Mathias Uhlen

Summary

Affiliation: Royal Institute of Technology
Country: Sweden

Publications

  1. ncbi Assembly of a gene sequence tag microarray by reversible biotin-streptavidin capture for transcript analysis of Arabidopsis thaliana
    Valtteri Wirta
    Department of Molecular Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, SE 106 91, Stockholm, Sweden
    BMC Biotechnol 5:5. 2005
  2. ncbi Antibody-based proteomics for human tissue profiling
    Mathias Uhlen
    Department of Biotechnology, AlbaNova University Center, Royal Institute of Technology, SE 10691 Stockholm, Sweden
    Mol Cell Proteomics 4:384-93. 2005
  3. ncbi A human protein atlas for normal and cancer tissues based on antibody proteomics
    Mathias Uhlen
    Department of Biotechnology, AlbaNova University Center, Royal Institute of Technology KTH, SE 106 91 Stockholm, Sweden
    Mol Cell Proteomics 4:1920-32. 2005
  4. ncbi A genecentric Human Protein Atlas for expression profiles based on antibodies
    Lisa Berglund
    Department of Proteomics, School of Biotechnology, AlbaNova University Center, Royal Institute of Technology, Stockholm, Sweden
    Mol Cell Proteomics 7:2019-27. 2008
  5. ncbi Staphylococcal surface display in combinatorial protein engineering and epitope mapping of antibodies
    Nina Kronqvist
    Department of Molecular Biotechnology, School of Biotechnology, Royal Institute of Technology KTH, AlbaNova University Center, SE 106 91 Stockholm, Sweden
    Recent Pat Biotechnol 4:171-82. 2010
  6. ncbi Validation of serum protein profiles by a dual antibody array approach
    Rebecca Rimini
    Department of Proteomics, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden
    J Proteomics 73:252-66. 2009
  7. ncbi The correlation between cellular size and protein expression levels--normalization for global protein profiling
    Emma Lundberg
    School of Biotechnology, AlbaNova University Center, Royal Institute of Technology KTH, SE 106 91 Stockholm, Sweden
    J Proteomics 71:448-60. 2008
  8. ncbi Prediction of the human membrane proteome
    Linn Fagerberg
    School of Biotechnology, AlbaNova University Center, Royal Institute of Technology KTH, Stockholm, Sweden
    Proteomics 10:1141-9. 2010
  9. ncbi Comparative protein profiling of serum and plasma using an antibody suspension bead array approach
    Jochen M Schwenk
    Department of Proteomics, School of Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden
    Proteomics 10:532-40. 2010
  10. ncbi A whole-genome bioinformatics approach to selection of antigens for systematic antibody generation
    Lisa Berglund
    School of Biotechnology, Royal Institute of Technology KTH, AlbaNova University Center, Stockholm, Sweden
    Proteomics 8:2832-9. 2008

Detail Information

Publications54

  1. ncbi Assembly of a gene sequence tag microarray by reversible biotin-streptavidin capture for transcript analysis of Arabidopsis thaliana
    Valtteri Wirta
    Department of Molecular Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, SE 106 91, Stockholm, Sweden
    BMC Biotechnol 5:5. 2005
    ....
  2. ncbi Antibody-based proteomics for human tissue profiling
    Mathias Uhlen
    Department of Biotechnology, AlbaNova University Center, Royal Institute of Technology, SE 10691 Stockholm, Sweden
    Mol Cell Proteomics 4:384-93. 2005
    ....
  3. ncbi A human protein atlas for normal and cancer tissues based on antibody proteomics
    Mathias Uhlen
    Department of Biotechnology, AlbaNova University Center, Royal Institute of Technology KTH, SE 106 91 Stockholm, Sweden
    Mol Cell Proteomics 4:1920-32. 2005
    ..Our results suggest it should be possible to extend this analysis to the majority of all human proteins thus providing a valuable tool for medical and biological research...
  4. ncbi A genecentric Human Protein Atlas for expression profiles based on antibodies
    Lisa Berglund
    Department of Proteomics, School of Biotechnology, AlbaNova University Center, Royal Institute of Technology, Stockholm, Sweden
    Mol Cell Proteomics 7:2019-27. 2008
    ..The new version of the protein atlas thus is a resource for many areas of biomedical research, including protein science and biomarker discovery...
  5. ncbi Staphylococcal surface display in combinatorial protein engineering and epitope mapping of antibodies
    Nina Kronqvist
    Department of Molecular Biotechnology, School of Biotechnology, Royal Institute of Technology KTH, AlbaNova University Center, SE 106 91 Stockholm, Sweden
    Recent Pat Biotechnol 4:171-82. 2010
    ..In addition, strategies for characterization of recombinant proteins on the staphylococcal cell surface, with an emphasis on an approach for epitope mapping of antibodies, are included...
