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Efficient visualization of high-throughput targeted proteomics experiments: TAPIR

Röst, Hannes L. ; Rosenberger, George ; Aebersold, Ruedi ; Malmström, Lars

In: Bioinformatics, 2015, vol. 31, no. 14, p. 2415-2417

Crosslinking-MS analysis reveals RNA polymerase I domain architecture and basis of rRNA cleavage

Jennebach, Stefan ; Herzog, Franz ; Aebersold, Ruedi ; Cramer, Patrick

In: Nucleic Acids Research, 2012, vol. 40, no. 12, p. 5591-5601

Proteome coverage prediction with infinite Markov models

Claassen, Manfred ; Aebersold, Ruedi ; Buhmann, Joachim M.

In: Bioinformatics, 2009, vol. 25, no. 12, p. i154-i160

aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data

Rosenberger, George ; Ludwig, Christina ; Röst, Hannes L. ; Aebersold, Ruedi ; Malmström, Lars

In: Bioinformatics, 2014, vol. 30, no. 17, p. 2511-2513

MS-BID: a Java package for label-free LC-MS-based comparative proteomic analysis

Hwang, Daehee ; Zhang, Ning ; Lee, Hookeun ; Yi, Eugene ; Zhang, Hui ; Lee, Inyoul Y. ; Hood, Leroy ; Aebersold, Ruedi

In: Bioinformatics, 2008, vol. 24, no. 22, p. 2641-2642

The PeptideAtlas project

Desiere, Frank ; Deutsch, Eric W. ; King, Nichole L. ; Nesvizhskii, Alexey I. ; Mallick, Parag ; Eng, Jimmy ; Chen, Sharon ; Eddes, James ; Loevenich, Sandra N. ; Aebersold, Ruedi

In: Nucleic Acids Research, 2006, vol. 34, p. D655-D658

Xwalk: computing and visualizing distances in cross-linking experiments

Kahraman, Abdullah ; Malmström, Lars ; Aebersold, Ruedi

In: Bioinformatics, 2011, vol. 27, no. 15, p. 2163-2164

Prequips—an extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data

Gehlenborg, Nils ; Yan, Wei ; Lee, Inyoul Y. ; Yoo, Hyuntae ; Nieselt, Kay ; Hwang, Daehee ; Aebersold, Ruedi ; Hood, Leroy

In: Bioinformatics, 2009, vol. 25, no. 5, p. 682-683

Yeast endosulfines control entry into quiescence and chronological life span by inhibiting protein phosphatase 2A

Bontron, Séverine ; Jaquenoud, Malika ; Vaga, Stefania ; Talarek, Nicolas ; Bodenmiller, Bernd ; Aebersold, Ruedi ; De Virgilio, Claudio

In: Cell Reports, 2012, vol. 3, no. 1, p. 16–22

The TORC1 and PKA protein kinases are central elements of signaling networks that regulate eukaryotic cell proliferation in response to growth factors and/or nutrients. In yeast, attenuation of signaling by these kinases following nitrogen and/or carbon limitation activates the protein kinase Rim15, which orchestrates the initiation of a reversible cellular quiescence program to ensure normal...