An independent evaluation in a CRC patient cohort of microbiome 16S rRNA sequence analysis methods: OTU clustering, DADA2, and Deblur
暂无分享,去创建一个
[1] S. Srikumar,et al. 16S rRNA Based Profiling of Bacterial Communities Colonizing Bakery-Production Environments. , 2022, Foodborne pathogens and disease.
[2] Xinxiang Li,et al. Dysbiosis of human gut microbiome in young-onset colorectal cancer , 2021, Nature Communications.
[3] Z. Soons,et al. Gut microbiota and short‐chain fatty acid alterations in cachectic cancer patients , 2021, Journal of cachexia, sarcopenia and muscle.
[4] H. Yoon,et al. Fecal Microbiota and Gut Microbe-Derived Extracellular Vesicles in Colorectal Cancer , 2021, Frontiers in Oncology.
[5] P. Solanki,et al. Gut microbiota-derived metabolites in CRC progression and causation , 2021, Journal of Cancer Research and Clinical Oncology.
[6] Pengfei Xu,et al. Global colorectal cancer burden in 2020 and projections to 2040 , 2021, Translational oncology.
[7] M. Tani,et al. The Comparison of Fecal Microbiota in Left-Side and Right-Side Human Colorectal Cancer , 2021, European Surgical Research.
[8] Benjamin D. Kaehler,et al. Beating Naive Bayes at Taxonomic Classification of 16S rRNA Gene Sequences , 2021, Frontiers in Microbiology.
[9] Charles J. Kahi,et al. ACG Clinical Guidelines: Colorectal Cancer Screening 2021. , 2021, The American journal of gastroenterology.
[10] Wei Chen,et al. Blautia—a new functional genus with potential probiotic properties? , 2021, Gut microbes.
[11] Fangfang Guo,et al. F. nucleatum targets lncRNA ENO1-IT1 to promote glycolysis and oncogenesis in colorectal cancer , 2020, Gut.
[12] Chi-Jung Huang,et al. A gut butyrate-producing bacterium Butyricicoccus pullicaecorum regulates short-chain fatty acid transporter and receptor to reduce the progression of 1,2-dimethylhydrazine-associated colorectal cancer , 2020, Oncology letters.
[13] K. Zhao,et al. Potential role of fecal microbiota in patients with constipation , 2020, Therapeutic advances in gastroenterology.
[14] R. Palmqvist,et al. Parvimonas micra as a putative non-invasive faecal biomarker for colorectal cancer , 2020, Scientific Reports.
[15] Ruixin Zhu,et al. Identification of microbial markers across populations in early detection of colorectal cancer , 2020, Nature Communications.
[16] Dong-yan Wang,et al. Alteration of the abundance of Parvimonas micra in the gut along the adenoma-carcinoma sequence , 2020, Oncology letters.
[17] Liangjing Wang,et al. Fusobacterium nucleatum promotes colorectal cancer metastasis by modulating KRT7-AS/KRT7 , 2020, Gut microbes.
[18] E. Stoffel,et al. Epidemiology and Mechanisms of the Increasing Incidence of Colon and Rectal Cancers in Young Adults. , 2020, Gastroenterology.
[19] Jun Yu,et al. A novel faecal Lachnoclostridium marker for the non-invasive diagnosis of colorectal adenoma and cancer , 2019, Gut.
[20] Benjamin D. Kaehler,et al. Species abundance information improves sequence taxonomy classification accuracy , 2019, Nature Communications.
[21] N. Qin,et al. Correlation of diet, microbiota and metabolite networks in inflammatory bowel disease , 2019, Journal of digestive diseases.
[22] Jun Yu,et al. Peptostreptococcus anaerobius promotes colorectal carcinogenesis and modulates tumour immunity , 2019, Nature Microbiology.
[23] Tomoyoshi Soga,et al. Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer , 2019, Nature Medicine.
[24] S. A. Boers,et al. Understanding and overcoming the pitfalls and biases of next-generation sequencing (NGS) methods for use in the routine clinical microbiological diagnostic laboratory , 2019, European Journal of Clinical Microbiology & Infectious Diseases.
[25] Varun Bhat,et al. Streptococcus gallolyticus Group Bacteremia and Colonic Adenocarcinoma , 2019, The Journal of the American Osteopathic Association.
[26] W. Wong,et al. Metabolomics and 16S rRNA sequencing of human colorectal cancers and adjacent mucosa , 2018, PloS one.
[27] W. Garrett,et al. Fusobacterium nucleatum — symbiont, opportunist and oncobacterium , 2018, Nature Reviews Microbiology.
[28] R. Marrie,et al. A comparative study of the gut microbiota in immune-mediated inflammatory diseases—does a common dysbiosis exist? , 2018, Microbiome.
[29] J. Diaz-Tasende. Colorectal cancer screening and survival. , 2018, Revista espanola de enfermedades digestivas : organo oficial de la Sociedad Espanola de Patologia Digestiva.
[30] Shuwen Han,et al. Intestinal microorganisms involved in colorectal cancer complicated with dyslipidosis , 2018, Cancer biology & therapy.
[31] Xiaotian Chen,et al. Faecalibacterium prausnitzii Produces Butyrate to Maintain Th17/Treg Balance and to Ameliorate Colorectal Colitis by Inhibiting Histone Deacetylase 1. , 2018, Inflammatory bowel diseases.
