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Items: 1 to 50 of 112

1.

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.

Torres PJ, Skarra DV, Ho BS, Sau L, Anvar AR, Kelley ST, Thackray VG.

BMC Microbiol. 2019 Mar 12;19(1):57. doi: 10.1186/s12866-019-1425-7.

2.

A new method for discovering EMAST sequences in animal models of cancer.

Bhaskaran N, Luu J, Kelley ST, Khan MW, Mamindla P, McGuire KL.

Sci Rep. 2018 Sep 13;8(1):13764. doi: 10.1038/s41598-018-32057-2.

3.

Discovery of a Novel Periodontal Disease-Associated Bacterium.

Torres PJ, Thompson J, McLean JS, Kelley ST, Edlund A.

Microb Ecol. 2019 Jan;77(1):267-276. doi: 10.1007/s00248-018-1200-6. Epub 2018 Jun 2.

4.

American Gut: an Open Platform for Citizen Science Microbiome Research.

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, Vázquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E, Zhu Q; American Gut Consortium , Knight R.

mSystems. 2018 May 15;3(3). pii: e00031-18. doi: 10.1128/mSystems.00031-18. eCollection 2018 May-Jun.

5.

Management of Research Animal Breeding Colonies.

Elliott JJ, Miller CT, Hagarman JA, Kelley ST, Tardif SD, Hacker SO, Bettis A.

In: Weichbrod RH, Thompson GAH, Norton JN, editors. Management of Animal Care and Use Programs in Research, Education, and Testing. 2nd edition. Boca Raton (FL): CRC Press/Taylor & Francis; 2018. Chapter 29.

6.

Effects of moderate, voluntary ethanol consumption on the rat and human gut microbiome.

Kosnicki KL, Penprase JC, Cintora P, Torres PJ, Harris GL, Brasser SM, Kelley ST.

Addict Biol. 2018 May 11. doi: 10.1111/adb.12626. [Epub ahead of print]

PMID:
29750384
7.

Periodontal disease and its connection to systemic biomarkers of cardiovascular disease in young American Indian/Alaskan natives.

Delange N, Lindsay S, Lemus H, Finlayson TL, Kelley ST, Gottlieb RA.

J Periodontol. 2018 Feb;89(2):219-227. doi: 10.1002/JPER.17-0319. Epub 2018 Feb 23.

8.

Gut Microbial Diversity in Women With Polycystic Ovary Syndrome Correlates With Hyperandrogenism.

Torres PJ, Siakowska M, Banaszewska B, Pawelczyk L, Duleba AJ, Kelley ST, Thackray VG.

J Clin Endocrinol Metab. 2018 Apr 1;103(4):1502-1511. doi: 10.1210/jc.2017-02153.

PMID:
29370410
9.

Draft Genome Sequence of USA100 Methicillin-Resistant Staphylococcus aureus Strain 209.

Chen Y, Crosby HA, Oosthuysen WF 2nd, Diekema DJ, Kelley ST, Horswill AR.

Genome Announc. 2018 Jan 4;6(1). pii: e01399-17. doi: 10.1128/genomeA.01399-17.

10.

Sampling, Extraction, and High-Throughput Sequencing Methods for Environmental Microbial and Viral Communities.

Torres PJ, Kelley ST.

Methods Mol Biol. 2018;1712:163-173. doi: 10.1007/978-1-4939-7514-3_11.

PMID:
29224074
11.

Multi-omics Analysis of Periodontal Pocket Microbial Communities Pre- and Posttreatment.

Califf KJ, Schwarzberg-Lipson K, Garg N, Gibbons SM, Caporaso JG, Slots J, Cohen C, Dorrestein PC, Kelley ST.

mSystems. 2017 Jun 20;2(3). pii: e00016-17. doi: 10.1128/mSystems.00016-17. eCollection 2017 May-Jun.

12.

Failure to replicate thrombomodulin genetic variant predictors of venous thromboembolism in African Americans.

Folsom AR, Roetker NS, Kelley ST, Tang W, Pankratz N.

