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Scott Kelley

Faculty RankProfessor
InstitutionSan Diego State University
Address5500 Campanile Dr
LS 373
San Diego CA 92182
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    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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    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. Rastegar K, Kelley ST, Thackray VG. Metagenome-Assembled Genomes from Murine Fecal Microbiomes Dominated by Uncharacterized Bacteria. Microbiol Resour Announc. 2023 Feb 13; e0116222. PMID: 36779794.
    2. Sisk-Hackworth L, Kelley ST, Thackray VG. Sex, puberty, and the gut microbiome. Reproduction. 2023 Feb 01; 165(2):R61-R74. PMID: 36445259.
      Citations:    Fields:    Translation:Humans
    3. Allsing N, Kelley ST, Fox AN, Sant KE. Metagenomic Analysis of Microbial Contamination in the U.S. Portion of the Tijuana River Watershed. Int J Environ Res Public Health. 2022 12 29; 20(1). PMID: 36612923.
      Citations:    Fields:    Translation:CellsPHPublic Health
    4. Liu S, Mathis KL, Graham RP, Kelley SR. Perianal Basal Cell Carcinoma: 35-Year Experience. Dis Colon Rectum. 2023 Feb 01; 66(2):217-220. PMID: 35714341.
      Citations:    Fields:    Translation:Humans
    5. Ansell J, Perry WRG, Mathis KL, Grass F, Yonkus JA, Hallemeier CL, Haddock MG, Graham RP, Merchea A, Colibaseanu DT, Mishra N, Kelley SR, Larson DW, Dozois EJ. Re-resection of Microscopically Positive Margins Found on Intraoperative Frozen Section Analysis Does Not Result in a Survival Benefit in Patients Undergoing Surgery and Intraoperative Radiation Therapy for Locally Recurrent Rectal Cancer. Dis Colon Rectum. 2022 09 01; 65(9):1094-1102. PMID: 35714345.
      Citations:    Fields:    Translation:Humans
    6. Bendik J, Kalia R, Sukumaran J, Richardot WH, Hoh E, Kelley ST. Automated high confidence compound identification of electron ionization mass spectra for nontargeted analysis. J Chromatogr A. 2021 Dec 20; 1660:462656. PMID: 34798444.
      Citations:    Fields:    Translation:HumansPHPublic Health
    7. Ho B, Ryback D, Benson B, Mason CN, Torres PJ, Quinn RA, Thackray VG, Kelley ST. Gut Metabolites Are More Predictive of Disease and Cohoused States than Gut Bacterial Features in a Polycystic Ovary Syndrome-Like Mouse Model. mSystems. 2021 Oct 26; 6(5):e0114920. PMID: 34519532.
    8. Sisk-Hackworth L, Ortiz-Velez A, Reed MB, Kelley ST. Compositional Data Analysis of Periodontal Disease Microbial Communities. Front Microbiol. 2021; 12:617949. PMID: 34079525.
    9. Kelley ST, Liu W, Quintana PJE, Hoh E, Dodder NG, Mahabee-Gittens EM, Padilla S, Ogden S, Frenzel S, Sisk-Hackworth L, Matt GE. Altered microbiomes in thirdhand smoke-exposed children and their home environments. Pediatr Res. 2021 12; 90(6):1153-1160. PMID: 33654287.
      Citations: 9     Fields:    Translation:HumansCellsPHPublic Health
    10. Yanagihara R, Berry MJ, Carson MJ, Chang SP, Corliss H, Cox MB, Haddad G, Hohmann C, Kelley ST, Lee ESY, Link BG, Noel RJ, Pickrel J, Porter JT, Quirk GJ, Samuel T, Stiles JK, Sy AU, Taira DA, Trepka MJ, Villalta F, Wiese TE. Building a Diverse Workforce and Thinkforce to Reduce Health Disparities. Int J Environ Res Public Health. 2021 02 07; 18(4). PMID: 33562262.
      Citations: 3     Fields:    Translation:Humans
    11. Sau L, Olmstead CM, Cui LJ, Chen A, Shah RS, Kelley ST, Thackray VG. Alterations in Gut Microbiota Do Not Play a Causal Role in Diet-independent Weight Gain Caused by Ovariectomy. J Endocr Soc. 2021 Jan 01; 5(1):bvaa173. PMID: 33324864.
