Xiaoli Dong

Publications

  1. DY Sorokin, D Mosier, JK Zorz, X Dong, M Strous (2020) Wenzhouxiangella Strain AB-CW3, a Proteolytic Bacterium From Hypersaline Soda Lakes That Preys on Cells of Gram-Positive Bacteria Frontiers in Microbiology, Dec 8, 2020, doi.org/10.3389/fmicb.2020.597686
  2. Yu, Jaicheng & Zhang, Tongwei & Xu, Huangtao & Dong, Xiaoli & Cai, Yao & Pan, Yongxin & Cao, Changqian. (2019). Thermostable iron oxide nanoparticle synthesis within recombinant ferritins from the hyperthermophile Pyrococcus yayanosii CH1. RSC Advances. vol. 9 67. 29 Nov. 2019, doi:10.1039/C9RA07397C
  3. Dong, Xiaoli, and Marc Strous. An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs. Frontiers in genetics vol. 10 999. 15 Oct. 2019, doi:10.3389/fgene.2019.00999
  4. Zorz, Jackie & Sharp, Christine & Kleiner, Manuel & Gordon, Paul & Pon, Richard & Dong, Xiaoli & Strous, Marc. (2019). A shared core microbiome in soda lakes separated by large distances. Nature Communications. 10. 1-10. 10.1038/s41467-019-12195-5.
  5. Manuel Kleiner, Xiaoli Dong, Tjorven Hinzke, Juliane Wippler, Erin Thorson, Bernhard Mayer, Marc Strous (2018) Metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities Proceedings of the National Academy of Sciences Jun 2018, 115 (24) E5576-E5584; DOI: 10.1073/pnas.1722325115i
  6. Kleiner M, Thorson E, Sharp CE, Dong X, Liu D, Li C, Strous M (2017) Assessing species biomass contributions in microbial communities via metaproteomics. Nat Commun. 2017 Nov 16;8(1):1558. doi: 10.1038/s41467-017-01544-x.
  7. Dong X, Kleiner M, Sharp CE, Thorson E, Li C, Liu D and Strous M (2017) Fast and Simple Analysis of MiSeq Amplicon Sequencing Data with MetaAmp. Front. Microbiol. 8:1461. doi: 10.3389/fmicb.2017.01461
  8. Rochman FF, Sheremet A, Tamas I, Saidi-Mehrabad A, Kim J-J, Dong X, Sensen CW, Gieg LM and Dunfield PF (2017) Benzene and Naphthalene Degrading Bacterial Communities in an Oil Sands Tailings Pond. Front. Microbiol. 8:1845. doi: 10.3389/fmicb.2017.01845
  9. Christine E. Sharp, Sydney Urschel, Xiaoli Dong, Allyson L. Brady, Greg F. Slater and Marc Strous. Robust, high-productivity phototrophic carbon capture at high pH and alkalinity using natural microbial communities. Biotechnology for Biofuels 10, 84 (2017). DOI: 10.1186/s13068-017-0769-1
  10. Emmo Hamann, Harald Gruber-Vodicka, Manuel Kleiner, Halina E. Tegetmeyer, Dietmar Riedel, Sten Littmann, Jianwei Chen, Jana Milucka, Bernhard Viehweger, Kevin W. Becker, Xiaoli Dong, Courtney W. Stairs, Kai-Uwe Hinrichs, Matthew W. Brown, Andrew J. Roger & Marc Strous (2016) Environmental Breviatea harbour mutualistic Arcobacter epibionts. Nature 534, 254–258(09 June 2016) doi:10.1038/nature18297
  11. An D, Dong X, An A, Park HS, Strous M and Voordouw G (2016) Metagenomic Analysis Indicates Epsilonproteobacteria as a Potential Cause of Microbial Corrosion in Pipelines Injected with Bisulfite. Front. Microbiol. 7:28. doi: 10.3389/fmicb.2016.00028
  12. Wong M, An D., Caffrey S., Soh J., Dong X., Sensen C., Oldenburg T., Larter S., Voordouw G.Roles of Thermophiles and Fungi in Bitumen Degradation in Mostly Cold Oil Sands Outcrops Applied and Environmental Microbiology, 2015 July 24. doi: 10.1128/AEM.02221-15
  13. Tan B, Jane Fowler S, Laban NA, Dong X, Sensen CW, Foght J, Gieg LM.(2015). Comparative analysis of metagenomes from three methanogenic hydrocarbon-degrading enrichment cultures with 41 environmental samples. ISME J. 2015 Mar 3. doi: 10.1038/ismej.2015.22.
