NDEx - sporedata/researchdesigneR GitHub Wiki

General description

The Network Data Exchange (NDEx) operates as a digital commons where researchers can upload, exchange, and widely disseminate biological networks and pathway models. The NDEx Project offers an open-source platform for the storage, sharing, modification, and publication of biological network information by scientists and organizations.

A key aim of the project is to establish a repository for models that are presently accessible only in formats like figures, tables, or supplementary materials. NDEx acts as a unique and shared distribution avenue for these projects, ensuring the preservation of their identity and proper attribution, rather than absorbing them into a larger collective.

Related publications

• A proteome-scale map of the SARS-CoV-2–human contactome
• Analyzing integrated network of methylation and gene expression profiles in lung squamous cell carcinoma
• Blood biomarkers representing maternal-fetal interface tissues used to predict early-and late-onset preeclampsia but not COVID-19 infection
• Computational exploration of the dual role of the phytochemical fortunellin: Antiviral activities against SARS-CoV-2 and immunomodulatory abilities against the host
• CTpathway: a CrossTalk-based pathway enrichment analysis method for cancer research
• Executable models of immune signaling pathways in HIV-associated atherosclerosis
• Identification of differentially expressed genes and their major pathways among the patient with COVID-19, cystic fibrosis, and chronic kidney disease
• Integrative weighted molecular network construction from transcriptomics and genome wide association data to identify shared genetic biomarkers for COPD and lung cancer
• Network-based drug repurposing for the treatment of COVID-19 patients in different clinical stages
• PIM1 promotes hepatic conversion by suppressing reprogramming-induced ferroptosis and cell cycle arrest
• Rescue of neuropsychiatric phenotypes in a mouse model of 16p11.2 duplication syndrome by genetic correction of an epilepsy network hub
• SUBATOMIC: a SUbgraph BAsed mulTi-OMIcs clustering framework to analyze integrated multi-edge networks
• The module triad: a novel network biology approach to utilize patients' multi-omics data for target discovery in ulcerative colitis
• The SARS-CoV-2 targeted human RNA binding proteins network biology to investigate COVID-19 associated manifestations
• TumorMet: A repository of tumor metabolic networks derived from context-specific Genome-Scale Metabolic Models

Data access

More information about NDEx can be found at https://home.ndexbio.org/index/