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Items: 1 to 50 of 114

1.

The Comprehensive Snack Parenting Questionnaire (CSPQ): Development and Test-Retest Reliability.

Gevers DWM, Kremers SPJ, de Vries NK, van Assema P.

Int J Environ Res Public Health. 2018 Apr 26;15(5). pii: E862. doi: 10.3390/ijerph15050862.

2.

The classroom microbiome and asthma morbidity in children attending 3 inner-city schools.

Lai PS, Kolde R, Franzosa EA, Gaffin JM, Baxi SN, Sheehan WJ, Gold DR, Gevers D, Xavier RJ, Phipatanakul W.

J Allergy Clin Immunol. 2018 Jun;141(6):2311-2313. doi: 10.1016/j.jaci.2018.02.022. Epub 2018 Mar 5. No abstract available.

PMID:
29518428
3.

Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation.

Smillie CS, Sauk J, Gevers D, Friedman J, Sung J, Youngster I, Hohmann EL, Staley C, Khoruts A, Sadowsky MJ, Allegretti JR, Smith MB, Xavier RJ, Alm EJ.

Cell Host Microbe. 2018 Feb 14;23(2):229-240.e5. doi: 10.1016/j.chom.2018.01.003.

PMID:
29447696
4.

Alterations in oral bacterial communities are associated with risk factors for oral and oropharyngeal cancer.

Börnigen D, Ren B, Pickard R, Li J, Ozer E, Hartmann EM, Xiao W, Tickle T, Rider J, Gevers D, Franzosa EA, Davey ME, Gillison ML, Huttenhower C.

Sci Rep. 2017 Dec 15;7(1):17686. doi: 10.1038/s41598-017-17795-z.

5.

A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients.

Hall AB, Yassour M, Sauk J, Garner A, Jiang X, Arthur T, Lagoudas GK, Vatanen T, Fornelos N, Wilson R, Bertha M, Cohen M, Garber J, Khalili H, Gevers D, Ananthakrishnan AN, Kugathasan S, Lander ES, Blainey P, Vlamakis H, Xavier RJ, Huttenhower C.

Genome Med. 2017 Nov 28;9(1):103. doi: 10.1186/s13073-017-0490-5.

6.

Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation.

Atarashi K, Suda W, Luo C, Kawaguchi T, Motoo I, Narushima S, Kiguchi Y, Yasuma K, Watanabe E, Tanoue T, Thaiss CA, Sato M, Toyooka K, Said HS, Yamagami H, Rice SA, Gevers D, Johnson RC, Segre JA, Chen K, Kolls JK, Elinav E, Morita H, Xavier RJ, Hattori M, Honda K.

Science. 2017 Oct 20;358(6361):359-365. doi: 10.1126/science.aan4526.

PMID:
29051379
7.

Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine.

Geller LT, Barzily-Rokni M, Danino T, Jonas OH, Shental N, Nejman D, Gavert N, Zwang Y, Cooper ZA, Shee K, Thaiss CA, Reuben A, Livny J, Avraham R, Frederick DT, Ligorio M, Chatman K, Johnston SE, Mosher CM, Brandis A, Fuks G, Gurbatri C, Gopalakrishnan V, Kim M, Hurd MW, Katz M, Fleming J, Maitra A, Smith DA, Skalak M, Bu J, Michaud M, Trauger SA, Barshack I, Golan T, Sandbank J, Flaherty KT, Mandinova A, Garrett WS, Thayer SP, Ferrone CR, Huttenhower C, Bhatia SN, Gevers D, Wargo JA, Golub TR, Straussman R.

Science. 2017 Sep 15;357(6356):1156-1160. doi: 10.1126/science.aah5043.

8.

Explaining use of food parenting practices: the importance of predisposing factors and parental cognitions.

Gevers DW, van Assema P, de Vries NK, Kremers SP.

Public Health Nutr. 2017 Sep;20(13):2355-2363. doi: 10.1017/S1368980017001112. Epub 2017 Jul 13.

PMID:
28703083
9.

Corrigendum: Mobile genes in the human microbiome are structured from global to individual scales.

Brito IL, Yilmaz S, Huang K, Xu L, Jupiter SD, Jenkins AP, Naisilisili W, Tamminen M, Smillie CS, Wortman JR, Birren BW, Xavier RJ, Blainey PC, Singh AK, Gevers D, Alm EJ.

