Justin Shaffer

Title(s)Postdoctoral Scholar, Pediatrics
SchoolVc-health Sciences-schools
Address9500 Gilman Drive #
La Jolla CA 92093
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    Collapse Biography 
    Collapse Education and Training
    University of California, Santa Cruz, Santa CruzB.A.12/2010Environmental Studies
    University of Arizona, TucsonPh.D.08/2017Plant Pathology

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Enhancing untargeted metabolomics using metadata-based source annotation. Nat Biotechnol. 2022 12; 40(12):1774-1779. Gauglitz JM, West KA, Bittremieux W, Williams CL, Weldon KC, Panitchpakdi M, Di Ottavio F, Aceves CM, Brown E, Sikora NC, Jarmusch AK, Martino C, Tripathi A, Meehan MJ, Dorrestein K, Shaffer JP, Coras R, Vargas F, Goldasich LD, Schwartz T, Bryant M, Humphrey G, Johnson AJ, Spengler K, Belda-Ferre P, Diaz E, McDonald D, Zhu Q, Elijah EO, Wang M, Marotz C, Sprecher KE, Vargas-Robles D, Withrow D, Ackermann G, Herrera L, Bradford BJ, Marques LMM, Amaral JG, Silva RM, Veras FP, Cunha TM, Oliveira RDR, Louzada-Junior P, Mills RH, Piotrowski PK, Servetas SL, Da Silva SM, Jones CM, Lin NJ, Lippa KA, Jackson SA, Daouk RK, Galasko D, Dulai PS, Kalashnikova TI, Wittenberg C, Terkeltaub R, Doty MM, Kim JH, Rhee KE, Beauchamp-Walters J, Wright KP, Dominguez-Bello MG, Manary M, Oliveira MF, Boland BS, Lopes NP, Guma M, Swafford AD, Dutton RJ, Knight R, Dorrestein PC. PMID: 35798960.
      View in: PubMed   Mentions:    Fields:    
    2. A comparison of six DNA extraction protocols for 16S, ITS and shotgun metagenomic sequencing of microbial communities. Biotechniques. 2022 06; 73(1):34-46. Shaffer JP, Carpenter CS, Martino C, Salido RA, Minich JJ, Bryant M, Sanders K, Schwartz T, Humphrey G, Swafford AD, Knight R. PMID: 35713407; PMCID: PMC9361692.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    3. Compositionally Aware Phylogenetic Beta-Diversity Measures Better Resolve Microbiomes Associated with Phenotype. mSystems. 2022 06 28; 7(3):e0005022. Martino C, McDonald D, Cantrell K, Dilmore AH, Vázquez-Baeza Y, Shenhav L, Shaffer JP, Rahman G, Armstrong G, Allaband C, Song SJ, Knight R. PMID: 35477286; PMCID: PMC9238373.
      View in: PubMed   Mentions:
    4. Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy. mSystems. 2022 04 26; 7(2):e0016722. Zhu Q, Huang S, Gonzalez A, McGrath I, McDonald D, Haiminen N, Armstrong G, Vázquez-Baeza Y, Yu J, Kuczynski J, Sepich-Poore GD, Swafford AD, Das P, Shaffer JP, Lejzerowicz F, Belda-Ferre P, Havulinna AS, Méric G, Niiranen T, Lahti L, Salomaa V, Kim HC, Jain M, Inouye M, Gilbert JA, Knight R. PMID: 35369727; PMCID: PMC9040630.
      View in: PubMed   Mentions: 1  
    5. Transcriptional Profiles of a Foliar Fungal Endophyte (Pestalotiopsis, Ascomycota) and Its Bacterial Symbiont (Luteibacter, Gammaproteobacteria) Reveal Sulfur Exchange and Growth Regulation during Early Phases of Symbiotic Interaction. mSystems. 2022 Apr 26; 7(2):e0009122. Shaffer JP, Carter ME, Spraker JE, Clark M, Smith BA, Hockett KL, Baltrus DA, Arnold AE. PMID: 35293790; PMCID: PMC9040847.
