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).

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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