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Items: 1 to 50 of 58

1.

Gut microbiome structure and metabolic activity in inflammatory bowel disease.

Franzosa EA, Sirota-Madi A, Avila-Pacheco J, Fornelos N, Haiser HJ, Reinker S, Vatanen T, Hall AB, Mallick H, McIver LJ, Sauk JS, Wilson RG, Stevens BW, Scott JM, Pierce K, Deik AA, Bullock K, Imhann F, Porter JA, Zhernakova A, Fu J, Weersma RK, Wijmenga C, Clish CB, Vlamakis H, Huttenhower C, Xavier RJ.

Nat Microbiol. 2018 Dec 10. doi: 10.1038/s41564-018-0306-4. [Epub ahead of print]

PMID:
30531976
2.

The human gut microbiome in early-onset type 1 diabetes from the TEDDY study.

Vatanen T, Franzosa EA, Schwager R, Tripathi S, Arthur TD, Vehik K, Lernmark Å, Hagopian WA, Rewers MJ, She JX, Toppari J, Ziegler AG, Akolkar B, Krischer JP, Stewart CJ, Ajami NJ, Petrosino JF, Gevers D, Lähdesmäki H, Vlamakis H, Huttenhower C, Xavier RJ.

Nature. 2018 Oct;562(7728):589-594. doi: 10.1038/s41586-018-0620-2. Epub 2018 Oct 24.

PMID:
30356183
3.

Compositional and Temporal Changes in the Gut Microbiome of Pediatric Ulcerative Colitis Patients Are Linked to Disease Course.

Schirmer M, Denson L, Vlamakis H, Franzosa EA, Thomas S, Gotman NM, Rufo P, Baker SS, Sauer C, Markowitz J, Pfefferkorn M, Oliva-Hemker M, Rosh J, Otley A, Boyle B, Mack D, Baldassano R, Keljo D, LeLeiko N, Heyman M, Griffiths A, Patel AS, Noe J, Kugathasan S, Walters T, Huttenhower C, Hyams J, Xavier RJ.

Cell Host Microbe. 2018 Oct 10;24(4):600-610.e4. doi: 10.1016/j.chom.2018.09.009.

PMID:
30308161
4.

Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life.

Yassour M, Jason E, Hogstrom LJ, Arthur TD, Tripathi S, Siljander H, Selvenius J, Oikarinen S, Hyöty H, Virtanen SM, Ilonen J, Ferretti P, Pasolli E, Tett A, Asnicar F, Segata N, Vlamakis H, Lander ES, Huttenhower C, Knip M, Xavier RJ.

Cell Host Microbe. 2018 Jul 11;24(1):146-154.e4. doi: 10.1016/j.chom.2018.06.007.

PMID:
30001517
5.

Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome.

Ferretti P, Pasolli E, Tett A, Asnicar F, Gorfer V, Fedi S, Armanini F, Truong DT, Manara S, Zolfo M, Beghini F, Bertorelli R, De Sanctis V, Bariletti I, Canto R, Clementi R, Cologna M, Crifò T, Cusumano G, Gottardi S, Innamorati C, Masè C, Postai D, Savoi D, Duranti S, Lugli GA, Mancabelli L, Turroni F, Ferrario C, Milani C, Mangifesta M, Anzalone R, Viappiani A, Yassour M, Vlamakis H, Xavier R, Collado CM, Koren O, Tateo S, Soffiati M, Pedrotti A, Ventura M, Huttenhower C, Bork P, Segata N.

Cell Host Microbe. 2018 Jul 11;24(1):133-145.e5. doi: 10.1016/j.chom.2018.06.005.

6.

A screen of Crohn's disease-associated microbial metabolites identifies ascorbate as a novel metabolic inhibitor of activated human T cells.

Chang YL, Rossetti M, Vlamakis H, Casero D, Sunga G, Harre N, Miller S, Humphries R, Stappenbeck T, Simpson KW, Sartor RB, Wu G, Lewis J, Bushman F, McGovern DPB, Salzman N, Borneman J, Xavier R, Huttenhower C, Braun J.

Mucosal Immunol. 2018 Apr 25. doi: 10.1038/s41385-018-0022-7. [Epub ahead of print]

7.

A Common Mechanism Links Activities of Butyrate in the Colon.

Verma MS, Fink MJ, Salmon GL, Fornelos N, Ohara TE, Ryu SH, Vlamakis H, Xavier RJ, Stappenbeck TS, Whitesides GM.

ACS Chem Biol. 2018 May 18;13(5):1291-1298. doi: 10.1021/acschembio.8b00073. Epub 2018 Apr 10.

PMID:
29584955
8.

Host genetic variation and its microbiome interactions within the Human Microbiome Project.

