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Publications

A continuously updated list of publications and citation metrics are available at ResearcherID:


Publications in reverse chronological order (equal contribution ¶, corrosponding author *)


  1. Ostenfeld, M.S., Jeppesen, D.K., Laurberg, J.R., Boysen, A.T., Bramsen, J.B., Primdal-Bengtson, B., Hendrix, A., Lamy, P., Dagnaes-Hansen, F., Rasmussen, M.H., Bui, K.H., Fristrup, N., Christensen, E.I., Nordentoft, I., Morth, J.P., Jensen, J.B., Pedersen, J.S., Beck, M., Theodorescu, D., Borre, M., Howard, K.A., Dyrskjot, L. and Orntoft, T.F. (2014). Cellular Disposal of miR23b by RAB27-Dependent Exosome Release Is Linked to Acquisition of Metastatic Properties.
    Cancer Res Sep 26. PUBMED
  2. Nuclear PoreTitan meets Orbi Winkler J., Ori A., Holzer K., Sticht C., Dauch D., Eiteneuer E.M., Pinna F., Geffers R., Ehemann V., Andres-Pons A., Breuhahn K., Longerich T., Lorenzo Bermejo J., Gretz N., Zender L., Schirmacher P., Beck M., and Singer S. (2014). Prosurvival function of the cellular apoptosis susceptibility/importin-α1 transport cycle is repressed by p53 in liver cancer.
    Hepatology 60(3):884-95. PUBMED
  3. Here we show that over-expression of CAS and importin alhpa 1 protects hepatocellular carcinoma cells from apoptosis in a p53-dependent manner.

  4. Piazza I., Rutkowska A., Ori A., Walczak M., Metz J., Pelechano V., Beck M., and Haering C.H. (2014). Association of condensin with chromosomes depends on DNA binding by its HEAT-repeat subunits.
    Nat Struct Mol Biol 21(6):560-8. PUBMED
  5. This study integrates biochemical and mass spectrometric with genomics approaches to analyze how Condensin complexes bind to chromatin.

  6. Ori, A., Andres-Pons, A. & Beck, M.* (2014). The Use of Targeted Proteomics to Determine the Stoichiometry of Large Macromolecular Assemblies.
    Methods Cell Biol 122C:117-146. PUBMED
  7. This methods chapter describes in high detail how subcellular fractionation can be combined with targeted proteomics to determine the stoichiometry of protein complexes.

  8. Nuclear Pore Beck, M.*, and Glavy, J.S.* (2014). Toward understanding the structure of the vertebrate nuclear pore complex.
    Nucleus 5(2). PUBMED
  9. This is a review article. We discuss technical developments in mass spectrometry and electron microscopy that might be beneficial for structure determination of nuclear pores.

  10. Nuclear PoreTitan meets Orbi Bui, K.H.¶, von Appen, A.¶, DiGuilio, A.L.,Ori, A., Sparks, L., Mackmull, M.T., Bock, T., Hagen, W. Andres-Pons, A., Glavy, J.S.*, and Beck, M.* (2013). Integrated structural analysis of the human nuclear pore complex scaffold.
    Cell 155(6):1233-1243. PUBMED
  11. The scaffold structure of the cytoplasmic and nuclear rings of the human nuclear pore complex was determined using electron microscopy, cross-linking and mass spectrometry. The basic architectural element is a double-vertex formed by the nucleoporin 107 subcomplex. The inter-subcomplex contacts are heavily phosphorylated in mitosis.

    Source data: hNup107 subcomplex structure NPC structure Nup214kd structure Fits as Chimera files

  12. Nuclear PoreTitan meets Orbi Thierbach, K., von Appen, A., Thoms, M., Beck, M., Flemming, D. and Hurt, E. (2013). Protein Interfaces of the Conserved Nup84 Complex from Chaetomium thermophilum Shown by Crosslinking Mass Spectrometry and Electron Microscopy.
    Structure 21:1672-82. PUBMED
  13. A structural model of the Chaetomium thermopilum Nup84 complex was derived using biochemical approaches, cross-linking MS and electron microscopy.

  14. computer Banterle, N.¶, Bui, K.H.¶, Lemke, E.A.*, and Beck, M.* (2013). Fourier ring correlation as a resolution criterion for super resolution microscopy.
    Journal of Structural Biology 183:3. PUBMED
  15. This study shows that Fourier Ring Correlation, a resolution measure developed for electron microscopy data sets, can be used to determine the resolution of super-resolved light microscopy images. A software tool for measuring the resolution is provided that requires the coordinates of the detected single fluorophores as input.

    Software tool: Files Instructions Source data: Super-resolution data

  16. Nuclear PoreTitan meets Orbi Ori, A., Banterle, N.¶, Iskar, M.¶, Andrés-Pons, A.¶, Escher, C., Huy Bui, K., Sparks, L., Solis-Mezarino, V., Rinner, O., Bork, P.*, Lemke, E.A.*, and Beck, M.* (2013). Cell type-specific nuclear pores: a case in point for context-dependent stoichiometry of molecular machines.
    Molecular Systems Biology 9:648. PUBMED
  17. The stoichiometry of the human nuclear pore complex is revealed by targeted mass spectrometry and super-resolution microscopy. The analysis reveals that the composition of the nuclear pore and other nuclear protein complexes is remodeled as a function of the cell type.

