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Protocol for refining metagenomic binning with BinSPreader.
Ochkalova S, Tolstoganov I, Lapidus A, Korobeynikov A. Ochkalova S, et al. Among authors: korobeynikov a. STAR Protoc. 2023 Sep 15;4(3):102417. doi: 10.1016/j.xpro.2023.102417. Epub 2023 Jul 4. STAR Protoc. 2023. PMID: 37405923 Free PMC article.
MGnify: the microbiome sequence data analysis resource in 2023.
Richardson L, Allen B, Baldi G, Beracochea M, Bileschi ML, Burdett T, Burgin J, Caballero-Pérez J, Cochrane G, Colwell LJ, Curtis T, Escobar-Zepeda A, Gurbich TA, Kale V, Korobeynikov A, Raj S, Rogers AB, Sakharova E, Sanchez S, Wilkinson DJ, Finn RD. Richardson L, et al. Among authors: korobeynikov a. Nucleic Acids Res. 2023 Jan 6;51(D1):D753-D759. doi: 10.1093/nar/gkac1080. Nucleic Acids Res. 2023. PMID: 36477304 Free PMC article.
BinSPreader: Refine binning results for fuller MAG reconstruction.
Tolstoganov I, Kamenev Y, Kruglikov R, Ochkalova S, Korobeynikov A. Tolstoganov I, et al. Among authors: korobeynikov a. iScience. 2022 Jul 19;25(8):104770. doi: 10.1016/j.isci.2022.104770. eCollection 2022 Aug 19. iScience. 2022. PMID: 35992057 Free PMC article.
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: korobeynikov a. 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.
Hi-C Metagenomics in the ICU: Exploring Clinically Relevant Features of Gut Microbiome in Chronically Critically Ill Patients.
Ivanova V, Chernevskaya E, Vasiluev P, Ivanov A, Tolstoganov I, Shafranskaya D, Ulyantsev V, Korobeynikov A, Razin SV, Beloborodova N, Ulianov SV, Tyakht A. Ivanova V, et al. Among authors: korobeynikov a. Front Microbiol. 2022 Feb 3;12:770323. doi: 10.3389/fmicb.2021.770323. eCollection 2021. Front Microbiol. 2022. PMID: 35185811 Free PMC article.
47 results