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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.


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.


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

Fouquier J, Schwartz T, Kelley ST.

Indoor Air. 2015 Dec 30. doi: 10.1111/ina.12279. [Epub ahead of print]


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.


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.


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

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

Microbiologyopen. 2015 Jan 6. doi: 10.1002/mbo3.236. [Epub ahead of print]


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.

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