Nature. 2017 Apr 6;544(7648):124. doi: 10.1038/nature20774. Epub 2017 Mar 22. No abstract available.

PMID:
28329759
10.

A Microbiome Foundation for the Study of Crohn's Disease.

Gevers D, Kugathasan S, Knights D, Kostic AD, Knight R, Xavier RJ.

Cell Host Microbe. 2017 Mar 8;21(3):301-304. doi: 10.1016/j.chom.2017.02.012.

11.

Metagenomic Characterization of Microbial Communities In Situ Within the Deeper Layers of the Ileum in Crohn's Disease.

Pedamallu CS, Bhatt AS, Bullman S, Fowler S, Freeman SS, Durand J, Jung J, Duke F, Manzo V, Cai D, Ananthakrishnan A, Ojesina AI, Ramachandran A, Gevers D, Xavier RJ, Bhan AK, Meyerson M, Yajnik V.

Cell Mol Gastroenterol Hepatol. 2016 May 26;2(5):563-566.e5. doi: 10.1016/j.jcmgh.2016.05.011. eCollection 2016 Sep.

12.

Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment.

Hsu T, Joice R, Vallarino J, Abu-Ali G, Hartmann EM, Shafquat A, DuLong C, Baranowski C, Gevers D, Green JL, Morgan XC, Spengler JD, Huttenhower C.

mSystems. 2016 Jun 28;1(3). pii: e00018-16. eCollection 2016 May-Jun.

13.

Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease.

Imhann F, Vich Vila A, Bonder MJ, Fu J, Gevers D, Visschedijk MC, Spekhorst LM, Alberts R, Franke L, van Dullemen HM, Ter Steege RWF, Huttenhower C, Dijkstra G, Xavier RJ, Festen EAM, Wijmenga C, Zhernakova A, Weersma RK.

Gut. 2018 Jan;67(1):108-119. doi: 10.1136/gutjnl-2016-312135. Epub 2016 Oct 8.

14.
15.

Increased Intestinal Microbial Diversity Following Fecal Microbiota Transplant for Active Crohn's Disease.

Vaughn BP, Vatanen T, Allegretti JR, Bai A, Xavier RJ, Korzenik J, Gevers D, Ting A, Robson SC, Moss AC.

Inflamm Bowel Dis. 2016 Sep;22(9):2182-90. doi: 10.1097/MIB.0000000000000893.

16.

Mobile genes in the human microbiome are structured from global to individual scales.

Brito IL, Yilmaz S, Huang K, Xu L, Jupiter SD, Jenkins AP, Naisilisili W, Tamminen M, Smillie CS, Wortman JR, Birren BW, Xavier RJ, Blainey PC, Singh AK, Gevers D, Alm EJ.

Nature. 2016 Jul 21;535(7612):435-439. doi: 10.1038/nature18927. Epub 2016 Jul 13. Erratum in: Nature. 2017 Apr 6;544(7648):124.

17.

Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability.

Yassour M, Vatanen T, Siljander H, Hämäläinen AM, Härkönen T, Ryhänen SJ, Franzosa EA, Vlamakis H, Huttenhower C, Gevers D, Lander ES, Knip M; DIABIMMUNE Study Group, Xavier RJ.

Sci Transl Med. 2016 Jun 15;8(343):343ra81. doi: 10.1126/scitranslmed.aad0917.

18.

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans.

Vatanen T, Kostic AD, d'Hennezel E, Siljander H, Franzosa EA, Yassour M, Kolde R, Vlamakis H, Arthur TD, Hämäläinen AM, Peet A, Tillmann V, Uibo R, Mokurov S, Dorshakova N, Ilonen J, Virtanen SM, Szabo SJ, Porter JA, Lähdesmäki H, Huttenhower C, Gevers D, Cullen TW, Knip M; DIABIMMUNE Study Group, Xavier RJ.

Cell. 2016 Jun 2;165(6):1551. doi: 10.1016/j.cell.2016.05.056. No abstract available.

19.

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans.

Vatanen T, Kostic AD, d'Hennezel E, Siljander H, Franzosa EA, Yassour M, Kolde R, Vlamakis H, Arthur TD, Hämäläinen AM, Peet A, Tillmann V, Uibo R, Mokurov S, Dorshakova N, Ilonen J, Virtanen SM, Szabo SJ, Porter JA, Lähdesmäki H, Huttenhower C, Gevers D, Cullen TW, Knip M; DIABIMMUNE Study Group, Xavier RJ.

