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Major data analysis errors invalidate cancer microbiome findings.
Gihawi A, Ge Y, Lu J, Puiu D, Xu A, Cooper CS, Brewer DS, Pertea M, Salzberg SL. Gihawi A, et al. Among authors: cooper cs. mBio. 2023 Oct 31;14(5):e0160723. doi: 10.1128/mbio.01607-23. Epub 2023 Oct 9. mBio. 2023. PMID: 37811944 Free PMC article.
Mutation detection in formalin-fixed prostate cancer biopsies taken at the time of diagnosis using next-generation DNA sequencing.
Manson-Bahr D, Ball R, Gundem G, Sethia K, Mills R, Rochester M, Goody V, Anderson E, O'Meara S, Flather M, Keeling M, Yazbek-Hanna M, Hurst R, Curley H, Clark J, Brewer DS, McDermott U, Cooper C. Manson-Bahr D, et al. J Clin Pathol. 2015 Mar;68(3):212-7. doi: 10.1136/jclinpath-2014-202754. Epub 2015 Jan 13. J Clin Pathol. 2015. PMID: 25586381
A urine-based DNA methylation assay, ProCUrE, to identify clinically significant prostate cancer.
Zhao F, Olkhov-Mitsel E, Kamdar S, Jeyapala R, Garcia J, Hurst R, Hanna MY, Mills R, Tuzova AV, O'Reilly E, Kelly S, Cooper C; Movember Urine Biomarker Consortium; Brewer D, Perry AS, Clark J, Fleshner N, Bapat B. Zhao F, et al. Clin Epigenetics. 2018 Nov 23;10(1):147. doi: 10.1186/s13148-018-0575-z. Clin Epigenetics. 2018. PMID: 30470249 Free PMC article.
A four-group urine risk classifier for predicting outcomes in patients with prostate cancer.
Connell SP, Yazbek-Hanna M, McCarthy F, Hurst R, Webb M, Curley H, Walker H, Mills R, Ball RY, Sanda MG, Pellegrini KL, Patil D, Perry AS, Schalken J, Pandha H, Whitaker H, Dennis N, Stuttle C, Mills IG, Guldvik I; Movember GAP1 Urine Biomarker Consortium; Parker C, Brewer DS, Cooper CS, Clark J. Connell SP, et al. Among authors: cooper cs. BJU Int. 2019 Oct;124(4):609-620. doi: 10.1111/bju.14811. Epub 2019 Jun 25. BJU Int. 2019. PMID: 31106513 Free PMC article.
Integrative pathway enrichment analysis of multivariate omics data.
Paczkowska M, Barenboim J, Sintupisut N, Fox NS, Zhu H, Abd-Rabbo D, Mee MW, Boutros PC; PCAWG Drivers and Functional Interpretation Working Group; Reimand J; PCAWG Consortium. Paczkowska M, et al. Nat Commun. 2020 Feb 5;11(1):735. doi: 10.1038/s41467-019-13983-9. Nat Commun. 2020. PMID: 32024846 Free PMC article.
Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition.
Rodriguez-Martin B, Alvarez EG, Baez-Ortega A, Zamora J, Supek F, Demeulemeester J, Santamarina M, Ju YS, Temes J, Garcia-Souto D, Detering H, Li Y, Rodriguez-Castro J, Dueso-Barroso A, Bruzos AL, Dentro SC, Blanco MG, Contino G, Ardeljan D, Tojo M, Roberts ND, Zumalave S, Edwards PA, Weischenfeldt J, Puiggròs M, Chong Z, Chen K, Lee EA, Wala JA, Raine KM, Butler A, Waszak SM, Navarro FCP, Schumacher SE, Monlong J, Maura F, Bolli N, Bourque G, Gerstein M, Park PJ, Wedge DC, Beroukhim R, Torrents D, Korbel JO, Martincorena I, Fitzgerald RC, Van Loo P, Kazazian HH, Burns KH; PCAWG Structural Variation Working Group; Campbell PJ, Tubio JMC; PCAWG Consortium. Rodriguez-Martin B, et al. Nat Genet. 2020 Mar;52(3):306-319. doi: 10.1038/s41588-019-0562-0. Epub 2020 Feb 5. Nat Genet. 2020. PMID: 32024998 Free PMC article.
Potential for diagnosis of infectious disease from the 100,000 Genomes Project Metagenomic Dataset: Recommendations for reporting results.
Magiorkinis G, Matthews PC, Wallace SE, Jeffery K, Dunbar K, Tedder R, Mbisa JL, Hannigan B, Vayena E, Simmonds P, Brewer DS, Gihawi A, Rallapalli G, Lahnstein L, Fowler T, Patch C, Maleady-Crowe F, Lucassen A, Cooper C. Magiorkinis G, et al. Wellcome Open Res. 2019 Oct 14;4:155. doi: 10.12688/wellcomeopenres.15499.1. eCollection 2019. Wellcome Open Res. 2019. PMID: 32055707 Free PMC article.
439 results