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2024
Pang, Z., Viau, C., JN Fobil, JN., Basu, N., and
Xia, J.@
(2024) "Comprehensive Blood Metabolome and Exposome Analysis, Annotation, and Interpretation in E-Waste Workers"
Metabolites
Metabolites 14 (12)
Viau, C., Nouar, A. and
Xia, J.@
(2024) "Use of Caenorhabditis elegans to Unravel the Tripartite Interaction of Kynurenine Pathway, UPRmt and Microbiome in Parkinson’s Disease"
Biomolecules
14 (11), 1370
Coutu, FA., Iorio, OC, Nabavi, S., Hadid, A., Jensen, D., Pamidi, S.,
Xia, J.
, Ross BA (2024) "Continuous characterisation of exacerbation pathophysiology using wearable technologies in free-living outpatients with COPD: a prospective observational cohort study"
Metabolites
eBioMedicine 110
Lu, Y., Hui, F., Zhou, G., and
Xia, J.@
(2024) "MicrobiomeNet: exploring microbial associations and metabolic profiles for mechanistic insights"
Nucleic Acids Research
(doi:10.1093/nar/gkae944)
Ewald J.D., Lu, Y., Ellis, C.E., Worton, J., Kolic, J., Sasaki, S., Zhang, D., dos Santos, T., Spigelman, A.F., Bautista, A., Dai, X. ....
Xia, J.@
and MacDonald, PE.@ (2024) "HumanIslets.com: Improving accessibility, integration, and usability of human research islet data"
Cell Metabolism
(doi:10.1016/j.cmet.2024.09.001)
Kolic, J., Sun, WQG, Cen, HH., Ewald, JD., Rogalski, JC., Sasaki, S., Sun, H., Rajesh,V., ....
Xia, J.
, Lynn, F.C., Gloyn,AL., Foster, LJ., MacDonald, PE., Johnson, JD. (2024) "Proteomic predictors of individualized nutrient-specific insulin secretion in health and disease"
Cell Metabolism
36 (7), 1619-1633. e5
Vigano, ML., Kubal, S., Lu, Y., Habib, S., Samarani, S., Cama, G., Viau, C., Farzin, H., Koudieh, N.,
Xia, J.
, Ahmad, A., Vigano, A., Costiniuk CT. (2024) "Impact of Cannabidiol and Exercise on Clinical Outcomes and Gut Microbiota for Chemotherapy-Induced Peripheral Neuropathy in Cancer Survivors: A Case Report"
Pharmaceuticals
2024, 17(7), 834
Mitchell, JM., Chi, Y., Thapa, M., Pang, Z.,
Xia, J.
, Li, S. (2024) "Common data models to streamline metabolomics processing and annotation, and implementation in a Python pipeline"
PLOS Computational Biology
20 (6), e1011912
Bayen, S., Elliott, C., Arlorio, M., Ballins, NZ., Birse, N., Brockmeyer, J., Chahal, S., ...
Xia, J.
(2024) "Towards a harmonized approach for food authenticity marker validation and accreditation"
Trends in Food Science & Technology
(doi: 10.1016/j.tifs.2024.104550)
Pang, Z., Xu, L., Viau, C., Lu, Y., Salavati, R., Basu, N., and
Xia, J. @
(2024) “MetaboAnalystR 4.0: a unified LC-MS workflow for global metabolomics”
Nature Communications
(doi: 10.1038/s41467-024-48009-6)
Jeon, YS, Sangiovanni, J., Boulanger, E., Crump, D., Liu, P., Ewald, J., Basu, N.,
Xia, J.
, Hecker, M., and Head J. (2024) “Hepatic Transcriptomic Responses to Ethinylestradiol in Embryonic Japanese Quail and Double‐crested Cormorant”
Environmental Toxicology & Chemistry
(doi: 10.1002/etc.5811)
Chang, L., Ewald, J., Hui, F., Bayen, S., and
Xia, J. @
(2024) “A data-centric perspective on exposomics data analysis”
Exposome
(doi: 10.1093/exposome/osae005)
Pang, Z., Lu, Y., Zhou, G., Hui, F., Xu, L., Viau, C., Spigelman, A., MacDonald, P., Wishart, D., Li, S., and
Xia, J. @
(2024) “MetaboAnalyst 6.0: towards a unified platform for metabolomics data processing, analysis and interpretation”
Nucleic Acids Research
(doi: 10.1093/nar/gkae253)
Ewald J., Zhou, G., Lu, Y., Kolic, J., Ellis, C., Johnson, J., Macdonald P., and
Xia, J. @
(2024) “Web-based Multi-omics Integration Using the Analyst Software Suite”,
Nature Protocols
(doi: 10.1038/s41596-023-00950-4)
2023
Ewald J., Zhou, G., Lu, Y., and
Xia, J.@
(2023) "Using ExpressAnalyst for Comprehensive Gene Expression Analysis in Model and Non‐Model Organisms"
Current Protocols
3 (11), e922
Wang, K., Liao, X.,
Xia, J.