    12. Sisk-Hackworth L, Kelley ST. An application of compositional data analysis to multiomic time-series data. NAR Genom Bioinform. 2020 Dec; 2(4):lqaa079. PMID: 33575625.
    13. Zhao D, Cardona C, Gottel N, Winton VJ, Thomas PM, Raba DA, Kelley ST, Henry C, Gilbert JA, Stephens B. Chemical composition of material extractives influences microbial growth and dynamics on wetted wood materials. Sci Rep. 2020 09 02; 10(1):14500. PMID: 32879425.
      Citations: 1     Fields:    Translation:AnimalsPHPublic Health
    14. Xu Y, Tandon R, Ancheta C, Arroyo P, Gilbert JA, Stephens B, Kelley ST. Quantitative profiling of built environment bacterial and fungal communities reveals dynamic material dependent growth patterns and microbial interactions. Indoor Air. 2021 01; 31(1):188-205. PMID: 32757488.
      Citations: 2     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    15. Chopyk J, Akrami K, Bavly T, Shin JH, Schwanemann LK, Ly M, Kalia R, Xu Y, Kelley ST, Malhotra A, Torriani FJ, Sweeney DA, Pride DT. Temporal variations in bacterial community diversity and composition throughout intensive care unit renovations. Microbiome. 2020 06 08; 8(1):86. PMID: 32513256.
      Citations: 5     Fields:    Translation:CellsPHPublic Health
    16. McGhee JJ, Rawson N, Bailey BA, Fernandez-Guerra A, Sisk-Hackworth L, Kelley ST. Meta-SourceTracker: application of Bayesian source tracking to shotgun metagenomics. PeerJ. 2020; 8:e8783. PMID: 32231882.
    17. Grass F, H?bner M, Mathis KL, Hahnloser D, Dozois EJ, Kelley SR, Demartines N, Larson DW. Challenges to accomplish stringent fluid management standards 7 years after enhanced recovery after surgery implementation-The surgeon's perspective. Surgery. 2020 Aug; 168(2):313-319. PMID: 32122658.
      Citations: 1     Fields:    Translation:Humans
    18. Prussin AJ, Belser JA, Bischoff W, Kelley ST, Lin K, Lindsley WG, Nshimyimana JP, Schuit M, Wu Z, Bibby K, Marr LC. Viruses in the Built Environment (VIBE) meeting report. Microbiome. 2020 01 04; 8(1):1. PMID: 31901242.
      Citations: 20     Fields:    Translation:HumansCells
    19. Arroyo P, Ho BS, Sau L, Kelley ST, Thackray VG. Letrozole treatment of pubertal female mice results in activational effects on reproduction, metabolism and the gut microbiome. PLoS One. 2019; 14(9):e0223274. PMID: 31568518.
      Citations: 17     Fields:    Translation:HumansAnimals
    20. Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodr?guez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, V?zquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019 08; 37(8):852-857. PMID: 31341288.
      Citations: 3581     Fields:    Translation:Humans
    21. Edwards RA, Vega AA, Norman HM, Ohaeri M, Levi K, Dinsdale EA, Cinek O, Aziz RK, McNair K, Barr JJ, Bibby K, Brouns SJJ, Cazares A, de Jonge PA, Desnues C, D?az Mu?oz SL, Fineran PC, Kurilshikov A, Lavigne R, Mazankova K, McCarthy DT, Nobrega FL, Reyes Mu?oz A, Tapia G, Trefault N, Tyakht AV, Vinuesa P, Wagemans J, Zhernakova A, Aarestrup FM, Ahmadov G, Alassaf A, Anton J, Asangba A, Billings EK, Cantu VA, Carlton JM, Cazares D, Cho GS, Condeff T, Cort?s P, Cranfield M, Cuevas DA, De la Iglesia R, Decewicz P, Doane MP, Dominy NJ, Dziewit L, Elwasila BM, Eren AM, Franz C, Fu J, Garcia-Aljaro C, Ghedin E, Gulino KM, Haggerty JM, Head SR, Hendriksen RS, Hill C, Hy?ty H, Ilina EN, Irwin MT, Jeffries TC, Jofre J, Junge RE, Kelley ST, Khan Mirzaei M, Kowalewski M, Kumaresan D, Leigh SR, Lipson D, Lisitsyna ES, Llagostera M, Maritz JM, Marr LC, McCann A, Molshanski-Mor S, Monteiro S, Moreira-Grez B, Morris M, Mugisha L, Muniesa M, Neve H, Nguyen NP, Nigro OD, Nilsson AS, O'Connell T, Odeh R, Oliver A, Piuri M, Prussin Ii AJ, Qimron U, Quan ZX, Rainetova P, Ram?rez-Rojas A, Raya R, Reasor K, Rice GAO, Rossi A, Santos R, Shimashita J, Stachler EN, Stene LC, Strain R, Stumpf R, Torres PJ, Twaddle A, Ugochi Ibekwe M, Villagra N, Wandro S, White B, Whiteley A, Whiteson KL, Wijmenga C, Zambrano MM, Zschach H, Dutilh BE. Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. Nat Microbiol. 2019 10; 4(10):1727-1736. PMID: 31285584.
