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Piphillin predicts metagenomic composition and dynamics from DADA2-corrected 16S rDNA sequences.

Narayan NR, Weinmaier T, Laserna-Mendieta EJ, Claesson MJ, Shanahan F, Dabbagh K, Iwai S, DeSantis TZ.

BMC Genomics. 2020 Jan 17;21(1):56. doi: 10.1186/s12864-019-6427-1.


Re-purposing 16S rRNA gene sequence data from within case paired tumor biopsy and tumor-adjacent biopsy or fecal samples to identify microbial markers for colorectal cancer.

Shah MS, DeSantis T, Yamal JM, Weir T, Ryan EP, Cope JL, Hollister EB.

PLoS One. 2018 Nov 9;13(11):e0207002. doi: 10.1371/journal.pone.0207002. eCollection 2018.


Maternal metabolic, immune, and microbial systems in late pregnancy vary with malnutrition in mice.

Connor KL, Chehoud C, Altrichter A, Chan L, DeSantis TZ, Lye SJ.

Biol Reprod. 2018 Apr 1;98(4):579-592. doi: 10.1093/biolre/ioy002.


Microbial markers in the diagnosis of colorectal cancer: the promise, reality and challenge.

DeSantis TZ, Shah MS, Cope JL, Hollister EB.

Future Microbiol. 2017 Nov;12:1341-1344. doi: 10.2217/fmb-2017-0185. Epub 2017 Oct 3. No abstract available.


Leveraging sequence-based faecal microbial community survey data to identify a composite biomarker for colorectal cancer.

Shah MS, DeSantis TZ, Weinmaier T, McMurdie PJ, Cope JL, Altrichter A, Yamal JM, Hollister EB.

Gut. 2018 May;67(5):882-891. doi: 10.1136/gutjnl-2016-313189. Epub 2017 Mar 24.


Piphillin: Improved Prediction of Metagenomic Content by Direct Inference from Human Microbiomes.

Iwai S, Weinmaier T, Schmidt BL, Albertson DG, Poloso NJ, Dabbagh K, DeSantis TZ.

PLoS One. 2016 Nov 7;11(11):e0166104. doi: 10.1371/journal.pone.0166104. eCollection 2016.


New perspectives on microbial community distortion after whole-genome amplification.

Probst AJ, Weinmaier T, DeSantis TZ, Santo Domingo JW, Ashbolt N.

PLoS One. 2015 May 26;10(5):e0124158. doi: 10.1371/journal.pone.0124158. eCollection 2015.


Gut microbiota in multiple sclerosis: possible influence of immunomodulators.

Cantarel BL, Waubant E, Chehoud C, Kuczynski J, DeSantis TZ, Warrington J, Venkatesan A, Fraser CM, Mowry EM.

J Investig Med. 2015 Jun;63(5):729-34. doi: 10.1097/JIM.0000000000000192.


The microbial community of the cystic fibrosis airway is disrupted in early life.

Renwick J, McNally P, John B, DeSantis T, Linnane B, Murphy P; SHIELD CF.

PLoS One. 2014 Dec 19;9(12):e109798. doi: 10.1371/journal.pone.0109798. eCollection 2014.


Comparing bacterial community composition of healthy and dark spot-affected Siderastrea siderea in Florida and the Caribbean.

Kellogg CA, Piceno YM, Tom LM, DeSantis TZ, Gray MA, Andersen GL.

PLoS One. 2014 Oct 7;9(10):e108767. doi: 10.1371/journal.pone.0108767. eCollection 2014.


An in vitro culture model to study the dynamics of colonic microbiota in Syrian golden hamsters and their susceptibility to infection with Clostridium difficile.

Miezeiewski M, Schnaufer T, Muravsky M, Wang S, Caro-Aguilar I, Secore S, Thiriot DS, Hsu C, Rogers I, DeSantis T, Kuczynski J, Probst AJ, Chehoud C, Steger R, Warrington J, Bodmer JL, Heinrichs JH.