, Xiao, C. Deng, J., Xu Z. "Metabolomics: A promising technique for uncovering quality-attribute of fresh and processed fruits and vegetables"
Trends in Food Science & Technology
, 104213
Shiri, TJ., Viau, C., Gu, X., Lu, Y., and
Xia, J.@
(2023) "The Native Microbiome Member Chryseobacterium sp. CHNTR56 MYb120 Induces Trehalose Production via a Shift in Central Carbon Metabolism during Early Life in C. elegans"
Metabolites
13 (8), 953
Zhou, Z., Wu, X., Wu, Y., ....
Xia J.
and 20 others, Shen S. (2023) “Indole-3-Propionic acid, A Gut Microbiota Metabolite, Protects Against the Development of Postoperative Delirium”.
Annals of Surgery
(doi: 10.1097/SLA.0000000000005886)
Chang, L., Zhou, G., and
Xia, J.@
(2023) "mGWAS-Explorer 2.0: Causal Analysis and Interpretation of Metabolite–Phenotype Associations"
Metabolites
13 (7), 826
Crump, D., Hickey G., Boulanger E., Masse, A., Head, JA., Hogan, N., Maguire, S.,
Xia, J.
, Hecker, M., Basu, N. (2023) "Development and initial testing of EcoToxChip, a novel toxicogenomics tool for environmental management and chemical risk assessment"
Environmental Toxicology and Chemistry
(doi: 10.1002/etc.5676)
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) "ExpressAnalyst: a unified platform for RNA-sequencing analysis in non-model species"
Nature Communications
14, 2995
Lu, Y., Zhou, G., Ewald, J., Pang, Z., Shiri, T., and
Xia, J.@
(2023) "MicrobiomeAnalyst 2.0: comprehensive statistical, functional and integrative analysis of microbiome data"
Nucleic Acids Research
(doi: 10.1093/nar/gkad407).
Majumder, S., Sackey, T., Viau, C., Park, S.,
Xia, J.
, Ronholm, J. and George S. (2023) "Genomic and phenotypic profiling of Staphylococcus aureus isolates from bovine mastitis for antibiotic resistance and intestinal infectivity"
BMC microbiology
23 (1), 1-18
Dridi, L., Altamura, F., Gonzalez, E., Lui, O., Kubinski, R., Pidgeon, R., Montagut, A., Chong, J.,
Xia, J.
, Maurice, C., Castagner B. (2023). Identifying glycan consumers in human gut microbiota samples using metabolic labeling coupled with fluorescence-activated cell sorting.
Nature Communications
662(14)
Ni, Z., Wölk, M., Jukes, G., 18 others,
Xia J.
, O’Donnell, V. and Fedorova M. (2023) “Guiding the choice of informatics software and tools for lipidomics research applications”.
Nature Methods
20, 193-204
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)"
Aquaculture
(doi: 10.1016/j.aquaculture.2022.738808)
Lu, Y., Pang, Z., and
Xia, J.@
(2023) "Comprehensive investigation of pathway enrichment methods for functional interpretation of LC-MS global metabolomics data"
Briefings In Bioinformatics
(doi: 10.1093/bib/bbac553).
2022
Jeon, Y.S., Crump, D., Boulanger, E., Soufan, O., Park, B., Basu, N., Hecker, M.,
Xia, J.
and Head, J. (2022) "Hepatic Transcriptomic Responses to Ethinylestradiol in Two Life Stages of Japanese Quail." Environmental Toxicology and Chemistry, 41 (11), 2769-2781
Chang, L.,
Xia, J.@
(2022) "MicroRNA Regulatory Network Analysis Using miRNet 2.0"
Transcription Factor Regulatory Networks
, 185-204, Humana Press, New York, NY.
Zhao H., Chong, J., Li D.,
Xia, J.@
(2022) "Integrated multiple-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)
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).
Marchand, H., Boulanger, BE, Vachon, N., Houde, M.,
Xia, J.
, Liu, P., Ewald, J., Bayen, S., Liu, L., Head JA (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 & Chemistry
(doi: 10.1002/etc.5391).
Chang, L., Zhou, G., Ou, H.,
Xia, J.@
(2022) "mGWAS-Explorer: linking SNPs, genes, metabolites and diseases for functional insights"
Metabolites
(doi: 10.3390/metabo12060526).
