Integrating knowledge and omics to decipher mechanisms via large‐scale models of signaling networks

Autor: Martin Garrido‐Rodriguez, Katharina Zirngibl, Olga Ivanova, Sebastian Lobentanzer, Julio Saez‐Rodriguez

Publikováno v: Molecular Systems Biology, Vol 18, Iss 7, Pp 1-15 (2022)

Abstract Signal transduction governs cellular behavior, and its dysregulation often leads to human disease. To understand this process, we can use network models based on prior knowledge, where nodes represent biomolecules, usually proteins, and edge

Externí odkaz: https://doaj.org/article/2407e044686f4858bdba6c6dc45f7460

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

Autor: Attila Gabor, Marco Tognetti, Alice Driessen, Jovan Tanevski, Baosen Guo, Wencai Cao, He Shen, Thomas Yu, Verena Chung, Single Cell Signaling in Breast Cancer DREAM Consortium members, Bernd Bodenmiller, Julio Saez‐Rodriguez, Augustinas Prusokas, Alidivinas Prusokas, Renata Retkute, Anand Rajasekar, Karthik Raman, Malvika Sudhakar, Raghunathan Rengaswamy, Edward S.C. Shih, Min‐jeong Kim, Changje Cho, Dohyang Kim, Hyeju Oh, Jinseub Hwang, Kim Jongtae, Yeongeun Nam, Sanghoo Yoon, Taeyong Kwon, Kyeongjun Lee, Sarika Chaudhary, Nehal Sharma, Shreya Bande, Gao Gao fan zhu Cankut Cubuk, Pelin Gundogdu, Joaquin Dopazo, Kinza Rian, Carlos Loucera, Matias M Falco, Martin Garrido‐Rodriguez, Maria Peña‐Chilet, Huiyuan Chen, Gabor Turu, Laszlo Hunyadi, Adam Misak, Lisheng Zhou, Xiaoqing Jiang, Pieta Zhang, Aakansha Rai, Rintu Kutum, Sadhna Rana, Rajgopal Srinivasan, Swatantra Pradhan, James Li, Vladimir Bajic, Christophe Van Neste, Didier Barradas‐bautista, Somayah Abdullah Albarade, Igor Nikolskiy, Musalula Sinkala, Duc Tran, Hung Nguyen, Tin Nguyen, Alexander Wu, Benjamin DeMeo, Brian Hie, Rohit Singh, Jiwei Liu, Xueer Chen, Leonor Saiz, Jose M. G Vilar, Peng Qiu, Akash Gosain, Anjali Dhall, Dinesh Bajaj, Harpreet Kaur, Krishna Bagaria, Mayank Chauhan, Neelam Sharma, Gajendra Raghava, Sumeet Patiyal, Jianye Hao, Jiajie Peng, Shangyi Ning, Yi Ma, Zhongyu Wei, Atte Aalto, Jorge Goncalves, Laurent Mombaerts, Xinnan Dai, Jie Zheng, Piyushkumar Mundra, Fan Xu, Jie Wang, Krishna Kant Singh, Mingyu Lee

Publikováno v: Molecular Systems Biology, Vol 17, Iss 10, Pp 1-16 (2021)

Abstract Recent technological developments allow us to measure the status of dozens of proteins in individual cells. This opens the way to understand the heterogeneity of complex multi‐signaling networks across cells and cell types, with important

Externí odkaz: https://doaj.org/article/bcd5b154a6e240949fe3c514a36f69b2

Etrinabdione (VCE-004.8), a B55α activator, promotes angiogenesis and arteriogenesis in critical limb ischemia

Autor: Adela García-Martín, María E. Prados, Isabel Lastres-Cubillo, Francisco J. Ponce-Diaz, Laura Cerero, Martin Garrido-Rodríguez, Carmen Navarrete, Rafael Pineda, Ana B. Rodríguez, Ignacio Muñoz, Javier Moya, Antonella Medeot, José A. Moreno, Antonio Chacón, José García-Revillo, Eduardo Muñoz

Publikováno v: Journal of Translational Medicine, Vol 22, Iss 1, Pp 1-24 (2024)

Abstract Background Vasculogenic therapies explored for the treatment of peripheral artery disease (PAD) have encountered minimal success in clinical trials. Addressing this, B55α, an isoform of protein phosphatase 2A (PP2A), emerges as pivotal in v

Externí odkaz: https://doaj.org/article/da0c42d747b54ca685b4758f5f0eacbf

Implementation of CRISPR/Cas9 Genome Editing to Generate Murine Lung Cancer Models That Depict the Mutational Landscape of Human Disease

Autor: Oliver, Hartmann, Michaela, Reissland, Carina R, Maier, Thomas, Fischer, Cristian, Prieto-Garcia, Apoorva, Baluapuri, Jessica, Schwarz, Werner, Schmitz, Martin, Garrido-Rodriguez, Nikolett, Pahor, Clare C, Davies, Florian, Bassermann, Amir, Orian, Elmar, Wolf, Almut, Schulze, Marco A, Calzado, Mathias T, Rosenfeldt, Markus E, Diefenbacher

Publikováno v: Frontiers in Cell and Developmental Biology

Lung cancer is the most common cancer worldwide and the leading cause of cancer-related deaths in both men and women. Despite the development of novel therapeutic interventions, the 5-year survival rate for non-small cell lung cancer (NSCLC) patients

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::128b3785858b29917ef488504ac8ebda
https://pubmed.ncbi.nlm.nih.gov/33738287

A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways.

Autor: Martín Garrido-Rodriguez, Daniel Lopez-Lopez, Francisco M Ortuno, María Peña-Chilet, Eduardo Muñoz, Marco A Calzado, Joaquin Dopazo

Publikováno v: PLoS Computational Biology, Vol 17, Iss 2, p e1008748 (2021)

MIGNON is a workflow for the analysis of RNA-Seq experiments, which not only efficiently manages the estimation of gene expression levels from raw sequencing reads, but also calls genomic variants present in the transcripts analyzed. Moreover, this i

Externí odkaz: https://doaj.org/article/65ddef7a579444e2b145e6b95460fc76