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Items: 1 to 50 of 321

1.

Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome.

Taylor BC, Lejzerowicz F, Poirel M, Shaffer JP, Jiang L, Aksenov A, Litwin N, Humphrey G, Martino C, Miller-Montgomery S, Dorrestein PC, Veiga P, Song SJ, McDonald D, Derrien M, Knight R.

mSystems. 2020 Mar 17;5(2). pii: e00901-19. doi: 10.1128/mSystems.00901-19.

2.

Global chemical effects of the microbiome include new bile-acid conjugations.

Quinn RA, Melnik AV, Vrbanac A, Fu T, Patras KA, Christy MP, Bodai Z, Belda-Ferre P, Tripathi A, Chung LK, Downes M, Welch RD, Quinn M, Humphrey G, Panitchpakdi M, Weldon KC, Aksenov A, da Silva R, Avila-Pacheco J, Clish C, Bae S, Mallick H, Franzosa EA, Lloyd-Price J, Bussell R, Thron T, Nelson AT, Wang M, Leszczynski E, Vargas F, Gauglitz JM, Meehan MJ, Gentry E, Arthur TD, Komor AC, Poulsen O, Boland BS, Chang JT, Sandborn WJ, Lim M, Garg N, Lumeng JC, Xavier RJ, Kazmierczak BI, Jain R, Egan M, Rhee KE, Ferguson D, Raffatellu M, Vlamakis H, Haddad GG, Siegel D, Huttenhower C, Mazmanian SK, Evans RM, Nizet V, Knight R, Dorrestein PC.

Nature. 2020 Mar;579(7797):123-129. doi: 10.1038/s41586-020-2047-9. Epub 2020 Feb 26.

PMID:
32103176
3.

The effect of legume supplementation on the gut microbiota in rural Malawian infants aged 6 to 12 months.

Ordiz MI, Janssen S, Humphrey G, Ackermann G, Stephenson K, Agapova S, Divala O, Kaimila Y, Maleta K, Zhong C, Knight R, Trehan I, Tarr PI, Rusconi B, Manary MJ.

Am J Clin Nutr. 2020 Feb 11. pii: nqaa011. doi: 10.1093/ajcn/nqaa011. [Epub ahead of print]

PMID:
32047925
4.

Manaaki - a cognitive behavioral therapy mobile health app to support people experiencing gambling problems: a randomized control trial protocol.

Humphrey G, Chu J, Dowling N, Rodda S, Merkouris S, Parag V, Newcombe D, Ho E, Nosa V, Ruwhui-Collins R, Whittaker R, Bullen C.

BMC Public Health. 2020 Feb 6;20(1):191. doi: 10.1186/s12889-020-8304-x.

5.

Comparative Analyses of Vertebrate Gut Microbiomes Reveal Convergence between Birds and Bats.

Song SJ, Sanders JG, Delsuc F, Metcalf J, Amato K, Taylor MW, Mazel F, Lutz HL, Winker K, Graves GR, Humphrey G, Gilbert JA, Hackett SJ, White KP, Skeen HR, Kurtis SM, Withrow J, Braile T, Miller M, McCracken KG, Maley JM, Ezenwa VO, Williams A, Blanton JM, McKenzie VJ, Knight R.

mBio. 2020 Jan 7;11(1). pii: e02901-19. doi: 10.1128/mBio.02901-19.

6.

A Web-Based Alcohol Risk Communication Tool: Development and Pretesting Study.

Kool B, Dobson R, Sharpe S, Humphrey G, Whittaker R, Ameratunga S.

JMIR Form Res. 2020 Jan 2;4(1):e13224. doi: 10.2196/13224.

7.

Understanding End-User Perspectives of Mobile Pulmonary Rehabilitation (mPR): Cross-Sectional Survey and Interviews.

Dobson R, Herbst P, Candy S, Brott T, Garrett J, Humphrey G, Reeve J, Tawhai M, Taylor D, Warren J, Whittaker R.

JMIR Form Res. 2019 Dec 20;3(4):e15466. doi: 10.2196/15466.

8.

Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads.