Legrand, E., Jeon, YS., Basu, N., Hecker, M., Crump, D.,
Xia, J.
, Chandramouli, B., Butler, H., Head, J. (2022) “Consideration of metabolomics and transcriptomics data in the context of using avian embryos for toxicity testing”
Comparative Biochemistry and Physiology, Part C
(doi: 10.1016/j.cbpc.2022.109370)
Zhou, G., Pang Z., Lu, Y., Ewald, J.,
Xia, J.@
(2022) "OmicsNet 2.0: a web-based platform for multi-omics integration and network visual analytics"
Nucleic Acids Research
(doi:10.1093/nar/gkac376).
Hacariz, O., Viau, C., Gu, X.,
Xia, J.@
(2022) “Native Microbiome Members of C. elegans Act Synergistically in Biosynthesis of Pyridoxal 5′-Phosphate”
Metabolites
(doi: 10.3390/metabo12020172)
Colville, C., Alcaraz, AJG., Green, D., Park, B.,
Xia, J.
, Soufan, O., Hruṧka, P., Potěšil, D., Zdráhal, Z., Crump, D., Basu, N., Hogan, N., Hecker, M. (2022) “Characterizing toxicity pathways of fluoxetine to predict adverse outcomes in adult fathead minnows (Pimephales promelas)”
Science of The Total Environment
(doi: 10.1016/j.scitotenv.2021.152747)
Ma, X., Li, J., Zhang, Y., Hacariz, O.,
Xia, J.
, Simpson, BK, Wang, Z. (2022) “Oxidative stress suppression in C. elegans by peptides from dogfish skin via regulation of transcription factors DAF-16 and HSF-1”
Food & function
(doi: 10.1039/D1FO02271G)
Lu, Y., Chong, J., Shen, S., Chammas, JB., Chalifour, L.,
Xia, J.@
(2022) “TrpNet: Understanding Tryptophan Metabolism across Gut Microbiome”
Metabolites
(doi: 10.3390/metabo12010010)
Alcaraz, AJG., Baraniuk, S., Mikulášek, K., Park, B., Lane, T., Burbridge, C., Ewald, J., Potěšil, D.,
Xia, J.
, Zdráhal, Z., Schneider, D., Crump, D., Basu, N., Hogan, N., Brinkmann, M., Hecker M. (2021) “Comparative analysis of transcriptomic points-of-departure (tPODs) and apical responses in embryo-larval fathead minnows exposed to fluoxetine”
Environmental Pollution
(doi: 10.1016/j.envpol.2021.118667)
2021
Legrand, E., Basu, N., Hecker, M., Crump, D.,
Xia, J.
, Chandramouli, B., Butler, H., Head J. “Targeted Metabolomics to Assess Exposure to Environmental Chemicals of Concern in Japanese Quail at Two Life Stages”
Metabolites
(doi: 10.3390/metabo11120850)
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)
Alcaraz, AJG., Potesil, D., Mikulasek, K., Potesil, D., Park, B., Shekh, K., Ewald, J., Burbridge, C., Zdrahal, Z., Schneider, D.,
Xia, J.
, Crump, D., Basu, N., and Hecker M. (2021) “Assessing the Toxicity of 17α-Ethinylestradiol in Rainbow Trout Using a 4-Day Transcriptomics Benchmark Dose (BMD) Embryo Assay”
Environmental Science & Technology
(doi: 10.1021/acs.est.1c02401)
Desforges, JP, Elena Legrand,E., Boulager, E., Liu, P.,
Xia, J.
, Butler, H., Chandramouli, B., Ewald, J., Basu, N., Hecker, M., Head, J., Crump D. (2021) “Using Transcriptomics and Metabolomics to Understand Species Differences in Sensitivity to Chlorpyrifos in Japanese Quail and Double‐Crested Cormorant Embryos”
Environmental Technology & Chemistry
(doi: 10.1002/etc.5174)
Zhou, G., Ewald, J., and
Xia, J.@
(2021) “OmicsAnalyst: a comprehensive web-based platform for visual analytics of multi-omics data”
Nucleic Acids Research
(10.1093/nar/gkab394)
Pang, Z., Chong, J., Zhou, G., Morais D., Chang, L., Barrette, M., Gauthier, C., Jacques, PE., Li, S., and
Xia, J.@
(2021) “MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights”
Nucleic Acids Research
(10.1093/nar/gkab382)
Haçariz, 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)
Alcaraz, AJG., Potěšil, D., Mikulášek, K., Green, D., Park, B., Burbridge, C., Bluhm, K., Soufan, O., Lane, T., Pipal, M., Brinkmann, M.,
Xia, J.