ISME J. 2015 Feb;9(2):321-32. doi: 10.1038/ismej.2014.127. Epub 2014 Jul 18.


Coupling genetic and chemical microbiome profiling reveals heterogeneity of archaeome and bacteriome in subsurface biofilms that are dominated by the same archaeal species.

Probst AJ, Birarda G, Holman HY, DeSantis TZ, Wanner G, Andersen GL, Perras AK, Meck S, Völkel J, Bechtel HA, Wirth R, Moissl-Eichinger C.

PLoS One. 2014 Jun 27;9(6):e99801. doi: 10.1371/journal.pone.0099801. eCollection 2014.


Coral transcriptome and bacterial community profiles reveal distinct Yellow Band Disease states in Orbicella faveolata.

Closek CJ, Sunagawa S, DeSalvo MK, Piceno YM, DeSantis TZ, Brodie EL, Weber MX, Voolstra CR, Andersen GL, Medina M.

ISME J. 2014 Dec;8(12):2411-22. doi: 10.1038/ismej.2014.85. Epub 2014 Jun 20.


Expansion of urease- and uricase-containing, indole- and p-cresol-forming and contraction of short-chain fatty acid-producing intestinal microbiota in ESRD.

Wong J, Piceno YM, DeSantis TZ, Pahl M, Andersen GL, Vaziri ND.

Am J Nephrol. 2014;39(3):230-237. doi: 10.1159/000360010. Epub 2014 Mar 8.


Microbial biogeography across a full-scale wastewater treatment plant transect: evidence for immigration between coupled processes.

Wells GF, Wu CH, Piceno YM, Eggleston B, Brodie EL, Desantis TZ, Andersen GL, Hazen TC, Francis CA, Criddle CS.

Appl Microbiol Biotechnol. 2014 May;98(10):4723-36. doi: 10.1007/s00253-014-5564-3. Epub 2014 Feb 20.


Analysis of Gut Microbiome and Diet Modification in Patients with Crohn's Disease.

Walters SS, Quiros A, Rolston M, Grishina I, Li J, Fenton A, DeSantis TZ, Thai A, Andersen GL, Papathakis P, Nieves R, Prindiville T, Dandekar S.

SOJ Microbiol Infect Dis. 2014;2(3):1-13. doi: 10.15226/sojmid/2/3/00122. Epub 2014 Jun 27.


Comparing bacterial community composition between healthy and white plague-like disease states in Orbicella annularis using PhyloChip™ G3 microarrays.

Kellogg CA, Piceno YM, Tom LM, DeSantis TZ, Gray MA, Zawada DG, Andersen GL.

PLoS One. 2013 Nov 20;8(11):e79801. doi: 10.1371/journal.pone.0079801. eCollection 2013.


Diversity of bacterioplankton in contrasting Tibetan lakes revealed by high-density microarray and clone library analysis.

Zhang R, Wu Q, Piceno YM, Desantis TZ, Saunders FM, Andersen GL, Liu WT.

FEMS Microbiol Ecol. 2013 Nov;86(2):277-87. doi: 10.1111/1574-6941.12160. Epub 2013 Jul 10.


Truffle brûlés have an impact on the diversity of soil bacterial communities.

Mello A, Ding GC, Piceno YM, Napoli C, Tom LM, DeSantis TZ, Andersen GL, Smalla K, Bonfante P.

PLoS One. 2013 Apr 30;8(4):e61945. doi: 10.1371/journal.pone.0061945. Print 2013.


A microbiota signature associated with experimental food allergy promotes allergic sensitization and anaphylaxis.

Noval Rivas M, Burton OT, Wise P, Zhang YQ, Hobson SA, Garcia Lloret M, Chehoud C, Kuczynski J, DeSantis T, Warrington J, Hyde ER, Petrosino JF, Gerber GK, Bry L, Oettgen HC, Mazmanian SK, Chatila TA.