Sanders JG, Nurk S, Salido RA, Minich J, Xu ZZ, Zhu Q, Martino C, Fedarko M, Arthur TD, Chen F, Boland BS, Humphrey GC, Brennan C, Sanders K, Gaffney J, Jepsen K, Khosroheidari M, Green C, Liyanage M, Dang JW, Phelan VV, Quinn RA, Bankevich A, Chang JT, Rana TM, Conrad DJ, Sandborn WJ, Smarr L, Dorrestein PC, Pevzner PA, Knight R.

Genome Biol. 2019 Oct 31;20(1):226. doi: 10.1186/s13059-019-1834-9.

9.

Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis.

Melnik AV, Vázquez-Baeza Y, Aksenov AA, Hyde E, McAvoy AC, Wang M, da Silva RR, Protsyuk I, Wu JV, Bouslimani A, Lim YW, Luzzatto-Knaan T, Comstock W, Quinn RA, Wong R, Humphrey G, Ackermann G, Spivey T, Brouha SS, Bandeira N, Lin GY, Rohwer F, Conrad DJ, Alexandrov T, Knight R, Dorrestein PC, Garg N.

mSystems. 2019 Sep 24;4(5). pii: e00375-19. doi: 10.1128/mSystems.00375-19.

10.

Quantifying and Understanding Well-to-Well Contamination in Microbiome Research.

Minich JJ, Sanders JG, Amir A, Humphrey G, Gilbert JA, Knight R.

mSystems. 2019 Jun 25;4(4). pii: e00186-19. doi: 10.1128/mSystems.00186-19.

11.

The Emergence of Universal Chromatographic Methods in the Research and Development of New Drug Substances.

Regalado EL, Haidar Ahmad IA, Bennett R, D'Atri V, Makarov AA, Humphrey GR, Mangion I, Guillarme D.

Acc Chem Res. 2019 Jul 16;52(7):1990-2002. doi: 10.1021/acs.accounts.9b00068. Epub 2019 Jun 14.

PMID:
31198042
12.

The impact of skin care products on skin chemistry and microbiome dynamics.

Bouslimani A, da Silva R, Kosciolek T, Janssen S, Callewaert C, Amir A, Dorrestein K, Melnik AV, Zaramela LS, Kim JN, Humphrey G, Schwartz T, Sanders K, Brennan C, Luzzatto-Knaan T, Ackermann G, McDonald D, Zengler K, Knight R, Dorrestein PC.

BMC Biol. 2019 Jun 12;17(1):47. doi: 10.1186/s12915-019-0660-6.

13.

Triplicate PCR reactions for 16S rRNA gene amplicon sequencing are unnecessary.

Marotz C, Sharma A, Humphrey G, Gottel N, Daum C, Gilbert JA, Eloe-Fadrosh E, Knight R.

Biotechniques. 2019 Jul;67(1):29-32. doi: 10.2144/btn-2018-0192. Epub 2019 May 24.

14.

Scalable Synthesis of Diazeniumdiolates: Application to the Preparation of MK-8150.

Zhong YL, Weisel M, Humphrey GR, Muzzio DJ, Zhang L, Huffman MA, Zhong W, Maloney KM, Campos KR.

Org Lett. 2019 Jun 7;21(11):4210-4214. doi: 10.1021/acs.orglett.9b01401. Epub 2019 May 22.

PMID:
31117712
15.

Detection of smoking status from retinal images; a Convolutional Neural Network study.

Vaghefi E, Yang S, Hill S, Humphrey G, Walker N, Squirrell D.

Sci Rep. 2019 May 9;9(1):7180. doi: 10.1038/s41598-019-43670-0.

16.

Intermittent Hypoxia and Hypercapnia Reproducibly Change the Gut Microbiome and Metabolome across Rodent Model Systems.

Tripathi A, Xu ZZ, Xue J, Poulsen O, Gonzalez A, Humphrey G, Meehan MJ, Melnik AV, Ackermann G, Zhou D, Malhotra A, Haddad GG, Dorrestein PC, Knight R.

mSystems. 2019 Apr 30;4(2). pii: e00058-19. doi: 10.1128/mSystems.00058-19. eCollection 2019 Mar-Apr.

17.

A gut microbiome signature for cirrhosis due to nonalcoholic fatty liver disease.

