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Items: 1 to 50 of 61


Evolution at the Edge of Expanding Populations.

Deforet M, Carmona-Fontaine C, Korolev KS, Xavier JB.

Am Nat. 2019 Sep;194(3):291-305. doi: 10.1086/704594. Epub 2019 Jul 24.


Antibiotic-Induced Shifts in Fecal Microbiota Density and Composition during Hematopoietic Stem Cell Transplantation.

Morjaria S, Schluter J, Taylor BP, Littmann ER, Carter RA, Fontana E, Peled JU, van den Brink MRM, Xavier JB, Taur Y.

Infect Immun. 2019 Aug 21;87(9). pii: e00206-19. doi: 10.1128/IAI.00206-19. Print 2019 Sep.


The Ultimate Guide to Bacterial Swarming: An Experimental Model to Study the Evolution of Cooperative Behavior.

Yan J, Monaco H, Xavier JB.

Annu Rev Microbiol. 2019 Sep 8;73:293-312. doi: 10.1146/annurev-micro-020518-120033. Epub 2019 Jun 10.


Intestinal Bile Acids Induce a Morphotype Switch in Vancomycin-Resistant Enterococcus that Facilitates Intestinal Colonization.

McKenney PT, Yan J, Vaubourgeix J, Becattini S, Lampen N, Motzer A, Larson PJ, Dannaoui D, Fujisawa S, Xavier JB, Pamer EG.

Cell Host Microbe. 2019 May 8;25(5):695-705.e5. doi: 10.1016/j.chom.2019.03.008. Epub 2019 Apr 25.


Diversification and Evolution of Vancomycin-Resistant Enterococcus faecium during Intestinal Domination.

Dubin KA, Mathur D, McKenney PT, Taylor BP, Littmann ER, Peled JU, van den Brink MRM, Taur Y, Pamer EG, Xavier JB.

Infect Immun. 2019 Jun 20;87(7). pii: e00102-19. doi: 10.1128/IAI.00102-19. Print 2019 Jul.


The impact of early-life sub-therapeutic antibiotic treatment (STAT) on excessive weight is robust despite transfer of intestinal microbes.

Schulfer AF, Schluter J, Zhang Y, Brown Q, Pathmasiri W, McRitchie S, Sumner S, Li H, Xavier JB, Blaser MJ.

ISME J. 2019 May;13(5):1280-1292. doi: 10.1038/s41396-019-0349-4. Epub 2019 Jan 16.


Reconstitution of the gut microbiota of antibiotic-treated patients by autologous fecal microbiota transplant.

Taur Y, Coyte K, Schluter J, Robilotti E, Figueroa C, Gjonbalaj M, Littmann ER, Ling L, Miller L, Gyaltshen Y, Fontana E, Morjaria S, Gyurkocza B, Perales MA, Castro-Malaspina H, Tamari R, Ponce D, Koehne G, Barker J, Jakubowski A, Papadopoulos E, Dahi P, Sauter C, Shaffer B, Young JW, Peled J, Meagher RC, Jenq RR, van den Brink MRM, Giralt SA, Pamer EG, Xavier JB.

Sci Transl Med. 2018 Sep 26;10(460). pii: eaap9489. doi: 10.1126/scitranslmed.aap9489.


The Vibrio cholerae type VI secretion system can modulate host intestinal mechanics to displace gut bacterial symbionts.

Logan SL, Thomas J, Yan J, Baker RP, Shields DS, Xavier JB, Hammer BK, Parthasarathy R.

Proc Natl Acad Sci U S A. 2018 Apr 17;115(16):E3779-E3787. doi: 10.1073/pnas.1720133115. Epub 2018 Apr 2.


Bow-tie signaling in c-di-GMP: Machine learning in a simple biochemical network.

Yan J, Deforet M, Boyle KE, Rahman R, Liang R, Okegbe C, Dietrich LEP, Qiu W, Xavier JB.

PLoS Comput Biol. 2017 Aug 2;13(8):e1005677. doi: 10.1371/journal.pcbi.1005677. eCollection 2017 Aug.


Metabolism and the Evolution of Social Behavior.