J Allergy Clin Immunol. 2013 Jan;131(1):201-12. doi: 10.1016/j.jaci.2012.10.026. Epub 2012 Nov 30.


Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm.

Probst AJ, Holman HY, DeSantis TZ, Andersen GL, Birarda G, Bechtel HA, Piceno YM, Sonnleitner M, Venkateswaran K, Moissl-Eichinger C.

ISME J. 2013 Mar;7(3):635-51. doi: 10.1038/ismej.2012.133. Epub 2012 Nov 22.


Changes in the microbial community structure of bacteria, archaea and fungi in response to elevated CO(2) and warming in an Australian native grassland soil.

Hayden HL, Mele PM, Bougoure DS, Allan CY, Norng S, Piceno YM, Brodie EL, Desantis TZ, Andersen GL, Williams AL, Hovenden MJ.

Environ Microbiol. 2012 Dec;14(12):3081-96. doi: 10.1111/j.1462-2920.2012.02855.x. Epub 2012 Oct 8.


Chronic kidney disease alters intestinal microbial flora.

Vaziri ND, Wong J, Pahl M, Piceno YM, Yuan J, DeSantis TZ, Ni Z, Nguyen TH, Andersen GL.

Kidney Int. 2013 Feb;83(2):308-15. doi: 10.1038/ki.2012.345. Epub 2012 Sep 19.


The "most wanted" taxa from the human microbiome for whole genome sequencing.

Fodor AA, DeSantis TZ, Wylie KM, Badger JH, Ye Y, Hepburn T, Hu P, Sodergren E, Liolios K, Huot-Creasy H, Birren BW, Earl AM.

PLoS One. 2012;7(7):e41294. doi: 10.1371/journal.pone.0041294. Epub 2012 Jul 26.


Influence of geogenic factors on microbial communities in metallogenic Australian soils.

Reith F, Brugger J, Zammit CM, Gregg AL, Goldfarb KC, Andersen GL, DeSantis TZ, Piceno YM, Brodie EL, Lu Z, He Z, Zhou J, Wakelin SA.

ISME J. 2012 Nov;6(11):2107-18. doi: 10.1038/ismej.2012.48. Epub 2012 Jun 7.


The response of marine picoplankton to ocean acidification.

Newbold LK, Oliver AE, Booth T, Tiwari B, Desantis T, Maguire M, Andersen G, van der Gast CJ, Whiteley AS.

Environ Microbiol. 2012 Sep;14(9):2293-307. doi: 10.1111/j.1462-2920.2012.02762.x. Epub 2012 May 16.


Bacterial communities in commercial aircraft high-efficiency particulate air (HEPA) filters assessed by PhyloChip analysis.

Korves TM, Piceno YM, Tom LM, Desantis TZ, Jones BW, Andersen GL, Hwang GM.

Indoor Air. 2013 Feb;23(1):50-61. doi: 10.1111/j.1600-0668.2012.00787.x. Epub 2012 Jun 8.


High-density PhyloChip profiling of stimulated aquifer microbial communities reveals a complex response to acetate amendment.

Handley KM, Wrighton KC, Piceno YM, Andersen GL, DeSantis TZ, Williams KH, Wilkins MJ, N'Guessan AL, Peacock A, Bargar J, Long PE, Banfield JF.

FEMS Microbiol Ecol. 2012 Jul;81(1):188-204. doi: 10.1111/j.1574-6941.2012.01363.x. Epub 2012 Apr 13.


An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea.

McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P.

ISME J. 2012 Mar;6(3):610-8. doi: 10.1038/ismej.2011.139. Epub 2011 Dec 1.


Bacterial communities associated with a mineral weathering profile at a sulphidic mine tailings dump in arid Western Australia.

