Selected Publications

Soste M, Charmpi K, Lampert F, Gerez JA, van Oostrum M, Malinovska L, Boersema PJ, Prymaczok NC, Riek R, Peter M, Vanni S, Beyer A, Picotti P.
Proteomics-based monitoring of pathway activity reveals that blocking diacylglycerol biosynthesis rescues from alpha-synuclein toxicity. Cell Systems (in press).

Andreas Lackner, Robert Sehlke , Marius Garmhausen, Giuliano Giuseppe Stirparo, Michelle Huth, Fabian Titz-Teixeira, Petra van der Lelij, Julia Ramesmayer, Henry F Thomas, Meryem Ralser, Laura Santini, Elena Galimberti, Mihail Sarov, A Francis Stewart, Austin Smith, Andreas Beyer, Martin Leeb (2021)
Cooperative genetic networks drive embryonic stem cell transition from naïve to formative pluripotency. EMBO J. 2021 Apr 15;40(8):e105776. doi: 10.15252/embj.2020105776. Epub 2021 Mar 9.

Valentina Cappelletti, Thomas Hauser, Ilaria Piazza, Monika Pepelnjak, Liliana Malinovska , Tobias Fuhrer, Yaozong Li, Christian Dörig, Paul Boersema, Ludovic Gillet, Jan Grossbach, Aurelien Dugourd, Julio Saez-Rodriguez, Andreas Beyer, Nicola Zamboni, Amedeo Caflisch, Natalie de Souza, Paola Picotti (2021)
Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ. Cell. 2021 Jan 21;184(2):545-559.e22. doi: 10.1016/j.cell.2020.12.021. Epub 2020 Dec 23.

Konstantina Charmpi , Tiannan Guo, Qing Zhong, Ulrich Wagner, Rui Sun, Nora C Toussaint, Christine E Fritz, Chunhui Yuan, Hao Chen, Niels J Rupp, Ailsa Christiansen, Dorothea Rutishauser , Jan H Rüschoff , Christian Fankhauser, Karim Saba, Cedric Poyet, Thomas Hermanns , Kathrin Oehl, Ariane L Moore, Christian Beisel, Laurence Calzone, Loredana Martignetti , Qiushi Zhang , Yi Zhu, María Rodríguez Martínez, Matteo Manica, Michael C Haffner, Ruedi Aebersold , Peter J Wild, Andreas Beyer (2020)
Convergent network effects along the axis of gene expression during prostate cancer progression. Genome Biol. 2020 Dec 14;21(1):302.

Stephan Kamrad, Jan Grossbach, Maria Rodríguez-López, Michael Müller , StJohn Townsend, Valentina Cappelletti, Gorjan Stojanovski, Clara Correia-Melo, Paola Picotti, Andreas Beyer, Markus Ralser, Jürg Bähler(2020)
Pyruvate kinase variant of fission yeast tunes carbon metabolism, cell regulation, growth and stress resistance. Mol Syst Biol 2020 Apr;16(4):e9270.

Oliver Hahn, Lisa F. Drews, An Nguyen, Takashi Tatsuta, Lisonia Gkioni, Oliver Hendrich, Qifeng Zhang, Thomas Langer, Scott Pletcher, Michael J. O. Wakelam, Andreas Beyer, Sebastian Grönke, and Linda Partridge (2019)
A nutritional memory effect counteracts benefits of dietary restriction in old mice. Nat Metab. 2019 Nov;1(11):1059-1073.

Debès C, Leote AC, Beyer A (2019)
Computational approaches for the systematic analysis of ageing-associated molecular alterations (Review). Drug Discovery Today: Disease Models 27:51-59.

Hahn O, Stubbs TM, Reik W, Grönke S, Beyer A, Partridge L. (2018)
Hepatic gene body hypermethylation is a shared epigenetic signature of murine longevity. PLoS Genet. 14(11):e1007766.

Liu Y, Borel C, Li L, Müller T, Williams EG, Germain P-L, Buljan M, Sajic T, Boersema PJ, Shao W, Faini M, Testa G, Beyer A, Antonarakis SE, Aebersold R. (2017)
Systematic proteome and proteostasis profiling in human Trisomy 21 fibroblast cells. Nat. Commun. 8:1212.

