Saez-Rodriguez J - Search Results

1

Cell-to-cell and type-to-type heterogeneity of signaling networks: insights from the crowd.

Gabor A, Tognetti M, Driessen A, Tanevski J, Guo B, Cao W, Shen H, Yu T, Chung V; Single Cell Signaling in Breast Cancer DREAM Consortium members; Bodenmiller B, Saez-Rodriguez J. Gabor A, et al. Mol Syst Biol. 2021 Oct;17(10):e10402. doi: 10.15252/msb.202110402. Mol Syst Biol. 2021. PMID: 34661974 Free PMC article.

2

Phosphoproteomic analyses reveal novel cross-modulation mechanisms between two signaling pathways in yeast.

Vaga S, Bernardo-Faura M, Cokelaer T, Maiolica A, Barnes CA, Gillet LC, Hegemann B, van Drogen F, Sharifian H, Klipp E, Peter M, Saez-Rodriguez J, Aebersold R. Vaga S, et al. Mol Syst Biol. 2014 Dec 9;10(12):767. doi: 10.15252/msb.20145112. Mol Syst Biol. 2014. PMID: 25492886 Free PMC article.

3

Inferring causal molecular networks: empirical assessment through a community-based effort.

Hill SM, Heiser LM, Cokelaer T, Unger M, Nesser NK, Carlin DE, Zhang Y, Sokolov A, Paull EO, Wong CK, Graim K, Bivol A, Wang H, Zhu F, Afsari B, Danilova LV, Favorov AV, Lee WS, Taylor D, Hu CW, Long BL, Noren DP, Bisberg AJ; HPN-DREAM Consortium; Mills GB, Gray JW, Kellen M, Norman T, Friend S, Qutub AA, Fertig EJ, Guan Y, Song M, Stuart JM, Spellman PT, Koeppl H, Stolovitzky G, Saez-Rodriguez J, Mukherjee S. Hill SM, et al. Nat Methods. 2016 Apr;13(4):310-8. doi: 10.1038/nmeth.3773. Epub 2016 Feb 22. Nat Methods. 2016. PMID: 26901648 Free PMC article.

4

Analysis of the Human Kinome and Phosphatome by Mass Cytometry Reveals Overexpression-Induced Effects on Cancer-Related Signaling.

Lun XK, Szklarczyk D, Gábor A, Dobberstein N, Zanotelli VRT, Saez-Rodriguez J, von Mering C, Bodenmiller B. Lun XK, et al. Mol Cell. 2019 Jun 6;74(5):1086-1102.e5. doi: 10.1016/j.molcel.2019.04.021. Epub 2019 May 14. Mol Cell. 2019. PMID: 31101498 Free PMC article.

5

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen.

Menden MP, Wang D, Mason MJ, Szalai B, Bulusu KC, Guan Y, Yu T, Kang J, Jeon M, Wolfinger R, Nguyen T, Zaslavskiy M; AstraZeneca-Sanger Drug Combination DREAM Consortium; Jang IS, Ghazoui Z, Ahsen ME, Vogel R, Neto EC, Norman T, Tang EKY, Garnett MJ, Veroli GYD, Fawell S, Stolovitzky G, Guinney J, Dry JR, Saez-Rodriguez J. Menden MP, et al. Nat Commun. 2019 Jun 17;10(1):2674. doi: 10.1038/s41467-019-09799-2. Nat Commun. 2019. PMID: 31209238 Free PMC article.

6

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

Schäfer A, Gjerga E, Welford RW, Renz I, Lehembre F, Groenen PM, Saez-Rodriguez J, Aebersold R, Gstaiger M. Schäfer A, et al. Mol Syst Biol. 2019 Aug;15(8):e8828. doi: 10.15252/msb.20198828. Mol Syst Biol. 2019. PMID: 31464372 Free PMC article.

7

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

Arnol D, Schapiro D, Bodenmiller B, Saez-Rodriguez J, Stegle O. Arnol D, et al. Cell Rep. 2019 Oct 1;29(1):202-211.e6. doi: 10.1016/j.celrep.2019.08.077. Cell Rep. 2019. PMID: 31577949 Free PMC article.

8

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

Liu A, Trairatphisan P, Gjerga E, Didangelos A, Barratt J, Saez-Rodriguez J. Liu A, et al. NPJ Syst Biol Appl. 2019 Nov 11;5:40. doi: 10.1038/s41540-019-0118-z. eCollection 2019. NPJ Syst Biol Appl. 2019. PMID: 31728204 Free PMC article.

9

Bringing data from curated pathway resources to Cytoscape with OmniPath.

Ceccarelli F, Turei D, Gabor A, Saez-Rodriguez J. Ceccarelli F, et al. Bioinformatics. 2020 Apr 15;36(8):2632-2633. doi: 10.1093/bioinformatics/btz968. Bioinformatics. 2020. PMID: 31886476

10

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

Holland CH, Tanevski J, Perales-Patón J, Gleixner J, Kumar MP, Mereu E, Joughin BA, Stegle O, Lauffenburger DA, Heyn H, Szalai B, Saez-Rodriguez J. Holland CH, et al. Genome Biol. 2020 Feb 12;21(1):36. doi: 10.1186/s13059-020-1949-z. Genome Biol. 2020. PMID: 32051003 Free PMC article.

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