Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 60

1.

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

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-Rodríguez 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 2nd, 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, Vázquez-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.

Nat Biotechnol. 2019 Aug 9. doi: 10.1038/s41587-019-0252-6. [Epub ahead of print]

PMID:
31399723
2.

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

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-Rodríguez 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 2nd, 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, Vázquez-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.

Nat Biotechnol. 2019 Aug;37(8):852-857. doi: 10.1038/s41587-019-0209-9. No abstract available. Erratum in: Nat Biotechnol. 2019 Aug 9;:.

PMID:
31341288
3.

Ground beef microbiome changes with antimicrobial decontamination interventions and product storage.

Weinroth MD, Britton BC, McCullough KR, Martin JN, Geornaras I, Knight R, Belk KE, Metcalf JL.

PLoS One. 2019 Jun 5;14(6):e0217947. doi: 10.1371/journal.pone.0217947. eCollection 2019.

4.

Is there convergence of gut microbes in blood-feeding vertebrates?

Song SJ, Sanders JG, Baldassarre DT, Chaves JA, Johnson NS, Piaggio AJ, Stuckey MJ, Nováková E, Metcalf JL, Chomel BB, Aguilar-Setién A, Knight R, McKenzie VJ.

Philos Trans R Soc Lond B Biol Sci. 2019 Jul 22;374(1777):20180249. doi: 10.1098/rstb.2018.0249. Epub 2019 Jun 3.

PMID:
31154984
5.

Equine Fecal Microbiota Changes Associated With Anthelmintic Administration.

Kunz IGZ, Reed KJ, Metcalf JL, Hassel DM, Coleman RJ, Hess TM, Coleman SJ.

J Equine Vet Sci. 2019 Jun;77:98-106. doi: 10.1016/j.jevs.2019.01.018. Epub 2019 Feb 13.

PMID:
31133326
6.

Request a woman scientist: A database for diversifying the public face of science.

McCullagh EA, Nowak K, Pogoriler A, Metcalf JL, Zaringhalam M, Zelikova TJ.

PLoS Biol. 2019 Apr 23;17(4):e3000212. doi: 10.1371/journal.pbio.3000212. eCollection 2019 Apr.

7.

Effects of a Saccharomyces cerevisiae fermentation product on liver abscesses, fecal microbiome, and resistome in feedlot cattle raised without antibiotics.

Huebner KL, Martin JN, Weissend CJ, Holzer KL, Parker JK, Lakin SM, Doster E, Weinroth MD, Abdo Z, Woerner DR, Metcalf JL, Geornaras I, Bryant TC, Morley PS, Belk KE.

Sci Rep. 2019 Feb 22;9(1):2559. doi: 10.1038/s41598-019-39181-7.

8.

Pre- and post-operative antibiotics in conjunction with cytoreductive surgery and heated intraperitoneal chemotherapy (HIPEC) should be considered for pseudomyxoma peritonei (PMP) treatment.

Merrell DS, McAvoy TJ, King MC, Sittig M, Millar EV, Nieroda C, Metcalf JL, Blum FC, Testerman TL, Sardi A.

Eur J Surg Oncol. 2019 Sep;45(9):1723-1726. doi: 10.1016/j.ejso.2019.01.223. Epub 2019 Jan 30.

PMID:
30770164
9.

Estimating the postmortem interval using microbes: Knowledge gaps and a path to technology adoption.

Metcalf JL.

Forensic Sci Int Genet. 2019 Jan;38:211-218. doi: 10.1016/j.fsigen.2018.11.004. Epub 2018 Nov 8. Review.

10.

Trace Evidence Potential in Postmortem Skin Microbiomes: From Death Scene to Morgue.

Kodama WA, Xu Z, Metcalf JL, Song SJ, Harrison N, Knight R, Carter DO, Happy CB.

J Forensic Sci. 2019 May;64(3):791-798. doi: 10.1111/1556-4029.13949. Epub 2018 Nov 8.

PMID:
30408195
11.

Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes.

