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Items: 40

1.

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
2.

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.

3.

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.

PMID:
29311644
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.

bioBakery: a meta'omic analysis environment.

McIver LJ, Abu-Ali G, Franzosa EA, Schwager R, Morgan XC, Waldron L, Segata N, Huttenhower C.

Bioinformatics. 2018 Apr 1;34(7):1235-1237. doi: 10.1093/bioinformatics/btx754.

6.

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.

7.

Erratum: Strains, functions and dynamics in the expanded Human Microbiome Project.

Lloyd-Price J, Mahurkar A, Rahnavard G, Crabtree J, Orvis J, Hall AB, Brady A, Creasy HH, McCracken C, Giglio MG, McDonald D, Franzosa EA, Knight R, White O, Huttenhower C.

Nature. 2017 Nov 9;551(7679):256. doi: 10.1038/nature24485. Epub 2017 Oct 12.

PMID:
29022944
8.

Strains, functions and dynamics in the expanded Human Microbiome Project.

Lloyd-Price J, Mahurkar A, Rahnavard G, Crabtree J, Orvis J, Hall AB, Brady A, Creasy HH, McCracken C, Giglio MG, McDonald D, Franzosa EA, Knight R, White O, Huttenhower C.

Nature. 2017 Oct 5;550(7674):61-66. doi: 10.1038/nature23889. Epub 2017 Sep 20. Erratum in: Nature. 2017 Oct 12;:.

9.

Fluoride Depletes Acidogenic Taxa in Oral but Not Gut Microbial Communities in Mice.

Yasuda K, Hsu T, Gallini CA, Mclver LJ, Schwager E, Shi A, DuLong CR, Schwager RN, Abu-Ali GS, Franzosa EA, Garrett WS, Huttenhower C, Morgan XC.

mSystems. 2017 Aug 8;2(4). pii: e00047-17. doi: 10.1128/mSystems.00047-17. eCollection 2017 Jul-Aug.

10.

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.

11.

A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans-4-hydroxy-l-proline.

Levin BJ, Huang YY, Peck SC, Wei Y, Martínez-Del Campo A, Marks JA, Franzosa EA, Huttenhower C, Balskus EP.

Science. 2017 Feb 10;355(6325). pii: eaai8386. doi: 10.1126/science.aai8386.

12.

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.

13.

A conserved bacterial protein induces pancreatic beta cell expansion during zebrafish development.

Hill JH, Franzosa EA, Huttenhower C, Guillemin K.

Elife. 2016 Dec 13;5. pii: e20145. doi: 10.7554/eLife.20145.

14.

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.

15.

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
16.

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.

17.

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.

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 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.

19.

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.

20.

High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED.

Kaminski J, Gibson MK, Franzosa EA, Segata N, Dantas G, Huttenhower C.

PLoS Comput Biol. 2015 Dec 18;11(12):e1004557. doi: 10.1371/journal.pcbi.1004557. eCollection 2015 Dec.

21.

MetaPhlAn2 for enhanced metagenomic taxonomic profiling.

Truong DT, Franzosa EA, Tickle TL, Scholz M, Weingart G, Pasolli E, Tett A, Huttenhower C, Segata N.

Nat Methods. 2015 Oct;12(10):902-3. doi: 10.1038/nmeth.3589. No abstract available. Erratum in: Nat Methods. 2016 Jan;13(1):101.

PMID:
26418763
22.

A reproducible approach to high-throughput biological data acquisition and integration.

Börnigen D, Moon YS, Rahnavard G, Waldron L, McIver L, Shafquat A, Franzosa EA, Miropolsky L, Sweeney C, Morgan XC, Garrett WS, Huttenhower C.

PeerJ. 2015 Mar 31;3:e791. doi: 10.7717/peerj.791. eCollection 2015.

23.

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.

24.

Sequencing and beyond: integrating molecular 'omics' for microbial community profiling.

Franzosa EA, Hsu T, Sirota-Madi A, Shafquat A, Abu-Ali G, Morgan XC, Huttenhower C.

Nat Rev Microbiol. 2015 Jun;13(6):360-72. doi: 10.1038/nrmicro3451. Epub 2015 Apr 27. Review.

25.

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.

26.

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.

27.

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.

28.

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.

29.

Signatures of pleiotropy, economy and convergent evolution in a domain-resolved map of human-virus protein-protein interaction networks.

Garamszegi S, Franzosa EA, Xia Y.

PLoS Pathog. 2013;9(12):e1003778. doi: 10.1371/journal.ppat.1003778. Epub 2013 Dec 5.

30.

Functional profiling of the gut microbiome in disease-associated inflammation.

Börnigen D, Morgan XC, Franzosa EA, Ren B, Xavier RJ, Garrett WS, Huttenhower C.

Genome Med. 2013 Jul 31;5(7):65. doi: 10.1186/gm469. eCollection 2013. Review.

31.

Quantitative residue-level structure-evolution relationships in the yeast membrane proteome.

Franzosa EA, Xue R, Xia Y.

Genome Biol Evol. 2013;5(4):734-44. doi: 10.1093/gbe/evt039.

32.

Toward a three-dimensional view of protein networks between species.

Franzosa EA, Garamszegi S, Xia Y.

Front Microbiol. 2012 Dec 21;3:428. doi: 10.3389/fmicb.2012.00428. eCollection 2012.

33.

Construction of functional linkage gene networks by data integration.

Linghu B, Franzosa EA, Xia Y.

Methods Mol Biol. 2013;939:215-32. doi: 10.1007/978-1-62703-107-3_14.

PMID:
23192549
34.

Independent effects of protein core size and expression on residue-level structure-evolution relationships.

Franzosa EA, Xia Y.

PLoS One. 2012;7(10):e46602. doi: 10.1371/journal.pone.0046602. Epub 2012 Oct 3.

35.
36.

Heterozygous yeast deletion collection screens reveal essential targets of Hsp90.

Franzosa EA, Albanèse V, Frydman J, Xia Y, McClellan AJ.

PLoS One. 2011;6(11):e28211. doi: 10.1371/journal.pone.0028211. Epub 2011 Nov 30.

37.

Structural principles within the human-virus protein-protein interaction network.

Franzosa EA, Xia Y.

Proc Natl Acad Sci U S A. 2011 Jun 28;108(26):10538-43. doi: 10.1073/pnas.1101440108. Epub 2011 Jun 16.

38.

Protein evolution in yeast transcription factor subnetworks.

Wang Y, Franzosa EA, Zhang XS, Xia Y.

Nucleic Acids Res. 2010 Oct;38(18):5959-69. doi: 10.1093/nar/gkq353. Epub 2010 May 13.

39.

Structural determinants of protein evolution are context-sensitive at the residue level.

Franzosa EA, Xia Y.

Mol Biol Evol. 2009 Oct;26(10):2387-95. doi: 10.1093/molbev/msp146. Epub 2009 Jul 13.

PMID:
19597162
40.

Integrated assessment of genomic correlates of protein evolutionary rate.

Xia Y, Franzosa EA, Gerstein MB.

PLoS Comput Biol. 2009 Jun;5(6):e1000413. doi: 10.1371/journal.pcbi.1000413. Epub 2009 Jun 12.

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