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Danielle S McDonald

TitleAsst Professor Adjoint
InstitutionUniversity of Colorado Denver - Anschutz Medical Campus
DepartmentSOM-FM General Operations

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Seitz VA, McGivern BB, Shaffer M, Borton MA, Belk AD, Ghadermazi P, Martino C, Shenhav L, Zhang AR, Shi P, Emmons A, Deel H, Xu ZZ, Nieciecki V, Zhu Q, Cantrell K, Ben-Hur A, Reed SC, Humphry GC, Ackermann G, McDonald D, Joshua Chan SH, Connor M, Boyd DA, Smith J, Watson JMS, Vidoli G, Steadman D, Lynne AM, Bucheli S, Carter DO, Burcham ZM, Knight R, Wrighton KC, Metcalf JL. CaDAVEr: a metagenome-assembled genome catalog of microbial decomposers across vertebrate environments. Microbiol Resour Announc. 2025 Nov 13; 14(11):e0132324. PMID: 40985699.
      View in: PubMed
    2. Burcham ZM, Belk AD, McGivern BB, Bouslimani A, Ghadermazi P, Martino C, Shenhav L, Zhang AR, Shi P, Emmons A, Deel HL, Xu ZZ, Nieciecki V, Zhu Q, Shaffer M, Panitchpakdi M, Weldon KC, Cantrell K, Ben-Hur A, Reed SC, Humphry GC, Ackermann G, McDonald D, Chan SHJ, Connor M, Boyd D, Smith J, Watson JMS, Vidoli G, Steadman D, Lynne AM, Bucheli S, Dorrestein PC, Wrighton KC, Carter DO, Knight R, Metcalf JL. A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables. Nat Microbiol. 2024 Mar; 9(3):595-613. PMID: 38347104.
      View in: PubMed
    3. Wischmeyer PE, McDonald D, Knight R. Role of the microbiome, probiotics, and 'dysbiosis therapy' in critical illness. Curr Opin Crit Care. 2016 08; 22(4):347-53. PMID: 27327243.
      View in: PubMed
    4. McDonald D, Birmingham A, Knight R. Context and the human microbiome. Microbiome. 2015 Nov 04; 3:52. PMID: 26530830; PMCID: PMC4632476.
      View in: PubMed, PubMed Central
    5. McDonald D, Xu Z, Hyde ER, Knight R. Ribosomal RNA, the lens into life. RNA. 2015 Apr; 21(4):692-4. PMID: 25780194; PMCID: PMC4371336.
      View in: PubMed, PubMed Central
    6. McDonald D, Hornig M, Lozupone C, Debelius J, Gilbert JA, Knight R. Towards large-cohort comparative studies to define the factors influencing the gut microbial community structure of ASD patients. Microb Ecol Health Dis. 2015; 26:26555. PMID: 25758371.
      View in: PubMed
    7. Insel PA, Wilderman A, Zambon AC, Snead AN, Murray F, Aroonsakool N, McDonald DS, Zhou S, McCann T, Zhang L, Sriram K, Chinn AM, Michkov AV, Lynch RM, Overland AC, Corriden R. G Protein-Coupled Receptor (GPCR) Expression in Native Cells: "Novel" endoGPCRs as Physiologic Regulators and Therapeutic Targets. Mol Pharmacol. 2015 Jul; 88(1):181-7. PMID: 25737495.
      View in: PubMed
    8. Ursell LK, Gunawardana M, Chang S, Mullen M, Moss JA, Herold BC, Keller MJ, McDonald D, González A, Knight R, Baum MM. Comparison of the vaginal microbial communities in women with recurrent genital HSV receiving acyclovir intravaginal rings. Antiviral Res. 2014 Feb; 102:87-94. PMID: 24361269; PMCID: PMC4006976.