Kolde R, Franzosa EA, Rahnavard G, Hall AB, Vlamakis H, Stevens C, Daly MJ, Xavier RJ, Huttenhower C.

Genome Med. 2018 Jan 29;10(1):6. doi: 10.1186/s13073-018-0515-8.

9.

Dynamics of metatranscription in the inflammatory bowel disease gut microbiome.

Schirmer M, Franzosa EA, Lloyd-Price J, McIver LJ, Schwager R, Poon TW, Ananthakrishnan AN, Andrews E, Barron G, Lake K, Prasad M, Sauk J, Stevens B, Wilson RG, Braun J, Denson LA, Kugathasan S, McGovern DPB, Vlamakis H, Xavier RJ, Huttenhower C.

Nat Microbiol. 2018 Mar;3(3):337-346. doi: 10.1038/s41564-017-0089-z. Epub 2018 Jan 8.

10.

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.

11.

Indoleacrylic Acid Produced by Commensal Peptostreptococcus Species Suppresses Inflammation.

Wlodarska M, Luo C, Kolde R, d'Hennezel E, Annand JW, Heim CE, Krastel P, Schmitt EK, Omar AS, Creasey EA, Garner AL, Mohammadi S, O'Connell DJ, Abubucker S, Arthur TD, Franzosa EA, Huttenhower C, Murphy LO, Haiser HJ, Vlamakis H, Porter JA, Xavier RJ.

Cell Host Microbe. 2017 Jul 12;22(1):25-37.e6. doi: 10.1016/j.chom.2017.06.007.

12.

Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children.

Zhao G, Vatanen T, Droit L, Park A, Kostic AD, Poon TW, Vlamakis H, Siljander H, Härkönen T, Hämäläinen AM, Peet A, Tillmann V, Ilonen J, Wang D, Knip M, Xavier RJ, Virgin HW.

Proc Natl Acad Sci U S A. 2017 Jul 25;114(30):E6166-E6175. doi: 10.1073/pnas.1706359114. Epub 2017 Jul 10. Erratum in: Proc Natl Acad Sci U S A. 2018 Nov 27;115(48):E11426.

13.

Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.

Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, Horst RT, Jansen T, Jacobs L, Bonder MJ, Kurilshikov A, Fu J, Joosten LAB, Zhernakova A, Huttenhower C, Wijmenga C, Netea MG, Xavier RJ.

Cell. 2016 Dec 15;167(7):1897. doi: 10.1016/j.cell.2016.11.046. No abstract available.

14.

Bacillus subtilis Early Colonization of Arabidopsis thaliana Roots Involves Multiple Chemotaxis Receptors.

Allard-Massicotte R, Tessier L, Lécuyer F, Lakshmanan V, Lucier JF, Garneau D, Caudwell L, Vlamakis H, Bais HP, Beauregard PB.

MBio. 2016 Nov 29;7(6). pii: e01664-16. doi: 10.1128/mBio.01664-16.

15.

Dynamic metabolic exchange governs a marine algal-bacterial interaction.

Segev E, Wyche TP, Kim KH, Petersen J, Ellebrandt C, Vlamakis H, Barteneva N, Paulson JN, Chai L, Clardy J, Kolter R.

Elife. 2016 Nov 18;5. pii: e17473. doi: 10.7554/eLife.17473.

16.

Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.

Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, Ter Horst R, Jansen T, Jacobs L, Bonder MJ, Kurilshikov A, Fu J, Joosten LAB, Zhernakova A, Huttenhower C, Wijmenga C, Netea MG, Xavier RJ.

Cell. 2016 Nov 3;167(4):1125-1136.e8. doi: 10.1016/j.cell.2016.10.020. Erratum in: Cell. 2016 Dec 15;167(7):1897. Cell. 2016 Dec 15;167(7):1897.

17.

Understanding human immune function using the resources from the Human Functional Genomics Project.

Netea MG, Joosten LA, Li Y, Kumar V, Oosting M, Smeekens S, Jaeger M, Ter Horst R, Schirmer M, Vlamakis H, Notebaart R, Pavelka N, Aguirre-Gamboa RR, Swertz MA, Tunjungputri RN, van de Heijden W, Franzosa EA, Ng A, Graham D, Lassen K, Schraa K, Netea-Maier R, Smit J, de Mast Q, van de Veerdonk F, Kullberg BJ, Tack C, van de Munckhof I, Rutten J, van der Graaf J, Franke L, Hofker M, Jonkers I, Platteel M, Maatman A, Fu J, Zhernakova A, van der Meer JW, Dinarello CA, van der Ven A, Huttenhouwer C, Koenen H, Joosten I, Xavier RJ, Wijmenga C.

Nat Med. 2016 Aug 4;22(8):831-3. doi: 10.1038/nm.4140. No abstract available.

PMID:
27490433
18.

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.

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

20.

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.

21.

