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Systems immunology: When systems biology meets immunology [PDF]

Frontiers in Immunology
The immune system is an intricate network of cells, proteins, and signaling pathways that coordinate protective responses and, when dysregulated, drive immune−related diseases.
Lucía Alfonso-González, Lucía Alfonso-González, Francisco J. Fernández, M. Cristina Vega   +3 more
doaj   +2 more sources

Pioneer factors in development and cancer

iScience, 2021
Summary: Transcription factors (TFs) are essential mediators of epigenetic regulation and modifiers of penetrance. Studies from the past decades have revealed a sub-class of TF that is capable of remodeling closed chromatin states through targeting ...
Benjamin D. Sunkel, Benjamin Z. Stanton
doaj   +1 more source

A persistent invasive phenotype in post-hypoxic tumor cells is revealed by fate mapping and computational modeling

iScience, 2021
Summary: Hypoxia is a critical factor in solid tumors that has been associated with cancer progression and aggressiveness. We recently developed a hypoxia fate mapping system to trace post-hypoxic cells within a tumor for the first time.
Heber L. Rocha, Inês Godet, Furkan Kurtoglu, John Metzcar, Kali Konstantinopoulos, Soumitra Bhoyar, Daniele M. Gilkes, Paul Macklin   +7 more
doaj   +1 more source

A network approach reveals driver genes associated with survival of patients with triple-negative breast cancer

iScience, 2021
Summary: We aimed to identify triple-negative breast cancer (TNBC) drivers that regulate survival time as predictive signatures that improve TNBC prognostication.
Courtney D. Dill, Eric B. Dammer, Ti'ara L. Griffen, Nicholas T. Seyfried, James W. Lillard, Jr.   +4 more
doaj   +1 more source

Genetic association and single-cell transcriptome analyses reveal distinct features connecting autoimmunity with cancers

iScience, 2022
Summary: Autoimmune diseases (ADs) are at a significantly higher risk of cancers with unclear mechanism. By searching GWAS catalog database and Medline, susceptible genes for five common ADs, including systemic lupus erythematosus (SLE), rheumatoid ...
Shasha Li, Chenyang Lu, Yuan Zhang, Xiaolu Zhao, Kequan Lin, Xiufang Kong, David Fox, Lixiang Xue, Lichao Sun, Yi Liu, Fengbiao Mao   +10 more
doaj   +1 more source

A metabolic regulatory network for the Caenorhabditis elegans intestine

iScience, 2022
Summary: Metabolic perturbations can affect gene expression, for instance to rewire metabolism. While numerous efforts have measured gene expression in response to individual metabolic perturbations, methods that determine all metabolic perturbations ...
Sushila Bhattacharya, Brent B. Horowitz, Jingyan Zhang, Xuhang Li, Hefei Zhang, Gabrielle E. Giese, Amy D. Holdorf, Albertha J.M. Walhout   +7 more
doaj   +1 more source

Specific arterio-venous transcriptomic and ncRNA-RNA interactions in human umbilical endothelial cells: A meta-analysis

iScience, 2021
Summary: Whether arterial-venous differences of primary endothelial cells commonly used for vascular research are preserved in vitro remains under debate.
Fabian Vega-Tapia, Estefania Peñaloza, Bernardo J. Krause   +2 more
doaj   +1 more source

Base editing-coupled survival screening enabled high-sensitive analysis of PAM compatibility and finding of the new possible off-target

iScience, 2021
Summary: Base editing (BE) is a promising genome engineering tool for modifying DNA or RNA and has been widely used in various microorganisms as well as eukaryotic cells.
Tianyuan Su, Qi Guo, Yi Zheng, Yizhao Chang, Fei Gu, Xuemei Lu, Qingsheng Qi   +6 more
doaj   +1 more source

A yeast chemogenomic screen identifies pathways that modulate adipic acid toxicity

iScience, 2021
Summary: Adipic acid production by yeast fermentation is gaining attention as a renewable source of platform chemicals for making nylon products. However, adipic acid toxicity inhibits yeast growth and fermentation.
Eugene Fletcher, Kevin Mercurio, Elizabeth A. Walden, Kristin Baetz   +3 more
doaj   +1 more source

CRIC-seq protocol for in situ profiling of proximal RNA-RNA contacts associated with RNA-binding proteins

STAR Protocols, 2023
Summary: RNA-binding proteins (RBPs) can bind and mediate RNA-RNA contacts. However, identifying specific RBP-organized RNA-RNA contacts remains challenging.
Rong Ye, Naijing Hu, Yuanchao Xue
doaj   +1 more source