[32] Gary Tse,et al. Association Between Bacteremia From Specific Microbes and Subsequent Diagnosis of Colorectal Cancer. , 2018, Gastroenterology.
[33] Benjamin D. Kaehler,et al. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin , 2018, Microbiome.
[34] Jacob T. Nearing,et al. Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches , 2018, PeerJ.
[35] Benjamin D. Kaehler,et al. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin , 2018, Microbiome.
[36] Donna Neuberg,et al. Analysis of Fusobacterium persistence and antibiotic response in colorectal cancer , 2017, Science.
[37] Hongyu Zhao,et al. Variable importance-weighted random forests , 2017, Quantitative Biology.
[38] H. Ashktorab,et al. Racial Disparity in Gastrointestinal Cancer Risk. , 2017, Gastroenterology.
[39] Yongzheng Peng,et al. Phascolarctobacterium faecium abundant colonization in human gastrointestinal tract. , 2017, Experimental and therapeutic medicine.
[40] Robert C. Edgar,et al. Updating the 97% identity threshold for 16S ribosomal RNA OTUs , 2017, bioRxiv.
[41] J. Roach,et al. A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome , 2017, BMC Microbiology.
[42] Kang Li,et al. Metabolomics for biomarker discovery in the diagnosis, prognosis, survival and recurrence of colorectal cancer: a systematic review , 2017, Oncotarget.
[43] Jose A Navas-Molina,et al. Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns , 2017, mSystems.
[44] S. Duncan,et al. Faecalibacterium prausnitzii: from microbiology to diagnostics and prognostics , 2017, The ISME Journal.
[45] Ben Nichols,et al. VSEARCH: a versatile open source tool for metagenomics , 2016, PeerJ.
[46] Paul J. McMurdie,et al. DADA2: High resolution sample inference from Illumina amplicon data , 2016, Nature Methods.
[47] E. Plummer,et al. A Comparison of Three Bioinformatics Pipelines for the Analysis ofPreterm Gut Microbiota using 16S rRNA Gene Sequencing Data , 2015 .
[48] Sarah L. Westcott,et al. De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units , 2015, PeerJ.
[49] Qiang Feng,et al. Gut microbiome development along the colorectal adenoma–carcinoma sequence , 2015, Nature Communications.
[50] É. Yergeau,et al. Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons , 2014, Journal of visualized experiments : JoVE.
[51] K. Schleifer,et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences , 2014, Nature Reviews Microbiology.
[52] Hermann Brenner,et al. Colorectal cancer , 2014, The Lancet.
[53] Jan Verhaegen,et al. A decrease of the butyrate-producing species Roseburia hominis and Faecalibacterium prausnitzii defines dysbiosis in patients with ulcerative colitis , 2013, Gut.
[54] Robert C. Edgar,et al. UPARSE: highly accurate OTU sequences from microbial amplicon reads , 2013, Nature Methods.
[55] H. Sokol,et al. Faecalibacterium prausnitzii and human intestinal health. , 2013, Current opinion in microbiology.
[56] V. Kunin,et al. Effects of OTU Clustering and PCR Artifacts on Microbial Diversity Estimates , 2013, Microbial Ecology.
[57] B. Birren,et al. Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. , 2012, Genome research.
[58] Richard A. Moore,et al. Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. , 2012, Genome research.
[59] Patrick D. Schloss,et al. Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies , 2011, PloS one.
[60] Liping Zhao,et al. Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers , 2011, The ISME Journal.
[61] C. Huttenhower,et al. Metagenomic biomarker discovery and explanation , 2011, Genome Biology.
[62] T. Fennell,et al. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries , 2011, Genome Biology.
[63] V. Kunin,et al. Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. , 2009, Environmental microbiology.
[64] Martin A. Nowak,et al. Comparative lesion sequencing provides insights into tumor evolution , 2008, Proceedings of the National Academy of Sciences.
[65] W. Ludwig,et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB , 2007, Nucleic acids research.
[66] N. Pace,et al. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases , 2007, Proceedings of the National Academy of Sciences.
[67] J. Garcia-Gil,et al. Abnormal microbiota composition in the ileocolonic mucosa of Crohn's disease patients as revealed by polymerase chain reaction‐denaturing gradient gel electrophoresis , 2006, Inflammatory bowel diseases.
[68] Tom Coenye,et al. Intragenomic heterogeneity between multiple 16S ribosomal RNA operons in sequenced bacterial genomes. , 2003, FEMS microbiology letters.
[69] B. Vogelstein,et al. A genetic model for colorectal tumorigenesis , 1990, Cell.
[70] D. Bauer. Constructing Confidence Sets Using Rank Statistics , 1972 .
[71] N. Qin,et al. Diet-microbiota-metabolite interaction networks reveal key players in inflammatory bowel disease. , 2019, Journal of digestive diseases.
[72] H. Wong,et al. Streptococcus gallolyticus Bacteremia and Colorectal Carcinoma. , 2019, Gastroenterology.
[73] Jacob T. Nearing,et al. Denoising the Denoisers: An independent evaluation of microbiome sequence error-correction methods , 2018 .
[74] Michael W. Hall,et al. 16S rRNA Gene Analysis with QIIME2. , 2018, Methods in molecular biology.