Cell. 2016 May 5;165(4):842-53. doi: 10.1016/j.cell.2016.04.007. Epub 2016 Apr 28. Erratum in: Cell. 2016 Jun 2;165(6):1551.

20.

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity.

Zhernakova A, Kurilshikov A, Bonder MJ, Tigchelaar EF, Schirmer M, Vatanen T, Mujagic Z, Vila AV, Falony G, Vieira-Silva S, Wang J, Imhann F, Brandsma E, Jankipersadsing SA, Joossens M, Cenit MC, Deelen P, Swertz MA; LifeLines cohort study, Weersma RK, Feskens EJ, Netea MG, Gevers D, Jonkers D, Franke L, Aulchenko YS, Huttenhower C, Raes J, Hofker MH, Xavier RJ, Wijmenga C, Fu J.

Science. 2016 Apr 29;352(6285):565-9. doi: 10.1126/science.aad3369. Epub 2016 Apr 28.

21.

The influence of a short-term gluten-free diet on the human gut microbiome.

Bonder MJ, Tigchelaar EF, Cai X, Trynka G, Cenit MC, Hrdlickova B, Zhong H, Vatanen T, Gevers D, Wijmenga C, Wang Y, Zhernakova A.

Genome Med. 2016 Apr 21;8(1):45. doi: 10.1186/s13073-016-0295-y.

22.

Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes.

Yassour M, Lim MY, Yun HS, Tickle TL, Sung J, Song YM, Lee K, Franzosa EA, Morgan XC, Gevers D, Lander ES, Xavier RJ, Birren BW, Ko G, Huttenhower C.

Genome Med. 2016 Feb 17;8(1):17. doi: 10.1186/s13073-016-0271-6.

23.

Characterization of Intestinal Microbiota in Ulcerative Colitis Patients with and without Primary Sclerosing Cholangitis.

Kevans D, Tyler AD, Holm K, Jørgensen KK, Vatn MH, Karlsen TH, Kaplan GG, Eksteen B, Gevers D, Hov JR, Silverberg MS.

J Crohns Colitis. 2016 Mar;10(3):330-7. doi: 10.1093/ecco-jcc/jjv204. Epub 2015 Nov 2.

24.

Host genetic variation impacts microbiome composition across human body sites.

Blekhman R, Goodrich JK, Huang K, Sun Q, Bukowski R, Bell JT, Spector TD, Keinan A, Ley RE, Gevers D, Clark AG.

Genome Biol. 2015 Sep 15;16:191. doi: 10.1186/s13059-015-0759-1.

25.

Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning.

Cleary B, Brito IL, Huang K, Gevers D, Shea T, Young S, Alm EJ.

Nat Biotechnol. 2015 Oct;33(10):1053-60. doi: 10.1038/nbt.3329. Epub 2015 Sep 14.

26.

The Gut Microbiome Contributes to a Substantial Proportion of the Variation in Blood Lipids.

Fu J, Bonder MJ, Cenit MC, Tigchelaar EF, Maatman A, Dekens JA, Brandsma E, Marczynska J, Imhann F, Weersma RK, Franke L, Poon TW, Xavier RJ, Gevers D, Hofker MH, Wijmenga C, Zhernakova A.

Circ Res. 2015 Oct 9;117(9):817-24. doi: 10.1161/CIRCRESAHA.115.306807. Epub 2015 Sep 10.

27.

ConStrains identifies microbial strains in metagenomic datasets.

Luo C, Knight R, Siljander H, Knip M, Xavier RJ, Gevers D.

Nat Biotechnol. 2015 Oct;33(10):1045-52. doi: 10.1038/nbt.3319. Epub 2015 Sep 7.

28.

Patterns of Food Parenting Practices and Children's Intake of Energy-Dense Snack Foods.

Gevers DW, Kremers SP, de Vries NK, van Assema P.

Nutrients. 2015 May 27;7(6):4093-106. doi: 10.3390/nu7064093.

29.

Identifying personal microbiomes using metagenomic codes.

Franzosa EA, Huang K, Meadow JF, Gevers D, Lemon KP, Bohannan BJ, Huttenhower C.

Proc Natl Acad Sci U S A. 2015 Jun 2;112(22):E2930-8. doi: 10.1073/pnas.1423854112. Epub 2015 May 11.

30.

Restrictive rules of Dutch mothers regarding their children's dietary intake between meals.

