is a major carrier of the cancer-associated sialyl-Tn antigen in intestinal metaplasia and gastric carcinomas
    Tim Conze
    Department of Genetics and Pathology, University of Uppsala, Uppsala, Sweden
    Glycobiology 20:199-206. 2010
    ..Identification of the mucin which is the carrier of a carbohydrate structure offers unique advantages for future development of more accurate diagnostic and prognostic markers...