Caussy C, Tripathi A, Humphrey G, Bassirian S, Singh S, Faulkner C, Bettencourt R, Rizo E, Richards L, Xu ZZ, Downes MR, Evans RM, Brenner DA, Sirlin CB, Knight R, Loomba R.

Nat Commun. 2019 Mar 29;10(1):1406. doi: 10.1038/s41467-019-09455-9.

18.

The genetic basis for adaptation of model-designed syntrophic co-cultures.

Lloyd CJ, King ZA, Sandberg TE, Hefner Y, Olson CA, Phaneuf PV, O'Brien EJ, Sanders JG, Salido RA, Sanders K, Brennan C, Humphrey G, Knight R, Feist AM.

PLoS Comput Biol. 2019 Mar 1;15(3):e1006213. doi: 10.1371/journal.pcbi.1006213. eCollection 2019 Mar.

19.

Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease.

Mills RH, Vázquez-Baeza Y, Zhu Q, Jiang L, Gaffney J, Humphrey G, Smarr L, Knight R, Gonzalez DJ.

mSystems. 2019 Feb 12;4(1). pii: e00337-18. doi: 10.1128/mSystems.00337-18. eCollection 2019 Jan-Feb.

20.

Neutrophilic proteolysis in the cystic fibrosis lung correlates with a pathogenic microbiome.

Quinn RA, Adem S, Mills RH, Comstock W, DeRight Goldasich L, Humphrey G, Aksenov AA, Melnik AV, da Silva R, Ackermann G, Bandeira N, Gonzalez DJ, Conrad D, O'Donoghue AJ, Knight R, Dorrestein PC.

Microbiome. 2019 Feb 13;7(1):23. doi: 10.1186/s40168-019-0636-3.

21.

Impact of a smartphone app on prescriber adherence to antibiotic guidelines in adult patients with community acquired pneumonia or urinary tract infections.

Yoon CH, Ritchie SR, Duffy EJ, Thomas MG, McBride S, Read K, Chen R, Humphrey G.

PLoS One. 2019 Jan 29;14(1):e0211157. doi: 10.1371/journal.pone.0211157. eCollection 2019.

22.

High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity.

Minich JJ, Humphrey G, Benitez RAS, Sanders J, Swafford A, Allen EE, Knight R.

mSystems. 2018 Nov 6;3(6). pii: e00166-18. doi: 10.1128/mSystems.00166-18. eCollection 2018 Nov-Dec.

23.

Using codesign to develop a culturally tailored, behavior change mHealth intervention for indigenous and other priority communities: A case study in New Zealand.

Verbiest MEA, Corrigan C, Dalhousie S, Firestone R, Funaki T, Goodwin D, Grey J, Henry A, Humphrey G, Jull A, Vano M, Pekepo C, Morenga LT, Whittaker R, Mhurchu CN.

Transl Behav Med. 2019 Jul 16;9(4):720-736. doi: 10.1093/tbm/iby093.

PMID:
30388262
24.

Combining traditional 2D and modern physical organic-derived descriptors to predict enhanced enantioselectivity for the key aza-Michael conjugate addition in the synthesis of Prevymis™ (letermovir).

Metsänen TT, Lexa KW, Santiago CB, Chung CK, Xu Y, Liu Z, Humphrey GR, Ruck RT, Sherer EC, Sigman MS.

Chem Sci. 2018 Jul 18;9(34):6922-6927. doi: 10.1039/c8sc02089b. eCollection 2018 Sep 14.

25.

A Co-Designed, Culturally-Tailored mHealth Tool to Support Healthy Lifestyles in Māori and Pasifika Communities in New Zealand: Protocol for a Cluster Randomized Controlled Trial.

Verbiest M, Borrell S, Dalhousie S, Tupa'i-Firestone R, Funaki T, Goodwin D, Grey J, Henry A, Hughes E, Humphrey G, Jiang Y, Jull A, Pekepo C, Schumacher J, Te Morenga L, Tunks M, Vano M, Whittaker R, Ni Mhurchu C.

JMIR Res Protoc. 2018 Aug 22;7(8):e10789. doi: 10.2196/10789.

26.
27.

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.

28.