Gevers DW, Raaijmakers LG, Bessems KM, Teuscher D, Kremers SP, van Assema P.

Eat Behav. 2015 Aug;18:62-5. doi: 10.1016/j.eatbeh.2015.04.002. Epub 2015 Apr 15.

PMID:
25913009
31.

Dirk Gevers.

Gevers D, Mullard A.

Nat Rev Drug Discov. 2015 May;14(5):305. doi: 10.1038/nrd4614. Epub 2015 Apr 24. No abstract available.

PMID:
25907337
32.

Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease.

Morgan XC, Kabakchiev B, Waldron L, Tyler AD, Tickle TL, Milgrom R, Stempak JM, Gevers D, Xavier RJ, Silverberg MS, Huttenhower C.

Genome Biol. 2015 Apr 8;16:67. doi: 10.1186/s13059-015-0637-x.

33.

Intake of energy-dense snack foods and drinks among Dutch children aged 7-12 years: how many, how much, when, where and which?

Gevers DW, Kremers SP, de Vries NK, van Assema P.

Public Health Nutr. 2016 Jan;19(1):83-92. doi: 10.1017/S1368980015000877. Epub 2015 Apr 8.

PMID:
25850560
34.

Biogeography of the intestinal mucosal and lumenal microbiome in the rhesus macaque.

Yasuda K, Oh K, Ren B, Tickle TL, Franzosa EA, Wachtman LM, Miller AD, Westmoreland SV, Mansfield KG, Vallender EJ, Miller GM, Rowlett JK, Gevers D, Huttenhower C, Morgan XC.

Cell Host Microbe. 2015 Mar 11;17(3):385-391. doi: 10.1016/j.chom.2015.01.015. Epub 2015 Feb 26.

35.

Corrigendum. Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature.

Haberman Y, Tickle TL, Dexheimer PJ, Kim MO, Tang D, Karns R, Baldassano RN, Noe JD, Rosh J, Markowitz J, Heyman MB, Griffiths AM, Crandall WV, Mack DR, Baker SS, Huttenhower C, Keljo DJ, Hyams JS, Kugathasan S, Walters TD, Aronow B, Xavier RJ, Gevers D, Denson LA.

J Clin Invest. 2015 Mar 2;125(3):1363. doi: 10.1172/JCI79657. Epub 2015 Mar 2. No abstract available.

36.

The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes.

Kostic AD, Gevers D, Siljander H, Vatanen T, Hyötyläinen T, Hämäläinen AM, Peet A, Tillmann V, Pöhö P, Mattila I, Lähdesmäki H, Franzosa EA, Vaarala O, de Goffau M, Harmsen H, Ilonen J, Virtanen SM, Clish CB, Orešič M, Huttenhower C, Knip M; DIABIMMUNE Study Group, Xavier RJ.

Cell Host Microbe. 2015 Feb 11;17(2):260-73. doi: 10.1016/j.chom.2015.01.001. Epub 2015 Feb 5.

37.

Disease-specific alterations in the enteric virome in inflammatory bowel disease.

Norman JM, Handley SA, Baldridge MT, Droit L, Liu CY, Keller BC, Kambal A, Monaco CL, Zhao G, Fleshner P, Stappenbeck TS, McGovern DP, Keshavarzian A, Mutlu EA, Sauk J, Gevers D, Xavier RJ, Wang D, Parkes M, Virgin HW.

Cell. 2015 Jan 29;160(3):447-60. doi: 10.1016/j.cell.2015.01.002. Epub 2015 Jan 22.

38.

Complex host genetics influence the microbiome in inflammatory bowel disease.

Knights D, Silverberg MS, Weersma RK, Gevers D, Dijkstra G, Huang H, Tyler AD, van Sommeren S, Imhann F, Stempak JM, Huang H, Vangay P, Al-Ghalith GA, Russell C, Sauk J, Knight J, Daly MJ, Huttenhower C, Xavier RJ.

Genome Med. 2014 Dec 2;6(12):107. doi: 10.1186/s13073-014-0107-1. eCollection 2014.

39.

Associations between general parenting, restrictive snacking rules, and adolescent's snack intake. The roles of fathers and mothers and interparental congruence.

Gevers DW, van Assema P, Sleddens EF, de Vries NK, Kremers SP.

Appetite. 2015 Apr;87:184-91. doi: 10.1016/j.appet.2014.12.220. Epub 2014 Dec 30.

