| Sleep-wake cycles drive daily dynamics of synaptic phosphorylation F Brüning, SB Noya, T Bange, S Koutsouli, JD Rudolph, SK Tyagarajan, ... Science 366 (6462), eaav3617, 2019 | 224 | 2019 |
| MaxDIA enables library-based and library-free data-independent acquisition proteomics P Sinitcyn, H Hamzeiy, F Salinas Soto, D Itzhak, F McCarthy, C Wichmann, ... Nature biotechnology 39 (12), 1563-1573, 2021 | 211 | 2021 |
| Computational methods for understanding mass spectrometry–based shotgun proteomics data P Sinitcyn, JD Rudolph, J Cox Annual Review of Biomedical Data Science 1 (1), 207-234, 2018 | 170 | 2018 |
| System-wide clinical proteomics of breast cancer reveals global remodeling of tissue homeostasis Y Pozniak, N Balint-Lahat, JD Rudolph, C Lindskog, R Katzir, C Avivi, ... Cell systems 2 (3), 172-184, 2016 | 100 | 2016 |
| A network module for the Perseus software for computational proteomics facilitates proteome interaction graph analysis JD Rudolph, J Cox Journal of proteome research 18 (5), 2052-2064, 2019 | 85 | 2019 |
| Elucidation of signaling pathways from large-scale phosphoproteomic data using protein interaction networks JD Rudolph, M de Graauw, B van de Water, T Geiger, R Sharan Cell systems 3 (6), 585-593. e3, 2016 | 74 | 2016 |
| JSBML 1.0: providing a smorgasbord of options to encode systems biology models N Rodriguez, A Thomas, L Watanabe, IY Vazirabad, V Kofia, HF Gómez, ... Bioinformatics 31 (20), 3383-3386, 2015 | 47 | 2015 |
| MaxQuant goes linux P Sinitcyn, S Tiwary, J Rudolph, P Gutenbrunner, C Wichmann, Ş Yılmaz, ... Nature methods 15 (6), 401-401, 2018 | 43 | 2018 |
| Expanding the perseus software for omics data analysis with custom plugins SH Yu, D Ferretti, JP Schessner, JD Rudolph, GHH Borner, J Cox Current protocols in bioinformatics 71 (1), e105, 2020 | 32 | 2020 |
| Development and application of software and algorithms for network approaches to proteomics data analysis JD Rudolph lmu, 2019 | | 2019 |