  14. Saidi-Mehrabad, A., He, Z., Tamas, I., Sharp, C.E., Brady, A.L., Rochman, R.F., Bodrossy, L., Abell, G.C., Penner, T., Dong, X., Sensen, C.W. and Dunfield P.F. (2013). Methanotrophic bacteria in oilsands tailings ponds of northern Alberta. The ISME Journal. 7(5):908-21.
  15. Soh, J., Dong, X., Caffrey, S.M., Voordouw, G., Sensen, C.W. (2013) Phoenix 2: a locally installable large-scale 16S rRNA gene sequence analysis pipeline with Web interface. Journal of Biotechnology 167(4):393-403.
  16. An, D., Brown, D., Chatterjee, I., Dong, X., Ramos-Padron, E., Wilson, S., Bordenave, S., Caffrey, S. M., Gieg, L. M., Sensen, C. W., and Gerrit Voordouw, G. (2013) Microbial community and potential functional gene diversity involved in anaerobic hydrocarbon degradation and methanogenesis in an oil sands tailings pond. Genome, 10.1139/gen-2013-0083.
  17. An, D., et al. (2013). Metagenomics of Hydrocarbon Resource Environments Indicates Aerobic Taxa and Genes to be Unexpectedly Common. Environmental Science & Technology, 47 (18), 10708-107717. DOI:10.1021/es4020184.
  18. B Tan, X Dong, CW Sensen, J Foght, S Scherer. Metagenomic analysis of an anaerobic alkane-degrading microbial culture: potential hydrocarbon-activating pathways and inferred roles of community members. Genome, 2013, 56(10): 599-611, 10.1139/gen-2013-0069
  19. Saidi-Mehrabad, A., He, Z., Tamas, I., Sharp, C.E., Brady, A.L., Rochman, R.F., Bodrossy, L., Abell, G.C., Penner, T., Dong, X., Sensen, C.W. and Dunfield P.F. (2012). Methanotrophic bacteria in oilsands tailings ponds of northern Alberta. ISME J. 2013 May;7(5):908-21. doi: 10.1038/ismej.2012.163. Epub 2012 Dec 20.
  20. Berdugo-Clavijo C, Dong X, Soh J, Sensen CW, Gieg LM. Methanogenic biodegradation of two-ringed polycyclic aromatic hydrocarbons. FEMS Microbiol Ecol. 2012 Jul;81(1):124-33. doi: 10.1111/j.1574-6941.2012.01328.x. Epub 2012 Mar 8. PMID:22324881
  21. Fowler SJ, Dong X, Sensen CW, Suflita JM, Gieg LM. Methanogenic toluene metabolism: community structure and intermediates. Environ Microbiol. 2011 Nov 1. doi: 10.1111/j.1462-2920.2011.02631.x. [Epub ahead of print] PubMed PMID: 22040260.
  22. Kryachko Y, Dong X, Sensen CW, Voordouw G. Compositions of microbial communities associated with oil and water in a mesothermic oil field. Antonie Van Leeuwenhoek. 2012 Mar;101(3):493-506. Epub 2011 Oct 29. PubMed PMID: 22038128.
  23. Park HS, Chatterjee I, Dong X, Wang SH, Sensen CW, Caffrey SM, Jack TR, Boivin J, Voordouw G. Effect of sodium bisulfite injection on the microbial community composition in a brackish-water-transporting pipeline. Appl Environ Microbiol. 2011 Oct;77(19):6908-17. Epub 2011 Aug 19. PubMed PMID: 21856836; PubMed Central PMCID: PMC3187121.
  24. Callbeck CM, Dong X, Chatterjee I, Agrawal A, Caffrey SM, Sensen CW, Voordouw G. Microbial community succession in a bioreactor modeling a souring low-temperature oil reservoir subjected to nitrate injection. Appl Microbiol Biotechnol. 2011 Aug;91(3):799-810. Epub 2011 May 3. PubMed PMID: 21538114.
  25. Ramos-Padrón E, Bordenave S, Lin S, Bhaskar IM, Dong X, Sensen CW, Fournier J, Voordouw G, Gieg LM. Carbon and sulfur cycling by microbial communities in a gypsum-treated oil sands tailings pond. Environ Sci Technol. 2011 Jan 15;45(2):439-46. Epub 2010 Dec 3. PubMed PMID: 21128661.