  6. ncbi Validation of serum protein profiles by a dual antibody array approach
    Rebecca Rimini
    Department of Proteomics, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden
    J Proteomics 73:252-66. 2009
    ....
  7. ncbi The correlation between cellular size and protein expression levels--normalization for global protein profiling
    Emma Lundberg
    School of Biotechnology, AlbaNova University Center, Royal Institute of Technology KTH, SE 106 91 Stockholm, Sweden
    J Proteomics 71:448-60. 2008
    ..The results demonstrate the value of large-scale, automated proteome analysis using immunohistochemistry, in revealing functional correlations and establishing methods to interpret and mine proteomic data...
  8. ncbi Prediction of the human membrane proteome
    Linn Fagerberg
    School of Biotechnology, AlbaNova University Center, Royal Institute of Technology KTH, Stockholm, Sweden
    Proteomics 10:1141-9. 2010
    ..A visualization tool displaying the topologies suggested by the eight prediction methods, for all predicted membrane proteins, is available on the public Human Protein Atlas portal (www.proteinatlas.org)...
  9. ncbi Comparative protein profiling of serum and plasma using an antibody suspension bead array approach
    Jochen M Schwenk
    Department of Proteomics, School of Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden
    Proteomics 10:532-40. 2010
    ....
  10. ncbi A whole-genome bioinformatics approach to selection of antigens for systematic antibody generation
    Lisa Berglund
    School of Biotechnology, Royal Institute of Technology KTH, AlbaNova University Center, Stockholm, Sweden
    Proteomics 8:2832-9. 2008
    ..A genome-wide analysis demonstrates that antigens for approximately 80% of the human protein-coding genes can be selected with this strategy...
  11. ncbi Antibodypedia, a portal for sharing antibody and antigen validation data
    Erik Björling
    School of Biotechnology, Royal Institute of Technology, AlbaNova University Center, SE 106 91 Stockholm, Sweden
    Mol Cell Proteomics 7:2028-37. 2008
    ..The database thus provides a virtual resource of publicly available antibodies toward human proteins with accompanying experimental evidence supporting an individual validation score for each antibody in an application-specific manner...
  12. ncbi Defining the transcriptome and proteome in three functionally different human cell lines
    Emma Lundberg
    Science for Life Laboratory, Royal Institute of Technology, Stockholm, Sweden
    Mol Syst Biol 6:450. 2010
    ..Thus, this study shows a path to characterize the transcriptome and proteome in human cells from different origins...
  13. ncbi Mapping the subcellular protein distribution in three human cell lines
    Linn Fagerberg
    School of Biotechnology, AlbaNova University Center, Royal Institute of Technology KTH, Stockholm, SE 106 91, Sweden
    J Proteome Res 10:3766-77. 2011
    ..Our results show distinct organelle proteomes, well conserved across the cell types, and demonstrate that biochemically similar organelles are grouped together...
  14. ncbi Antibody suspension bead arrays within serum proteomics
    Jochen M Schwenk
    Department of Proteomics, School of Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden
    J Proteome Res 7:3168-79. 2008
    ..The feasibility of this workflow was shown in a study with more than 200 clinical serum samples tested for 20 serum proteins...
  15. ncbi Toward next generation plasma profiling via heat-induced epitope retrieval and array-based assays
    Jochen M Schwenk
    Science for Life Laboratory, Royal Institute of Technology KTH, Stockholm, Sweden
    Mol Cell Proteomics 9:2497-507. 2010
    ..The study shows a path of pursuit for large scale screening of biobank repositories in a flexible and proteome-wide fashion by utilizing heat-induced epitope retrieval and using an antibody suspension bead array format...
  16. ncbi A web-based tool for in silico biomarker discovery based on tissue-specific protein profiles in normal and cancer tissues
    Erik Björling
    School of Biotechnology, AlbaNova University Center, Royal Institute of Technology KTH, SE 10691 Stockholm, Sweden
    Mol Cell Proteomics 7:825-44. 2008
    ..The lists of candidate proteins can be used as a starting point for further validation in larger patient cohorts using both immunological approaches and technologies utilizing more classical proteomics tools...
  17. ncbi Epitope mapping using gram-positive surface display
    Johan Rockberg
    School of Biotechnology, Royal Institute of Technology KTH, AlbaNova University Center, Stockholm, Sweden
    Curr Protoc Immunol . 2010
    ..The protocol described here has been shown useful for mapping of both monoclonal and polyclonal binders with varying epitope lengths...
