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bioRxiv · 10.1101/2025.09.27.679001

XomicsDB: a database of paired multi-omics datasets for systems biology

Zhang, T.·Liu, L.·Wu, Y.·Jung, S.·Liu, X.·Jiang, Q.·Yang, N.·Kim, S.·Tao, Y.·Li, G.·Cao, H.
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Abstract

Life science research is primarily driven by data integration on the basis of theoretical development. Broad applications of multiomics (xomics) data calls for efficient integration of xomics data to infer cellular operation and regulation. To that end, it is urgently needed good-quality xomics data should be curated and shared for the community. Here we present XomicsDB, a database curating paired xomics datasets at both bulk and single-cell levels in model organisms. It contains 183 datasets from 13 model organisms, with a total of seven xomics data types. Users can download these datasets individually or in a batch from the ftp server provided. Users can also upload their paired xomics datasets for sharing. Incoporation of xomics data intom GSMs are demonstrated in model organisms Escherichia coli and human. Future efforts will be on collecting more single-cell xomics data and curating non-model oragnisms. The XomicsDB can be found at: http://xomicsdb.com.

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Zhang, T., Liu, L., Wu, Y., Jung, S., Liu, X., Jiang, Q., Yang, N., Kim, S., Tao, Y., Li, G., Cao, H.. 2025-09-29. XomicsDB: a database of paired multi-omics datasets for systems biology. https://doi.org/10.1101/2025.09.27.679001

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