Xia Lab @ McGill
The latest publication list can also be found on my Google Scholar Profile
2020
  1. 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)
  2. 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)
  3. 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)
  4. 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)
  5. Viau, C., Hacariz, O., Karimian, F., and Xia J.@ (2020) “Comprehensive phenotyping and transcriptome profiling to study nanotoxicity in C. elegans”. PeerJ 8, e8684
  6. 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)
  7. 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)
  8. 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
  1. 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
  2. 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)
  3. Chong, J., Yamamoto, M., and Xia, J@. (2019) “MetaboAnalystR 2.0: from raw spectra to biological insights” Metabolites 9, 57
  4. 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)
  5. 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)
  6. 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)
  7. 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
  1. Chong, J. and Xia, J@. (2018) “MetaboAnalystR: an R package for flexible and reproducible analysis of metabolomics data” Bioinformatics 34 4313-4314
  2. 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
  3. 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
  4. 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)
  5. 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
  6. 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
  7. 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)
  8. 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)
  9. 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
  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
  1. Chong, J. and Xia, J@. (2017) “Computational approaches for integrative analysis of the metabolome and microbiome” Metabolites 7(4), 62
  2. 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
  3. 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
  4. 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
  5. 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
  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  1. 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.
  2. 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
  3. 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
  4. 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
  5. 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
  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. Xia, J., Broadhurst, D., Wilson, M. and Wishart, D. (2013) “Translational biomarker discovery in clinical metabolomics: an introductory tutorial”. Metabolomics, 9, 280-299
  11. 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.
  12. 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
  13. 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
  14. 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
  15. 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.
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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.
  21. 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
  22. 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.
  23. 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.
  24. Xia, J. and Wishart, D.S. (2010) “MetPA: a web-based metabolomics tool for pathway analysis and visualization”. Bioinformatics 26, 2342-2344.
  25. 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.
  26. 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.
  27. 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.
  28. 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.
  29. 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.
  30. 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.
  31. 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.
  32. 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.
  33. 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.
  34. 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.