, Zdráhal, Z., Schneider, D., Crump, D., Basu, N., Hogan, N., and Hecker M. (2021) “Development of a Comprehensive Toxicity Pathway Model for 17α-Ethinylestradiol in Early Life Stage Fathead Minnows (Pimephales promelas)”
Environmental Science & Technology
(doi: 10.1021/acs.est.0c05942)
Liu, P., Ewald, J., Galvez, J., Head, J., Crump, D., Basu, N. and
Xia, J.@
(2021) “Ultrafast functional profiling of RNA-seq data for nonmodel organisms”
Genome Research
(doi: 10.1101/gr.269894.120)
Chang, HY., Colby, SM., Du, X., Gomez, J., Helf, M., Kechris, K., Kirkpatrick, C., Li, S., Patti, G., Renslow, R., Subramaniam, S., Verma, M.,
Xia, J.
, and Young JD (2021) “A Practical Guide to Metabolomics Software Development”
Anal. Chem
(doi: 10.1021/acs.analchem.0c03581)
Pang, Z., Zhou, G., Chong, J. and
Xia, J.@
(2021) “Comprehensive Meta-Analysis of COVID-19 Global Metabolomics Datasets”
Metabolites
(doi: 10.3390/metabo11010044)
2020
Ewald, J., Soufan, O., Soufan, O.
Xia, J.@
and Basu, N.@(2020) “FastBMD: an online tool for rapid benchmark dose-response analysis of transcriptomics data”
Bioinformatics
(doi: 10.1093/bioinformatics/btaa700)
Chang, L., Zhou, G., Soufan, O. and
Xia, J.@
(2020) “miRNet 2.0: network-based visual analytics for miRNA functional analysis and systems biology”
Nucl. Acids Res.
(doi: 10.1093/nar/gkaa467)
Pang, Z., Chong, J., Li, S. and
Xia, J.@
(2020) “MetaboAnalystR 3.0: Toward an Optimized Workflow for Global Metabolomics”
Metabolites
(doi: 10.3390/metabo10050186)
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)
Viau, C., Hacariz, O., Karimian, F., and
Xia J.@
(2020) “Comprehensive phenotyping and transcriptome profiling to study nanotoxicity in C. elegans”.
PeerJ
8, e8684
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 and Technology
(doi: 10.1021/acs.est.9b06607)
Chong, J. and
Xia, J@.
(2020) “Metabolomics Data Analysis using MetaboAnalyst 4.0”
Computational Methods and Data Analysis for Metabolomics
. vol 2104. Humana, New York, NY (doi: 10.1007/978-1-0716-0239-3_17)
Zhou, G., Li, S. and
Xia, J@.
(2020) “Network-based Approaches for Multi-omics Integration”
Computational Methods and Data Analysis for Metabolomics
, vol 2104. Humana, New York, NY (doi: 10.1007/978-1-0716-0239-3_23)
2019
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
Soufan O., Ewald J., Viau C., Crump D., Hecker M., Basu N., and
Xia, J.
@ (2019) "T1000: a reduced gene set prioritized for toxicogenomic studies".
PeerJ
7: e7975 (doi.org/10.7717/peerj.7975)
Chong, J., Yamamoto, M., and
Xia, J@.
(2019) “MetaboAnalystR 2.0: from raw spectra to biological insights”
Metabolites
9, 57
Khan, N., Mendonca1, L., Dhariwal, A., Fontes, G., Menzies, D.,
Xia, J.
, Divangahi, M., King. I. (2019) “Intestinal dysbiosis compromises alveolar macrophage immunity to Mycobacterium tuberculosis”
Mucosal Immunology
(doi: 10.1038/s41385-019-0147-3)
Basu, N., Crump, D., Head, J., Hickey, G., Hogan, N., Maguire, S.,
Xia, J.
, and Hecker, M. (2019) “EcoToxChip: A next-generation toxicogenomics tool for chemical prioritization and environmental management”
Environmental Toxicology and Chemistry
38 (2), 279–288 (doi: 10.1002/etc.4309)
Zhao H., Soufan, O.,
Xia, J.
, Tang R., Li L., and Li, D. (2019) “Transcriptome and physiological analysis reveal alterations in muscle metabolisms and immune responses of grass carp (Ctenopharyngodon idellus) cultured at different stocking densities”
Aquaculture
(doi: 10.1016/j.aquaculture.2019.01.003)
Chong, J., Wishart, D.S. and
Xia, J.
@ (2019) "Using MetaboAnalyst 4.0 for Comprehensive and Integrative Metabolomics Data Analysis".
