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Items: 20

1.

Experimental design and quantitative analysis of microbial community multiomics.

Mallick H, Ma S, Franzosa EA, Vatanen T, Morgan XC, Huttenhower C.

Genome Biol. 2017 Nov 30;18(1):228. doi: 10.1186/s13059-017-1359-z. Review.

2.

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.

3.

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.

4.

High-throughput automated microfluidic sample preparation for accurate microbial genomics.

Kim S, De Jonghe J, Kulesa AB, Feldman D, Vatanen T, Bhattacharyya RP, Berdy B, Gomez J, Nolan J, Epstein S, Blainey PC.

Nat Commun. 2017 Jan 27;8:13919. doi: 10.1038/ncomms13919.

5.

The effect of host genetics on the gut microbiome.

Bonder MJ, Kurilshikov A, Tigchelaar EF, Mujagic Z, Imhann F, Vila AV, Deelen P, Vatanen T, Schirmer M, Smeekens SP, Zhernakova DV, Jankipersadsing SA, Jaeger M, Oosting M, Cenit MC, Masclee AA, Swertz MA, Li Y, Kumar V, Joosten L, Harmsen H, Weersma RK, Franke L, Hofker MH, Xavier RJ, Jonkers D, Netea MG, Wijmenga C, Fu J, Zhernakova A.

Nat Genet. 2016 Nov;48(11):1407-1412. doi: 10.1038/ng.3663. Epub 2016 Oct 3.

PMID:
27694959
6.

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.

7.

Dysbiosis, inflammation, and response to treatment: a longitudinal study of pediatric subjects with newly diagnosed inflammatory bowel disease.

Shaw KA, Bertha M, Hofmekler T, Chopra P, Vatanen T, Srivatsa A, Prince J, Kumar A, Sauer C, Zwick ME, Satten GA, Kostic AD, Mulle JG, Xavier RJ, Kugathasan S.

Genome Med. 2016 Jul 13;8(1):75. doi: 10.1186/s13073-016-0331-y.

8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

The absence of macrophage Nrf2 promotes early atherogenesis.

Ruotsalainen AK, Inkala M, Partanen ME, Lappalainen JP, Kansanen E, Mäkinen PI, Heinonen SE, Laitinen HM, Heikkilä J, Vatanen T, Hörkkö S, Yamamoto M, Ylä-Herttuala S, Jauhiainen M, Levonen AL.

Cardiovasc Res. 2013 Apr 1;98(1):107-15. doi: 10.1093/cvr/cvt008. Epub 2013 Jan 22.

PMID:
23341579
15.

The effect of electron collimator leaf shape on the build-up dose in narrow electron MLC fields.

Vatanen T, Traneus E, Väänänen A, Lahtinen T.

Phys Med Biol. 2009 Dec 7;54(23):7211-26. doi: 10.1088/0031-9155/54/23/012. Epub 2009 Nov 17.

PMID:
19920308
16.

Enhancement of electron-beam surface dose with an electron multi-leaf collimator (eMLC): a feasibility study.

Vatanen T, Traneus E, Lahtinen T.

Phys Med Biol. 2009 Apr 21;54(8):2407-19. doi: 10.1088/0031-9155/54/8/010. Epub 2009 Apr 1.

PMID:
19336845
17.

Comparison of conventional inserts and an add-on electron MLC for chest wall irradiation of left-sided breast cancer.

Vatanen T, Traneus E, Lahtinen T.

Acta Oncol. 2009;48(3):446-51. doi: 10.1080/02841860802477907.

PMID:
18932098
18.

Minocycline reduces engraftment and activation of bone marrow-derived cells but sustains their phagocytic activity in a mouse model of Alzheimer's disease.

Malm TM, Magga J, Kuh GF, Vatanen T, Koistinaho M, Koistinaho J.

Glia. 2008 Dec;56(16):1767-79. doi: 10.1002/glia.20726.

PMID:
18649403
19.

Dosimetric verification of a Monte Carlo electron beam model for an add-on eMLC.

Vatanen T, Traneus E, Lahtinen T.

Phys Med Biol. 2008 Jan 21;53(2):391-404. doi: 10.1088/0031-9155/53/2/007. Epub 2007 Dec 28.

PMID:
18184994
20.

Bone-marrow-derived cells contribute to the recruitment of microglial cells in response to beta-amyloid deposition in APP/PS1 double transgenic Alzheimer mice.

Malm TM, Koistinaho M, Pärepalo M, Vatanen T, Ooka A, Karlsson S, Koistinaho J.

Neurobiol Dis. 2005 Feb;18(1):134-42.

PMID:
15649704

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