Amato KR, G Sanders J, Song SJ, Nute M, Metcalf JL, Thompson LR, Morton JT, Amir A, J McKenzie V, Humphrey G, Gogul G, Gaffney J, L Baden A, A O Britton G, P Cuozzo F, Di Fiore A, J Dominy N, L Goldberg T, Gomez A, Kowalewski MM, J Lewis R, Link A, L Sauther M, Tecot S, A White B, E Nelson K, M Stumpf R, Knight R, R Leigh S.

ISME J. 2019 Mar;13(3):576-587. doi: 10.1038/s41396-018-0175-0. Epub 2018 Jul 11.

PMID:
29995839
12.

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.

13.

Microbiome Data Accurately Predicts the Postmortem Interval Using Random Forest Regression Models.

Belk A, Xu ZZ, Carter DO, Lynne A, Bucheli S, Knight R, Metcalf JL.

Genes (Basel). 2018 Feb 16;9(2). pii: E104. doi: 10.3390/genes9020104.

14.

Coprolites reveal ecological interactions lost with the extinction of New Zealand birds.

Boast AP, Weyrich LS, Wood JR, Metcalf JL, Knight R, Cooper A.

Proc Natl Acad Sci U S A. 2018 Feb 13;115(7):1546-1551. doi: 10.1073/pnas.1712337115.

15.

Correction for Morton et al., "Uncovering the Horseshoe Effect in Microbial Analyses".

Morton JT, Toran L, Edlund A, Metcalf JL, Lauber C, Knight R.

mSystems. 2018 Feb 6;3(1). pii: e00006-18. doi: 10.1128/mSystems.00006-18. eCollection 2018 Jan-Feb.

16.

Evaluating the impact of domestication and captivity on the horse gut microbiome.

Metcalf JL, Song SJ, Morton JT, Weiss S, Seguin-Orlando A, Joly F, Feh C, Taberlet P, Coissac E, Amir A, Willerslev E, Knight R, McKenzie V, Orlando L.

Sci Rep. 2017 Nov 14;7(1):15497. doi: 10.1038/s41598-017-15375-9.

17.

Rapid Communication: 16S ribosomal ribonucleic acid characterization of liver abscesses in feedlot cattle from three states in the United States.

Weinroth MD, Carlson CR, Martin JN, Metcalf JL, Morley PS, Belk KE.

J Anim Sci. 2017 Oct;95(10):4520-4525. doi: 10.2527/jas2017.1743.

PMID:
29108068
18.

The Effects of Captivity on the Mammalian Gut Microbiome.

McKenzie VJ, Song SJ, Delsuc F, Prest TL, Oliverio AM, Korpita TM, Alexiev A, Amato KR, Metcalf JL, Kowalewski M, Avenant NL, Link A, Di Fiore A, Seguin-Orlando A, Feh C, Orlando L, Mendelson JR, Sanders J, Knight R.

Integr Comp Biol. 2017 Oct 1;57(4):690-704. doi: 10.1093/icb/icx090.

19.

Microbiome Tools for Forensic Science.

Metcalf JL, Xu ZZ, Bouslimani A, Dorrestein P, Carter DO, Knight R.

Trends Biotechnol. 2017 Sep;35(9):814-823. doi: 10.1016/j.tibtech.2017.03.006. Epub 2017 Mar 30. Review.

PMID:
28366290
20.

Uncovering the Horseshoe Effect in Microbial Analyses.

Morton JT, Toran L, Edlund A, Metcalf JL, Lauber C, Knight R.

mSystems. 2017 Feb 21;2(1). pii: e00166-16. doi: 10.1128/mSystems.00166-16. eCollection 2017 Jan-Feb. Erratum in: mSystems. 2018 Feb 6;3(1):.

21.

Balance Trees Reveal Microbial Niche Differentiation.

Morton JT, Sanders J, Quinn RA, McDonald D, Gonzalez A, Vázquez-Baeza Y, Navas-Molina JA, Song SJ, Metcalf JL, Hyde ER, Lladser M, Dorrestein PC, Knight R.

mSystems. 2017 Jan 17;2(1). pii: e00162-16. doi: 10.1128/mSystems.00162-16. eCollection 2017 Jan-Feb.