      Citations: 80     Fields:    Translation:HumansAnimalsCells
    22. Shariq OA, Hanson KT, McKenna NP, Kelley SR, Dozois EJ, Lightner AL, Mathis KL, Habermann EB. Does Metabolic Syndrome Increase the Risk of Postoperative Complications in Patients Undergoing Colorectal Cancer Surgery? Dis Colon Rectum. 2019 07; 62(7):849-858. PMID: 31188186.
      Citations: 11     Fields:    Translation:Humans
    23. de la Cuesta-Zuluaga J, Kelley ST, Chen Y, Escobar JS, Mueller NT, Ley RE, McDonald D, Huang S, Swafford AD, Knight R, Thackray VG. Age- and Sex-Dependent Patterns of Gut Microbial Diversity in Human Adults. mSystems. 2019 Jul-Aug; 4(4). PMID: 31098397.
    24. Torres PJ, Ho BS, Arroyo P, Sau L, Chen A, Kelley ST, Thackray VG. Exposure to a Healthy Gut Microbiome Protects Against Reproductive and Metabolic Dysregulation in a PCOS Mouse Model. Endocrinology. 2019 05 01; 160(5):1193-1204. PMID: 30924862.
      Citations: 24     Fields:    Translation:HumansAnimals
    25. Lax S, Cardona C, Zhao D, Winton VJ, Goodney G, Gao P, Gottel N, Hartmann EM, Henry C, Thomas PM, Kelley ST, Stephens B, Gilbert JA. Microbial and metabolic succession on common building materials under high humidity conditions. Nat Commun. 2019 04 16; 10(1):1767. PMID: 30992445.
      Citations: 14     Fields:    Translation:AnimalsCellsPHPublic Health
    26. Prussin AJ, Torres PJ, Shimashita J, Head SR, Bibby KJ, Kelley ST, Marr LC. Seasonal dynamics of DNA and RNA viral bioaerosol communities in a daycare center. Microbiome. 2019 04 01; 7(1):53. PMID: 30935423.
      Citations: 12     Fields:    Translation:HumansCellsPHPublic Health
    27. Torres PJ, Skarra DV, Ho BS, Sau L, Anvar AR, Kelley ST, Thackray VG. Letrozole treatment of adult female mice results in a similar reproductive phenotype but distinct changes in metabolism and the gut microbiome compared to pubertal mice. BMC Microbiol. 2019 03 12; 19(1):57. PMID: 30871463.
      Citations: 13     Fields:    Translation:Animals
    28. Bhaskaran N, Luu J, Kelley ST, Khan MW, Mamindla P, McGuire KL. A new method for discovering EMAST sequences in animal models of cancer. Sci Rep. 2018 09 13; 8(1):13764. PMID: 30214002.
      Citations: 1     Fields:    Translation:HumansAnimalsCells
    29. Torres PJ, Thompson J, McLean JS, Kelley ST, Edlund A. Discovery of a Novel Periodontal Disease-Associated Bacterium. Microb Ecol. 2019 Jan; 77(1):267-276. PMID: 29860637.
      Citations: 9     Fields:    Translation:HumansCells
    30. McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jackson MA, Janssen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko D, Melnik AV, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song SJ, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, V?zquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E, Zhu Q, Knight R. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. 2018 May-Jun; 3(3). PMID: 29795809.