      View in: PubMed, PubMed Central
    9. Bates ST, Ahrendt S, Bik HM, Bruns TD, Caporaso JG, Cole J, Dwan M, Fierer N, Gu D, Houston S, Knight R, Leff J, Lewis C, Maestre JP, McDonald D, Nilsson RH, Porras-Alfaro A, Robert V, Schoch C, Scott J, Taylor DL, Parfrey LW, Stajich JE. Meeting report: fungal its workshop (october 2012). Stand Genomic Sci. 2013 Apr 15; 8(1):118-23. PMID: 23961317.
      View in: PubMed
    10. McDonald D, Vázquez-Baeza Y, Walters WA, Caporaso JG, Knight R. From molecules to dynamic biological communities. Biol Philos. 2013 Mar; 28(2):241-259. PMID: 23483075.
      View in: PubMed
    11. Harris JK, Caporaso JG, Walker JJ, Spear JR, Gold NJ, Robertson CE, Hugenholtz P, Goodrich J, McDonald D, Knights D, Marshall P, Tufo H, Knight R, Pace NR. Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat. ISME J. 2013 Jan; 7(1):50-60. PMID: 22832344.
      View in: PubMed
    12. Widmann J, Stombaugh J, McDonald D, Chocholousova J, Gardner P, Iyer MK, Liu Z, Lozupone CA, Quinn J, Smit S, Wikman S, Zaneveld JR, Knight R. RNASTAR: an RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs. RNA. 2012 Jul; 18(7):1319-27. PMID: 22645380.
      View in: PubMed
    13. Almodovar S, Knight R, Allshouse AA, Roemer S, Lozupone C, McDonald D, Widmann J, Voelkel NF, Shelton RJ, Suarez EB, Hammer KW, Goujard C, Petrosillo N, Simonneau G, Hsue PY, Humbert M, Flores SC. Human Immunodeficiency Virus nef signature sequences are associated with pulmonary hypertension. AIDS Res Hum Retroviruses. 2012 Jun; 28(6):607-18. PMID: 22066947.
      View in: PubMed
    14. McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 2012 Mar; 6(3):610-8. PMID: 22134646; PMCID: PMC3280142.
      View in: PubMed, PubMed Central
    15. Kuczynski J, Liu Z, Lozupone C, McDonald D, Fierer N, Knight R. Microbial community resemblance methods differ in their ability to detect biologically relevant patterns. Nat Methods. 2010 Oct; 7(10):813-9. PMID: 20818378.
      View in: PubMed
    16. Majerfeld I, Chocholousova J, Malaiya V, Widmann J, McDonald D, Reeder J, Iyer M, Illangasekare M, Yarus M, Knight R. Nucleotides that are essential but not conserved; a sufficient L-tryptophan site in RNA. RNA. 2010 Oct; 16(10):1915-24. PMID: 20699302; PMCID: PMC2941100.
      View in: PubMed, PubMed Central
    17. Fierer N, Lauber CL, Zhou N, McDonald D, Costello EK, Knight R. Forensic identification using skin bacterial communities. Proc Natl Acad Sci U S A. 2010 Apr 06; 107(14):6477-81. PMID: 20231444.
      View in: PubMed
    18. McDonald D, Waterbury L, Knight R, Betterton MD. Activating and inhibiting connections in biological network dynamics. Biol Direct. 2008 Dec 04; 3:49. PMID: 19055800.
      View in: PubMed
    19. Oscamou M, McDonald D, Yap VB, Huttley GA, Lladser ME, Knight R. Comparison of methods for estimating the nucleotide substitution matrix. BMC Bioinformatics. 2008 Dec 01; 9:511. PMID: 19046431.
      View in: PubMed
    20. Knight R, Maxwell P, Birmingham A, Carnes J, Caporaso JG, Easton BC, Eaton M, Hamady M, Lindsay H, Liu Z, Lozupone C, McDonald D, Robeson M, Sammut R, Smit S, Wakefield MJ, Widmann J, Wikman S, Wilson S, Ying H, Huttley GA. PyCogent: a toolkit for making sense from sequence. Genome Biol. 2007; 8(8):R171. PMID: 17708774.
      View in: PubMed
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