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Zhenjiang Xu

TitleAssistant Project Scientist
InstitutionUniversity of California San Diego
DepartmentPediatrics
Address9500 Gilman Drive #0763
La Jolla CA 92093
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Minich JJ, Zhu Q, Xu ZZ, Amir A, Ngochera M, Simwaka M, Allen EE, Zidana H, Knight R. Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus). Microbiologyopen. 2018 Aug 31; e00716. PMID: 30168288.
      View in: PubMed
    2. Zarrinpar A, Chaix A, Xu ZZ, Chang MW, Marotz CA, Saghatelian A, Knight R, Panda S. Antibiotic-induced microbiome depletion alters metabolic homeostasis by affecting gut signaling and colonic metabolism. Nat Commun. 2018 Jul 20; 9(1):2872. PMID: 30030441.
      View in: PubMed
    3. Knight R, Vrbanac A, Taylor BC, Aksenov A, Callewaert C, Debelius J, Gonzalez A, Kosciolek T, McCall LI, McDonald D, Melnik AV, Morton JT, Navas J, Quinn RA, Sanders JG, Swafford AD, Thompson LR, Tripathi A, Xu ZZ, Zaneveld JR, Zhu Q, Caporaso JG, Dorrestein PC. Best practices for analysing microbiomes. Nat Rev Microbiol. 2018 May 23. PMID: 29795328.
      View in: PubMed
    4. Michaud JM, Thompson LR, Kaul D, Espinoza JL, Richter RA, Xu ZZ, Lee C, Pham KM, Beall CM, Malfatti F, Azam F, Knight R, Burkart MD, Dupont CL, Prather KA. Taxon-specific aerosolization of bacteria and viruses in an experimental ocean-atmosphere mesocosm. Nat Commun. 2018 May 22; 9(1):2017. PMID: 29789621.
      View in: PubMed
    5. Richardson JB, Dancy BCR, Horton CL, Lee YS, Madejczyk MS, Xu ZZ, Ackermann G, Humphrey G, Palacios G, Knight R, Lewis JA. Exposure to toxic metals triggers unique responses from the rat gut microbiota. Sci Rep. 2018 Apr 26; 8(1):6578. PMID: 29700420.
      View in: PubMed
    6. Janssen S, McDonald D, Gonzalez A, Navas-Molina JA, Jiang L, Xu ZZ, Winker K, Kado DM, Orwoll E, Manary M, Mirarab S, Knight R. Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information. mSystems. 2018 May-Jun; 3(3). PMID: 29719869.
      View in: PubMed
    7. Belk A, Xu ZZ, Carter DO, Lynne A, Bucheli S, Knight R, Metcalf JL. Microbiome Data Accurately Predicts the Postmortem Interval Using Random Forest Regression Models. Genes (Basel). 2018 Feb 16; 9(2). PMID: 29462950.
      View in: PubMed
    8. Zhou Y, Xu ZZ, He Y, Yang Y, Liu L, Lin Q, Nie Y, Li M, Zhi F, Liu S, Amir A, González A, Tripathi A, Chen M, Wu GD, Knight R, Zhou H, Chen Y. Gut Microbiota Offers Universal Biomarkers across Ethnicity in Inflammatory Bowel Disease Diagnosis and Infliximab Response Prediction. mSystems. 2018 Jan-Feb; 3(1). PMID: 29404425.
      View in: PubMed
    9. Vázquez-Baeza Y, Gonzalez A, Xu ZZ, Washburne A, Herfarth HH, Sartor RB, Knight R. Guiding longitudinal sampling in IBD cohorts. Gut. 2017 Oct 21. PMID: 29055911.
      View in: PubMed
    10. Metcalf JL, Xu ZZ, Bouslimani A, Dorrestein P, Carter DO, Knight R. Microbiome Tools for Forensic Science. Trends Biotechnol. 2017 09; 35(9):814-823. PMID: 28366290.