    31. Kosnicki KL, Penprase JC, Cintora P, Torres PJ, Harris GL, Brasser SM, Kelley ST. Effects of moderate, voluntary ethanol consumption on the rat and human gut microbiome. Addict Biol. 2019 07; 24(4):617-630. PMID: 29750384.
      Citations: 14     Fields:    Translation:HumansAnimals
    32. Torres PJ, Siakowska M, Banaszewska B, Pawelczyk L, Duleba AJ, Kelley ST, Thackray VG. Gut Microbial Diversity in Women With Polycystic Ovary Syndrome Correlates With Hyperandrogenism. J Clin Endocrinol Metab. 2018 04 01; 103(4):1502-1511. PMID: 29370410.
      Citations: 98     Fields:    Translation:Humans
    33. Delange N, Lindsay S, Lemus H, Finlayson TL, Kelley ST, Gottlieb RA. Periodontal disease and its connection to systemic biomarkers of cardiovascular disease in young American Indian/Alaskan natives. J Periodontol. 2018 02; 89(2):219-227. PMID: 29520828.
      Citations: 6     Fields:    Translation:Humans
    34. Chen Y, Crosby HA, Oosthuysen WF, Diekema DJ, Kelley ST, Horswill AR. Draft Genome Sequence of USA100 Methicillin-Resistant Staphylococcus aureus Strain 209. Genome Announc. 2018 Jan 04; 6(1). PMID: 29301880.
    35. Torres PJ, Kelley ST. Sampling, Extraction, and High-Throughput Sequencing Methods for Environmental Microbial and Viral Communities. Methods Mol Biol. 2018; 1712:163-173. PMID: 29224074.
      Citations:    Fields:    Translation:HumansAnimalsCellsPHPublic Health
    36. Parker ME, Mathis KL, Kelley SR. Severity of diverticulitis in patients with polycystic kidney disease without transplantation. Int J Colorectal Dis. 2017 Dec; 32(12):1767-1770. PMID: 28965236.
      Citations: 2     Fields:    Translation:Humans
    37. Califf KJ, Schwarzberg-Lipson K, Garg N, Gibbons SM, Caporaso JG, Slots J, Cohen C, Dorrestein PC, Kelley ST. Multi-omics Analysis of Periodontal Pocket Microbial Communities Pre- and Posttreatment. mSystems. 2017 May-Jun; 2(3). PMID: 28744486.
    38. Gurfield N, Grewal S, Cua LS, Torres PJ, Kelley ST. Endosymbiont interference and microbial diversity of the Pacific coast tick, Dermacentor occidentalis, in San Diego County, California. PeerJ. 2017; 5:e3202. PMID: 28503372.
    39. Chase J, Fouquier J, Zare M, Sonderegger DL, Knight R, Kelley ST, Siegel J, Caporaso JG. Geography and Location Are the Primary Drivers of Office Microbiome Composition. mSystems. 2016 Mar-Apr; 1(2). PMID: 27822521.
    40. Fouquier J, Rideout JR, Bolyen E, Chase J, Shiffer A, McDonald D, Knight R, Caporaso JG, Kelley ST. Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses. Microbiome. 2016 Feb 24; 4:11. PMID: 26905735.
      Citations: 18     Fields:    Translation:HumansAnimals
    41. Kelley ST, Skarra DV, Rivera AJ, Thackray VG. The Gut Microbiome Is Altered in a Letrozole-Induced Mouse Model of Polycystic Ovary Syndrome. PLoS One. 2016; 11(1):e0146509. PMID: 26731268.
      Citations: 59     Fields:    Translation:Animals
    42. McLean JS, Liu Q, Thompson J, Edlund A, Kelley S. Draft Genome Sequence of "Candidatus Bacteroides periocalifornicus," a New Member of the Bacteriodetes Phylum Found within the Oral Microbiome of Periodontitis Patients. Genome Announc. 2015 Dec 23; 3(6). PMID: 26701081.
    43. Torres PJ, Fletcher EM, Gibbons SM, Bouvet M, Doran KS, Kelley ST. Characterization of the salivary microbiome in patients with pancreatic cancer. PeerJ. 2015; 3:e1373. PMID: 26587342.