Blood. 2017 Aug 3;130(5):688-690. doi: 10.1182/blood-2017-03-771329. Epub 2017 Jun 15. No abstract available.

13.

Endosymbiont interference and microbial diversity of the Pacific coast tick, Dermacentor occidentalis, in San Diego County, California.

Gurfield N, Grewal S, Cua LS, Torres PJ, Kelley ST.

PeerJ. 2017 Apr 13;5:e3202. doi: 10.7717/peerj.3202. eCollection 2017.

14.

Geography and Location Are the Primary Drivers of Office Microbiome Composition.

Chase J, Fouquier J, Zare M, Sonderegger DL, Knight R, Kelley ST, Siegel J, Caporaso JG.

mSystems. 2016 Apr 19;1(2). pii: e00022-16. eCollection 2016 Mar-Apr.

15.

Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses.

Fouquier J, Rideout JR, Bolyen E, Chase J, Shiffer A, McDonald D, Knight R, Caporaso JG, Kelley ST.

Microbiome. 2016 Feb 24;4:11. doi: 10.1186/s40168-016-0153-6.

16.

The Gut Microbiome Is Altered in a Letrozole-Induced Mouse Model of Polycystic Ovary Syndrome.

Kelley ST, Skarra DV, Rivera AJ, Thackray VG.

PLoS One. 2016 Jan 5;11(1):e0146509. doi: 10.1371/journal.pone.0146509. eCollection 2016.

17.

Rapid assemblage of diverse environmental fungal communities on public restroom floors.

Fouquier J, Schwartz T, Kelley ST.

Indoor Air. 2016 Dec;26(6):869-879. doi: 10.1111/ina.12279. Epub 2016 Jan 28.

PMID:
26717555
18.

Characterization of the salivary microbiome in patients with pancreatic cancer.

Torres PJ, Fletcher EM, Gibbons SM, Bouvet M, Doran KS, Kelley ST.

PeerJ. 2015 Nov 5;3:e1373. doi: 10.7717/peerj.1373. eCollection 2015.

19.

Changes in microbial communities along redox gradients in polygonized Arctic wet tundra soils.

Lipson DA, Raab TK, Parker M, Kelley ST, Brislawn CJ, Jansson J.

Environ Microbiol Rep. 2015 Aug;7(4):649-57. doi: 10.1111/1758-2229.12301.

PMID:
26034016
20.

Biodiversity hot spot on a hot spot: novel extremophile diversity in Hawaiian fumaroles.

Wall K, Cornell J, Bizzoco RW, Kelley ST.

Microbiologyopen. 2015 Apr;4(2):267-281. doi: 10.1002/mbo3.236. Epub 2015 Jan 6.

21.

Ecological succession and viability of human-associated microbiota on restroom surfaces.

Gibbons SM, Schwartz T, Fouquier J, Mitchell M, Sangwan N, Gilbert JA, Kelley ST.

Appl Environ Microbiol. 2015 Jan;81(2):765-73. doi: 10.1128/AEM.03117-14. Epub 2014 Nov 14.

22.

Advancing the microbiome research community.

Huttenhower C, Knight R, Brown CT, Caporaso JG, Clemente JC, Gevers D, Franzosa EA, Kelley ST, Knights D, Ley RE, Mahurkar A, Ravel J; Scientists for Advancement of Microbiome Research, White O.

Cell. 2014 Oct 9;159(2):227-30. doi: 10.1016/j.cell.2014.09.022.

23.

The Hospital Microbiome Project: Meeting report for the 2nd Hospital Microbiome Project, Chicago, USA, January 15(th), 2013.

Shogan BD, Smith DP, Packman AI, Kelley ST, Landon EM, Bhangar S, Vora GJ, Jones RM, Keegan K, Stephens B, Ramos T, Kirkup BC Jr, 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.

Stand Genomic Sci. 2013 Jul 25;8(3):571-9. doi: 10.4056/sigs.4187859. eCollection 2013 Jul 30. No abstract available.

24.

The personal human oral microbiome obscures the effects of treatment on periodontal disease.