Current Protocols in Bioinformatics
68, e86 (doi: 10.1002/cpbi.86)
2018
Chong, J. and
Xia, J@.
(2018) “MetaboAnalystR: an R package for flexible and reproducible analysis of metabolomics data”
Bioinformatics
34 4313-4314
Zhou G. and
Xia, J@.
(2018) “OmicsNet - A web-based tool for creation and visual analysis of biological networks in 3D space”
Nucleic Acids Research
46 W514-522
Chong, J., Soufan, O., Li, C., Caraus, I., Li, S., Bourque, B., Wishart, DS., and
Xia, J@.
(2018) “MetaboAnalyst 4.0 – Towards More Transparent and Integrative Metabolomics Analysis”
Nucleic Acids Research
46 W486-494
Fan, Y., Habib. M., and
Xia, J@.
(2018) “Xeno-miRNet: a comprehensive database and analytics platform to explore xeno-miRNAs and their potential targets”
PeerJ
6:e5650 (doi: 10.7717/peerj.5650)
Zhao, H., Chong, J. Tang, R., Li, L.,
Xia, J.
and Li. D. (2018) “Metabolomics Analysis Reveals Correlations between Fish Flesh Quality and Muscle Metabolite Profiles in Grass Carp (Ctenopharyngodon idellus)”
GigaScience
7, 2018, 1-18
Zhao, H.,
Xia, J.
, Zhang, X., He, X., Li, L., Tang, R., Chi, W., Li D. (2018) “Diet Affects Muscle Quality and Growth Traits of Grass Carp (Ctenopharyngodon idellus): A Comparison Between Grass and Artificial Feed”
Frontiers in physiology
9, 283
Kang, E., Zhou, G., Yousef, M., Cayrol, R.,
Xia, J.
, and Gruenheid S. (2018), “Loss of disease tolerance during Citrobacter rodentium infection is associated with impaired epithelial differentiation and hyperactivation of T cell responses”
Scientific Reports
8:847 (doi: 10.1038/s41598-017-17386-y)
Zhou, G. and
Xia, J@.
(2018) “Using OmicsNet for Network Integration and 3D Visualization”
Current Protocols in Bioinformatics
, 45 pages (doi: 10.1002/cpbi.69)
Fan, Y. and
Xia, J@.
(2018) “miRNet – functional analysis and visual exploration of miRNA-target interactions in a network context”
Computational Cell Biology
, Springer, doi: 10.1007/978-1-4939-8618-7_10
Dayalan, S.,
Xia, J.
, Spicer, R. A., Salek, R., and Roessner, U. (2018) “Metabolome Analysis”
Reference Module in Life Sciences
(Elsevier), 24 pages, doi: 10.1016/B978-0-12-809633-8.20251-3
2017
Chong, J. and
Xia, J@.
(2017) “Computational approaches for integrative analysis of the metabolome and microbiome”
Metabolites
7(4), 62
Bourguinat, C., Keller, K.,
Xia, J.
, Lepage, P., McTier,T.L., Woods, D.J., and Prichard R. K. (2017) “Genetic profiles of ten Dirofilaria immitis isolates susceptible or resistant to macrocyclic lactone heartworm preventives”
Parasites and Vectors
, 10 (Suppl 2) :504
Dhariwal, A., Chong, J., Habib, S., King, I., Agellon, LB., and
Xia, J@.
(2017) “MicrobiomeAnalyst – a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data”.
Nucleic Acids Research
45 W180-188
Gardinassi, L.G.,
Xia, J.
, Safo, S.E., Li, S. (2017) “Bioinformatics Tools for the Interpretation of Metabolomics Data”
Current Pharmacology Reports
3: 374 doi: 10.1007/s40495-017-0107-0
Xia, J@.
(2017) “Computational strategies for biological interpretation of metabolomics data”
Metabolomics: From Fundamentals to Clinical Applications
, doi: 10.1007/978-3-319-47656-8
2016
Fan, Y., Siklenka, K., Arora, S.K., Ribeiro, P., Kimmins, S., and
Xia, J@.
(2016) “miRNet - dissecting miRNA-target interactions and functional associations through network-based visual analysis”
Nucleic Acids Research
44 W135-41
O’Neill, M., Ballesteros, C., Tritten, L., Burkman, E., Zaky, W.I.,
Xia, J.
, Moorhead, A., Williams, S. A., and Geary, T. G. (2016) “Profiling the macrofilaricidal effects of flubendazole on adult female Brugia malayi using RNAseq”
International Journal for Parasitology: Drugs and Drug Resistance
6 (3): 288-296
Zhou, G., Stevenson, MM., Geary, T.G., and
Xia, J@.