      View in: PubMed   Mentions:
    6. Swapping Metagenomics Preprocessing Pipeline Components Offers Speed and Sensitivity Increases. mSystems. 2022 Apr 26; 7(2):e0137821. Armstrong G, Martino C, Morris J, Khaleghi B, Kang J, DeReus J, Zhu Q, Roush D, McDonald D, Gonazlez A, Shaffer JP, Carpenter C, Estaki M, Wandro S, Eilert S, Akel A, Eno J, Curewitz K, Swafford AD, Moshiri N, Rosing T, Knight R. PMID: 35293792; PMCID: PMC9040843.
      View in: PubMed   Mentions:
    7. SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment. Microbiome. 2021 06 08; 9(1):132. Marotz C, Belda-Ferre P, Ali F, Das P, Huang S, Cantrell K, Jiang L, Martino C, Diner RE, Rahman G, McDonald D, Armstrong G, Kodera S, Donato S, Ecklu-Mensah G, Gottel N, Salas Garcia MC, Chiang LY, Salido RA, Shaffer JP, Bryant MK, Sanders K, Humphrey G, Ackermann G, Haiminen N, Beck KL, Kim HC, Carrieri AP, Parida L, Vázquez-Baeza Y, Torriani FJ, Knight R, Gilbert J, Sweeney DA, Allard SM. PMID: 34103074; PMCID: PMC8186369.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCellsPHPublic Health
    8. Correction for Vangay et al., "Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities". mSystems. 2021 May 04; 6(3). Vangay P, Burgin J, Johnston A, Beck KL, Berrios DC, Blumberg K, Canon S, Chain P, Chandonia JM, Christianson D, Costes SV, Damerow J, Duncan WD, Dundore-Arias JP, Fagnan K, Galazka JM, Gibbons SM, Hays D, Hervey J, Hu B, Hurwitz BL, Jaiswal P, Joachimiak MP, Kinkel L, Ladau J, Martin SL, McCue LA, Miller K, Mouncey N, Mungall C, Pafilis E, Reddy TBK, Richardson L, Roux S, Schriml LM, Shaffer JP, Sundaramurthi JC, Thompson LR, Timme RE, Zheng J, Wood-Charlson EM, Eloe-Fadrosh EA. PMID: 33947809; PMCID: PMC8269219.
      View in: PubMed   Mentions:
    9. Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities. mSystems. 2021 02 23; 6(1). Vangay P, Burgin J, Johnston A, Beck KL, Berrios DC, Blumberg K, Canon S, Chain P, Chandonia JM, Christianson D, Costes SV, Damerow J, Duncan WD, Dundore-Arias JP, Fagnan K, Galazka JM, Gibbons SM, Hays D, Hervey J, Hu B, Hurwitz BL, Jaiswal P, Joachimiak MP, Kinkel L, Ladau J, Martin SL, McCue LA, Miller K, Mouncey N, Mungall C, Pafilis E, Reddy TBK, Richardson L, Roux S, Schriml LM, Shaffer JP, Sundaramurthi JC, Thompson LR, Timme RE, Zheng J, Wood-Charlson EM, Eloe-Fadrosh EA. PMID: 33622857; PMCID: PMC8573954.
      View in: PubMed   Mentions: 9  
    10. A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities. Biotechniques. 2021 03; 70(3):149-159. Shaffer JP, Marotz C, Belda-Ferre P, Martino C, Wandro S, Estaki M, Salido RA, Carpenter CS, Zaramela LS, Minich JJ, Bryant M, Sanders K, Fraraccio S, Ackermann G, Humphrey G, Swafford AD, Miller-Montgomery S, Knight R. PMID: 33512248; PMCID: PMC7931620.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    11. Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment. Microbiome. 2021 01 22; 9(1):25. Minich JJ, Ali F, Marotz C, Belda-Ferre P, Chiang L, Shaffer JP, Carpenter CS, McDonald D, Gilbert J, Allard SM, Allen EE, Knight R, Sweeney DA, Swafford AD. PMID: 33482920; PMCID: PMC7821463.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    12. Early life gut microbiota is associated with rapid infant growth in Hispanics from Southern California. Gut Microbes. 2021 Jan-Dec; 13(1):1961203. Alderete TL, Jones RB, Shaffer JP, Holzhausen EA, Patterson WB, Kazemian E, Chatzi L, Knight R, Plows JF, Berger PK, Goran MI. PMID: 34424832; PMCID: PMC8386720.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    13. Microbial context predicts SARS-CoV-2 prevalence in patients and the hospital built environment. medRxiv. 2020 Nov 22. Marotz C, Belda-Ferre P, Ali F, Das P, Huang S, Cantrell K, Jiang L, Martino C, Diner RE, Rahman G, McDonald D, Armstrong G, Kodera S, Donato S, Ecklu-Mensah G, Gottel N, Garcia MCS, Chiang LY, Salido RA, Shaffer JP, Bryant M, Sanders K, Humphrey G, Ackermann G, Haiminen N, Beck KL, Kim HC, Carrieri AP, Parida L, Vázquez-Baeza Y, Torriani FJ, Knight R, Gilbert JA, Sweeney DA, Allard SM. PMID: 33236030; PMCID: PMC7685343.