  18. ncbi Toward a confocal subcellular atlas of the human proteome
    Laurent Barbe
    Department of Biotechnology, AlbaNova University Center, Royal Institute of Technology, SE 106 91 Stockholm, Sweden
    Mol Cell Proteomics 7:499-508. 2008
    ..The results suggest that this approach might be a valuable tool in conjunction with predictive models for protein localization...
  19. ncbi Prediction of antibody response using recombinant human protein fragments as antigen
    Johan Rockberg
    School of Biotechnology, Royal Institute of Technology, AlbaNova University Center, Stockholm SE 106 91, Sweden
    Protein Sci 18:2346-55. 2009
    ..The data set presented here can be used for further studies to design new prediction tools for the generation of antibodies to specific protein targets...
  20. ncbi Generation of monospecific antibodies based on affinity capture of polyclonal antibodies
    Barbara Hjelm
    Department of Biotechnology, AlbaNova University Center, Royal Institute of Technology, 10691 Stockholm, Sweden
    Protein Sci 20:1824-35. 2011
    ....
  21. ncbi Correlations between RNA and protein expression profiles in 23 human cell lines
    Marcus Gry
    Department of Proteomics, School of Biotechnology, AlbaNova University Center, KTH Royal Institute of Technology, Stockholm, Sweden
    BMC Genomics 10:365. 2009
    ....
  22. ncbi Exploring epitopes of antibodies toward the human tryptophanyl-tRNA synthetase
    Barbara Hjelm
    Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden
    N Biotechnol 27:129-37. 2010
    ..An alanine-scanning experiment showed binding to four specific residues. The implications for the systematic analysis of antibody epitopes on the basis of these results are discussed...
  23. ncbi Automated sample preparation method for mass spectrometry analysis on recombinant proteins
    Johanna Steen
    School of Biotechnology, Department of Proteomics, AlbaNova University Center, Royal Institute of Technology, 106 91 Stockholm, Sweden
    J Chromatogr A 1216:4457-64. 2009
    ....
  24. ncbi A human protein atlas based on antibody proteomics
    Anja Persson
    Royal Institute of Technology, School of Biotechnology, AlbaNova University Center, SE 106 91 Stockholm, Sweden
    Curr Opin Mol Ther 8:185-90. 2006
    ..The Human Protein Atlas is related to four other expression atlas initiatives, including, in particular, an upcoming protein atlas developed by the Sanger Institute...
  25. ncbi Large-scale protein profiling in human cell lines using antibody-based proteomics
    Linn Fagerberg
    Department of Proteomics, School of Biotechnology, AlbaNova University Center, KTH Royal Institute of Technology, SE 10691 Stockholm, Sweden
    J Proteome Res 10:4066-75. 2011
    ..This work also provides an extensive list of antibodies, for which high-resolution images as well as validation data are available on the Human Protein Atlas ( www.proteinatlas.org ), that are of potential use in cell line studies...
  26. ncbi Analysis of transcript and protein overlap in a human osteosarcoma cell line
    Daniel Klevebring
    Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Royal Institute of Technology, SE 171 65 Solna, Sweden
    BMC Genomics 11:684. 2010
    ....
  27. ncbi Determination of binding specificities in highly multiplexed bead-based assays for antibody proteomics
    Jochen M Schwenk
    Department of Proteomics, Royal Institute of Technology KTH, SE 10691 Stockholm, Sweden
    Mol Cell Proteomics 6:125-32. 2007
    ..This high throughput analysis will potentially have great impact on the possibility for the utilization of different antibody proteomics approaches where the quality assessment of antibodies is of the utmost importance...
  28. ncbi Creation of an antibody-based subcellular protein atlas
    Emma Lundberg
    School of Biotechnology, AlbaNova University Center, Royal Institute of Technology KTH, Stockholm, Sweden
    Proteomics 10:3984-96. 2010
    ..The considerations made when creating the subcellular protein atlas and critical parameters of this approach are discussed...
  29. ncbi A single fixation protocol for proteome-wide immunofluorescence localization studies
    Charlotte Stadler
    School of Biotechnology, AlbaNova University Center, Royal Institute of Technology KTH, SE 106 91 Stockholm, Sweden
    J Proteomics 73:1067-78. 2010
    ....
  30. ncbi A transcriptional timetable of autumn senescence
    Anders Andersson
    Department of Biotechnology, KTH - Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
    Genome Biol 5:R24. 2004
    ..We also found evidence for increased transcriptional activity before the appearance of visible signs of senescence, presumably preparing the leaf for degradation of its components...