(2016) “Comprehensive Transcriptome Meta-analysis to Characterize Host Immune Responses in Helminth Infections”
PLOS Neglected Tropical Diseases
10 (4): e0004624
Ballesteros C, Tritten, L., O’Neill, M., Burkman, E., Zaky, W.I.,
Xia, J.
, A Moorhead, A., Williams, S.A., and Geary, T.G. (2016) “The Effects of Ivermectin on Brugia malayi Females In Vitro: A Transcriptomic Approach”
PLOS Neglected Tropical Diseases
, 10(8): e0004929
Gruber M.,
Xia, J.
, Yu, M., Steppuhn, H., Wall, K., Messer, D., Sharpe A.G., Acharya, S., Wishart, D.S., Johnson, D.W., Miller, D., Taheri, A. (2016) “Transcript analysis in two alfalfa salt tolerance selected breeding populations relative to a non-tolerant population”
Genome
, doi: 10.1139/gen-2016-0111
Paudel, JR., Amirizian, A., Krosse, S., Giddings, J., Ismail, SAA.,
Xia, J.
, Gloer, JB., van Dam, NM., and Bede, JC. (2016) “Effect of atmospheric carbon dioxide levels and nitrate fertilization on glucosinolate biosynthesis in mechanically damaged Arabidopsis plants”
BMC Plant Biology
16:68
Ballesteros, C., Tritten, L., O’Neill, M., Burkman, E., Zaky, W.I.,
Xia, J.
, Moorhead, A., Williams, S.A., and Geary, T.G. (2016) “The effect of in vitro cultivation on the transcriptome of adult Brugia malayi”.
PLOS Neglected Tropical Diseases
, 10 (1): e0004311
Xia, J@.
and Wishart D.S.@ (2016) “Using MetaboAnalyst 3.0 for Comprehensive Metabolomics Data Analysis”
Current Protocols in Bioinformatics
, 55:14.10.1-14.10.91, 91 pages
2015
Xia, J@.
, Gill, E., and Hancock, R.E.W@. (2015) “NetworkAnalyst for Statistical, Visual and Network-based Approaches for Meta-analysis of Expression Data”
Nature Protocols
10 (6), 823-844.
Siklenka, K., Erkek, S., Godmann, M., Lambrot, R., McGraw, S., Lafleur,C., Cohen, T.,
Xia, J.
, Suderman, M., Hallett, M., Trasler, J., Peters, A.H.F.M. and Kimmins, S. (2015) “Disruption of histone methylation in developing sperm impairs offspring health transgenerationally”
Science
350: 6261
Xia, J@.
, Sinelnikov, I.V., Han B., and Wishart D.S. (2015) “MetaboAnalyst 3.0 – Making Metabolomics More Meaningful”.
Nucleic Acids Research
43 (W1): W251-257
Bahado-Singh, R.O., Akolekar, A., Mandal, R., Dong, E.,
Xia, J.
, Kruger, M., Wishart D. S. and Nicolaides, K. (2015) “Metabolomic Analysis for First Trimester Down Syndrome Prediction”
Obstetric Anesthesia Digest
35 (1), 35-36
Yeung, A., Hale, C.,
Xia, J.
, Tate, P., Goulding, D., Keane, J., Mukhopadhyay, S., Forrester, L., Billker, O., Skarnes, W., Hancock R.E.W., and Dougan G. (2015) “Conditional-ready mouse embryonic stem cell derived macrophages enable the study of essential genes in macrophage function”
Scientific Reports
5:8908
Before 2015
Xia, J.
, Benner, M.J. and Hancock, REW. (2014) “NetworkAnalyst – integrative approaches for protein-protein interaction network analysis and visual exploration”.
Nucleic Acid Research
, 42, W167-174
34. Peng, J., Guo, K.,
Xia, J.
, Zhou, J., Yang, J., Westaway, D., Wishart, D.S. and Li., L. (2014) “Development of Isotope Labeling Liquid Chromatography Mass Spectrometry for Mouse Urine Metabolomics: Quantitative Metabolomic Study of Transgenic Mice Related to Alzheimer’s Disease”
Journal of Proteome Research
, 13(10): 4457-69
35. Pena, O.M., Hancock, D.G., Lyle, N.H., Linder, A., James A., Russell, J.A.,
Xia, J.
, Fjell, C.D., Boyd, J.H., and Hancock, R.E.W. (2014) “An Endotoxin Tolerance Signature Predicts Sepsis and Organ Dysfunction at Initial Clinical Presentation”
EbioMedicine
, 1(1): 64-71
36. Fan, L., Wang, Q., de la Fuente-Núñez, C., Sun, F.,
Xia, J.