PMID:
25555538
40.

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.

41.

Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature.

Haberman Y, Tickle TL, Dexheimer PJ, Kim MO, Tang D, Karns R, Baldassano RN, Noe JD, Rosh J, Markowitz J, Heyman MB, Griffiths AM, Crandall WV, Mack DR, Baker SS, Huttenhower C, Keljo DJ, Hyams JS, Kugathasan S, Walters TD, Aronow B, Xavier RJ, Gevers D, Denson LA.

J Clin Invest. 2014 Aug;124(8):3617-33. doi: 10.1172/JCI75436. Epub 2014 Jul 8. Erratum in: J Clin Invest. 2015 Mar 2;125(3):1363.

42.

Relating the metatranscriptome and metagenome of the human gut.

Franzosa EA, Morgan XC, Segata N, Waldron L, Reyes J, Earl AM, Giannoukos G, Boylan MR, Ciulla D, Gevers D, Izard J, Garrett WS, Chan AT, Huttenhower C.

Proc Natl Acad Sci U S A. 2014 Jun 3;111(22):E2329-38. doi: 10.1073/pnas.1319284111. Epub 2014 May 19.

43.

Fecal microbiota transplant for relapsing Clostridium difficile infection using a frozen inoculum from unrelated donors: a randomized, open-label, controlled pilot study.

Youngster I, Sauk J, Pindar C, Wilson RG, Kaplan JL, Smith MB, Alm EJ, Gevers D, Russell GH, Hohmann EL.

Clin Infect Dis. 2014 Jun;58(11):1515-22. doi: 10.1093/cid/ciu135. Epub 2014 Apr 23.

44.

Clarifying concepts of food parenting practices. A Delphi study with an application to snacking behavior.

Gevers DW, Kremers SP, de Vries NK, van Assema P.

Appetite. 2014 Aug;79:51-7. doi: 10.1016/j.appet.2014.04.002. Epub 2014 Apr 13.

PMID:
24732407
45.

The treatment-naive microbiome in new-onset Crohn's disease.

Gevers D, Kugathasan S, Denson LA, Vázquez-Baeza Y, Van Treuren W, Ren B, Schwager E, Knights D, Song SJ, Yassour M, Morgan XC, Kostic AD, Luo C, González A, McDonald D, Haberman Y, Walters T, Baker S, Rosh J, Stephens M, Heyman M, Markowitz J, Baldassano R, Griffiths A, Sylvester F, Mack D, Kim S, Crandall W, Hyams J, Huttenhower C, Knight R, Xavier RJ.

Cell Host Microbe. 2014 Mar 12;15(3):382-392. doi: 10.1016/j.chom.2014.02.005.

46.

The intestinal microbiome in type 1 diabetes.

Dunne JL, Triplett EW, Gevers D, Xavier R, Insel R, Danska J, Atkinson MA.

Clin Exp Immunol. 2014 Jul;177(1):30-7. doi: 10.1111/cei.12321. Review.

47.

The microbiome in inflammatory bowel disease: current status and the future ahead.

Kostic AD, Xavier RJ, Gevers D.

Gastroenterology. 2014 May;146(6):1489-99. doi: 10.1053/j.gastro.2014.02.009. Epub 2014 Feb 19. Review.

48.

Emotional and instrumental feeding practices of Dutch mothers regarding foods eaten between main meals.

Raaijmakers LG, Gevers DW, Teuscher D, Kremers SP, van Assema P.

BMC Public Health. 2014 Feb 17;14:171. doi: 10.1186/1471-2458-14-171.

49.

Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission.

Rooks MG, Veiga P, Wardwell-Scott LH, Tickle T, Segata N, Michaud M, Gallini CA, Beal C, van Hylckama-Vlieg JE, Ballal SA, Morgan XC, Glickman JN, Gevers D, Huttenhower C, Garrett WS.

ISME J. 2014 Jul;8(7):1403-17. doi: 10.1038/ismej.2014.3. Epub 2014 Feb 6.

50.

Early microbial and metabolomic signatures predict later onset of necrotizing enterocolitis in preterm infants.

Morrow AL, Lagomarcino AJ, Schibler KR, Taft DH, Yu Z, Wang B, Altaye M, Wagner M, Gevers D, Ward DV, Kennedy MA, Huttenhower C, Newburg DS.

Microbiome. 2013 Apr 16;1(1):13. doi: 10.1186/2049-2618-1-13.

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