Sáez-Rodríguez J - Search Results

1

A comprehensive database for integrated analysis of omics data in autoimmune diseases.

Martorell-Marugán J, López-Domínguez R, García-Moreno A, Toro-Domínguez D, Villatoro-García JA, Barturen G, Martín-Gómez A, Troule K, Gómez-López G, Al-Shahrour F, González-Rumayor V, Peña-Chilet M, Dopazo J, Sáez-Rodríguez J, Alarcón-Riquelme ME, Carmona-Sáez P. Martorell-Marugán J, et al. BMC Bioinformatics. 2021 Jun 24;22(1):343. doi: 10.1186/s12859-021-04268-4. BMC Bioinformatics. 2021. PMID: 34167460 Free PMC article.

2

CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms.

Terfve C, Cokelaer T, Henriques D, MacNamara A, Goncalves E, Morris MK, van Iersel M, Lauffenburger DA, Saez-Rodriguez J. Terfve C, et al. BMC Syst Biol. 2012 Oct 18;6:133. doi: 10.1186/1752-0509-6-133. BMC Syst Biol. 2012. PMID: 23079107 Free PMC article.

3

CySBGN: a Cytoscape plug-in to integrate SBGN maps.

Gonçalves E, van Iersel M, Saez-Rodriguez J. Gonçalves E, et al. BMC Bioinformatics. 2013 Jan 16;14:17. doi: 10.1186/1471-2105-14-17. BMC Bioinformatics. 2013. PMID: 23324051 Free PMC article.

4

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics.

Egea JA, Henriques D, Cokelaer T, Villaverde AF, MacNamara A, Danciu DP, Banga JR, Saez-Rodriguez J. Egea JA, et al. BMC Bioinformatics. 2014 May 10;15:136. doi: 10.1186/1471-2105-15-136. BMC Bioinformatics. 2014. PMID: 24885957 Free PMC article.

5

Efficient randomization of biological networks while preserving functional characterization of individual nodes.

Iorio F, Bernardo-Faura M, Gobbi A, Cokelaer T, Jurman G, Saez-Rodriguez J. Iorio F, et al. BMC Bioinformatics. 2016 Dec 20;17(1):542. doi: 10.1186/s12859-016-1402-1. BMC Bioinformatics. 2016. PMID: 27998275 Free PMC article.

6

GDSCTools for mining pharmacogenomic interactions in cancer.

Cokelaer T, Chen E, Iorio F, Menden MP, Lightfoot H, Saez-Rodriguez J, Garnett MJ. Cokelaer T, et al. Bioinformatics. 2018 Apr 1;34(7):1226-1228. doi: 10.1093/bioinformatics/btx744. Bioinformatics. 2018. PMID: 29186349 Free PMC article.

7

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

8

Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses.

Dugourd A, Kuppe C, Sciacovelli M, Gjerga E, Gabor A, Emdal KB, Vieira V, Bekker-Jensen DB, Kranz J, Bindels EMJ, Costa ASH, Sousa A, Beltrao P, Rocha M, Olsen JV, Frezza C, Kramann R, Saez-Rodriguez J. Dugourd A, et al. Mol Syst Biol. 2021 Jan;17(1):e9730. doi: 10.15252/msb.20209730. Mol Syst Biol. 2021. PMID: 33502086 Free PMC article.

9

Integrated intra- and intercellular signaling knowledge for multicellular omics analysis.

Türei D, Valdeolivas A, Gul L, Palacio-Escat N, Klein M, Ivanova O, Ölbei M, Gábor A, Theis F, Módos D, Korcsmáros T, Saez-Rodriguez J. Türei D, et al. Mol Syst Biol. 2021 Mar;17(3):e9923. doi: 10.15252/msb.20209923. Mol Syst Biol. 2021. PMID: 33749993 Free PMC article.

10

Transcription Factor Activity Inference in Systemic Lupus Erythematosus.

Lopez-Dominguez R, Toro-Dominguez D, Martorell-Marugan J, Garcia-Moreno A, Holland CH, Saez-Rodriguez J, Goldman D, Petri MA, Alarcon-Riquelme ME, Carmona-Saez P. Lopez-Dominguez R, et al. Life (Basel). 2021 Apr 1;11(4):299. doi: 10.3390/life11040299. Life (Basel). 2021. PMID: 33915751 Free PMC article.

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