Tain LS, Sehlke R, Jain C, Chokkalingam M, Nagarajuna N, Essers P, Rassner M, Grönke S, Froelich J, Dieterich C, Mann M, Alic N, Beyer A, Partridge L. (2017)
A proteomic atlas of insulin signaling reveals tissue-specific mechanisms of longevity-assurance. Mol. Syst. Biol. 13(9):939. doi: 10.15252/msb.20177663.

Liu Y, Beyer A, Aebersold R (2016)
On the Dependency of Cellular Protein Levels on mRNA Abundance. Cell, 165(3):535-50.

Johannes Stephan, Oliver Stegle, Andreas Beyer (2015)
A random forest approach to capture genetic effects in the presence of population structure. Nature Communications, doi:10.1038/ncomms8432

Mathieu Clément-Ziza, Francesc X Marsellach, Sandra Codlin, Manos A Papadakis, Susanne Reinhardt, María Rodriguez-López, Stuart Martin, Samuel Marguerat, Alexander Schmidt, Eunhye Lee, Christopher T Workman, Jürg Bahler & Andreas Beyer (2014)
Natural genetic variation impacts expression levels of coding, non-coding, and antisense transcripts in fission yeast. Molec. Syst. Biol. 10:764.

Kuhn M, Hyman AA, Beyer A (2014)
Coiled-Coil Proteins Facilitated the Functional Expansion of the Centrosome. PLoS Comp. Biol., 10(6):e1003657

Sikora-Wohlfeld W, Ackermann M, Christodoulou EG, Singaravelu K, Beyer A. (2013)
Assessing computational methods for transcription factor target gene identication based on ChIP-seq data. PLoS Comp. Biol.,9(11):e1003342

Ackermann M, Sikora-Wohlfeld W, Beyer A. (2013)
Impact of natural genetic variation on gene expression dynamics. PLoS Genetics, 9(6):e1003514

Paola Picotti, Mathieu Clément-Ziza, Henry Lam, David S. Campbell, Alexander Schmidt, Eric W. Deutsch, Hannes Röst, Zhi Sun, Oliver Rinner, Lukas Reiter, Qin Shen, Jacob J. Michaelson, Andreas Frei, Simon Alberti, Ulrike Kusebauch, Bernd Wollscheid, Robert L. Moritz, Andreas Beyer and Ruedi Aebersold (2013)
A complete mass spectrometric map of the yeast proteome applied to quantitative trait analysis. Nature, doi:10.1038/nature11835

Elefsinioti A, Saraç ÖS, Hegele A, Plake C, Hubner NC, Poser I, Sarov M, Hyman A, Mann M, Schroeder M, Stelzl U, Beyer A. (2011)
Large-scale de novo prediction of physical protein-protein association. Mol Cell Proteomics. 10(11):M111.010629.

Michaelson JJ, Alberts R, Schughart K, Beyer A. (2010)
Data-driven assessment of eQTL mapping methods.BMC Genomics. 7;11:502.

Michaelson JJ, Loguercio S, Beyer A. (2009)
Detection and interpretation of expression quantitative trait loci (eQTL). Methods 48(3):265-76.

Suthram S, Beyer A, Ideker T. (2008)
eQED: an efficient method for interpreting eQTL associations using protein networks. Molec. Syst. Biol. 4:162.

Beyer A, Bandyopadhyay S, Ideker T. (2007)
Integrating physical and genetic maps: from genomes to interaction networks. Nat. Rev. Genet. 8(9):699-710.

R. Brockman, A.Beyer, J. Heinisch, T. Wilhelm (2007)
Posttranscriptional expression regulation: what determines translation rates? PLoS Comput. Biol. 3(3):e57.

A. Beyer, C. Workman, J. Hollunder, D. Radke, U. Möller, T. Wilhelm, T.G. Ideker (2006)
Integrated assessment and prediction of transcription factor binding. PLoS Comput. Biol. 2(6):e70.

J. Hollunder, A. Beyer, T. Wilhelm (2005)
Identification and characterization of protein subcomplexes in yeast. Proteomics 5(8):2082-9.

A. Beyer, T. Wilhelm (2005)
Dynamic simulation of protein complex formation on a genomic scale. Bioinformatics 21(8):1610-6.

A. Beyer, J. Hollunder, H.P. Nasheuer, T. Wilhelm (2004)
Post-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale. Mol. Cell. Proteomics 3(11):1083-92.

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