      View in: PubMed
    11. Weiss S, Xu ZZ, Peddada S, Amir A, Bittinger K, Gonzalez A, Lozupone C, Zaneveld JR, Vázquez-Baeza Y, Birmingham A, Hyde ER, Knight R. Normalization and microbial differential abundance strategies depend upon data characteristics. Microbiome. 2017 03 03; 5(1):27. PMID: 28253908.
      View in: PubMed
    12. Debelius J, Song SJ, Vazquez-Baeza Y, Xu ZZ, Gonzalez A, Knight R. Tiny microbes, enormous impacts: what matters in gut microbiome studies? Genome Biol. 2016 10 19; 17(1):217. PMID: 27760558.
      View in: PubMed
    13. Gilbert JA, Quinn RA, Debelius J, Xu ZZ, Morton J, Garg N, Jansson JK, Dorrestein PC, Knight R. Microbiome-wide association studies link dynamic microbial consortia to disease. Nature. 2016 07 07; 535(7610):94-103. PMID: 27383984.
      View in: PubMed
    14. Song SJ, Amir A, Metcalf JL, Amato KR, Xu ZZ, Humphrey G, Knight R. Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies. mSystems. 2016 May-Jun; 1(3). PMID: 27822526.
      View in: PubMed
    15. Weiss S, Van Treuren W, Lozupone C, Faust K, Friedman J, Deng Y, Xia LC, Xu ZZ, Ursell L, Alm EJ, Birmingham A, Cram JA, Fuhrman JA, Raes J, Sun F, Zhou J, Knight R. Correlation detection strategies in microbial data sets vary widely in sensitivity and precision. ISME J. 2016 07; 10(7):1669-81. PMID: 26905627; PMCID: PMC4918442 [Available on 07/01/17].
    16. Kopylova E, Navas-Molina JA, Mercier C, Xu ZZ, Mahé F, He Y, Zhou HW, Rognes T, Caporaso JG, Knight R. Open-Source Sequence Clustering Methods Improve the State Of the Art. mSystems. 2016 Jan-Feb; 1(1). PMID: 27822515.
      View in: PubMed
    17. Xu ZZ, Mathews DH. Prediction of Secondary Structures Conserved in Multiple RNA Sequences. Methods Mol Biol. 2016; 1490:35-50. PMID: 27665591.
      View in: PubMed
    18. Xu ZZ, Mathews DH. Secondary Structure Prediction of Single Sequences Using RNAstructure. Methods Mol Biol. 2016; 1490:15-34. PMID: 27665590.
      View in: PubMed
    19. Xu ZZ, Mathews DH. Experiment-Assisted Secondary Structure Prediction with RNAstructure. Methods Mol Biol. 2016; 1490:163-76. PMID: 27665598.
      View in: PubMed
    20. Metcalf JL, Xu ZZ, Weiss S, Lax S, Van Treuren W, Hyde ER, Song SJ, Amir A, Larsen P, Sangwan N, Haarmann D, Humphrey GC, Ackermann G, Thompson LR, Lauber C, Bibat A, Nicholas C, Gebert MJ, Petrosino JF, Reed SC, Gilbert JA, Lynne AM, Bucheli SR, Carter DO, Knight R. Microbial community assembly and metabolic function during mammalian corpse decomposition. Science. 2016 Jan 08; 351(6269):158-62. PMID: 26657285.
      View in: PubMed
    21. Teng F, Yang F, Huang S, Bo C, Xu ZZ, Amir A, Knight R, Ling J, Xu J. Prediction of Early Childhood Caries via Spatial-Temporal Variations of Oral Microbiota. Cell Host Microbe. 2015 Sep 09; 18(3):296-306. PMID: 26355216.
      View in: PubMed
    22. Fu Y, Xu ZZ, Lu ZJ, Zhao S, Mathews DH. Discovery of Novel ncRNA Sequences in Multiple Genome Alignments on the Basis of Conserved and Stable Secondary Structures. PLoS One. 2015; 10(6):e0130200. PMID: 26075601; PMCID: PMC4468099.
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