Boyle KE, Monaco HT, Deforet M, Yan J, Wang Z, Rhee K, Xavier JB.

Mol Biol Evol. 2017 Sep 1;34(9):2367-2379. doi: 10.1093/molbev/msx174.


Image-Based Measurement of H2O2 Reaction-Diffusion in Wounded Zebrafish Larvae.

Jelcic M, Enyedi B, Xavier JB, Niethammer P.

Biophys J. 2017 May 9;112(9):2011-2018. doi: 10.1016/j.bpj.2017.03.021.


Metabolic origins of spatial organization in the tumor microenvironment.

Carmona-Fontaine C, Deforet M, Akkari L, Thompson CB, Joyce JA, Xavier JB.

Proc Natl Acad Sci U S A. 2017 Mar 14;114(11):2934-2939. doi: 10.1073/pnas.1700600114. Epub 2017 Feb 28.


Microenvironment-derived factors driving metastatic plasticity in melanoma.

Kim IS, Heilmann S, Kansler ER, Zhang Y, Zimmer M, Ratnakumar K, Bowman RL, Simon-Vermot T, Fennell M, Garippa R, Lu L, Lee W, Hollmann T, Xavier JB, White RM.

Nat Commun. 2017 Feb 9;8:14343. doi: 10.1038/ncomms14343.


Sociomicrobiology and Pathogenic Bacteria.

Xavier JB.

Microbiol Spectr. 2016 Jun;4(3). doi: 10.1128/microbiolspec.VMBF-0019-2015. Review.


Human symbionts inject and neutralize antibacterial toxins to persist in the gut.

Wexler AG, Bao Y, Whitney JC, Bobay LM, Xavier JB, Schofield WB, Barry NA, Russell AB, Tran BQ, Goo YA, Goodlett DR, Ochman H, Mougous JD, Goodman AL.

Proc Natl Acad Sci U S A. 2016 Mar 29;113(13):3639-44. doi: 10.1073/pnas.1525637113. Epub 2016 Mar 8.


Facultative control of matrix production optimizes competitive fitness in Pseudomonas aeruginosa PA14 biofilm models.

Madsen JS, Lin YC, Squyres GR, Price-Whelan A, de Santiago Torio A, Song A, Cornell WC, Sørensen SJ, Xavier JB, Dietrich LE.

Appl Environ Microbiol. 2015 Dec;81(24):8414-26. doi: 10.1128/AEM.02628-15. Epub 2015 Oct 2.


Cell-Size Homeostasis and the Incremental Rule in a Bacterial Pathogen.

Deforet M, van Ditmarsch D, Xavier JB.

Biophys J. 2015 Aug 4;109(3):521-8. doi: 10.1016/j.bpj.2015.07.002.


Integration of Metabolic and Quorum Sensing Signals Governing the Decision to Cooperate in a Bacterial Social Trait.

Boyle KE, Monaco H, van Ditmarsch D, Deforet M, Xavier JB.

PLoS Comput Biol. 2015 Jun 23;11(5):e1004279. doi: 10.1371/journal.pcbi.1004279. eCollection 2015 May.


Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile.

Buffie CG, Bucci V, Stein RR, McKenney PT, Ling L, Gobourne A, No D, Liu H, Kinnebrew M, Viale A, Littmann E, van den Brink MR, Jenq RR, Taur Y, Sander C, Cross JR, Toussaint NC, Xavier JB, Pamer EG.

Nature. 2015 Jan 8;517(7533):205-8. doi: 10.1038/nature13828. Epub 2014 Oct 22.


Turning ecology and evolution against cancer.

Korolev KS, Xavier JB, Gore J.

Nat Rev Cancer. 2014 May;14(5):371-80. doi: 10.1038/nrc3712. Epub 2014 Apr 17. Review.


Towards predictive models of the human gut microbiome.

Bucci V, Xavier JB.

J Mol Biol. 2014 Nov 25;426(23):3907-16. doi: 10.1016/j.jmb.2014.03.017. Epub 2014 Apr 12. Review.


Hyperswarming adaptations in a bacterium improve collective motility without enhancing single cell motility.

Deforet M, van Ditmarsch D, Carmona-Fontaine C, Xavier JB.