  26. Soh J, Turinsky AL, Trinh QM, Chang J, Sabhaney A, Dong X, Gordon PM, Janzen RP, Hau D, Xia J, Wishart DS, Sensen CW. Spatiotemporal integration of molecular and anatomical data in virtual reality using semantic mapping. Int J Nanomedicine. 2009;4:79-89. Epub 2009 Apr 1.
  27. Turinsky AL, Fanea E, Trinh Q, Wat S, Hallgrímsson B, Dong X, Shu X, Stromer JN, Hill JW, Edwards C, Grosenick B, Yajima M, Sensen CW. CAVEman: Standardized anatomical context for biomedical data mapping. Anat Sci Educ. 2008 Jan;1(1):10-8. PubMed PMID: 19177373.
  28. Turinsky AL, Fanea E, Trinh Q, Dong X, Stromer JN, Shu X, Wat S, Hallgrímsson B, Hill JW, Edwards C, Grosenick B, Yajima M, Sensen CW. Integration of genomic and medical data into a 3D atlas of human anatomy. Stud Health Technol Inform. 2008;132:526-31. PubMed PMID: 18391362.
  29. Van Domselaar GH, Stothard P, Shrivastava S, Cruz JA, Guo A, Dong X, Lu P, Szafron D, Greiner R, Wishart DS. BASys: a web server for automated bacterial genome annotation. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W455-9. PubMed PMID: 15980511; PubMed Central PMCID: PMC1160269.
  30. Xiaoli Dong, Paul Stothard, Ian J. Forsythe, and David S. Wishart. 2004. PlasMapper: a web server for drawing and auto-annotating plasmid maps. Nucl. Acids. Res. Vol. 32: W660-W664. Web Server Issue
  31. Van Domselaar GH, Stothard P, Shrivastava S, Cruz JA, Guo A, Dong X, Lu P, Szafron D, Greiner R, Wishart DS (2005) BASys: a web server for automated bacterial genome annotation. Nucleic Acids Res 33:W455-W459.
  32. W. Jin, L. Song, X. Dong, and D. Wu. 1998. Impact factors of bioremediation efficiency of oil polluted soil. Environmental Protection, No. 252, Oct. 1998.
  33. W. Jin, L. Song, and X. Dong. 1998. The effect of salinity on treatment of oil-polluted soil. Drilling and Production Technology, Vol. 21, No. 4.
  34. W. Jin, L. Song, X. Dong, X. Li, and P. Xie. 1998. Apply oil degradation microbes to treat oil-polluted soil. Environmental Engineering, Vol. 16, No.4.J.
  35. W. Jin, L.Song, and X.Dong. 1997. Screening technology of oil degradation microbes with high efficiency. The 5th Technology Symposium, RIPED Branch of PetroChina, Langfang, Hebei.
  36. W. Jin, P. Xie, X. Li, and X. Dong. 1997. Microorganism flocculant: solving problems of treating drilling wasted water. Environmental Protection of Oil and Gas Fields, Vol. 7, No. 1.
  37. Li, X. Liu, Z. Kang, and X. Dong. 1995. Effect of seed coating formulation No. 17 on the development of puccinia striformis in host wheat. J. of Plant Protection, Vol. 22, No. 2.

Posters

  1. 13th International Symposium on Microbial Ecology ISME 2010 in Seattle: Chatterjee I., Caffrey S.M., Dong X., Sensen C.W., Voordouw G.: Analysis of the composition of microbial communities in hydrocarbon resource environments by pyrosequencing of 16S genes.
  2. 13th International Symposium on Microbial Ecology ISME 2010 in Seattle: Ramos-Padron, E., Bordenave, S., Lin, S., Dong, X., Sensen, S., Gieg, L.: Microbial activities and communities in oil sands tailings ponds: Towards improved pond management.
  3. 13th International Symposium on Microbial Ecology ISME 2010 in Seattle: Callbeck, C., Dong,X. and Voordouw, G. 2010. A bioreactor simulating nitrate injection into a low temperature oil reservoir.
  4. iCORE Summit 2006 in Banff: Sensen C.W., Turinsky A., Dong X., Fanea E., Shu X., Stromer J., Wat S.: 4D Bioinformatics: Mining Medical and Genomics Data in Virtual Patients.

ISMOS-3 Metagenomics Workshop 2011 in Calgary

  1. Sean M. Caffrey, Xiaoli Dong: Tools for pyrotag analysis