Publications

The papers below are publications related to the EcoOmicsAnalyst project (2018 - 2023)

• Zhou, G., Soufan, O., Ewald, J., Hancock, REW, Basu, N. and Xia, J. (2019) “NetworkAnalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and meta-analysis” Nucleic Acids Research 47 W234-241
• Ewald, J., Soufan, O., Xia, J., Basu, N. (2020) “FastBMD: an online tool for rapid benchmark dose-response analysis of transcriptomics data” Bioinformatics (10.1093/bioinformatics/btaa700)
• Viau, C., Hacariz, O., Karimian, F., and Xia J. (2020) “Comprehensive phenotyping and transcriptome profiling to study nanotoxicity in C. elegans”. PeerJ 8, e8684
• Chong, J., Liu, P. and Xia, J@. (2020) “Using MicrobiomeAnalyst for comprehensive statistical, functional and meta-analysis of microbiome data” Nature Protocols (doi: 10.1038/s41596-019-0264-1)
• Ewald, J., Soufan, O., Crump, D., Hecker, M., Xia, J., and Basu, N. (2020) “EcoToxModules: Custom gene sets to organize and analyze toxicogenomics data from ecological species” Environmental Science & Technology (doi: 10.1021/acs.est.9b06607)
• Hacariz, O., Viau, C., Karimian, F., Xia, J. (2021) “The Symbiotic Relationship Between Caenorhabditis elegans and Members of Its Microbiome Contributes to Worm Fitness and Lifespan Extension” BMC Genomics 22 (364)
• Soufan, O., Ewald, J., Zhou, G., Hacariz, O., Boulanger, E., Alcaraz, AJG., Hickey, G., Maguire, S., Pain, G., Hogan, N., Hecker, M., Crump, D., Head, J., Basu, N., Xia, J. (2021) “EcoToxXplorer: Leveraging Design Thinking to Develop a Standardized Web-Based Transcriptomics Analytics Platform for Diverse Users” Environmental Toxicology & Chemistry (doi: 10.1002/etc.5251)
• Liu, P., Ewald, J., Galvez, J. H., Bourque, G., Basu, N., and Xia, J. (2021) “Seq2Fun: ultra-fast functional profiling of RNA-seq data for non-model organisms” Genome Research (doi: 10.1101/gr.269894.120)
• Pang, Z., Zhou, G., Ewald, J., Chang, L., Hacariz, O., Basu, N., Xia, J. (2022) "Using MetaboAnalyst 5.0 for LC-HRMS spectra processing, multi-omics integration and covariate adjustment of global metabolomics data" Nature Protocols (doi: 10.1038/s41596-022-00710-w).
• Jeon, Y. S., D. Crump, E. Boulanger, O. Soufan, B. Park, N. Basu, M. Hecker, J. Xia and J. A. Head (2022). "Hepatic Transcriptomic Responses to Ethinylestradiol in Two Life Stages of Japanese Quail." Environmental Toxicology and Chemistry 41(11): 2769-2781.
• Hacariz, O., Viau C., Gu, X., and Xia, J. (2022) “Native Microbiome Members of C. elegans Act Synergistically in Biosynthesis of Pyridoxal 5’-Phosphate” Metabolites (doi: 10.3390/metabo12020172)
• Marchand, H., B. Barst, E. Boulanger, N. Vachon, M. Houde, J. Xia, P. Liu, J. Ewald, S. Bayen and L. Liu (2022). "Exposure to Contaminated River Water is Associated with Early Hatching and Dysregulation of Gene Expression in Early Life Stages of the Endangered Copper Redhorse (Moxostoma hubbsi)." Environmental Toxicology and Chemistry 41(8): 1950-1966.
• Zhao, H., Chong, J. Li, D. and Xia, J. (2023) Integrated multi-omics reveals the regulatory mechanism underlying the effects of artificial feed and grass feeding on growth and muscle quality of grass carp (Ctenopharyngodon idellus) (doi: 10.1016/j.aquaculture.2022.738808)
• Liu, P., Ewald J., Legrand E., Jeon, Y.S., Sangiovanni, J., Hacariz, O., Pang, Z., Zhou, G., Head, J., Basu, N., and Xia, J. (2023) “A unified platform for RNA-seq analysis in non-model species”, Nature Communications (doi:10.1038/s41467-023-38785-y)