Intermittent Hypoxia and Hypercapnia, a Hallmark of Obstructive Sleep Apnea, Alters the Gut Microbiome and Metabolome.

Tripathi A, Melnik AV, Xue J, Poulsen O, Meehan MJ, Humphrey G, Jiang L, Ackermann G, McDonald D, Zhou D, Knight R, Dorrestein PC, Haddad GG.

mSystems. 2018 Jun 5;3(3). pii: e00020-18. doi: 10.1128/mSystems.00020-18. eCollection 2018 May-Jun.

29.

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.

30.

Exposure to toxic metals triggers unique responses from the rat gut microbiota.

Richardson JB, Dancy BCR, Horton CL, Lee YS, Madejczyk MS, Xu ZZ, Ackermann G, Humphrey G, Palacios G, Knight R, Lewis JA.

Sci Rep. 2018 Apr 26;8(1):6578. doi: 10.1038/s41598-018-24931-w.

31.

A communal catalogue reveals Earth's multiscale microbial diversity.

Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, Prill RJ, Tripathi A, Gibbons SM, Ackermann G, Navas-Molina JA, Janssen S, Kopylova E, Vázquez-Baeza Y, González A, Morton JT, Mirarab S, Zech Xu Z, Jiang L, Haroon MF, Kanbar J, Zhu Q, Jin Song S, Kosciolek T, Bokulich NA, Lefler J, Brislawn CJ, Humphrey G, Owens SM, Hampton-Marcell J, Berg-Lyons D, McKenzie V, Fierer N, Fuhrman JA, Clauset A, Stevens RL, Shade A, Pollard KS, Goodwin KD, Jansson JK, Gilbert JA, Knight R; Earth Microbiome Project Consortium.

Nature. 2017 Nov 23;551(7681):457-463. doi: 10.1038/nature24621. Epub 2017 Nov 1.

32.

Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung.

Garg N, Wang M, Hyde E, da Silva RR, Melnik AV, Protsyuk I, Bouslimani A, Lim YW, Wong R, Humphrey G, Ackermann G, Spivey T, Brouha SS, Bandeira N, Lin GY, Rohwer F, Conrad DJ, Alexandrov T, Knight R, Dorrestein PC.

Cell Host Microbe. 2017 Nov 8;22(5):705-716.e4. doi: 10.1016/j.chom.2017.10.001. Epub 2017 Oct 19.

33.

Asymmetric Synthesis of Functionalized trans-Cyclopropoxy Building Block for Grazoprevir.

Xu F, Zhong YL, Li H, Qi J, Desmond R, Song ZJ, Park J, Wang T, Truppo M, Humphrey GR, Ruck RT.

Org Lett. 2017 Nov 3;19(21):5880-5883. doi: 10.1021/acs.orglett.7b02867.

PMID:
29052413
34.

Asymmetric Hydrogen Bonding Catalysis for the Synthesis of Dihydroquinazoline-Containing Antiviral, Letermovir.

Chung CK, Liu Z, Lexa KW, Andreani T, Xu Y, Ji Y, DiRocco DA, Humphrey GR, Ruck RT.

J Am Chem Soc. 2017 Aug 9;139(31):10637-10640. doi: 10.1021/jacs.7b05806. Epub 2017 Jul 25.

PMID:
28737937
35.

DNA extraction for streamlined metagenomics of diverse environmental samples.

Marotz C, Amir A, Humphrey G, Gaffney J, Gogul G, Knight R.

Biotechniques. 2017 Jun 1;62(6):290-293. doi: 10.2144/000114559.

36.

The Oral and Skin Microbiomes of Captive Komodo Dragons Are Significantly Shared with Their Habitat.

Hyde ER, Navas-Molina JA, Song SJ, Kueneman JG, Ackermann G, Cardona C, Humphrey G, Boyer D, Weaver T, Mendelson JR 3rd, McKenzie VJ, Gilbert JA, Knight R.

mSystems. 2016 Aug 2;1(4). pii: e00046-16. eCollection 2016 Jul-Aug.

37.

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.

38.

From Sample to Multi-Omics Conclusions in under 48 Hours.

