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Fecal dysbiosis in infants with cystic fibrosis is associated with early linear growth failure.

Hayden HS, Eng A, Pope CE, Brittnacher MJ, Vo AT, Weiss EJ, Hager KR, Martin BD, Leung DH, Heltshe SL, Borenstein E, Miller SI, Hoffman LR.

Nat Med. 2020 Feb;26(2):215-221. doi: 10.1038/s41591-019-0714-x. Epub 2020 Jan 20.


Defining and Evaluating Microbial Contributions to Metabolite Variation in Microbiome-Metabolome Association Studies.

Noecker C, Chiu HC, McNally CP, Borenstein E.

mSystems. 2019 Dec 17;4(6). pii: e00579-19. doi: 10.1128/mSystems.00579-19.


Human gut bacteria contain acquired interbacterial defence systems.

Ross BD, Verster AJ, Radey MC, Schmidtke DT, Pope CE, Hoffman LR, Hajjar AM, Peterson SB, Borenstein E, Mougous JD.

Nature. 2019 Nov;575(7781):224-228. doi: 10.1038/s41586-019-1708-z. Epub 2019 Oct 30.


Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice.

Sharon G, Cruz NJ, Kang DW, Gandal MJ, Wang B, Kim YM, Zink EM, Casey CP, Taylor BC, Lane CJ, Bramer LM, Isern NG, Hoyt DW, Noecker C, Sweredoski MJ, Moradian A, Borenstein E, Jansson JK, Knight R, Metz TO, Lois C, Geschwind DH, Krajmalnik-Brown R, Mazmanian SK.

Cell. 2019 May 30;177(6):1600-1618.e17. doi: 10.1016/j.cell.2019.05.004.


Microbial community design: methods, applications, and opportunities.

Eng A, Borenstein E.

Curr Opin Biotechnol. 2019 Aug;58:117-128. doi: 10.1016/j.copbio.2019.03.002. Epub 2019 Apr 3. Review.


Human and Extracellular DNA Depletion for Metagenomic Analysis of Complex Clinical Infection Samples Yields Optimized Viable Microbiome Profiles.

Nelson MT, Pope CE, Marsh RL, Wolter DJ, Weiss EJ, Hager KR, Vo AT, Brittnacher MJ, Radey MC, Hayden HS, Eng A, Miller SI, Borenstein E, Hoffman LR.

Cell Rep. 2019 Feb 19;26(8):2227-2240.e5. doi: 10.1016/j.celrep.2019.01.091.


The ketogenic diet influences taxonomic and functional composition of the gut microbiota in children with severe epilepsy.

Lindefeldt M, Eng A, Darban H, Bjerkner A, Zetterström CK, Allander T, Andersson B, Borenstein E, Dahlin M, Prast-Nielsen S.

NPJ Biofilms Microbiomes. 2019 Jan 23;5:5. doi: 10.1038/s41522-018-0073-2. eCollection 2019.


Competitive lottery-based assembly of selected clades in the human gut microbiome.

Verster AJ, Borenstein E.

Microbiome. 2018 Oct 19;6(1):186. doi: 10.1186/s40168-018-0571-8.


Metabolic model-based analysis of the emergence of bacterial cross-feeding via extensive gene loss.

McNally CP, Borenstein E.

BMC Syst Biol. 2018 Jun 15;12(1):69. doi: 10.1186/s12918-018-0588-4.


The Skin Microbiome of the Neotropical Frog Craugastor fitzingeri: Inferring Potential Bacterial-Host-Pathogen Interactions From Metagenomic Data.

Rebollar EA, Gutiérrez-Preciado A, Noecker C, Eng A, Hughey MC, Medina D, Walke JB, Borenstein E, Jensen RV, Belden LK, Harris RN.

Front Microbiol. 2018 Mar 20;9:466. doi: 10.3389/fmicb.2018.00466. eCollection 2018.


BURRITO: An Interactive Multi-Omic Tool for Visualizing Taxa-Function Relationships in Microbiome Data.

McNally CP, Eng A, Noecker C, Gagne-Maynard WC, Borenstein E.