    44. Lipson DA, Raab TK, Parker M, Kelley ST, Brislawn CJ, Jansson J. Changes in microbial communities along redox gradients in polygonized Arctic wet tundra soils. Environ Microbiol Rep. 2015 Aug; 7(4):649-57. PMID: 26034016.
      Citations: 15     Fields:    Translation:CellsPHPublic Health
    45. Wall K, Cornell J, Bizzoco RW, Kelley ST. Biodiversity hot spot on a hot spot: novel extremophile diversity in Hawaiian fumaroles. Microbiologyopen. 2015 Apr; 4(2):267-281. PMID: 25565172.
      Citations: 8     Fields:    
    46. Gibbons SM, Schwartz T, Fouquier J, Mitchell M, Sangwan N, Gilbert JA, Kelley ST. Ecological succession and viability of human-associated microbiota on restroom surfaces. Appl Environ Microbiol. 2015 Jan; 81(2):765-73. PMID: 25398865.
      Citations: 48     Fields:    Translation:HumansCellsPHPublic Health
    47. Huttenhower C, Knight R, Brown CT, Caporaso JG, Clemente JC, Gevers D, Franzosa EA, Kelley ST, Knights D, Ley RE, Mahurkar A, Ravel J, White O. Advancing the microbiome research community. Cell. 2014 Oct 09; 159(2):227-30. PMID: 25303518.
      Citations: 35     Fields:    Translation:HumansAnimals
    48. Schwarzberg K, Le R, Bharti B, Lindsay S, Casaburi G, Salvatore F, Saber MH, Alonaizan F, Slots J, Gottlieb RA, Caporaso JG, Kelley ST. The personal human oral microbiome obscures the effects of treatment on periodontal disease. PLoS One. 2014; 9(1):e86708. PMID: 24489772.
      Citations: 40     Fields:    Translation:HumansCellsCTClinical Trials
    49. Sherman MP, Minnerly J, Curtiss W, Rangwala S, Kelley ST. Research on neonatal microbiomes: what neonatologists need to know. Neonatology. 2014; 105(1):14-24. PMID: 24193200.
      Citations: 2     Fields:    Translation:Humans
    50. Anthony EG, Richard E, Lipkowitz MS, Kelley ST, Alcaraz JE, Shaffer RA, Bhatnagar V. Association of phosphodiesterase 4 polymorphism (rs702553) with blood pressure in the African American Study of Kidney Disease and Hypertension Genomics Study. Pharmacogenet Genomics. 2013 Aug; 23(8):442-4. PMID: 23778321.
      Citations: 1     Fields:    Translation:Humans
    51. Shogan BD, Smith DP, Packman AI, Kelley ST, Landon EM, Bhangar S, Vora GJ, Jones RM, Keegan K, Stephens B, Ramos T, Kirkup BC, Levin H, Rosenthal M, Foxman B, Chang EB, Siegel J, Cobey S, An G, Alverdy JC, Olsiewski PJ, Martin MO, Marrs R, Hernandez M, Christley S, Morowitz M, Weber S, Gilbert J. The Hospital Microbiome Project: Meeting report for the 2nd Hospital Microbiome Project, Chicago, USA, January 15(th), 2013. Stand Genomic Sci. 2013 Jul 30; 8(3):571-9. PMID: 24501640.
    52. Smith D, Alverdy J, An G, Coleman M, Garcia-Houchins S, Green J, Keegan K, Kelley ST, Kirkup BC, Kociolek L, Levin H, Landon E, Olsiewski P, Knight R, Siegel J, Weber S, Gilbert J. The Hospital Microbiome Project: Meeting Report for the 1st Hospital Microbiome Project Workshop on sampling design and building science measurements, Chicago, USA, June 7th-8th 2012. Stand Genomic Sci. 2013 Apr 15; 8(1):112-7. PMID: 23961316.
    53. Kelley ST, Gilbert JA. Studying the microbiology of the indoor environment. Genome Biol. 2013 Feb 28; 14(2):202. PMID: 23514020.
      Citations: 62     Fields:    Translation:CellsPHPublic Health
    54. Hewitt KM, Mannino FL, Gonzalez A, Chase JH, Caporaso JG, Knight R, Kelley ST. Bacterial diversity in two Neonatal Intensive Care Units (NICUs). PLoS One. 2013; 8(1):e54703. PMID: 23372757.
