Network Biology Publications

Highlights in the development and application of Network Biology tools and resources. Share relevant articles and join the discussion at the Network Biology Group.

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NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange. Pillich et al., Bioinformatics, Volume 39, Issue 3, March 2023, btad118, https://doi.org/10.1093/bioinformatics/btad118

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An integrated in-silico Pharmaco-BioInformatics approaches to identify synergistic effects of COVID-19 to HIV patients. Hossain et al., Comput Biol Med. 2023 Mar; 155: 106656.

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Multi-omics characterization of RNA binding proteins reveals disease comorbidities and potential drugs in COVID-19. Pan et al., Comput Biol Med. 2023 Mar; 155: 106651.

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Network-based drug repurposing for the treatment of COVID-19 patients in different clinical stages. Wang et al., Heliyon. 2023 Feb 24 : e14059.

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Rescue of neuropsychiatric phenotypes in a mouse model of 16p11.2 duplication syndrome by genetic correction of an epilepsy network hub. Nat Commun. 2023; 14: 825.

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Functional impact of multi-omic interactions in breast cancer subtypes Ochoa and Hernández-Lemus, Front Genet. 2022; 13: 1078609.

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The module triad: a novel network biology approach to utilize patients’ multi-omics data for target discovery in ulcerative colitis Voitalov et al., Sci Rep. 2022; 12: 21685.

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Network-based approach for targeting human kinases commonly associated with amyotrophic lateral sclerosis and cancer. Khatoon et al., Front Mol Neurosci. 2022; 15: 1023286.

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TumorMet: A repository of tumor metabolic networks derived from context-specific Genome-Scale Metabolic Models. Granata et al., Sci Data. 2022; 9: 607.

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CTpathway: a CrossTalk-based pathway enrichment analysis method for cancer research. Liu et al., Genome Med. 2022; 14: 118.

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A proteome-scale map of the SARS-CoV-2–human contactome. Kim et al., Nat Biotechnol. 2023; 41(1): 140–149.

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Integrative weighted molecular network construction from transcriptomics and genome wide association data to identify shared genetic biomarkers for COPD and lung cancer. Banaganapalli, et al., PloS one doi: 10.1371/journal.pone.0274629.

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Executable models of immune signaling pathways in HIV-associated atherosclerosis. Palshikar et al., NPJ Syst Biol Appl. 2022; 8: 35.

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Analyzing integrated network of methylation and gene expression profiles in lung squamous cell carcinoma. Heryanto et al., Sci Rep. 2022; 12: 15799.

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PIM1 promotes hepatic conversion by suppressing reprogramming-induced ferroptosis and cell cycle arrest. Yuan, et al., Nature communications doi: 10.1038/s41467-022-32976-9.

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Computational exploration of the dual role of the phytochemical fortunellin: Antiviral activities against SARS-CoV-2 and immunomodulatory abilities against the host. Agrawal et al., Comput Biol Med. 2022 Sep 8 : 106049.

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SUBATOMIC: a SUbgraph BAsed mulTi-OMIcs clustering framework to analyze integrated multi-edge networks. Loers and Vermeirssen, BMC Bioinformatics 2022 Sep 5;23(1):363. doi: 10.1186/s12859-022-04908-3.