, Xia, P., Hancock, R.E.W. (2014) “Increased IL-8 Production in Human Bronchial Epithelial Cells after exposure to Azithromycin pre-treated Pseudomonas aeruginosa in vitro”
FEMS Microbiology Letters
, 355(1): 43-50
37. Kleensang A., Maertens A., Rosenberg M., Fitzpatrick S., Lamb J., Auerbach S., Brennan R., Crofton K., Gordon B., Fornace A.J., Gaido K., Gerhold D., Haw R., Henney A., Ma’ayan A., McBride M., Monti S., Ochs M.F., Pandey A., Sharan R., Stierum R., Tugendreich S., Willett C., Wittwehr C.,
Xia, J.
, and 12 more authors. (2014) “T4 Workshop Report – Pathways of Toxicity”.
ALTEX
31(1): 53-61
Xia, J.
, Lyle, N.H., Mayer, M., Pena, O.M. and Hancock, R.E.W. (2013) “INVEX – a web-based tool for integrative visualization of expression data”.
Bioinformatics
, 29 (24), 3232-3234
Ghobakhlou, A., Laberge, S., Antoun, H., Wishart, D.S.,
Xia, J.
, Krishnamurthy, R., Mandal, R. (2013) “Metabolomic Analysis of Cold Acclimation of Arctic Mesorhizobium sp. Strain N33”.
PloS One
, 8 (12), e84801
Xia, J.
, Fjell, C.D., Mayer, M., Pena, O.M., Wishart, D.S. and Hancock, R.E.W. (2013) “INMEX – a web-based tool for integrative meta-analysis of expression data”.
Nucleic Acids Research
, 41, W63-W70
Bahado-Singh, R.O., Akolekar, R., Mandal, R., Dong, E.,
Xia, J.
, Kruger, M., Wishart, D.S. and Nicolaides, K. (2013) “Metabolomic analysis for first-trimester Down syndrome prediction”.
American Journal of Obstetrics and Gynecology
, 208:371.e1-8
Xia, J.
, Broadhurst, D., Wilson, M. and Wishart, D. (2013) “Translational biomarker discovery in clinical metabolomics: an introductory tutorial”.
Metabolomics
, 9, 280-299
Canam, T., Li, X., Holowachuk, J., Yu, M.,
Xia, J.
, Mandal, R., Krishnamurthy, R., Bouatra, S., Sinelnikov, I. and Yu, B. (2013) “Differential metabolite profiles and salinity tolerance between two genetically-related brown-seeded and yellow-seeded Brassica carinata lines”.
Plant Science
, 198, 17–26.
Wishart, D.S., Jewison, T., Guo, A.C., Wilson, M., Knox, C., Liu, Y., Djoumbou, Y., Mandal, R., Aziat, F., Dong, E., Bouatra, S., Sinelnikov, I., Arndt, D.,
Xia, J.
, Liu, P. et al. (2013) “HMDB 3.0 – The Human Metabolome Database in 2013”.
Nucleic Acids Research
, 41, D801-D807
Bahado-Singh, R.O., Akolekar, R., Mandal, R., Dong, E.,
Xia, J.
, Kruger, M., Wishart, D.S. and Nicolaides, K. (2013) “First Trimester Metabolomic Detection of late-onset preeclampsia”.
American Journal of Obstetrics and Gynecology
, 208, 58.e1–58.e7
Xia, J.
, Mandal, R., Sinelnikov, I., Broadhurst, D., and Wishart, DS. (2012) “MetaboAnalyst 2.0 – a comprehensive server for metabolomic data analysis”
Nucleic Acids Research
, W127-133
Arndt, D.,
Xia, J.
, Yifeng Liu, Y., Zhou, Y., Guo, AC., Cruz, JA., Sinelnikov, I., Budwill, K., Nesbø, CL., and Wishart DS (2012) “METAGENassist: a comprehensive web server for comparative metagenomics”:
Nucleic Acids Research
, W88-W95.
Bahado-Singh, R.O., Akolekar, R., Mandal, R., Dong, E.,
Xia, J.
, Kruger, M., Wishart, D.S. and Nicolaides, K. (2012) Metabolomics and first-trimester prediction of early-onset preeclampsia.
Journal of Maternal-Fetal and Neonatal Medicine
, 25, 1840-1847
Fleming-Canepa, X., Brusnyk, C., Aldridge, J.R., Ross, K.L., Moon, D., Wang, D.,
Xia, J.
, Barber, M.R.W., Webster, R.G. and Magor, K.E. (2011) “Expression of duck CCL19 and CCL21 and CCR7 receptor in lymphoid and influenza-infected tissues”.