      Citations: 68     Fields:    Translation:HumansCells
    55. Saber MH, Schwarzberg K, Alonaizan FA, Kelley ST, Sedghizadeh PP, Furlan M, Levy TA, Simon JH, Slots J. Bacterial flora of dental periradicular lesions analyzed by the 454-pyrosequencing technology. J Endod. 2012 Nov; 38(11):1484-8. PMID: 23063222.
      Citations: 10     Fields:    Translation:Humans
    56. Abubucker S, Segata N, Goll J, Schubert AM, Izard J, Cantarel BL, Rodriguez-Mueller B, Zucker J, Thiagarajan M, Henrissat B, White O, Kelley ST, Meth? B, Schloss PD, Gevers D, Mitreva M, Huttenhower C. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol. 2012; 8(6):e1002358. PMID: 22719234.
      Citations: 516     Fields:    Translation:Humans
    57. Hewitt KM, Gerba CP, Maxwell SL, Kelley ST. Office space bacterial abundance and diversity in three metropolitan areas. PLoS One. 2012; 7(5):e37849. PMID: 22666400.
      Citations: 57     Fields:    Translation:HumansCells
    58. Knights D, Kuczynski J, Charlson ES, Zaneveld J, Mozer MC, Collman RG, Bushman FD, Knight R, Kelley ST. Bayesian community-wide culture-independent microbial source tracking. Nat Methods. 2011 Jul 17; 8(9):761-3. PMID: 21765408.
      Citations: 506     Fields:    Translation:HumansPHPublic Health
    59. Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, Sterk P, Arumugam M, Bailey M, Baumgartner L, Birren BW, Blaser MJ, Bonazzi V, Booth T, Bork P, Bushman FD, Buttigieg PL, Chain PS, Charlson E, Costello EK, Huot-Creasy H, Dawyndt P, DeSantis T, Fierer N, Fuhrman JA, Gallery RE, Gevers D, Gibbs RA, San Gil I, Gonzalez A, Gordon JI, Guralnick R, Hankeln W, Highlander S, Hugenholtz P, Jansson J, Kau AL, Kelley ST, Kennedy J, Knights D, Koren O, Kuczynski J, Kyrpides N, Larsen R, Lauber CL, Legg T, Ley RE, Lozupone CA, Ludwig W, Lyons D, Maguire E, Meth? BA, Meyer F, Muegge B, Nakielny S, Nelson KE, Nemergut D, Neufeld JD, Newbold LK, Oliver AE, Pace NR, Palanisamy G, Peplies J, Petrosino J, Proctor L, Pruesse E, Quast C, Raes J, Ratnasingham S, Ravel J, Relman DA, Assunta-Sansone S, Schloss PD, Schriml L, Sinha R, Smith MI, Sodergren E, Spo A, Stombaugh J, Tiedje JM, Ward DV, Weinstock GM, Wendel D, White O, Whiteley A, Wilke A, Wortman JR, Yatsunenko T, Gl?ckner FO. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol. 2011 May; 29(5):415-20. PMID: 21552244.
      Citations: 278     Fields:    Translation:Humans
    60. Tin S, Bizzoco RW, Kelley ST. Role of the terrestrial subsurface in shaping geothermal spring microbial communities. Environ Microbiol Rep. 2011 Aug; 3(4):491-9. PMID: 23761312.
      Citations: 2     Fields:    
    61. Caporaso JG, Knight R, Kelley ST. Host-associated and free-living phage communities differ profoundly in phylogenetic composition. PLoS One. 2011 Feb 24; 6(2):e16900. PMID: 21383980.
      Citations: 13     Fields:    Translation:HumansCells
    62. Benson CA, Bizzoco RW, Lipson DA, Kelley ST. Microbial diversity in nonsulfur, sulfur and iron geothermal steam vents. FEMS Microbiol Ecol. 2011 Apr; 76(1):74-88. PMID: 21223339.
      Citations: 18     Fields:    Translation:Cells
    63. Casas V, Magbanua J, Sobrepe?a G, Kelley ST, Maloy SR. Reservoir of bacterial exotoxin genes in the environment. Int J Microbiol. 2010; 2010:754368. PMID: 21318166.