22.

Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies.

Song SJ, Amir A, Metcalf JL, Amato KR, Xu ZZ, Humphrey G, Knight R.

mSystems. 2016 May 3;1(3). pii: e00021-16. eCollection 2016 May-Jun.

23.

Microbiology of death.

Metcalf JL, Carter DO, Knight R.

Curr Biol. 2016 Jul 11;26(13):R561-R563. doi: 10.1016/j.cub.2016.03.042.

24.

Synergistic roles of climate warming and human occupation in Patagonian megafaunal extinctions during the Last Deglaciation.

Metcalf JL, Turney C, Barnett R, Martin F, Bray SC, Vilstrup JT, Orlando L, Salas-Gismondi R, Loponte D, Medina M, De Nigris M, Civalero T, Fernández PM, Gasco A, Duran V, Seymour KL, Otaola C, Gil A, Paunero R, Prevosti FJ, Bradshaw CJ, Wheeler JC, Borrero L, Austin JJ, Cooper A.

Sci Adv. 2016 Jun 17;2(6):e1501682. doi: 10.1126/sciadv.1501682. eCollection 2016 Jun.

25.

Microbial community assembly and metabolic function during mammalian corpse decomposition.

Metcalf JL, Xu ZZ, Weiss S, Lax S, Van Treuren W, Hyde ER, Song SJ, Amir A, Larsen P, Sangwan N, Haarmann D, Humphrey GC, Ackermann G, Thompson LR, Lauber C, Bibat A, Nicholas C, Gebert MJ, Petrosino JF, Reed SC, Gilbert JA, Lynne AM, Bucheli SR, Carter DO, Knight R.

Science. 2016 Jan 8;351(6269):158-62. doi: 10.1126/science.aad2646. Epub 2015 Dec 10.

26.

Carcass mass has little influence on the structure of gravesoil microbial communities.

Weiss S, Carter DO, Metcalf JL, Knight R.

Int J Legal Med. 2016 Jan;130(1):253-63. doi: 10.1007/s00414-015-1206-2. Epub 2015 May 30.

PMID:
26024793
27.

Seasonal variation of postmortem microbial communities.

Carter DO, Metcalf JL, Bibat A, Knight R.

Forensic Sci Med Pathol. 2015 Jun;11(2):202-7. doi: 10.1007/s12024-015-9667-7. Epub 2015 Mar 4.

PMID:
25737335
28.

Tracking down the sources of experimental contamination in microbiome studies.

Weiss S, Amir A, Hyde ER, Metcalf JL, Song SJ, Knight R.

Genome Biol. 2014 Dec 17;15(12):564. doi: 10.1186/s13059-014-0564-2.

29.

Late pleistocene Australian marsupial DNA clarifies the affinities of extinct megafaunal kangaroos and wallabies.

Llamas B, Brotherton P, Mitchell KJ, Templeton JE, Thomson VA, Metcalf JL, Armstrong KN, Kasper M, Richards SM, Camens AB, Lee MS, Cooper A.

Mol Biol Evol. 2015 Mar;32(3):574-84. doi: 10.1093/molbev/msu338. Epub 2014 Dec 18.

PMID:
25526902
30.

Young children's causal explanations are biased by post-action associative information.

Atance CM, Metcalf JL, Martin-Ordas G, Walker CL.

Dev Psychol. 2014 Dec;50(12):2675-85. doi: 10.1037/a0038186. Epub 2014 Nov 3.

PMID:
25365120
31.

Longitudinal analysis of microbial interaction between humans and the indoor environment.

Lax S, Smith DP, Hampton-Marcell J, Owens SM, Handley KM, Scott NM, Gibbons SM, Larsen P, Shogan BD, Weiss S, Metcalf JL, Ursell LK, Vázquez-Baeza Y, Van Treuren W, Hasan NA, Gibson MK, Colwell R, Dantas G, Knight R, Gilbert JA.

