Sean Davis, MD, PhD

Publications

• Manghi P, Antonello G, Schiffer L, Golzato D, Wokaty A, Beghini F, Mirzayi C, Long K, Gravel-Pucillo K, Piccinno G, Gamboa-Tuz SD, Bonetti A, D'Amato G, Azhar R, Eckenrode K, Zohra F, Giunchiglia V, Keller M, Pedrotti A, Likhotkin I, Elsafoury S, Geistlinger L, Blanco-Miguez A, Thomas AM, Zolfo M, Ramos M, Valles-Colomer M, Tamburini S, Asnicar F, Jones HE, Huttenhower C, Carey V, Davis S, Pasolli E, Oh S, Segata N, Waldron L. Meta-analysis of 22,710 human microbiome metagenomes defines an oral-to-gut microbial enrichment score and associations with host health and disease. Nat Commun. 2025 Dec 23;17(1):196. PubMed PMID: 41436448
• Huang BL, Davis S, Koyama E, Pacifici M, Mackem S. A pivotal role for Wnt antagonists in constraining Wnt activity to promote digit joint specification. bioRxiv. 2025 Jul 21. PubMed PMID: 40747425
• Drnevich J, Tan FJ, Almeida-Silva F, Castelo R, Culhane AC, Davis S, Doyle MA, Geistlinger L, Ghazi AR, Holmes S, Lahti L, Mahmoud A, Nishida K, Ramos M, Rue-Albrecht K, Shih DJH, Gatto L, Soneson C. Learning and teaching biological data science in the Bioconductor community. PLoS Comput Biol. 2025 Apr;21(4):e1012925. PubMed PMID: 40261894
• Abdill RJ, Graham SP, Rubinetti V, Ahmadian M, Hicks P, Chetty A, McDonald D, Ferretti P, Gibbons E, Rossi M, Krishnan A, Albert FW, Greene CS, Davis S, Blekhman R. Integration of 168,000 samples reveals global patterns of the human gut microbiome. Cell. 2025 Feb 20;188(4):1100-1118.e17. PubMed PMID: 39848248
• Long K, Gravel-Pucillo K, Waldron L, Davis S, Oh S. Large-scale Manual Curation and Harmonization of Metadata from Metagenomic and Cancer Genomic Repositories: Challenges and Solutions. bioRxiv. 2025 Dec 1. PubMed PMID: 41377518
• Huang YP, Harmon L, Deering-Gardner E, Ma X, Harsh J, Xue Z, Wen H, Ramos M, Davis S, Triche TJ Jr. bamSliceR: a Bioconductor package for rapid, cross-cohort variant and allelic bias analysis. Bioinform Adv. 2025;5(1):vbaf098. PubMed PMID: 40395503
• Fungtammasan A, Lee A, Taroni J, Wheeler K, Chin CS, Davis S, Greene C. Ten simple rules for large-scale data processing. PLoS Comput Biol. 2022 Feb;18(2):e1009757. PubMed PMID: 35143491
• Oh S, Geistlinger L, Ramos M, Blankenberg D, van den Beek M, Taroni JN, Carey VJ, Greene CS, Waldron L, Davis S. GenomicSuperSignature facilitates interpretation of RNA-seq experiments through robust, efficient comparison to public databases. Nat Commun. 2022 Jun 27;13(1):3695. PubMed PMID: 35760813

Practice Locations

UCHealth Anschutz Outpatient Pavilion - Anschutz Medical Campus
1635 Aurora Ct
Aurora, CO 80045
720-848-0000