Saez-Rodriguez Group

1. Increased CXCL4 expression in hematopoietic cells links inflammation and progression of bone marrow fibrosis in MPN

Gleitz H Blood, 2020

2. Community Assessment of the predictability of cancer protein and phosphoprotein levels from genomics and transcriptomics

Yang M Cell Systems, 2020

3. The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST)

Touré V Bioinformatics, 2020

4. Converting networks to predictive logic models from perturbation signalling data with CellNOpt

Gjerga E Bioinformatics, 2020

5. Stratification and prediction of drug synergy based on target functional similarity

Yang M npj Systems Biology and Applications, 2020

6. CELLector: Genomics Guided Selection of Cancer in vitro Models

Najgebauer H Cell Systems, 2020

7. Setting the basis of best practices and standards for curation and annotation of logical models in biology—highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop

Niarakis A Briefings in Bioinformatics, 2020

8. Patient‐specific logic models of signaling pathways from screenings on cancer biopsies to prioritize personalized combination therapies

Eduati F Molecular systems biology, 2020

9. Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data

Holland CH Genome Biology, 2020

10. Dysregulated mesenchymal PDGFR-β drives kidney fibrosis

Buhl E EMBO Mol Med, 2020

11. Personalized signaling models for personalized treatments

Saez‐Rodriguez J Mol Syst Biol, 2020

12. Quantitative Systems Toxicology Modeling To Address Key Safety Questions in Drug Development: A Focus of the TransQST Consortium

Ferreira S Chem Res Toxicol, 2020

13. Bringing data from curated pathway resources to Cytoscape with OmniPath

Ceccarelli F Bioinformatics, 2019

14. Kinetic modelling of quantitative proteome data predicts metabolic reprogramming of liver cancer

Berndt N British Journal of Cancer , 2019

15. Metabolic rewiring of the hypertensive kidney

Rinschen M Science Signaling, 2019

16. Influence of Liver Fibrosis on Lobular Zonation

Ghallab A MDPI cells, 2019

17. A Functional Landscape of CKD Entities From Public Transcriptomic Data

Tajti F Kidney International Reports, 2019

18. From expression footprints to causal pathways: contextualizing large signaling networks with CARNIVAL

Liu A npj Systems Biology and Applications, 2019

19. Modeling Cell-Cell Interactions from Spatial Molecular Data with Spatial Variance Component Analysis

Arnol D Cell reports, 2019

20. Signatures of cell death and proliferation in perturbation transcriptomics data—from confounding factor to effective prediction

Szalai B Nucleic Acids Research, 2019

21. Transfer of regulatory knowledge from human to mouse for functional genomic analysis.

Holland CH Biochim Biophys Acta Gene Regul Mech, 2019

22. Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges.

Ellrott K Genome Biol, 2019

23. Assessment of network module identification across complex diseases.

Choobdar S Nat Methods, 2019

24. Novel plasma peptide markers involved in the pathology of CKD identified using mass spectrometric approach.

Gajjala PR J Mol Med (Berl), 2019

25. Elucidating essential kinases of endothelin signalling by logic modelling of phosphoproteomics data.

Schäfer A Mol Syst Biol, 2019