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Publications

Diana M. Proctor, Christof Seiler, Adam R. Burns, Samuel Walker, Tina Jung, Jonathan Weng, Shanne Sastiel, Yoga Rajendran, Yvonne Kapila, Meredith E. Millman, Gary C. Armitage, Peter M. Loomer, Susan P. Holmes, Mark I. Ryder, David A. Relman medRxiv 2021.10.04.21264534. Submitted: JDR.
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Proctor DM, Dangana T, Sexton DJ, Fukuda C, Yelin RD, Stanley M, Bell PB, Baskaran S, Deming C, Chen Q, Conlan S, NISC Comparative Sequencing Program4, Welsh RM, Vallabhaneni S, Chiller T, Forsberg L, Black SRR, Pacilli M, Kong HH, Lin MY, Schoeny ME, Litvintseva AP, Segre JA, Hayden MK. Integrated genomic, epidemiologic investigation of Candida auris skin colonization, 2021. Nature Medicine, 27: 1401–1409. PMID: 34155414.

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Lisco A, Hsu AP, Dimitrova D, Proctor DM, Mace EM, Ye P1, Anderson MV, et al. Hicks SN, Grivas C, Hammoud DA, Manion M, Starrett GJ, Farrel A, Dobbs K, Brownell I, Buck C, LD, Orange JS, Leonard WJ, Orestes MI, Peters AT, Kanakry JA, Segre JA, Kong HH, and Sereti I, 2021. Treatment of HPV Skin Virome Expansion and Relapsing HPV Diseases with Restored Cytotoxic Function of Natural Killer, 2021. New England Journal of Medicine. 385:921-929.

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Huang X, Welsh R, Deming C, Proctor DM, Thomas P, Gussin G, Huang S, Bentz M, Vallabhaneni S, Chiller T, Jackson B, Forsberg K, Conlan S, Litvintseva A, Segre JA. Skin metagenomic sequence analysis of early Candida auris outbreaks in United States nursing homes, 2021. 6(4): 25. mSphere. PMID: 34346704.

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Proctor DM, Shelef KM, Gonzalez A, Long C, Dethlefsen L, Burns A, Loomer PL, Armitage GC, Ryder MI, Millman ME, Knight R, Holmes SP, Relman DA. Microbial biogeography and ecology of the mouth and implications for periodontal diseases, 2020. Periodontology 2000, 2020.82(1): 26-41. PMID 31850642.

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Davis, NM, Proctor DM, Holmes, SP, Relman DR, Callahan BJ. Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data. Microbiome, 2018. 17(6): 226.PMID:30558668.
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Goltsman, DSA, Sun CL, Proctor DM, Diguilio DB, Robaczewska A, Thomas BC, Shaw, GM, Stevenson DK, Holmes SP, Banfield JF, Relman DA. Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome. Genome Research, 2018. 28(10):1467-1480. PMID 30232199.

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Proctor DM, Fukuyama JF, Loomer PM, Armitage GC, Lee SA, Davis, NM, Ryder MI, Holmes SP, Relman DA, 2018. A spatial gradient of bacterial diversity in the human oral cavity shaped by salivary flow, Nature Communications, 2018. 9(681). PMID: 29445174.

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Proctor DM and Relman DA. The Landscape ecology and microbiota of the human nose, mouth and throat. Cell Host Microbe, 2017. 21(4): 421-432. PMID: 28407480.

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Callahan BJ, Proctor DM, Relman DA, Fukuyama JA, Holmes SP, 2016. Reproducible research workflow in R for the analysis of personalized human microbiome data. Pac Symp Biocomput. 21:183-94. PMID: 26776185.

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Book chapters

Kicza A, Pureka C, Proctor D, Riley M, Dorit R, 2016. The Bacteriocins: Current Knowledge and Future Prospects. Caister Academic Press, Norfolk, UK. Chapter 8: The phenotypic and genotypic landscape of colicin resistance. Pages 141-154.

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In preparation

Liang H, Jo JH, Zhang Z, Han J, Che Y Taylor M, Proctor DM, Apolo AB, McCulloch JA, Davar D, Zarour HM, Dzutsev AK, Brownell I, Trinchieri G, Gulley JM, Kong HH. Identifying microbiome-based biomarkers for clinical response in cancer immunotherapy. Submitted: Nature Communications.

Sim CK, Kashaf SS, Conlan S, Stacy A, Proctor DM, Deming C, Almeida A, Nicolas Bouladoux N, Chen M, NISC Comparative Sequencing Program, Palmore, TN, Finn RD, Belkaid Y, Segre JA. A mouse model of intestinal occult colonization demonstrating antibiotic-induced outgrowth of carbapenem-resistant Enterobacteriaceae, 2021. bioxRiv.

Jeganatha P, Callahan BJ, Proctor DM, Relman DA, Holmes SP, The Block Bootstrap Method for Longitudinal Microbiome Data. 2018. arXiv:1809.01832v2.

Other publications

Proctor DM, 2021. At the root of widespread dental disease in the United States: the separation of dental and medical health. Science Policy for All. June 10.

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Relman DA & Proctor DM, 2015. Times of drought: a study of the oral microbial ecosystem under conditions of hyposalivation. Sjögren’s Quarterly: The Professionals’ Resource of Sjögren’s. 10: 1-6.

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Proctor DM, 2014. Using phyloseq for the reproducible analysis of high-throughput sequencing data in microbial ecology. The Computational, evolutionary and human genomics (CEHG) at Stanford blog. January 9.

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