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In-Depth Characterization of the Clostridioides difficile Phosphoproteome to Identify Ser/Thr Kinase Substrates2022 Molecular & Cellular Proteomics article Medicine Clostridium difficile and Clostridium perfringens research Open access
Tránsito García‐García, Thibaut Douché, Quentin Giai Gianetto, Sandrine Poncet, Nesrine El Omrani, Wiep Klaas Smits, +3 more
20citations -
Comparative phosphoproteome analysis of primary and metastatic uveal melanoma cell lines2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Ocular Oncology and Treatments Open access
Kseniya Glinkina, Román González‐Prieto, Amina F.A.S. Teunisse, Maria Chiara Gelmi, Martine Johanna Jager, Alfred C.O. Vertegaal, +1 more
0citations -
Multiomics Analyses Reveal Dynamic Bioenergetic Pathways and Functional Remodeling of the Heart During Intermittent Fasting2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Dietary Effects on Health Open access
Thiruma Valavan Arumugam, Asfa Alli Shaik, Elisa Anamaria Liehn, Sharmelee Selvaraji, Luting Poh, Vismitha Rajeev, +19 more
2citations -
Clostridioides difficile phosphoproteomics shows an expansion of phosphorylated proteins in stationary growth phase2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Clostridium difficile and Clostridium perfringens research Open access
Wiep Klaas Smits, Yassene Mohammed, Arnoud de Ru, Valentina Cordo’, Annemieke H. Friggen, Peter A. van Veelen, +1 more
0citations -
Causal integration of multi‐omics data with prior knowledge to generate mechanistic hypotheses2021 Molecular Systems Biology article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Aurélien J. F. Dugourd, Christoph Kuppe, Marco Sciacovelli, Enio Gjerga, Attila Gábor, Kristina Bennet Emdal, +12 more
156citations -
Integrated Proteomics Unveils Nuclear PDE3A2 as a Regulator of Cardiac Myocyte Hypertrophy2023 Circulation Research article Biochemistry, Genetics and Molecular Biology Phosphodiesterase function and regulation Open access
Gunasekaran Subramaniam, Katharina Schleicher, Duangnapa Kovanich, Anna Zerio, Milda Folkmanaite, Ying‐Chi Chao, +15 more
29citations -
Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Aurélien J. F. Dugourd, Christoph Kuppe, Marco Sciacovelli, Enio Gjerga, Kristina Bennet Emdal, Dorte B. Bekker‐Jensen, +7 more
16citations -
A structural machine learning approach for rapid prediction of thermodynamically destabilizing tyrosine phosphorylations2025 Cell Reports Methods article Biochemistry, Genetics and Molecular Biology Machine Learning in Bioinformatics Open access
Jaie C. Woodard, Atena Malemir Chegini, Jian Tian, Rupa Bhowmick, Subramaniam Pennathur, Alireza Mashaghi, +2 more
3citations -
Rapid prediction of thermodynamically destabilizing tyrosine phosphorylations in cancers2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Machine Learning in Bioinformatics Open access
Jaie C. Woodard, Atena Malemir Chegini, Jian Tian, Rupa Bhowmick, Subramanium Pennathur, Alireza Mashaghi, +2 more
2citations -
Proteome-wide quantitative RNA interactome capture (qRIC) identifies phosphorylation sites with regulatory potential in RBM202021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology RNA Research and Splicing Open access
Carlos H. Vieira-Vieira, Vita Dauksaite, Michael Gotthardt, Matthias Selbach
0citations -
Functional and spatial proteomics profiling reveals intra- and intercellular signaling crosstalk in colorectal cancer2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Colorectal Cancer Treatments and Studies Open access
Christina Plattner, Giorgia Lamberti, Peter Blattmann, Alexander Kirchmair, Dietmar Rieder, Zuzana Loncová, +23 more
0citations -
PHONEMeS: Efficient Modeling of Signaling Networks Derived from Large-Scale Mass Spectrometry Data2021 Journal of Proteome Research article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Enio Gjerga, Aurélien J. F. Dugourd, Luis Tobalina, Abel Sousa, Julio Sáez-Rodríguez
32citations -
Combined Quantitative (Phospho)proteomics and Mass Spectrometry Imaging Reveal Temporal and Spatial Protein Changes in Human Intestinal Ischemia–Reperfusion2021 Journal of Proteome Research article Chemistry Advanced Proteomics Techniques and Applications Open access
Anna M. Kip, Juan Manuel Valverde, Maarten A. F. Altelaar, Ron M. A. Heeren, Inca H. R. Hundscheid, Cornelis H.C. Dejong, +3 more
18citations -
Quantitative phosphoproteomics to unravel the cellular response to chemical stressors with different modes of action2020 Archives of Toxicology article Chemistry Advanced Proteomics Techniques and Applications Open access
Bharath K. Sampadi, Alex Pines, Stephanie Munk, Branislav Mišovic, Anton J.L. de Groot, Bob van de Water, +3 more
17citations -
Modulation of nucleotide metabolism by picornaviruses2024 PLoS Pathogens article Biochemistry, Genetics and Molecular Biology Biochemical and Molecular Research Open access
Lonneke V. Nouwen, Martijn Breeuwsma, Esther A. Zaal, Chris H.A. van de Lest, Inge Buitendijk, Marleen Zwaagstra, +4 more
14citations