Schwarzberg K, Le R, Bharti B, Lindsay S, Casaburi G, Salvatore F, Saber MH, Alonaizan F, Slots J, Gottlieb RA, Caporaso JG, Kelley ST.

PLoS One. 2014 Jan 29;9(1):e86708. doi: 10.1371/journal.pone.0086708. eCollection 2014.

25.

Research on neonatal microbiomes: what neonatologists need to know.

Sherman MP, Minnerly J, Curtiss W, Rangwala S, Kelley ST.

Neonatology. 2014;105(1):14-24. doi: 10.1159/000354944. Epub 2013 Nov 2. Review.

26.

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.

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.

Stand Genomic Sci. 2013 Apr 15;8(1):112-7. doi: 10.4056/sigs.3717348. eCollection 2013 Apr 15.

27.

Association of phosphodiesterase 4 polymorphism (rs702553) with blood pressure in the African American Study of Kidney Disease and Hypertension Genomics Study.

Anthony EG, Richard E, Lipkowitz MS, Kelley ST, Alcaraz JE, Shaffer RA, Bhatnagar V.

Pharmacogenet Genomics. 2013 Aug;23(8):442-4. doi: 10.1097/FPC.0b013e3283636840.

PMID:
23778321
28.

Studying the microbiology of the indoor environment.

Kelley ST, Gilbert JA.

Genome Biol. 2013 Feb 28;14(2):202. doi: 10.1186/gb-2013-14-2-202. Review.

29.

Bacterial diversity in two Neonatal Intensive Care Units (NICUs).

Hewitt KM, Mannino FL, Gonzalez A, Chase JH, Caporaso JG, Knight R, Kelley ST.

PLoS One. 2013;8(1):e54703. doi: 10.1371/journal.pone.0054703. Epub 2013 Jan 23.

30.

Bacterial flora of dental periradicular lesions analyzed by the 454-pyrosequencing technology.

Saber MH, Schwarzberg K, Alonaizan FA, Kelley ST, Sedghizadeh PP, Furlan M, Levy TA, Simon JH, Slots J.

J Endod. 2012 Nov;38(11):1484-8. doi: 10.1016/j.joen.2012.06.037. Epub 2012 Aug 9.

PMID:
23063222
31.

Ancestral state reconstruction for Dendroctonus bark beetles: evolution of a tree killer.

Reeve JD, Anderson FE, Kelley ST.

Environ Entomol. 2012 Jun;41(3):723-30. doi: 10.1603/EN11281.

PMID:
22732632
32.

Metabolic reconstruction for metagenomic data and its application to the human microbiome.

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, Methé B, Schloss PD, Gevers D, Mitreva M, Huttenhower C.

PLoS Comput Biol. 2012;8(6):e1002358. doi: 10.1371/journal.pcbi.1002358. Epub 2012 Jun 13.

33.

Office space bacterial abundance and diversity in three metropolitan areas.

Hewitt KM, Gerba CP, Maxwell SL, Kelley ST.

PLoS One. 2012;7(5):e37849. doi: 10.1371/journal.pone.0037849. Epub 2012 May 30.

34.

Role of the terrestrial subsurface in shaping geothermal spring microbial communities.

Tin S, Bizzoco RW, Kelley ST.

Environ Microbiol Rep. 2011 Aug;3(4):491-9. doi: 10.1111/j.1758-2229.2011.00248.x. Epub 2011 Mar 21.

PMID:
23761312
35.

Bayesian community-wide culture-independent microbial source tracking.

Knights D, Kuczynski J, Charlson ES, Zaneveld J, Mozer MC, Collman RG, Bushman FD, Knight R, Kelley ST.

Nat Methods. 2011 Jul 17;8(9):761-3. doi: 10.1038/nmeth.1650.

36.

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.

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, Methé 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, Glöckner FO.

Nat Biotechnol. 2011 May;29(5):415-20. doi: 10.1038/nbt.1823.

37.

Host-associated and free-living phage communities differ profoundly in phylogenetic composition.