Wakelin SA, Anand RR, Reith F, Gregg AL, Noble RR, Goldfarb KC, Andersen GL, DeSantis TZ, Piceno YM, Brodie EL.

FEMS Microbiol Ecol. 2012 Feb;79(2):298-311. doi: 10.1111/j.1574-6941.2011.01215.x. Epub 2011 Oct 24.


PhyloChip™ microarray comparison of sampling methods used for coral microbial ecology.

Kellogg CA, Piceno YM, Tom LM, DeSantis TZ, Zawada DG, Andersen GL.

J Microbiol Methods. 2012 Jan;88(1):103-9. doi: 10.1016/j.mimet.2011.10.019. Epub 2011 Nov 4.


The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide.

He Z, Piceno Y, Deng Y, Xu M, Lu Z, Desantis T, Andersen G, Hobbie SE, Reich PB, Zhou J.

ISME J. 2012 Feb;6(2):259-72. doi: 10.1038/ismej.2011.99. Epub 2011 Jul 28.


PCR amplification-independent methods for detection of microbial communities by the high-density microarray PhyloChip.

DeAngelis KM, Wu CH, Beller HR, Brodie EL, Chakraborty R, DeSantis TZ, Fortney JL, Hazen TC, Osman SR, Singer ME, Tom LM, Andersen GL.

Appl Environ Microbiol. 2011 Sep;77(18):6313-22. doi: 10.1128/AEM.05262-11. Epub 2011 Jul 15.


Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys.

Werner JJ, Koren O, Hugenholtz P, DeSantis TZ, Walters WA, Caporaso JG, Angenent LT, Knight R, Ley RE.

ISME J. 2012 Jan;6(1):94-103. doi: 10.1038/ismej.2011.82. Epub 2011 Jun 30.


Bacterial diversity of terrestrial crystalline volcanic rocks, Iceland.

Kelly LC, Cockell CS, Herrera-Belaroussi A, Piceno Y, Andersen G, DeSantis T, Brodie E, Thorsteinsson T, Marteinsson V, Poly F, LeRoux X.

Microb Ecol. 2011 Jul;62(1):69-79. doi: 10.1007/s00248-011-9864-1. Epub 2011 May 17.


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.


Deciphering the rhizosphere microbiome for disease-suppressive bacteria.

Mendes R, Kruijt M, de Bruijn I, Dekkers E, van der Voort M, Schneider JH, Piceno YM, DeSantis TZ, Andersen GL, Bakker PA, Raaijmakers JM.

Science. 2011 May 27;332(6033):1097-100. doi: 10.1126/science.1203980. Epub 2011 May 5.


Simrank: Rapid and sensitive general-purpose k-mer search tool.

DeSantis TZ, Keller K, Karaoz U, Alekseyenko AV, Singh NN, Brodie EL, Pei Z, Andersen GL, Larsen N.

BMC Ecol. 2011 Apr 27;11:11. doi: 10.1186/1472-6785-11-11.


Bacterial community analysis of beef cattle feedlots reveals that pen surface is distinct from feces.

Durso LM, Harhay GP, Smith TP, Bono JL, DeSantis TZ, Clawson ML.

Foodborne Pathog Dis. 2011 May;8(5):647-9. doi: 10.1089/fpd.2010.0774. Epub 2011 Jan 9.


Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons.

Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methé B, DeSantis TZ; Human Microbiome Consortium, Petrosino JF, Knight R, Birren BW.

Genome Res. 2011 Mar;21(3):494-504. doi: 10.1101/gr.112730.110. Epub 2011 Jan 6.


Airway microbiota and bronchial hyperresponsiveness in patients with suboptimally controlled asthma.

Huang YJ, Nelson CE, Brodie EL, Desantis TZ, Baek MS, Liu J, Woyke T, Allgaier M, Bristow J, Wiener-Kronish JP, Sutherland ER, King TS, Icitovic N, Martin RJ, Calhoun WJ, Castro M, Denlinger LC, Dimango E, Kraft M, Peters SP, Wasserman SI, Wechsler ME, Boushey HA, Lynch SV; National Heart, Lung, and Blood Institute's Asthma Clinical Research Network.