Bacterial influence on alkenones in live microalgae.

Segev E, Castañeda IS, Sikes EL, Vlamakis H, Kolter R.

J Phycol. 2016 Feb;52(1):125-30. doi: 10.1111/jpy.12370. Epub 2016 Jan 12.

22.

Morphological Heterogeneity and Attachment of Phaeobacter inhibens.

Segev E, Tellez A, Vlamakis H, Kolter R.

PLoS One. 2015 Nov 11;10(11):e0141300. doi: 10.1371/journal.pone.0141300. eCollection 2015.

23.

Division of Labor in Biofilms: the Ecology of Cell Differentiation.

van Gestel J, Vlamakis H, Kolter R.

Microbiol Spectr. 2015 Apr;3(2):MB-0002-2014. doi: 10.1128/microbiolspec.MB-0002-2014. Review.

PMID:
26104716
24.

From cell differentiation to cell collectives: Bacillus subtilis uses division of labor to migrate.

van Gestel J, Vlamakis H, Kolter R.

PLoS Biol. 2015 Apr 20;13(4):e1002141. doi: 10.1371/journal.pbio.1002141. eCollection 2015 Apr.

25.

Directed natural product biosynthesis gene cluster capture and expression in the model bacterium Bacillus subtilis.

Li Y, Li Z, Yamanaka K, Xu Y, Zhang W, Vlamakis H, Kolter R, Moore BS, Qian PY.

Sci Rep. 2015 Mar 24;5:9383. doi: 10.1038/srep09383.

26.

New tools for comparing microscopy images: quantitative analysis of cell types in Bacillus subtilis.

van Gestel J, Vlamakis H, Kolter R.

J Bacteriol. 2015 Feb 15;197(4):699-709. doi: 10.1128/JB.02501-14. Epub 2014 Dec 1.

27.

Mutualistic interaction between Salmonella enterica and Aspergillus niger and its effects on Zea mays colonization.

Balbontín R, Vlamakis H, Kolter R.

Microb Biotechnol. 2014 Nov;7(6):589-600. doi: 10.1111/1751-7915.12182.

28.

Genome Sequence of Serratia plymuthica V4.

Cleto S, Van der Auwera G, Almeida C, Vieira MJ, Vlamakis H, Kolter R.

Genome Announc. 2014 May 15;2(3). pii: e00340-14. doi: 10.1128/genomeA.00340-14.

29.

Functional analysis of the accessory protein TapA in Bacillus subtilis amyloid fiber assembly.

Romero D, Vlamakis H, Losick R, Kolter R.

J Bacteriol. 2014 Apr;196(8):1505-13. doi: 10.1128/JB.01363-13. Epub 2014 Jan 31.

30.

Draft Genome of a Type 4 Pilus Defective Myxococcus xanthus Strain, DZF1.

Müller S, Willett JW, Bahr SM, Scott JC, Wilson JM, Darnell CL, Vlamakis HC, Kirby JR.

Genome Announc. 2013 Jun 20;1(3). pii: e00392-13. doi: 10.1128/genomeA.00392-13.

31.

Draft Genome Sequence of Myxococcus xanthus Wild-Type Strain DZ2, a Model Organism for Predation and Development.

Müller S, Willett JW, Bahr SM, Darnell CL, Hummels KR, Dong CK, Vlamakis HC, Kirby JR.

Genome Announc. 2013 May 9;1(3). pii: e00217-13. doi: 10.1128/genomeA.00217-13.

32.

Isolation, characterization, and aggregation of a structured bacterial matrix precursor.

Chai L, Romero D, Kayatekin C, Akabayov B, Vlamakis H, Losick R, Kolter R.

J Biol Chem. 2013 Jun 14;288(24):17559-68. doi: 10.1074/jbc.M113.453605. Epub 2013 Apr 30.

33.

Bacillus subtilis biofilm induction by plant polysaccharides.

Beauregard PB, Chai Y, Vlamakis H, Losick R, Kolter R.

Proc Natl Acad Sci U S A. 2013 Apr 23;110(17):E1621-30. doi: 10.1073/pnas.1218984110. Epub 2013 Apr 8.

34.

Bacterial flagella explore microscale hummocks and hollows to increase adhesion.

Friedlander RS, Vlamakis H, Kim P, Khan M, Kolter R, Aizenberg J.

Proc Natl Acad Sci U S A. 2013 Apr 2;110(14):5624-9. doi: 10.1073/pnas.1219662110. Epub 2013 Mar 18.

35.

Sticking together: building a biofilm the Bacillus subtilis way.

Vlamakis H, Chai Y, Beauregard P, Losick R, Kolter R.

Nat Rev Microbiol. 2013 Mar;11(3):157-68. doi: 10.1038/nrmicro2960. Epub 2013 Jan 28. Review.