    Source data: Absolute quantification Relative Quantification Fluorophore counting

  18. Nuclear Pore Milles, S., Bui, K.H., Koehler, C., Eltsov, M., Beck, M.*, Lemke, E.A.* (2013). Facilitated aggregation of FG nucleoporins under molecular crowding conditions.
    EMBO reports 14:178. PUBMED
  19. This study reveals that FG-nucleoporins rapidely aggregate into amyloid fibers under molecular crowding conditions.

  20. Herzog, F.¶, Kahraman, A.¶, Boehringer, D., Mak, R., Bracher, A., Walzthoeni, T., Leitner, A., Beck, M., Hartl, F.U., Ban, N., Malmström, L., Aebersold R. (2012). Structural probing of a protein phosphatase 2A network by chemical cross-linking and mass spectrometry.
    Science 337:1348. PUBMED
  21. Structures of the protein phosphatase 2A network are systematically characterized by cross-linking mass spectrometry.

  22. computer Walzthoeni, T., Claassen, M., Leitner, A., Herzog, F., Bohn, S., Förster, F., Beck, M.*, and Aebersold, R.* (2012). False discovery rate estimation for cross-linked peptides identified by mass spectrometry.
    Nature Methods 9:901. PUBMED
  23. This paper introduces xProphet, a tool that using a target-decoy strategy, determines false discovery rate in mass-spectrometry data of chemically cross-linked peptides.

  24. computer Xu, M., Beck, M., and Alber, F. (2012). High-throughput subtomogram alignment and classification by Fourier space constrained fast volumetric matching.
    Journal of Structural Biology 178:152. PUBMED
  25. This study introduces an improved algorithm for subtomogram averaging.

  26. Beck, M. ¶, Schmidt, A. ¶, Malmstroem, J., Claassen, M., Ori, A., Szymborska, A., Herzog, F., Rinner, O., Ellenberg, J., and Aebersold R. (2011). The quantitative proteome of a human cell line.
    Molecular Systems Biology 7:549. PUBMED
  27. This study demonstrates that human tissue culture cell lines express at least 10,000 proteins. Copy numbers per cell were calculated for the majority of these proteins. A link between protein function, domain duplication and protein abundance is detected and discussed.

  28. Schmidt, A. ¶, Beck, M. ¶, Malmström, J., Lam, H., Claassen, M., Campbell, D., and Aebersold, R. (2011). Absolute quantification of microbial proteomes at different states by directed mass spectrometry.
    Molecular Systems Biology 7:510. PUBMED
  29. This study demonstrates that proteomes of microbes can be absolutely quantified in a high-throughput manner. A comparative analysis of 25 quantitative proteome maps revealed how the proteome of Leptospira interrogans is changed upon pathogenic progression and antibiotic defense.

  30. computer Xu, M., Beck, M., and Alber, F. (2011). Template-free detection of macromolecular complexes in cryo electron tomograms.
    Bioinformatics 27, I69-I76. PUBMED
  31. An algorithm for the recognition of reoccurring features in cryo electron tomograms is introduced and validated in silico.

  32. computer Reiter, L., Rinner, O., Picotti, P., Hüttenhain, R., Beck, M., Brusniak, M., Hengartner, M.O., and Aebersold, R. (2011) mProphet: automated data processing and statistical validation for large-scale SRM experiments.
    Nature Methods 8, 430-U85. PUBMED
  33. This publication introduces mProphet, a tool for the statistical validation of Selected Reaction Monitoring. In particular, a scoring function and decoy transitions are used for automated data validation and to calculate false positive discovery rates.

  34. Beck, M., Topf, M., Frazier, Z., Tjong, H., Xu, M., Zhang, S.H., and Alber, F. (2011). Exploring the spatial and temporal organization of a cell's proteome.
    Journal of Structural Biology 173, 483-496. PUBMED
  35. This review discusses progress in the fields of structure determination and spatial modeling towards describing the proteome of a cell in time and space.

  36. Beck, M., Claassen, M., and Aebersold, R. (2011). Comprehensive proteomics.
    Current Opinion in Biotechnology 22, 3-8. PUBMED
  37. This review discusses the comprehensiveness of mass spectrometry based proteomics, in particular the difficulty of distinguishing absent from non-detected peptides.

  38. Bohn, S., Beck, F., Sakata, E., Walzthoeni, T., Beck, M., Aebersold, R., Forster, F., Baumeister, W., and Nickell, S. (2010). Structure of the 26S proteasome from Schizosaccharomyces pombe at subnanometer resolution.
    Proceedings of the National Academy of Sciences of the United States of America 49, 20992 – 20997. PUBMED
  39. This study uses an integrated approach to refine the structure of the 26S proteasome to sub-nanometer resolution.