J Allergy Clin Immunol. 2011 Feb;127(2):372-381.e1-3. doi: 10.1016/j.jaci.2010.10.048. Epub 2010 Dec 30.


PhyloChip microarray analysis reveals altered gastrointestinal microbial communities in a rat model of colonic hypersensitivity.

Nelson TA, Holmes S, Alekseyenko AV, Shenoy M, Desantis T, Wu CH, Andersen GL, Winston J, Sonnenburg J, Pasricha PJ, Spormann A.

Neurogastroenterol Motil. 2011 Feb;23(2):169-77, e41-2. doi: 10.1111/j.1365-2982.2010.01637.x. Epub 2010 Dec 3.


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.


Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome.

Nossa CW, Oberdorf WE, Yang L, Aas JA, Paster BJ, Desantis TZ, Brodie EL, Malamud D, Poles MA, Pei Z.

World J Gastroenterol. 2010 Sep 7;16(33):4135-44.


Deep-sea oil plume enriches indigenous oil-degrading bacteria.

Hazen TC, Dubinsky EA, DeSantis TZ, Andersen GL, Piceno YM, Singh N, Jansson JK, Probst A, Borglin SE, Fortney JL, Stringfellow WT, Bill M, Conrad ME, Tom LM, Chavarria KL, Alusi TR, Lamendella R, Joyner DC, Spier C, Baelum J, Auer M, Zemla ML, Chakraborty R, Sonnenthal EL, D'haeseleer P, Holman HY, Osman S, Lu Z, Van Nostrand JD, Deng Y, Zhou J, Mason OU.

Science. 2010 Oct 8;330(6001):204-8. doi: 10.1126/science.1195979. Epub 2010 Aug 24.


Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators.

Wu CH, Sercu B, Van de Werfhorst LC, Wong J, DeSantis TZ, Brodie EL, Hazen TC, Holden PA, Andersen GL.

PLoS One. 2010 Jun 23;5(6):e11285. doi: 10.1371/journal.pone.0011285.


Integrated microbial survey analysis of prokaryotic communities for the PhyloChip microarray.

Schatz MC, Phillippy AM, Gajer P, DeSantis TZ, Andersen GL, Ravel J.

Appl Environ Microbiol. 2010 Aug;76(16):5636-8. doi: 10.1128/AEM.00303-10. Epub 2010 Jun 25.


Animal-to-animal variation in fecal microbial diversity among beef cattle.

Durso LM, Harhay GP, Smith TP, Bono JL, Desantis TZ, Harhay DM, Andersen GL, Keen JE, Laegreid WW, Clawson ML.

Appl Environ Microbiol. 2010 Jul;76(14):4858-62. doi: 10.1128/AEM.00207-10. Epub 2010 May 14.


Diversity of 16S rRNA genes within individual prokaryotic genomes.

Pei AY, Oberdorf WE, Nossa CW, Agarwal A, Chokshi P, Gerz EA, Jin Z, Lee P, Yang L, Poles M, Brown SM, Sotero S, Desantis T, Brodie E, Nelson K, Pei Z.

Appl Environ Microbiol. 2010 Jun;76(12):3886-97. doi: 10.1128/AEM.02953-09. Epub 2010 Apr 23. Erratum in: Appl Environ Microbiol. 2010 Aug;76(15):5333.


Microbial secondary succession in a chronosequence of chalk grasslands.

Kuramae EE, Gamper HA, Yergeau E, Piceno YM, Brodie EL, Desantis TZ, Andersen GL, van Veen JA, Kowalchuk GA.

ISME J. 2010 May;4(5):711-5. doi: 10.1038/ismej.2010.11. Epub 2010 Feb 18.


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