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npj Systems Biology and Applications Volume 4 Issue 1

Subject Areas: Biochemistry, Genetics and Molecular Biology (miscellaneous); ; ; ; ; ; ;
Publisher: Nature Publishing Group UK - Springer Journals
SJR: 25

Open Access

Journal Article

PECAplus: statistical analysis of time-dependent regulatory changes in dynamic single-omics and dual-omics experiments

Teo, Guoshou; Zhang, Yun; Vogel, Christine; Choi, Hyungwon

2017 npj Systems Biology and Applications

doi:10.1038/s41540-017-0040-1 pmid:29263799

Simultaneous dynamic profiling of mRNA and protein expression is increasingly popular, and there is a critical need for algorithms to identify regulatory layers and time dependency of gene expression. A group of scientists from United States and Singapore present PECAplus, a comprehensive set of...
Open Access

Journal Article

VEGFR1 promotes cell migration and proliferation through PLCγ and PI3K pathways

Weddell, Jared; Chen, Si; Imoukhuede, P.

2017 npj Systems Biology and Applications

doi:10.1038/s41540-017-0037-9 pmid:29263797

The ability to control vascular endothelial growth factor (VEGF) signaling offers promising therapeutic potential for vascular diseases and cancer. Despite this promise, VEGF-targeted therapies are not clinically effective for many pathologies, such as breast cancer. VEGFR1 has recently emerged...
Open Access

Journal Article

Classification of gene signatures for their information value and functional redundancy

Cantini, Laura; Calzone, Laurence; Martignetti, Loredana; Rydenfelt, Mattias; Blüthgen, Nils; Barillot, Emmanuel; Zinovyev, Andrei

2017 npj Systems Biology and Applications

doi:10.1038/s41540-017-0038-8 pmid:29263798

Gene signatures are more and more used to interpret results of omics data analyses but suffer from compositional (large overlap) and functional (correlated read-outs) redundancy. Moreover, many gene signatures rarely come out as significant in statistical tests. Based on pan-cancer data analysis,...

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