  31. ncbi Targeted protein pullout from human tissue samples using competitive elution
    Ronny Falk
    Royal Institute of Technology, AlbaNova University Center, Department of Biotechnology, Stockholm, Sweden
    Biotechnol J 6:28-37. 2011
    ..Competitive elution has thus been shown to offer an effective approach for wide-scale pullout experiments where proteins and their interaction partners are to be studied...
  32. ncbi The 6th HUPO Antibody Initiative (HAI) workshop: sharing data about affinity reagents and other recent developments. September 2009, Toronto, Canada
    Kalle Jonasson
    School of Biotechnology, AlbaNova University Center, Royal Institute of Technology KTH, Stockholm, Sweden
    Proteomics 10:2066-8. 2010
    ..workshop for the HUPO Antibody Initiative (HAI) held in September 2009 was co-chaired by Michael Snyder and Mathias Uhlen and discussed several aspects of antibody production, their validation, and attempts to standardise this ..
  33. ncbi A novel method for reproducible fluorescent labeling of small amounts of antibodies on solid phase
    Emma Lundberg
    Department of Biotechnology, Royal Institute of Technology, Roslagstullsbacken 21, SE 106 91 Stockholm, Sweden
    J Immunol Methods 322:40-9. 2007
    ..This novel solid-phase antibody labeling method may also be applicable for other conjugation chemistries and labels, and has potential for high-throughput applications...
  34. ncbi Towards a human proteome atlas: high-throughput generation of mono-specific antibodies for tissue profiling
    Peter Nilsson
    Department of Biotechnology, Royal Institute of Technology (KTH, Stockholm, Sweden
    Proteomics 5:4327-37. 2005
    ..The results suggest that a comprehensive atlas containing extensive protein expression and subcellular localization data of the human proteome can be generated in an efficient manner with mono-specific antibodies...
  35. ncbi Droplet size based separation by deterministic lateral displacement-separating droplets by cell--induced shrinking
    Haakan N Joensson
    Div of Nanobiotechnology, Royal Institute of Technology, KTH, AlbaNova University Center, SE 10691 Stockholm, Sweden
    Lab Chip 11:1305-10. 2011
    ..g. clonal selection. The same device also separates 11 µm from 30 µm droplets at a rate of 12,000 droplets per second, more than twofold faster than previously demonstrated passive hydrodynamic separation devices...
  36. ncbi Generation and validation of affinity reagents on a proteome-wide level
    Mathias Uhlen
    Department of Proteomics, School of Biotechnology, Royal Institute of Technology KTH, AlbaNova University Center, Stockholm, Sweden
    J Mol Recognit 22:57-64. 2009
    ..proteinatlas.org) showing the human protein profiles in a large number of normal and cancer tissues as well as a large set of human cell lines...
  37. ncbi Epitope mapping of antibodies using bacterial surface display
    Johan Rockberg
    Department of Molecular Biotechnology, School of Biotechnology, Royal Institute of Technology KTH, AlbaNova University Center, SE 106 91 Stockholm, Sweden
    Nat Methods 5:1039-45. 2008
    ..Our approach shows a path forward for systematic validation of antibodies for epitope specificity and cross-reactivity on a whole-proteome level...
  38. ncbi Affinity recovery of eight HER2-binding affibody variants using an anti-idiotypic affibody molecule as capture ligand
    Helena Wållberg
    Division of Molecular Biotechnology, School of Biotechnology, AlbaNova University Center, Royal Institute of Technology KTH, SE 106 91 Stockholm, Sweden
    Protein Expr Purif 76:127-35. 2011
    ....
  39. ncbi The epitope space of the human proteome
    Lisa Berglund
    School of Biotechnology, AlbaNova University Center, Royal Institute of Technology, SE 106 91 Stockholm, Sweden
    Protein Sci 17:606-13. 2008
    ..The implications for human antibody-based proteomics efforts are discussed...
  40. ncbi High nuclear RBM3 expression is associated with an improved prognosis in colorectal cancer
    Barbara Hjelm
    Department of Proteomics, AlbaNova University Center, Royal Institute of Technology, Stockholm, Sweden
    Proteomics Clin Appl 5:624-35. 2011
    ..In this study, we investigated the prognostic impact of human RBM3 expression in colorectal cancer using tissue microarray-based immunohistochemical analysis...
  41. ncbi Discovery of epitopes for targeting the human epidermal growth factor receptor 2 (HER2) with antibodies
    Johan Rockberg
    School of Biotechnology, Royal Institute of Technology KTH, AlbaNova University Center, SE 106 91 Stockholm, Sweden
    Mol Oncol 3:238-47. 2009
    ..The work describes a new strategy to develop antibodies directed to non-overlapping epitopes and shows a path of pursuit to explore the epitope space of a target protein...