Front Microbiol. 2018 Mar 1;9:365. doi: 10.3389/fmicb.2018.00365. eCollection 2018.


Taxa-function robustness in microbial communities.

Eng A, Borenstein E.

Microbiome. 2018 Mar 2;6(1):45. doi: 10.1186/s40168-018-0425-4.


Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis.

Matamouros S, Hayden HS, Hager KR, Brittnacher MJ, Lachance K, Weiss EJ, Pope CE, Imhaus AF, McNally CP, Borenstein E, Hoffman LR, Miller SI.

Proc Natl Acad Sci U S A. 2018 Feb 13;115(7):1605-1610. doi: 10.1073/pnas.1714373115. Epub 2018 Jan 29.


The Landscape of Type VI Secretion across Human Gut Microbiomes Reveals Its Role in Community Composition.

Verster AJ, Ross BD, Radey MC, Bao Y, Goodman AL, Mougous JD, Borenstein E.

Cell Host Microbe. 2017 Sep 13;22(3):411-419.e4. doi: 10.1016/j.chom.2017.08.010.


A broadly distributed toxin family mediates contact-dependent antagonism between gram-positive bacteria.

Whitney JC, Peterson SB, Kim J, Pazos M, Verster AJ, Radey MC, Kulasekara HD, Ching MQ, Bullen NP, Bryant D, Goo YA, Surette MG, Borenstein E, Vollmer W, Mougous JD.

Elife. 2017 Jul 11;6. pii: e26938. doi: 10.7554/eLife.26938.


Microbiome sharing between children, livestock and household surfaces in western Kenya.

Mosites E, Sammons M, Otiang E, Eng A, Noecker C, Manor O, Hilton S, Thumbi SM, Onyango C, Garland-Lewis G, Call DR, Njenga MK, Wasserheit JN, Zambriski JA, Walson JL, Palmer GH, Montgomery J, Borenstein E, Omore R, Rabinowitz PM.

PLoS One. 2017 Feb 2;12(2):e0171017. doi: 10.1371/journal.pone.0171017. eCollection 2017.


Systematic Characterization and Analysis of the Taxonomic Drivers of Functional Shifts in the Human Microbiome.

Manor O, Borenstein E.

Cell Host Microbe. 2017 Feb 8;21(2):254-267. doi: 10.1016/j.chom.2016.12.014. Epub 2017 Jan 19.


Influence of early life exposure, host genetics and diet on the mouse gut microbiome and metabolome.

Snijders AM, Langley SA, Kim YM, Brislawn CJ, Noecker C, Zink EM, Fansler SJ, Casey CP, Miller DR, Huang Y, Karpen GH, Celniker SE, Brown JB, Borenstein E, Jansson JK, Metz TO, Mao JH.

Nat Microbiol. 2016 Nov 28;2:16221. doi: 10.1038/nmicrobiol.2016.221.


High-resolution characterization of the human microbiome.

Noecker C, McNally CP, Eng A, Borenstein E.

Transl Res. 2017 Jan;179:7-23. doi: 10.1016/j.trsl.2016.07.012. Epub 2016 Jul 25. Review.


An Alignment-Free "Metapeptide" Strategy for Metaproteomic Characterization of Microbiome Samples Using Shotgun Metagenomic Sequencing.

May DH, Timmins-Schiffman E, Mikan MP, Harvey HR, Borenstein E, Nunn BL, Noble WS.

J Proteome Res. 2016 Aug 5;15(8):2697-705. doi: 10.1021/acs.jproteome.6b00239. Epub 2016 Jul 19.


Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation.

Noecker C, Eng A, Srinivasan S, Theriot CM, Young VB, Jansson JK, Fredricks DN, Borenstein E.

mSystems. 2016 Jan-Feb;1(1). pii: e00013-15. Epub 2016 Jan 19.


Evolutionary assembly patterns of prokaryotic genomes.

Press MO, Queitsch C, Borenstein E.

Genome Res. 2016 Jun;26(6):826-33. doi: 10.1101/gr.200097.115. Epub 2016 Apr 14.


An algorithm for designing minimal microbial communities with desired metabolic capacities.

Eng A, Borenstein E.