Caporaso JG, Knight R, Kelley ST.

PLoS One. 2011 Feb 24;6(2):e16900. doi: 10.1371/journal.pone.0016900.

38.

Reservoir of bacterial exotoxin genes in the environment.

Casas V, Magbanua J, Sobrepeña G, Kelley ST, Maloy SR.

Int J Microbiol. 2010;2010:754368. doi: 10.1155/2010/754368. Epub 2011 Jan 9.

39.

Microbial diversity in nonsulfur, sulfur and iron geothermal steam vents.

Benson CA, Bizzoco RW, Lipson DA, Kelley ST.

FEMS Microbiol Ecol. 2011 Apr;76(1):74-88. doi: 10.1111/j.1574-6941.2011.01047.x. Epub 2011 Feb 1.

40.

Supervised classification of microbiota mitigates mislabeling errors.

Knights D, Kuczynski J, Koren O, Ley RE, Field D, Knight R, DeSantis TZ, Kelley ST.

ISME J. 2011 Apr;5(4):570-3. doi: 10.1038/ismej.2010.148. Epub 2010 Oct 7. No abstract available.

41.

Comparative analysis of microbial diversity in Longitarsus flea beetles (Coleoptera: Chrysomelidae).

Kelley ST, Dobler S.

Genetica. 2011 May;139(5):541-50. doi: 10.1007/s10709-010-9498-0. Epub 2010 Sep 16.

PMID:
20844936
42.

Direct sequencing of the human microbiome readily reveals community differences.

Kuczynski J, Costello EK, Nemergut DR, Zaneveld J, Lauber CL, Knights D, Koren O, Fierer N, Kelley ST, Ley RE, Gordon JI, Knight R.

Genome Biol. 2010;11(5):210. doi: 10.1186/gb-2010-11-5-210. Epub 2010 May 5. Review.

43.

QIIME allows analysis of high-throughput community sequencing data.

Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña 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.

Nat Methods. 2010 May;7(5):335-6. doi: 10.1038/nmeth.f.303. Epub 2010 Apr 11. No abstract available.

44.

Simian varicella virus in pigtailed macaques (Macaca nemestrina): clinical, pathologic, and virologic features.

Hukkanen RR, Gillen M, Grant R, Liggitt HD, Kiem HP, Kelley ST.

Comp Med. 2009 Oct;59(5):482-7.

45.

Parallelization and optimization of genetic analyses in isolation by distance web service.

Turner JL, Kelley ST, Otto JS, Valafar F, Bohonak AJ.

BMC Genet. 2009 Jun 19;10:28. doi: 10.1186/1471-2156-10-28.

46.

Mate availability contributes to maintain the mixed-mating system in a scolytid beetle.

Gottlieb D, Holzman JP, Lubin Y, Bouskila A, Kelley ST, Harari AR.

J Evol Biol. 2009 Jul;22(7):1526-34. doi: 10.1111/j.1420-9101.2009.01763.x. Epub 2009 Jun 3.

47.

Inbreeding variability and population structure in the invasive haplodiploid palm-seed borer (Coccotrypes dactyliperda).

Holzman JP, Bohonak AJ, Kirkendall LR, Gottlieb D, Harari AR, Kelley ST.

J Evol Biol. 2009 May;22(5):1076-87. doi: 10.1111/j.1420-9101.2009.01722.x. Epub 2009 Mar 19.

48.

Correlations between neoadjuvant treatment, anemia, and perioperative complications in patients undergoing esophagectomy for cancer.

Melis M, McLoughlin JM, Dean EM, Siegel EM, Weber JM, Shah N, Kelley ST, Karl RC.

J Surg Res. 2009 May 1;153(1):114-20. doi: 10.1016/j.jss.2008.06.005. Epub 2008 Jul 31.

PMID:
19201421
50.

Minimally invasive surgery for esophageal cancer.

Santillan AA, Farma JM, Meredith KL, Shah NR, Kelley ST.

J Natl Compr Canc Netw. 2008 Oct;6(9):879-84. Review.

PMID:
18926097

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