  42. ncbi Mapping the human proteome using antibodies
    Mathias Uhlen
    School of Biotechnology, AlbaNova University Center, Royal Institute of Technology (KTH, S-106 91 Stockholm, Sweden
    Mol Cell Proteomics 6:1455-6. 2007
  43. ncbi Expression and immunogenicity of six putative variable surface proteins in Mycoplasma mycoides subsp. mycoides SC
    Carl Hamsten
    Department of Proteomics, School of Biotechnology, Royal Institute of Technology KTH, AlbaNova University Center, Stockholm, Sweden
    Microbiology 154:539-49. 2008
    ..Vmm and one of the putative Vmm-type proteins showed variable expression in vitro...
  44. ncbi A new era for proteomics research?
    Mathias Uhlen
    School of Biotechnology, AlbaNova University Center, Royal Institute of Technology KTH, Stockholm SE 10691, Sweden
    Genome Biol 9:325. 2008
    ..A report of the 7th Annual Human Proteome Organization (HUPO) Conference, Amsterdam, the Netherlands, 16-20 August 2008...
  45. ncbi High-throughput protein production--lessons from scaling up from 10 to 288 recombinant proteins per week
    Hanna Tegel
    School of Biotechnology, Royal Institute of Technology, Stockholm, Sweden
    Biotechnol J 4:51-7. 2009
    ..The number of manual handling steps has been significantly reduced (from 18 to 9) and the protein purification has been completely automated...
  46. ncbi Affinity as a tool in life science
    Mathias Uhlen
    School of Biotechnology, AlbaNova University Center, Royal Institute of Technology, Stockholm, Sweden
    Biotechniques 44:649-54. 2008
    ..Recently, such affinity proteomics have allowed the detailed analysis of human protein expression in a comprehensive manner both in normal and disease tissue using tissue microarrays and confocal microscopy...
  47. ncbi Affibody molecules in protein capture microarrays: evaluation of multidomain ligands and different detection formats
    Björn Renberg
    School of Biotechnology, Division of Molecular Biotechnology, Royal Institute of Technology, AlbaNova University Center, SE 106 91 Stockholm, Sweden
    J Proteome Res 6:171-9. 2007
    ..Finally, the presence of IgA was determined using detection of directly Cy5-labeled normal or IgA-deficient serum samples...
  48. ncbi Detection and analysis of low-abundance cell-surface biomarkers using enzymatic amplification in microfluidic droplets
    Haakan N Joensson
    Department of Nano Biotechnology, Royal Institute of Technology, AlbaNova University Center, 10691 Stockholm, Sweden
    Angew Chem Int Ed Engl 48:2518-21. 2009
    ..Droplet optical labels allow concurrent analysis of several samples...
  49. ncbi Analysis of protein expression in cell microarrays: a tool for antibody-based proteomics
    Ann-Catrin Andersson
    Department of Genetics and Pathology, Rudbeck Laboratory, University Hospital, Uppsala, Sweden
    J Histochem Cytochem 54:1413-23. 2006
    ..We conclude that a modified TMA technique, including cell samples, provides a valuable tool for high-throughput analysis of protein expression, and that this technique can be used for global approaches to explore the human proteome...
  50. ncbi A high-throughput strategy for protein profiling in cell microarrays using automated image analysis
    Sara Strömberg
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
    Proteomics 7:2142-50. 2007
    ....
  51. ncbi Human Proteinpedia enables sharing of human protein data
    Suresh Mathivanan
    Nat Biotechnol 26:164-7. 2008
  52. ncbi Publication Committee meeting. HUPO 5th annual World Congress. Long Beach, CA, USA 30 October 2006
    Sandra Orchard
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
    Proteomics 7:1009-11. 2007
    ..Discussions centred on how best to structure interactions between journals, databases and researchers to improve accessibility to data, and facilitate comparisons between datasets...
  53. ncbi A reagent resource to identify proteins and peptides of interest for the cancer community: a workshop report
    Brian B Haab
    Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
    Mol Cell Proteomics 5:1996-2007. 2006
    ..This workshop report explores various approaches to develop a framework that will most effectively fulfill the needs of the NCI and the cancer research community...
  54. ncbi Large-scale proteomics analysis of human ovarian cancer for biomarkers
    Sofia Bengtsson
    Department of Protein Technology, Lund University, 221 84 Lund, Sweden
    J Proteome Res 6:1440-50. 2007
    ..Currently, we have validated 5 of these antibodies for use in immunohistochemical analysis using tissue microarrays of healthy and diseased ovarian, as well as other, human tissues...