Science. 2014 Aug 29;345(6200):1048-52. doi: 10.1126/science.1254529.

32.

Vertebrate decomposition is accelerated by soil microbes.

Lauber CL, Metcalf JL, Keepers K, Ackermann G, Carter DO, Knight R.

Appl Environ Microbiol. 2014 Aug;80(16):4920-9. doi: 10.1128/AEM.00957-14. Epub 2014 Jun 6.

33.

Ancient human oral plaque preserves a wealth of biological data.

Metcalf JL, Ursell LK, Knight R.

Nat Genet. 2014 Apr;46(4):321-3. doi: 10.1038/ng.2930.

PMID:
24675519
34.

Integrating multiple lines of evidence into historical biogeography hypothesis testing: a Bison bison case study.

Metcalf JL, Prost S, Nogués-Bravo D, DeChaine EG, Anderson C, Batra P, Araújo MB, Cooper A, Guralnick RP.

Proc Biol Sci. 2014 Jan 8;281(1777):20132782. doi: 10.1098/rspb.2013.2782. Print 2014 Feb 22.

35.

A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system.

Metcalf JL, Wegener Parfrey L, Gonzalez A, Lauber CL, Knights D, Ackermann G, Humphrey GC, Gebert MJ, Van Treuren W, Berg-Lyons D, Keepers K, Guo Y, Bullard J, Fierer N, Carter DO, Knight R.

Elife. 2013 Oct 15;2:e01104. doi: 10.7554/eLife.01104.

36.

Convergence of gut microbiomes in myrmecophagous mammals.

Delsuc F, Metcalf JL, Wegener Parfrey L, Song SJ, González A, Knight R.

Mol Ecol. 2014 Mar;23(6):1301-17. doi: 10.1111/mec.12501. Epub 2013 Oct 7.

37.

Replenishing our defensive microbes.

Ursell LK, Van Treuren W, Metcalf JL, Pirrung M, Gewirtz A, Knight R.

Bioessays. 2013 Sep;35(9):810-7. doi: 10.1002/bies.201300018. Epub 2013 Jul 8. Review.

38.

K63-ubiquitylation of VHL by SOCS1 mediates DNA double-strand break repair.

Metcalf JL, Bradshaw PS, Komosa M, Greer SN, Stephen Meyn M, Ohh M.

Oncogene. 2014 Feb 20;33(8):1055-65. doi: 10.1038/onc.2013.22. Epub 2013 Mar 4.

PMID:
23455319
39.

Animals in a bacterial world, a new imperative for the life sciences.

McFall-Ngai M, Hadfield MG, Bosch TC, Carey HV, Domazet-Lošo T, Douglas AE, Dubilier N, Eberl G, Fukami T, Gilbert SF, Hentschel U, King N, Kjelleberg S, Knoll AH, Kremer N, Mazmanian SK, Metcalf JL, Nealson K, Pierce NE, Rawls JF, Reid A, Ruby EG, Rumpho M, Sanders JG, Tautz D, Wernegreen JJ.

Proc Natl Acad Sci U S A. 2013 Feb 26;110(9):3229-36. doi: 10.1073/pnas.1218525110. Epub 2013 Feb 7. Review.

40.

Historical stocking data and 19th century DNA reveal human-induced changes to native diversity and distribution of cutthroat trout.

Metcalf JL, Love Stowell S, Kennedy CM, Rogers KB, McDonald D, Epp J, Keepers K, Cooper A, Austin JJ, Martin AP.

Mol Ecol. 2012 Nov;21(21):5194-207. doi: 10.1111/mec.12028. Epub 2012 Sep 24.

PMID:
22998121
41.

Defining the human microbiome.

Ursell LK, Metcalf JL, Parfrey LW, Knight R.

Nutr Rev. 2012 Aug;70 Suppl 1:S38-44. doi: 10.1111/j.1753-4887.2012.00493.x. Review.

42.

Functional importance of Dicer protein in the adaptive cellular response to hypoxia.