Bioinformatics. 2016 Jul 1;32(13):2008-16. doi: 10.1093/bioinformatics/btw107. Epub 2016 Feb 26.


Metagenomic evidence for taxonomic dysbiosis and functional imbalance in the gastrointestinal tracts of children with cystic fibrosis.

Manor O, Levy R, Pope CE, Hayden HS, Brittnacher MJ, Carr R, Radey MC, Hager KR, Heltshe SL, Ramsey BW, Miller SI, Hoffman LR, Borenstein E.

Sci Rep. 2016 Mar 4;6:22493. doi: 10.1038/srep22493.


Getting Personal About Nutrition.

Noecker C, Borenstein E.

Trends Mol Med. 2016 Feb;22(2):83-85. doi: 10.1016/j.molmed.2015.12.010. Epub 2016 Jan 14.


NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation.

Levy R, Carr R, Kreimer A, Freilich S, Borenstein E.

BMC Bioinformatics. 2015 May 17;16:164. doi: 10.1186/s12859-015-0588-y.


Extensive strain-level copy-number variation across human gut microbiome species.

Greenblum S, Carr R, Borenstein E.

Cell. 2015 Feb 12;160(4):583-594. doi: 10.1016/j.cell.2014.12.038. Epub 2015 Jan 29.


Where next for microbiome research?

Waldor MK, Tyson G, Borenstein E, Ochman H, Moeller A, Finlay BB, Kong HH, Gordon JI, Nelson KE, Dabbagh K, Smith H.

PLoS Biol. 2015 Jan 20;13(1):e1002050. doi: 10.1371/journal.pbio.1002050. eCollection 2015 Jan.


Conservation of trans-acting circuitry during mammalian regulatory evolution.

Stergachis AB, Neph S, Sandstrom R, Haugen E, Reynolds AP, Zhang M, Byron R, Canfield T, Stelhing-Sun S, Lee K, Thurman RE, Vong S, Bates D, Neri F, Diegel M, Giste E, Dunn D, Vierstra J, Hansen RS, Johnson AK, Sabo PJ, Wilken MS, Reh TA, Treuting PM, Kaul R, Groudine M, Bender MA, Borenstein E, Stamatoyannopoulos JA.

Nature. 2014 Nov 20;515(7527):365-70. doi: 10.1038/nature13972.


The discovery of integrated gene networks for autism and related disorders.

Hormozdiari F, Penn O, Borenstein E, Eichler EE.

Genome Res. 2015 Jan;25(1):142-54. doi: 10.1101/gr.178855.114. Epub 2014 Nov 5.


Hsp90 promotes kinase evolution.

Lachowiec J, Lemus T, Borenstein E, Queitsch C.

Mol Biol Evol. 2015 Jan;32(1):91-9. doi: 10.1093/molbev/msu270. Epub 2014 Sep 21.


Mapping the inner workings of the microbiome: genomic- and metagenomic-based study of metabolism and metabolic interactions in the human microbiome.

Manor O, Levy R, Borenstein E.

Cell Metab. 2014 Nov 4;20(5):742-752. doi: 10.1016/j.cmet.2014.07.021. Epub 2014 Aug 28. Review.


Comparative analysis of functional metagenomic annotation and the mappability of short reads.

Carr R, Borenstein E.

PLoS One. 2014 Aug 22;9(8):e105776. doi: 10.1371/journal.pone.0105776. eCollection 2014.


Emergent biosynthetic capacity in simple microbial communities.

Chiu HC, Levy R, Borenstein E.

PLoS Comput Biol. 2014 Jul 3;10(7):e1003695. doi: 10.1371/journal.pcbi.1003695. eCollection 2014 Jul.


Metagenomic systems biology and metabolic modeling of the human microbiome: from species composition to community assembly rules.

Levy R, Borenstein E.

Gut Microbes. 2014 Mar-Apr;5(2):265-70. doi: 10.4161/gmic.28261. Epub 2014 Feb 20.


Escherichia coli dysbiosis correlates with gastrointestinal dysfunction in children with cystic fibrosis.

