BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

122 related articles for article (PubMed ID: 34387940)

  • 1. mOTUs: Profiling Taxonomic Composition, Transcriptional Activity and Strain Populations of Microbial Communities.
    Ruscheweyh HJ; Milanese A; Paoli L; Sintsova A; Mende DR; Zeller G; Sunagawa S
    Curr Protoc; 2021 Aug; 1(8):e218. PubMed ID: 34387940
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments.
    Ruscheweyh HJ; Milanese A; Paoli L; Karcher N; Clayssen Q; Keller MI; Wirbel J; Bork P; Mende DR; Zeller G; Sunagawa S
    Microbiome; 2022 Dec; 10(1):212. PubMed ID: 36464731
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Genotyping Microbial Communities with MIDAS2: From Metagenomic Reads to Allele Tables.
    Zhao C; Goldman M; Smith BJ; Pollard KS
    Curr Protoc; 2022 Dec; 2(12):e604. PubMed ID: 36469554
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Microbial abundance, activity and population genomic profiling with mOTUs2.
    Milanese A; Mende DR; Paoli L; Salazar G; Ruscheweyh HJ; Cuenca M; Hingamp P; Alves R; Costea PI; Coelho LP; Schmidt TSB; Almeida A; Mitchell AL; Finn RD; Huerta-Cepas J; Bork P; Zeller G; Sunagawa S
    Nat Commun; 2019 Mar; 10(1):1014. PubMed ID: 30833550
    [TBL] [Abstract][Full Text] [Related]  

  • 5. A Guide to Gene-Centric Analysis Using TreeSAPP.
    Morgan-Lang C; Hallam SJ
    Curr Protoc; 2023 Feb; 3(2):e671. PubMed ID: 36801973
    [TBL] [Abstract][Full Text] [Related]  

  • 6. VITCOMIC2: visualization tool for the phylogenetic composition of microbial communities based on 16S rRNA gene amplicons and metagenomic shotgun sequencing.
    Mori H; Maruyama T; Yano M; Yamada T; Kurokawa K
    BMC Syst Biol; 2018 Mar; 12(Suppl 2):30. PubMed ID: 29560821
    [TBL] [Abstract][Full Text] [Related]  

  • 7. SPIRE: a Searchable, Planetary-scale mIcrobiome REsource.
    Schmidt TSB; Fullam A; Ferretti P; Orakov A; Maistrenko OM; Ruscheweyh HJ; Letunic I; Duan Y; Van Rossum T; Sunagawa S; Mende DR; Finn RD; Kuhn M; Pedro Coelho L; Bork P
    Nucleic Acids Res; 2024 Jan; 52(D1):D777-D783. PubMed ID: 37897342
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Metagenomic species profiling using universal phylogenetic marker genes.
    Sunagawa S; Mende DR; Zeller G; Izquierdo-Carrasco F; Berger SA; Kultima JR; Coelho LP; Arumugam M; Tap J; Nielsen HB; Rasmussen S; Brunak S; Pedersen O; Guarner F; de Vos WM; Wang J; Li J; Doré J; Ehrlich SD; Stamatakis A; Bork P
    Nat Methods; 2013 Dec; 10(12):1196-9. PubMed ID: 24141494
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Biogeochemical profiling and taxonomic characterization of municipal landfill site by metagenomic sequencing.
    Gupta J; Rathour R; Dupont C; Mishra A; Shekhar Thakur I
    Bioresour Technol; 2022 May; 351():126936. PubMed ID: 35247565
    [TBL] [Abstract][Full Text] [Related]  

  • 10. The selection of software and database for metagenomics sequence analysis impacts the outcome of microbial profiling and pathogen detection.
    Xu R; Rajeev S; Salvador LCM
    PLoS One; 2023; 18(4):e0284031. PubMed ID: 37027361
    [TBL] [Abstract][Full Text] [Related]  

  • 11. TIPP: taxonomic identification and phylogenetic profiling.
    Nguyen NP; Mirarab S; Liu B; Pop M; Warnow T
    Bioinformatics; 2014 Dec; 30(24):3548-55. PubMed ID: 25359891
    [TBL] [Abstract][Full Text] [Related]  

  • 12. The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples.
    Gweon HS; Shaw LP; Swann J; De Maio N; AbuOun M; Niehus R; Hubbard ATM; Bowes MJ; Bailey MJ; Peto TEA; Hoosdally SJ; Walker AS; Sebra RP; Crook DW; Anjum MF; Read DS; Stoesser N;
    Environ Microbiome; 2019 Oct; 14(1):7. PubMed ID: 33902704
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality.
    Jiang Y; Xiong X; Danska J; Parkinson J
    Microbiome; 2016 Jan; 4():2. PubMed ID: 26757703
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Selection of marker genes for genetic barcoding of microorganisms and binning of metagenomic reads by Barcoder software tools.
    Rotimi AM; Pierneef R; Reva ON
    BMC Bioinformatics; 2018 Aug; 19(1):309. PubMed ID: 30165813
    [TBL] [Abstract][Full Text] [Related]  

  • 15. A metagenomic assessment of microbial eukaryotic diversity in the global ocean.
    Obiol A; Giner CR; Sánchez P; Duarte CM; Acinas SG; Massana R
    Mol Ecol Resour; 2020 May; 20(3):. PubMed ID: 32065492
    [TBL] [Abstract][Full Text] [Related]  

  • 16. CAMISIM: simulating metagenomes and microbial communities.
    Fritz A; Hofmann P; Majda S; Dahms E; Dröge J; Fiedler J; Lesker TR; Belmann P; DeMaere MZ; Darling AE; Sczyrba A; Bremges A; McHardy AC
    Microbiome; 2019 Feb; 7(1):17. PubMed ID: 30736849
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3.
    Beghini F; McIver LJ; Blanco-Míguez A; Dubois L; Asnicar F; Maharjan S; Mailyan A; Manghi P; Scholz M; Thomas AM; Valles-Colomer M; Weingart G; Zhang Y; Zolfo M; Huttenhower C; Franzosa EA; Segata N
    Elife; 2021 May; 10():. PubMed ID: 33944776
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Culture-enriched metagenomic sequencing enables in-depth profiling of the cystic fibrosis lung microbiota.
    Whelan FJ; Waddell B; Syed SA; Shekarriz S; Rabin HR; Parkins MD; Surette MG
    Nat Microbiol; 2020 Feb; 5(2):379-390. PubMed ID: 31959969
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Massive metagenomic data analysis using abundance-based machine learning.
    Harris ZN; Dhungel E; Mosior M; Ahn TH
    Biol Direct; 2019 Aug; 14(1):12. PubMed ID: 31370905
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Profiling microbial strains in urban environments using metagenomic sequencing data.
    Zolfo M; Asnicar F; Manghi P; Pasolli E; Tett A; Segata N
    Biol Direct; 2018 May; 13(1):9. PubMed ID: 29743119
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 7.