Ho JJ, Metcalf JL, Yan MS, Turgeon PJ, Wang JJ, Chalsev M, Petruzziello-Pellegrini TN, Tsui AK, He JZ, Dhamko H, Man HS, Robb GB, Teh BT, Ohh M, Marsden PA.

J Biol Chem. 2012 Aug 17;287(34):29003-20. doi: 10.1074/jbc.M112.373365. Epub 2012 Jun 28.

43.

The updated biology of hypoxia-inducible factor.

Greer SN, Metcalf JL, Wang Y, Ohh M.

EMBO J. 2012 May 30;31(11):2448-60. doi: 10.1038/emboj.2012.125. Epub 2012 May 4. Review.

44.

Characterizing microbial communities through space and time.

Gonzalez A, King A, Robeson MS 2nd, Song S, Shade A, Metcalf JL, Knight R.

Curr Opin Biotechnol. 2012 Jun;23(3):431-6. doi: 10.1016/j.copbio.2011.11.017. Epub 2011 Dec 7. Review.

45.

Our microbial selves: what ecology can teach us.

Gonzalez A, Clemente JC, Shade A, Metcalf JL, Song S, Prithiviraj B, Palmer BE, Knight R.

EMBO Rep. 2011 Jul 1;12(8):775-84. doi: 10.1038/embor.2011.137. Review.

46.

Revising the recent evolutionary history of equids using ancient DNA.

Orlando L, Metcalf JL, Alberdi MT, Telles-Antunes M, Bonjean D, Otte M, Martin F, Eisenmann V, Mashkour M, Morello F, Prado JL, Salas-Gismondi R, Shockey BJ, Wrinn PJ, Vasil'ev SK, Ovodov ND, Cherry MI, Hopwood B, Male D, Austin JJ, Hänni C, Cooper A.

Proc Natl Acad Sci U S A. 2009 Dec 22;106(51):21754-9. doi: 10.1073/pnas.0903672106. Epub 2009 Dec 9.

47.

Regulation of endocytosis via the oxygen-sensing pathway.

Wang Y, Roche O, Yan MS, Finak G, Evans AJ, Metcalf JL, Hast BE, Hanna SC, Wondergem B, Furge KA, Irwin MS, Kim WY, Teh BT, Grinstein S, Park M, Marsden PA, Ohh M.

Nat Med. 2009 Mar;15(3):319-24. doi: 10.1038/nm.1922. Epub 2009 Mar 1.

PMID:
19252501
48.

Regioselective nitration of N(alpha),N(1)-bis(trifluoroacetyl)-L-tryptophan methyl ester: efficient synthesis of 2-nitro and 6-nitro-N-trifluoroacetyl-L-tryptophan methyl ester.

Osborne AS, Som P, Metcalf JL, Phillips RS.

Bioorg Med Chem Lett. 2008 Nov 1;18(21):5750-2. doi: 10.1016/j.bmcl.2008.09.086. Epub 2008 Sep 26.

49.

Somatic pairing of chromosome 19 in renal oncocytoma is associated with deregulated EGLN2-mediated [corrected] oxygen-sensing response.

Koeman JM, Russell RC, Tan MH, Petillo D, Westphal M, Koelzer K, Metcalf JL, Zhang Z, Matsuda D, Dykema KJ, Houseman HL, Kort EJ, Furge LL, Kahnoski RJ, Richard S, Vieillefond A, Swiatek PJ, Teh BT, Ohh M, Furge KA.

PLoS Genet. 2008 Sep 5;4(9):e1000176. doi: 10.1371/journal.pgen.1000176. Erratum in: PLoS Genet. 2008 Jul;4(7). doi: 10.1371/annotation/7f57058f-cc02-45a6-bfab-a835619e3916.

50.

Hybridization dynamics between Colorado's native cutthroat trout and introduced rainbow trout.

Metcalf JL, Siegle MR, Martin AP.

J Hered. 2008 Mar-Apr;99(2):149-56. doi: 10.1093/jhered/esm118. Epub 2008 Jan 30.

PMID:
18238784

Supplemental Content

Loading ...
Support Center