Here, you find all resources for our open-access publications including databases, computational tools, and code. We believe that following the FAIR (Findable, Accessible, Interoperable, Reusable) and 3R (Replicability, Reproducibility, and Robustness) principles for data sharing are crucial for maintaining the integrity of science.
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A network-based tool for microRNA-oritened enrichment analysis.
microRNA enrichment analysis R
RingNet is a web-based tool for visualizing multi-modal data in networks.
network visualization multi-omics data visualization R
The biologically informed classifier uses the graph convolutional neural network to do multi-label classification for hierarchical tumor subtypes with tiers.
explainable AI tumor subtype classification Python
The tool automates biomedical literature analysis from PubMed. It builds networks of gene and concept co-occurrences from user-selected publications, expands research through new article discovery, and identifies relevant interactions, including novel ones.
literature parsing network-based text mining Python
The pipeline allows users to perform end-to-end analysis of bulk miRNA sequencing data, including quality control of FastQ files, mapping of read counts to miRNA genes using miRBase or Reference genome, quantification of miRNA read counts, differential gene expression analysis using DEseq2, gene set enrichment analysis using curated cancer hallmark gene sets, and identification of miRNA targets.
leukemia mircoRNA Shell/R
The pipeline presents a network-based method for identifying cancer genes that can be used as prognostic and prognostic biomarkers and a advanced drug repurposing method targeting those cancer.
drug repurposing network biology R
The pipeline builds a deep learning model based on disease networks. The learned representations are used for patient stratification, and in turn, the data mined in the network provides biomedical explanation to the deep learning model.
melanoma AI Python
We characterized miRNA-gene interactions in over 2000 REACTOME pathways in dendritic cells used for immunotherapy. All the identified interactions are visualized in complex heat maps accompanied with a table for detailed information for further research.
dentritic cell network biology R
The database contains cooperative miRNA pairs that are predicted for efficiently modulating the expression of protein-coding genes of cancer driver genes underlying metastatic melanoma.
microRNA network biology database
The multi-level mathematical model accounts for the anti-cancer effects of an immune vaccine at the molecular level and can be used for optimizing the vaccine design.
cancer vaccine mathematical model Matlab
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