    64. Knights D, Kuczynski J, Koren O, Ley RE, Field D, Knight R, DeSantis TZ, Kelley ST. Supervised classification of microbiota mitigates mislabeling errors. ISME J. 2011 Apr; 5(4):570-3. PMID: 20927137.
      Citations: 25     Fields:    Translation:Cells
    65. Kelley ST, Dobler S. Comparative analysis of microbial diversity in Longitarsus flea beetles (Coleoptera: Chrysomelidae). Genetica. 2011 May; 139(5):541-50. PMID: 20844936.
      Citations: 15     Fields:    Translation:AnimalsCellsPHPublic Health
    66. Kuczynski J, Costello EK, Nemergut DR, Zaneveld J, Lauber CL, Knights D, Koren O, Fierer N, Kelley ST, Ley RE, Gordon JI, Knight R. Direct sequencing of the human microbiome readily reveals community differences. Genome Biol. 2010; 11(5):210. PMID: 20441597.
      Citations: 86     Fields:    Translation:HumansCells
    67. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pe?a AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010 May; 7(5):335-6. PMID: 20383131.
      Citations: 12751     Fields:    Translation:HumansAnimals
    68. Turner JL, Kelley ST, Otto JS, Valafar F, Bohonak AJ. Parallelization and optimization of genetic analyses in isolation by distance web service. BMC Genet. 2009 Jun 19; 10:28. PMID: 19545374.
      Citations:    Fields:    
    69. Breitbart M, Haynes M, Kelley S, Angly F, Edwards RA, Felts B, Mahaffy JM, Mueller J, Nulton J, Rayhawk S, Rodriguez-Brito B, Salamon P, Rohwer F. Viral diversity and dynamics in an infant gut. Res Microbiol. 2008 Jun; 159(5):367-73. PMID: 18541415.
      Citations: 141     Fields:    Translation:HumansCells
    70. Ellis DG, Bizzoco RW, Kelley ST. Halophilic Archaea determined from geothermal steam vent aerosols. Environ Microbiol. 2008 Jun; 10(6):1582-90. PMID: 18331336.
      Citations: 10     Fields:    Translation:Cells
    71. Desnues C, Rodriguez-Brito B, Rayhawk S, Kelley S, Tran T, Haynes M, Liu H, Furlan M, Wegley L, Chau B, Ruan Y, Hall D, Angly FE, Edwards RA, Li L, Thurber RV, Reid RP, Siefert J, Souza V, Valentine DL, Swan BK, Breitbart M, Rohwer F. Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature. 2008 Mar 20; 452(7185):340-3. PMID: 18311127.
      Citations: 115     Fields:    Translation:CellsPHPublic Health
    72. Krause L, Diaz NN, Goesmann A, Kelley S, Nattkemper TW, Rohwer F, Edwards RA, Stoye J. Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Res. 2008 Apr; 36(7):2230-9. PMID: 18285365.
      Citations: 116     Fields:    Translation:PHPublic Health
    73. Townsend TM, Alegre RE, Kelley ST, Wiens JJ, Reeder TW. Rapid development of multiple nuclear loci for phylogenetic analysis using genomic resources: an example from squamate reptiles. Mol Phylogenet Evol. 2008 Apr; 47(1):129-42. PMID: 18313331.
      Citations: 32     Fields:    Translation:HumansAnimalsCells
    74. Thackray LB, Wobus CE, Chachu KA, Liu B, Alegre ER, Henderson KS, Kelley ST, Virgin HW. Murine noroviruses comprising a single genogroup exhibit biological diversity despite limited sequence divergence. J Virol. 2007 Oct; 81(19):10460-73. PMID: 17652401.
      Citations: 143     Fields:    Translation:AnimalsCells
    75. Lee L, Tin S, Kelley ST. Culture-independent analysis of bacterial diversity in a child-care facility. BMC Microbiol. 2007 Apr 05; 7:27. PMID: 17411442.
      Citations: 31     Fields:    Translation:HumansCellsPHPublic Health
    76. Mathur J, Bizzoco RW, Ellis DG, Lipson DA, Poole AW, Levine R, Kelley ST. Effects of abiotic factors on the phylogenetic diversity of bacterial communities in acidic thermal springs. Appl Environ Microbiol. 2007 Apr; 73(8):2612-23. PMID: 17220248.