Molecular Immunology
, 48, 1950-1957
Xia, J.
, Sinelnikov, I., and Wishart, D.S. (2011) “MetATT – a web-based metabolomic tool for analyzing time-series and two-factor data sets”.
Bioinformatics
, 27, 2455-2456
Xia, J.
and Wishart, D.S. (2011) “Web-based inference of biological patterns, functions and pathways from metabolomic data using MetaboAnalyst”.
Nature Protocols
, 6, 743-760
Psychogios, N., Hau, DD., Peng, J., Guo, AC., Mandal, R., Bouatra, S., Sinelnikov, I., Krishnamurthy, R., Eisner, R., Gautam, B., Nelson, Y.,
Xia, J.
, et al. (2011) “The Human Serum Metabolome”.
PloS One
, 6: e16957.
Eisner, R., Stretch, C., Eastman, T.,
Xia, J.
, Hau, D., Damaraju, S., Greiner, R., Wishart, D.S. and Baracos, V.E. (2011) “Learning to predict cancer-associated skeletal muscle wasting from 1H-NMR profiles of urinary metabolites”.
Metabolomics
, 7, 25-34
Xia, J.
and Wishart, D.S.@ (2011) “Metabolomic Data Processing, Analysis and Interpretation using MetaboAnalyst”.
Current Protocols in Bioinformatics
, 34:14.10.1-14.10.48.
Xia, J.
and Wishart, D.S. (2010) “MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data”.
Nucleic Acids Res
38, W71-77.
Xia, J.
and Wishart, D.S. (2010) “MetPA: a web-based metabolomics tool for pathway analysis and visualization”.
Bioinformatics
26, 2342-2344.
Frolkis, A., Knox, C., Lim, E., Jewison, T., Law, V., Hau, D., Liu, P., Gautam, B., Ly, S., Guo, A.C.,
Xia, J.
, Liang, Y., Shrivastava, S. and Wishart D.S. (2010) “SMPDB: The Small Molecule Pathway Database”.
Nucleic Acids Res
38, D480-487.
Ametaj, B.N., Zebeli, Q., Saleem, F., Psychogios, N., Lewis, J.L., Dunn, S.M.,
Xia, J.
, and Wishart, D.S. (2010) “Metabolomics reveals unhealthy alterations in rumen metabolism with increased proportion of cereal grain in the diet of dairy cows.”
Metabolomics
6, 583-594.
Xia, J.
, Psychogios, N., Young, N. and Wishart, D.S. (2009) “MetaboAnalyst: a web server for metabolomic data analysis and interpretation”.
Nucleic Acids Res
37, W652-660.
Wishart, D.S., Knox, C., Guo, A.C., Eisner, R., Young, N., Gautam, B., Hau, D.D., Psychogios, N., Dong, E., Bouatra, S., Mandal, R., Sinelnikov I.,
Xia, J.
, et al. (2009) “HMDB: a knowledgebase for the human metabolome”.
Nucleic Acids Res
37, D603-610.
Soh, J., Turinsky, A.L., Trinh, Q., Chang, J., Sabhaney, A., Dong, X., Gordon, P., Janzen, R., D., H.,
Xia, J.
, Wishart D.S. and Sensen C.W. (2009) “Spatiotemporal integration of molecular and anatomical data in virtual reality using semantic mapping”.
Int J Nanomed
4, 79-89.
Xia, J.
, Bjorndahl, T. C., Tang, P. and Wishart, D.S. (2008) “MetaboMiner–semi-automated identification of metabolites from 2D NMR spectra of complex biofluids”.
BMC Bioinformatics
9, 507.
MacDonald, M. R.,
Xia, J.
, Smith, A. L. and Magor, K. E. (2008) “The duck toll like receptor 7: genomic organization, expression and function”.
Mol Immunol
45, 2055-2061.
Guo, X., Branton, W.G., Moon, D.A.,
Xia, J.
, Macdonald, M.R. and Magor, K.E. (2008) “Dendritic cell inhibitory and activating immunoreceptors (DCIR and DCAR) in duck: Genomic organization and expression”.
Mol Immunol
45, 3942-3946.
MacDonald, M.R., Veniamin, S.M., Guo, X.,
Xia, J.
, Moon, D.A. and Magor, K.E. (2007) “Genomics of antiviral defenses in the duck, a natural host of influenza and hepatitis B viruses”.
Cytogenet Genome Res
117, 195-206.
Xia, J.
, Radford, C., Guo, X. and Magor, K.E. (2007) “Immune gene discovery by expressed sequence tag analysis of spleen in the duck (Anas platyrhynchos)”.
Dev Comp Immunol
31, 272-285.