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Critical Assessment of Metagenome Interpretation: the second round of challenges.
Meyer F, Fritz A, Deng ZL, Koslicki D, Lesker TR, Gurevich A, Robertson G, Alser M, Antipov D, Beghini F, Bertrand D, Brito JJ, Brown CT, Buchmann J, Buluç A, Chen B, Chikhi R, Clausen PTLC, Cristian A, Dabrowski PW, Darling AE, Egan R, Eskin E, Georganas E, Goltsman E, Gray MA, Hansen LH, Hofmeyr S, Huang P, Irber L, Jia H, Jørgensen TS, Kieser SD, Klemetsen T, Kola A, Kolmogorov M, Korobeynikov A, Kwan J, LaPierre N, Lemaitre C, Li C, Limasset A, Malcher-Miranda F, Mangul S, Marcelino VR, Marchet C, Marijon P, Meleshko D, Mende DR, Milanese A, Nagarajan N, Nissen J, Nurk S, Oliker L, Paoli L, Peterlongo P, Piro VC, Porter JS, Rasmussen S, Rees ER, Reinert K, Renard B, Robertsen EM, Rosen GL, Ruscheweyh HJ, Sarwal V, Segata N, Seiler E, Shi L, Sun F, Sunagawa S, Sørensen SJ, Thomas A, Tong C, Trajkovski M, Tremblay J, Uritskiy G, Vicedomini R, Wang Z, Wang Z, Wang Z, Warren A, Willassen NP, Yelick K, You R, Zeller G, Zhao Z, Zhu S, Zhu J, Garrido-Oter R, Gastmeier P, Hacquard S, Häußler S, Khaledi A, Maechler F, Mesny F, Radutoiu S, Schulze-Lefert P, Smit N, Strowig T, Bremges A, Sczyrba A, McHardy AC. Meyer F, et al. Among authors: zhu s, zhu j. Nat Methods. 2022 Apr;19(4):429-440. doi: 10.1038/s41592-022-01431-4. Epub 2022 Apr 8. Nat Methods. 2022. PMID: 35396482 Free PMC article.
A gene catalogue of the Sprague-Dawley rat gut metagenome.
Pan H, Guo R, Zhu J, Wang Q, Ju Y, Xie Y, Zheng Y, Wang Z, Li T, Liu Z, Lu L, Li F, Tong B, Xiao L, Xu X, Li R, Yuan Z, Yang H, Wang J, Kristiansen K, Jia H, Liu L. Pan H, et al. Among authors: zhu j. Gigascience. 2018 May 1;7(5):giy055. doi: 10.1093/gigascience/giy055. Gigascience. 2018. PMID: 29762673 Free PMC article.
Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa.
Zhu J, Tian L, Chen P, Han M, Song L, Tong X, Sun X, Yang F, Lin Z, Liu X, Liu C, Wang X, Lin Y, Cai K, Hou Y, Xu X, Yang H, Wang J, Kristiansen K, Xiao L, Zhang T, Jia H, Jie Z. Zhu J, et al. Genomics Proteomics Bioinformatics. 2022 Apr;20(2):246-259. doi: 10.1016/j.gpb.2021.05.001. Epub 2021 Sep 4. Genomics Proteomics Bioinformatics. 2022. PMID: 34492339 Free PMC article.
Cervicovaginal microbiome dynamics after taking oral probiotics.
Chen C, Hao L, Zhang Z, Tian L, Zhang X, Zhu J, Jie Z, Tong X, Xiao L, Zhang T, Jin X, Xu X, Yang H, Wang J, Kristiansen K, Jia H. Chen C, et al. Among authors: zhu j. J Genet Genomics. 2021 Aug 20;48(8):716-726. doi: 10.1016/j.jgg.2021.03.019. Epub 2021 Jun 26. J Genet Genomics. 2021. PMID: 34391676
Sex differences in the oral microbiome, host traits, and their causal relationships.
Liu X, Tong X, Jie Z, Zhu J, Tian L, Sun Q, Ju Y, Zou L, Lu H, Qiu X, Li Q, Liao Y, Lian H, Zuo Y, Chen X, Rao W, Ren Y, Wang Y, Zi J, Wang R, Xu X, Yang H, Wang J, Zong Y, Liu W, Hou Y, Jin X, Xiao L, Kristiansen K, Jia H, Zhang T. Liu X, et al. Among authors: zhu j. iScience. 2022 Dec 22;26(1):105839. doi: 10.1016/j.isci.2022.105839. eCollection 2023 Jan 20. iScience. 2022. PMID: 36660475 Free PMC article.
Life History Recorded in the Vagino-cervical Microbiome Along with Multi-omes.
Jie Z, Chen C, Hao L, Li F, Song L, Zhang X, Zhu J, Tian L, Tong X, Cai K, Zhang Z, Ju Y, Yu X, Li Y, Zhou H, Lu H, Qiu X, Li Q, Liao Y, Zhou D, Lian H, Zuo Y, Chen X, Rao W, Ren Y, Wang Y, Zi J, Wang R, Liu N, Wu J, Zhang W, Liu X, Zong Y, Liu W, Xiao L, Hou Y, Xu X, Yang H, Wang J, Kristiansen K, Jia H. Jie Z, et al. Among authors: zhu j. Genomics Proteomics Bioinformatics. 2022 Apr;20(2):304-321. doi: 10.1016/j.gpb.2021.01.005. Epub 2021 Jun 9. Genomics Proteomics Bioinformatics. 2022. PMID: 34118463 Free PMC article.
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