      View in: PubMed   Mentions:
    14. A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities. bioRxiv. 2020 Nov 14. Shaffer JP, Marotz C, Belda-Ferre P, Martino C, Wandro S, Estaki M, Salido RA, Carpenter CS, Zaramela LS, Minich JJ, Bryant M, Sanders K, Fraraccio S, Ackermann G, Humphrey G, Swafford AD, Miller-Montgomery S, Knight R. PMID: 33200135; PMCID: PMC7668742.
      View in: PubMed   Mentions:
    15. Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment. Res Sq. 2020 Aug 18. Minich J, Ali F, Marotz C, Belda-Ferre P, Chiang L, Shaffer JP, Carpenter CS, McDonald D, Gilbert J, Allard SM, Allen EE, Knight R, Sweeney DA, Swafford AD. PMID: 32839765; PMCID: PMC7444291.
      View in: PubMed   Mentions:
    16. Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment. medRxiv. 2020 Aug 13. Minich JJ, Ali F, Marotz C, Belda-Ferre P, Chiang L, Shaffer JP, Carpenter CS, McDonald D, Gilbert JA, Allard SM, Allen EE, Knight R, Sweeney DA, Swafford AD. PMID: 32511552; PMCID: PMC7274233.
      View in: PubMed   Mentions:
    17. Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome. mSystems. 2020 Mar 17; 5(2). Taylor BC, Lejzerowicz F, Poirel M, Shaffer JP, Jiang L, Aksenov A, Litwin N, Humphrey G, Martino C, Miller-Montgomery S, Dorrestein PC, Veiga P, Song SJ, McDonald D, Derrien M, Knight R. PMID: 32184365; PMCID: PMC7380580.
      View in: PubMed   Mentions: 28  
    18. Soil-borne fungi influence seed germination and mortality, with implications for coexistence of desert winter annual plants. PLoS One. 2019; 14(10):e0224417. Li YM, Shaffer JP, Hall B, Ko H. PMID: 31671129; PMCID: PMC6822719.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsPHPublic Health
    19. Bacterial Endosymbionts: Master Modulators of Fungal Phenotypes. Microbiol Spectr. 2017 09; 5(5). Araldi-Brondolo SJ, Spraker J, Shaffer JP, Woytenko EH, Baltrus DA, Gallery RE, Arnold AE. PMID: 28936944.
      View in: PubMed   Mentions: 7     Fields:    Translation:AnimalsCells
    20. An Endohyphal Bacterium (Chitinophaga, Bacteroidetes) Alters Carbon Source Use by Fusarium keratoplasticum (F. solani Species Complex, Nectriaceae). Front Microbiol. 2017; 8:350. Shaffer JP, U'Ren JM, Gallery RE, Baltrus DA, Arnold AE. PMID: 28382021; PMCID: PMC5361657.
      View in: PubMed   Mentions: 20  
    21. Diversity, specificity, and phylogenetic relationships of bacteria in fungi that inhabit tropical seeds and leaves. Frontiers in Ecology and Evolution. 2016; 4(Oct 2016):1-20. Shaffer JP, Sarmiento C, Zalamea P-C, Gallery RE, Davis AS, Baltrus DA, Arnold AE. View Publication.
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