  40. Forster, F., Han, B.G., Beck, M.* (2010). Visual Proteomics.
    Methods in Enzymology 483, 215-243. PUBMED
  41. This book chapter provides a practical guide for detecting the structural signatures of protein complexes in cryo electron tomograms.

  42. Leitner, A., Walzthoeni, T., Kahraman, A., Herzog, F., Rinner, O., Beck, M., and Aebersold, R. (2010). Probing Native Protein Structures by Chemical Cross-linking, Mass Spectrometry, and Bioinformatics.
    Molecular & Cellular Proteomics 9, 1634 – 1649. PUBMED
  43. This review discusses how cross-linked peptides are identified by mass spectrometry in order to determine spatial restraints describing protein folds and interfaces.

    Commencement at EMBL

  44. Titan meets Orbi Beck, M. ¶, Malmström, J. ¶, Lange, V., Schmidt, A., Deutsch, E., and Aebersold, R. (2009). Visual proteomics of the human pathogen Leptospira interrogans.
    Nature Methods 6, 817-823. PUBMED
  45. This paper assesses the feasibility and performance of the visual proteomics approach. Thereby, the structural signatures of the major protein complexes are detected in cryo electron tomograms of Leptospira interrogans cells in a cross-correlation based approach in order to define their position and orientation.

  46. Medalia, N., Beer, A., Zwickl, P., Mihalache, O., Beck, M., Medalia, O., and Navon, A. (2009). Architecture and Molecular Mechanism of PAN, the Archaeal Proteasome Regulatory ATPase.
    The Journal of Biological Chemistry 284, 22952-22960. PUBMED
  47. This study provides a 3D model of the ATPase PAN.

  48. Titan meets Orbi Malmström, J. ¶, Beck, M. ¶, Schmidt, A., Lange, V., Deutsch, E., and Aebersold, R. (2009). Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans.
    Nature 460, 762-765. PUBMED
  49. A mass-spectrometry based approach is used to estimate cellular copy number of the majority of all Leptospira proteins. The accuracy is statistically validated and underlined with independent experimental data obtained by cryo electron tomography.

  50. computer Rinner, O., Seebacher, J., Walzthoeni, T., Mueller, L., Beck, M., Schmidt, A., Mueller, M., and Aebersold, R. (2008). Identification of cross-linked peptides from large sequence databases.
    Nature methods 5 315-318. PUBMED
  51. This study introduces xQuest, a search engine for the identification of cross-linked peptides.

  52. Nuclear Pore Beck, M.*, and Medalia, O. (2008). Structural and functional insights into nucleocytoplasmic transport.
    Histology and Histopathology 23, 1025-1033. PUBMED
  53. Progress in the field of structure determination of Nuclear Pore Complexes at the time, including cryo-EM, X-ray crystallography and NMR studies, is reviewed. We furthermore showed that most Dichtyostelium nucleoporins are sufficiently conserved on the primary sequence level to identify them using Blast and human reference sequences.

  54. Medalia, O., Beck, M., Ecke, M., Weber, I., Neujahr, R., Baumeister, W., and Gerisch, G. (2007). Organization of actin networks in intact filopodia.
    Current Biology 17, 79-84. PUBMED
  55. This study uses cryo electron tomography to elucidate the organization of actin in filopodia.

  56. Nuclear Pore Beck, M., Lucic, V., Forster, F., Baumeister, W., and Medalia, O. (2007). Snapshots of nuclear pore complexes in action captured by cryo-electron tomography.
    Nature 449, 611-615. PUBMED
  57. Here we showed that biological plasticity rather than technical parameters limit the attainable resolution of Nuclear Pores. We quantified deviations from the 8-fold rotational symmetry and introduce a symmetry-independent subtomogram averaging strategy in order to resolve the structure of the Nuclear Pore Complex to 58 Å.

  58. Garvalov, B. K., Zuber, B., Bouchet-Marquis, C., Kudryashev, M., Gruska, M., Beck, M., Leis, A., Frischknecht, F., Bradke, F., Baumeister, W., et al. (2006). Luminal particles within cellular microtubules.
    Journal of Cell Biology 174 759-765. PUBMED
  59. This study describes densities inside of microtubules.

  60. Leis, A. P., Beck, M., Gruska, M., Best, C., Hegerl, R., Baumeister, W., and Leis, J. W. (2006). Cryo-electron tomography of biological specimens.
    IEEE Signal Processing Magazine 23, 95-103. ISI
  61. This review discusses algorithms for the processing of tomographic data sets.

  62. Nuclear Pore Beck, M., Forster, F., Ecke, M., Plitzko, J. M., Melchior, F., Gerisch, G., Baumeister, W., and Medalia, O. (2004). Nuclear pore complex structure and dynamics revealed by cryoelectron tomography.
    Science 306, 1387-1390. PUBMED
  63. In this study we showed that the structure of nuclear pores can be determined from cryo electron tomograms of intact nuclei. We put forward the first isotropically resolved structure of the Nuclear Pore Complex. For this purpose a novel, 'missing wedge-weighted' subtomogram alignment algorithm was developed that is described in more detail in Forster et al., PNAS 2005.


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