Antonios Papadakis, Akos Gyenis, Joris Pothof, Jan H J Hoeijmakers, Argyris Papantonis, Andreas Beyer (2023)
Age-associated transcriptional stress due to accelerated elongation and increased stalling of RNAPII Nat Genet (2023) https://doi.org/10.1038/s41588-023-01601-w
Matthias Weith, Jan Großbach, Mathieu Clement-Ziza, Ludovic Gillet, María Rodríguez-López, Samuel Marguerat, Christopher T Workman, Paola Picotti, Jürg Bähler, Ruedi Aebersold, Andreas Beyer (2023)
Genetic effects on molecular network states explain complex traits Molecular Systems Biology (2023) 19:e11493 https://doi.org/10.15252/msb.202211493
Leonid Kruglyak, Andreas Beyer, Joshua S Bloom, Jan Grossbach, Tami D Lieberman, Christopher P Mancuso, Matthew S Rich, Gavin Sherlock, Craig D Kaplan (2023)
Insufficient evidence for non-neutrality of synonymous mutations Nature (2023) PMID: 37076734 DOI: 10.1038/s41586-023-05865-4
Cédric Debès, Antonios Papadakis, Sebastian Grönke, Özlem Karalay, Luke S. Tain, Athanasia Mizi, Shuhei Nakamura, Oliver Hahn, Carina Weigelt, Natasa Josipovic, Anne Zirkel, Isabell Brusius, Konstantinos Sofiadis, Mantha Lamprousi, Yu-Xuan Lu, Wenming Huang, Reza Esmaillie, Torsten Kubacki, Martin R. Späth, Bernhard Schermer, Thomas Benzing, Roman-Ulrich Müller, Adam Antebi, Linda Partridge, Argyris Papantonis & Andreas Beyer (2023)
Ageing-associated changes in transcriptional elongation influence longevity. Nature, DOI 10.1038/s41586-023-05922-y
Leote AC, Wu X, Beyer A (2022)
Regulatory network-based imputation of dropouts in single-cell RNA sequencing data. PLoS Comput Biol. 18(2):e1009849.
Mackmull MT, Nagel L, Sesterhenn F, Muntel J, Grossbach J, Stalder P, Bruderer R, Reiter L, van de Berg WDJ, de Souza N, Beyer A#, Picotti P# (2022)
Global, in situ analysis of the structural proteome in individuals with Parkinson’s disease to identify a new class of biomarker. Nat. Struct. Mol. Biology PMID: 36224378 DOI: 10.1038/s41594-022-00837-0
Dewald F, Suárez I, Johnen R, Grossbach J, Moran-Tovar R, Steger G, Joachim A, Rubio GH, Fries M, Behr F, Kley J, Lingnau A, Kretschmer A, Gude C, Baeza-Flores G, Del Valle DL, Roblero-Hernandez A, Magana-Cerino J, Hernandez AT, Ruiz-Quinones J, Schega K, Linne V, Junker L, Wunsch M, Heger E, Knops E, Di Cristanziano V, Meyer M, Hünseler C, Weber LT, Lüers JC, Quade G, Wisplinghoff H, Tiemann C, Zotz R, Jomaa H, Pranada A, Herzum I, Cullen P, Schmitz FJ, Philipsen P, Kirchner G, Knabbe C, Hellmich M, Buess M, Wolff A, Kossow A, Niessen J, Jeworutzki S, Schräpler JP, Lässig M, Dötsch J, Fätkenheuer G, Kaiser R, Beyer A, Rybniker J, Klein F. (2022)
Effective high-throughput RT-qPCR screening for SARS-CoV-2 infections in children Nat Commun. 13(1):3640. doi: 10.1038/s41467-022-30664-2.
Jan Grossbach , Ludovic Gillet , Mathieu Clément-Ziza , Corinna L Schmalohr , Olga T Schubert , Maximilian Schütter , Julia S P Mawer , Christopher A Barnes , Isabell Bludau , Matthias Weith, Peter Tessarz, Martin Graef, Ruedi Aebersold, Andreas Beyer (2022)
The impact of genomic variation on protein phosphorylation states and regulatory networks. Molecular Systems Biology (2022)18:e10712
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. (2022)
Proteomics-based monitoring of pathway activity reveals that blocking diacylglycerol biosynthesis rescues from alpha-synuclein toxicity. Cell Systems (2022) doi: 10.1016/j.cels.2019.07.010
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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