      Citations: 25     Fields:    Translation:CellsPHPublic Health
    77. Lozupone CA, Hamady M, Kelley ST, Knight R. Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Appl Environ Microbiol. 2007 Mar; 73(5):1576-85. PMID: 17220268.
      Citations: 925     Fields:    Translation:AnimalsCells
    78. Angly FE, Felts B, Breitbart M, Salamon P, Edwards RA, Carlson C, Chan AM, Haynes M, Kelley S, Liu H, Mahaffy JM, Mueller JE, Nulton J, Olson R, Parsons R, Rayhawk S, Suttle CA, Rohwer F. The marine viromes of four oceanic regions. PLoS Biol. 2006 Nov; 4(11):e368. PMID: 17090214.
      Citations: 402     Fields:    Translation:Cells
    79. Safaee S, Weiser GC, Cassirer EF, Ramey RR, Kelley ST. Microbial diversity in bighorn sheep revealed by culture-independent methods. J Wildl Dis. 2006 Jul; 42(3):545-55. PMID: 17092885.
      Citations: 9     Fields:    Translation:AnimalsCells
    80. Kelley ST, Cassirer EF, Weiser GC, Safaee S. Phylogenetic diversity of Pasteurellaceae and horizontal gene transfer of leukotoxin in wild and domestic sheep. Infect Genet Evol. 2007 Jan; 7(1):13-23. PMID: 16635591.
      Citations: 3     Fields:    Translation:AnimalsCells
    81. Nguyen TX, Alegre ER, Kelley ST. Phylogenetic analysis of general bacterial porins: a phylogenomic case study. J Mol Microbiol Biotechnol. 2006; 11(6):291-301. PMID: 17114893.
      Citations: 9     Fields:    Translation:Cells
    82. Marquez SM, Harris JK, Kelley ST, Brown JW, Dawson SC, Roberts EC, Pace NR. Structural implications of novel diversity in eucaryal RNase P RNA. RNA. 2005 May; 11(5):739-51. PMID: 15811915.
      Citations: 31     Fields:    Translation:AnimalsCells
    83. Angenent LT, Kelley ST, St Amand A, Pace NR, Hernandez MT. Molecular identification of potential pathogens in water and air of a hospital therapy pool. Proc Natl Acad Sci U S A. 2005 Mar 29; 102(13):4860-5. PMID: 15769858.
      Citations: 56     Fields:    Translation:CellsPHPublic Health
    84. Jensen JL, Bohonak AJ, Kelley ST. Isolation by distance, web service. BMC Genet. 2005 Mar 11; 6:13. PMID: 15760479.
      Citations: 345     Fields:    Translation:Humans
    85. Crawford NP, Colliver DW, Funke AA, Young MN, Kelley S, Cobbs GA, Petras RE, Galandiuk S. Characterization of genotype-phenotype relationships and stratification by the CARD15 variant genotype for inflammatory bowel disease susceptibility loci using multiple short tandem repeat genetic markers. Hum Mutat. 2005 Feb; 25(2):156-66. PMID: 15643611.
      Citations: 7     Fields:    Translation:HumansCells
    86. Kelley ST, Theisen U, Angenent LT, St Amand A, Pace NR. Molecular analysis of shower curtain biofilm microbes. Appl Environ Microbiol. 2004 Jul; 70(7):4187-92. PMID: 15240300.
      Citations: 46     Fields:    Translation:CellsPHPublic Health
    87. Breitbart M, Felts B, Kelley S, Mahaffy JM, Nulton J, Salamon P, Rohwer F. Diversity and population structure of a near-shore marine-sediment viral community. Proc Biol Sci. 2004 Mar 22; 271(1539):565-74. PMID: 15156913.
      Citations: 119     Fields:    Translation:Cells
    88. Harris JK, Kelley ST, Pace NR. New perspective on uncultured bacterial phylogenetic division OP11. Appl Environ Microbiol. 2004 Feb; 70(2):845-9. PMID: 14766563.
      Citations: 75     Fields:    Translation:CellsPHPublic Health
    89. Harris JK, Kelley ST, Spiegelman GB, Pace NR. The genetic core of the universal ancestor. Genome Res. 2003 Mar; 13(3):407-12. PMID: 12618371.
      Citations: 124     Fields:    Translation:AnimalsCells
      Citations: 48     Fields:    
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