Hoffman LR, Pope CE, Hayden HS, Heltshe S, Levy R, McNamara S, Jacobs MA, Rohmer L, Radey M, Ramsey BW, Brittnacher MJ, Borenstein E, Miller SI.

Clin Infect Dis. 2014 Feb;58(3):396-9. doi: 10.1093/cid/cit715. Epub 2013 Oct 30.


Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution.

Carr R, Shen-Orr SS, Borenstein E.

PLoS Comput Biol. 2013;9(10):e1003292. doi: 10.1371/journal.pcbi.1003292. Epub 2013 Oct 17.


Genome-scale co-evolutionary inference identifies functions and clients of bacterial Hsp90.

Press MO, Li H, Creanza N, Kramer G, Queitsch C, Sourjik V, Borenstein E.

PLoS Genet. 2013;9(7):e1003631. doi: 10.1371/journal.pgen.1003631. Epub 2013 Jul 11.


Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules.

Levy R, Borenstein E.

Proc Natl Acad Sci U S A. 2013 Jul 30;110(31):12804-9. doi: 10.1073/pnas.1300926110. Epub 2013 Jul 15.


Towards a predictive systems-level model of the human microbiome: progress, challenges, and opportunities.

Greenblum S, Chiu HC, Levy R, Carr R, Borenstein E.

Curr Opin Biotechnol. 2013 Aug;24(4):810-20. doi: 10.1016/j.copbio.2013.04.001. Epub 2013 Apr 23. Review.


Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders.

O'Roak BJ, Vives L, Fu W, Egertson JD, Stanaway IB, Phelps IG, Carvill G, Kumar A, Lee C, Ankenman K, Munson J, Hiatt JB, Turner EH, Levy R, O'Day DR, Krumm N, Coe BP, Martin BK, Borenstein E, Nickerson DA, Mefford HC, Doherty D, Akey JM, Bernier R, Eichler EE, Shendure J.

Science. 2012 Dec 21;338(6114):1619-22. doi: 10.1126/science.1227764. Epub 2012 Nov 15.


Circuitry and dynamics of human transcription factor regulatory networks.

Neph S, Stergachis AB, Reynolds A, Sandstrom R, Borenstein E, Stamatoyannopoulos JA.

Cell. 2012 Sep 14;150(6):1274-86. doi: 10.1016/j.cell.2012.04.040. Epub 2012 Sep 5.


Reverse Ecology: from systems to environments and back.

Levy R, Borenstein E.

Adv Exp Med Biol. 2012;751:329-45. doi: 10.1007/978-1-4614-3567-9_15.


NetCmpt: a network-based tool for calculating the metabolic competition between bacterial species.

Kreimer A, Doron-Faigenboim A, Borenstein E, Freilich S.

Bioinformatics. 2012 Aug 15;28(16):2195-7. doi: 10.1093/bioinformatics/bts323. Epub 2012 Jun 4. Erratum in: Bioinformatics. 2012 Oct 1;28(19):2560.


Computational systems biology and in silico modeling of the human microbiome.

Borenstein E.

Brief Bioinform. 2012 Nov;13(6):769-80. doi: 10.1093/bib/bbs022. Epub 2012 May 15. Review.


Most networks in Wagner's model are cycling.

Pinho R, Borenstein E, Feldman MW.

PLoS One. 2012;7(4):e34285. doi: 10.1371/journal.pone.0034285. Epub 2012 Apr 12.


Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations.

O'Roak BJ, Vives L, Girirajan S, Karakoc E, Krumm N, Coe BP, Levy R, Ko A, Lee C, Smith JD, Turner EH, Stanaway IB, Vernot B, Malig M, Baker C, Reilly B, Akey JM, Borenstein E, Rieder MJ, Nickerson DA, Bernier R, Shendure J, Eichler EE.

Nature. 2012 Apr 4;485(7397):246-50. doi: 10.1038/nature10989.


NetSeed: a network-based reverse-ecology tool for calculating the metabolic interface of an organism with its environment.

Carr R, Borenstein E.

Bioinformatics. 2012 Mar 1;28(5):734-5. doi: 10.1093/bioinformatics/btr721. Epub 2012 Jan 4.


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