Quinn RA, Navas-Molina JA, Hyde ER, Song SJ, Vázquez-Baeza Y, Humphrey G, Gaffney J, Minich JJ, Melnik AV, Herschend J, DeReus J, Durant A, Dutton RJ, Khosroheidari M, Green C, da Silva R, Dorrestein PC, Knight R.

mSystems. 2016 Apr 26;1(2). pii: e00038-16. eCollection 2016 Mar-Apr.

39.

Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys.

Walters W, Hyde ER, Berg-Lyons D, Ackermann G, Humphrey G, Parada A, Gilbert JA, Jansson JK, Caporaso JG, Fuhrman JA, Apprill A, Knight R.

mSystems. 2015 Dec 22;1(1). pii: e00009-15. eCollection 2016 Jan-Feb.

40.

Asymmetric Synthesis of a Potent HIV-1 Integrase Inhibitor.

Kuethe JT, Humphrey GR, Journet M, Peng Z, Childers KG.

J Org Chem. 2016 Nov 4;81(21):10256-10265. Epub 2016 Aug 10.

PMID:
27471910
41.

Parental smoking during pregnancy: findings from the Growing Up in New Zealand cohort.

Humphrey G, Rossen F, Walker N, Bullen C.

N Z Med J. 2016 Sep 23;129(1442):60-74.

PMID:
27657160
42.

Development of Risk-Taking, Perspective-Taking, and Inhibitory Control During Adolescence.

Humphrey G, Dumontheil I.

Dev Neuropsychol. 2016 Jan-Mar;41(1-2):59-76. doi: 10.1080/87565641.2016.1161764. Epub 2016 Apr 12.

PMID:
27070826
43.

A Synthesis of a Spirocyclic Macrocyclic Protease Inhibitor for the Treatment of Hepatitis C.

Chung CK, Cleator E, Dumas AM, Hicks JD, Humphrey GR, Maligres PE, Nolting AF, Rivera N, Ruck RT, Shevlin M.

Org Lett. 2016 Mar 18;18(6):1394-7. doi: 10.1021/acs.orglett.6b00331. Epub 2016 Mar 7.

PMID:
26950496
44.

Angiomyxoma in Accessory Hepatic Lobe.

Rossi A, Pederiva F, Santos R, Wood S, Humphrey G.

APSP J Case Rep. 2016 Jan 1;7(1):10. eCollection 2016 Jan-Apr. No abstract available.

45.

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.

46.

Phylogenetic and ecological factors impact the gut microbiota of two Neotropical primate species.

Amato KR, Martinez-Mota R, Righini N, Raguet-Schofield M, Corcione FP, Marini E, Humphrey G, Gogul G, Gaffney J, Lovelace E, Williams L, Luong A, Dominguez-Bello MG, Stumpf RM, White B, Nelson KE, Knight R, Leigh SR.

Oecologia. 2016 Mar;180(3):717-33. doi: 10.1007/s00442-015-3507-z. Epub 2015 Nov 24.

PMID:
26597549
47.

Gram-negative organisms in peritoneal dialysis peritonitis: an early indication for surgery in patients with haemolytic uraemic syndrome?

Harwood R, Wilkinson D, Ramkumar S, Humphrey G.

Pediatr Surg Int. 2016 Mar;32(3):235-8. doi: 10.1007/s00383-015-3833-6. Epub 2015 Nov 17.

PMID:
26578260
48.

Highly efficient synthesis of HIV NNRTI doravirine.

Gauthier DR Jr, Sherry BD, Cao Y, Journet M, Humphrey G, Itoh T, Mangion I, Tschaen DM.

Org Lett. 2015 Mar 20;17(6):1353-6. doi: 10.1021/ol503625z. Epub 2015 Mar 9.

PMID:
25751537
49.

Lung biopsy for chronic pulmonary disease in children.

Greenhalgh RM, Yardley IE, Child F, Bruce J, Humphrey GM.

J Pediatr Surg. 2014 Jul;49(7):1075-7. doi: 10.1016/j.jpedsurg.2013.10.026. Epub 2013 Nov 15.

PMID:
24952791
50.

The power of persuasion.

Humphrey GB.

Narrat Inq Bioeth. 2013 Fall;3(2):101-3. doi: 10.1353/nib.2013.0030. No abstract available.

PMID:
24407075

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