36.

Biofilm inhibitors that target amyloid proteins.

Romero D, Sanabria-Valentín E, Vlamakis H, Kolter R.

Chem Biol. 2013 Jan 24;20(1):102-10. doi: 10.1016/j.chembiol.2012.10.021.

37.

Galactose metabolism plays a crucial role in biofilm formation by Bacillus subtilis.

Chai Y, Beauregard PB, Vlamakis H, Losick R, Kolter R.

MBio. 2012 Aug 14;3(4):e00184-12. doi: 10.1128/mBio.00184-12. Print 2012. Erratum in: MBio. 2013;4(1). doi:10.1128/mBio.00555-12.

38.

The biofilm formation defect of a Bacillus subtilis flotillin-defective mutant involves the protease FtsH.

Yepes A, Schneider J, Mielich B, Koch G, García-Betancur JC, Ramamurthi KS, Vlamakis H, López D.

Mol Microbiol. 2012 Oct;86(2):457-71. doi: 10.1111/j.1365-2958.2012.08205.x. Epub 2012 Aug 24.

39.

Mixing and matching siderophore clusters: structure and biosynthesis of serratiochelins from Serratia sp. V4.

Seyedsayamdost MR, Cleto S, Carr G, Vlamakis H, João Vieira M, Kolter R, Clardy J.

J Am Chem Soc. 2012 Aug 22;134(33):13550-3. doi: 10.1021/ja304941d. Epub 2012 Aug 13.

40.

Osmotic spreading of Bacillus subtilis biofilms driven by an extracellular matrix.

Seminara A, Angelini TE, Wilking JN, Vlamakis H, Ebrahim S, Kolter R, Weitz DA, Brenner MP.

Proc Natl Acad Sci U S A. 2012 Jan 24;109(4):1116-21. doi: 10.1073/pnas.1109261108. Epub 2012 Jan 9.

41.

The world of biofilms.

Vlamakis H.

Virulence. 2011 Sep-Oct;2(5):431-4. doi: 10.4161/viru.2.5.17902. Epub 2011 Sep 1. No abstract available.

PMID:
21921689
42.

An accessory protein required for anchoring and assembly of amyloid fibres in B. subtilis biofilms.

Romero D, Vlamakis H, Losick R, Kolter R.

Mol Microbiol. 2011 Jun;80(5):1155-68. doi: 10.1111/j.1365-2958.2011.07653.x. Epub 2011 May 5.

43.

Metal-enhanced fluorescence to quantify bacterial adhesion.

Lee K, Hahn LD, Yuen WW, Vlamakis H, Kolter R, Mooney DJ.

Adv Mater. 2011 Mar 25;23(12):H101-4. doi: 10.1002/adma.201004096. Epub 2011 Feb 22. No abstract available.

PMID:
21433096
44.

Shear stress increases the residence time of adhesion of Pseudomonas aeruginosa.

Lecuyer S, Rusconi R, Shen Y, Forsyth A, Vlamakis H, Kolter R, Stone HA.

Biophys J. 2011 Jan 19;100(2):341-50. doi: 10.1016/j.bpj.2010.11.078. Erratum in: Biophys J. 2011 Mar 2;100(5):1381.

45.

KinD is a checkpoint protein linking spore formation to extracellular-matrix production in Bacillus subtilis biofilms.

Aguilar C, Vlamakis H, Guzman A, Losick R, Kolter R.

MBio. 2010 May 18;1(1). pii: e00035-10. doi: 10.1128/mBio.00035-10.

46.

Biofilms.

López D, Vlamakis H, Kolter R.

Cold Spring Harb Perspect Biol. 2010 Jul;2(7):a000398. doi: 10.1101/cshperspect.a000398. Epub 2010 Jun 2. Review.

47.

Cannibalism enhances biofilm development in Bacillus subtilis.

López D, Vlamakis H, Losick R, Kolter R.

Mol Microbiol. 2009 Nov;74(3):609-18. doi: 10.1111/j.1365-2958.2009.06882.x. Epub 2009 Sep 22.

48.

Paracrine signaling in a bacterium.

López D, Vlamakis H, Losick R, Kolter R.

Genes Dev. 2009 Jul 15;23(14):1631-8. doi: 10.1101/gad.1813709.

49.

Generation of multiple cell types in Bacillus subtilis.

Lopez D, Vlamakis H, Kolter R.

FEMS Microbiol Rev. 2009 Jan;33(1):152-63. doi: 10.1111/j.1574-6976.2008.00148.x. Epub 2008 Nov 19. Review.

50.

Biofilm development with an emphasis on Bacillus subtilis.

Lemon KP, Earl AM, Vlamakis HC, Aguilar C, Kolter R.

Curr Top Microbiol Immunol. 2008;322:1-16. Review.

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