Soft Matter. 2014 Apr 14;10(14):2405-13. doi: 10.1039/c3sm53127a.


The ecological basis of morphogenesis: branching patterns in swarming colonies of bacteria.

Deng P, de Vargas Roditi L, van Ditmarsch D, Xavier JB.

New J Phys. 2014 Jan;16:015006-15006.


Tumour-stromal interactions generate emergent persistence in collective cancer cell migration.

Chang WK, Carmona-Fontaine C, Xavier JB.

Interface Focus. 2013 Aug 6;3(4):20130017. doi: 10.1098/rsfs.2013.0017.


Different levels of catabolite repression optimize growth in stable and variable environments.

New AM, Cerulus B, Govers SK, Perez-Samper G, Zhu B, Boogmans S, Xavier JB, Verstrepen KJ.

PLoS Biol. 2014 Jan;12(1):e1001764. doi: 10.1371/journal.pbio.1001764. Epub 2014 Jan 14.


Seeing is believing: what experiments with microbes reveal about evolution.

van Ditmarsch D, Xavier JB.

Trends Microbiol. 2014 Jan;22(1):2-4. doi: 10.1016/j.tim.2013.11.004.


Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota.

Stein RR, Bucci V, Toussaint NC, Buffie CG, Rätsch G, Pamer EG, Sander C, Xavier JB.

PLoS Comput Biol. 2013;9(12):e1003388. doi: 10.1371/journal.pcbi.1003388. Epub 2013 Dec 12.


Emergence of spatial structure in the tumor microenvironment due to the Warburg effect.

Carmona-Fontaine C, Bucci V, Akkari L, Deforet M, Joyce JA, Xavier JB.

Proc Natl Acad Sci U S A. 2013 Nov 26;110(48):19402-7. doi: 10.1073/pnas.1311939110. Epub 2013 Nov 11.


Multilevel selection analysis of a microbial social trait.

de Vargas Roditi L, Boyle KE, Xavier JB.

Mol Syst Biol. 2013 Aug 20;9:684. doi: 10.1038/msb.2013.42.


Convergent evolution of hyperswarming leads to impaired biofilm formation in pathogenic bacteria.

van Ditmarsch D, Boyle KE, Sakhtah H, Oyler JE, Nadell CD, Déziel É, Dietrich LE, Xavier JB.

Cell Rep. 2013 Aug 29;4(4):697-708. doi: 10.1016/j.celrep.2013.07.026. Epub 2013 Aug 15.


Cutting through the complexity of cell collectives.

Nadell CD, Bucci V, Drescher K, Levin SA, Bassler BL, Xavier JB.

Proc Biol Sci. 2013 Jan 30;280(1755):20122770. doi: 10.1098/rspb.2012.2770. Print 2013 Mar 22. Review.


Exploiting social evolution in biofilms.

Boyle KE, Heilmann S, van Ditmarsch D, Xavier JB.

Curr Opin Microbiol. 2013 Apr;16(2):207-12. doi: 10.1016/j.mib.2013.01.003. Epub 2013 Jan 26. Review.


Intestinal microbiota containing Barnesiella species cures vancomycin-resistant Enterococcus faecium colonization.

Ubeda C, Bucci V, Caballero S, Djukovic A, Toussaint NC, Equinda M, Lipuma L, Ling L, Gobourne A, No D, Taur Y, Jenq RR, van den Brink MR, Xavier JB, Pamer EG.

Infect Immun. 2013 Mar;81(3):965-73. doi: 10.1128/IAI.01197-12. Epub 2013 Jan 14.


Altruistic cell death and collective drug resistance.

Carmona-Fontaine C, Xavier JB.

Mol Syst Biol. 2012;8:627. doi: 10.1038/msb.2012.60. No abstract available.


Microbiology. Animal behavior and the microbiome.

Ezenwa VO, Gerardo NM, Inouye DW, Medina M, Xavier JB.

Science. 2012 Oct 12;338(6104):198-9. doi: 10.1126/science.1227412. No abstract available.


Intestinal domination and the risk of bacteremia in patients undergoing allogeneic hematopoietic stem cell transplantation.

Taur Y, Xavier JB, Lipuma L, Ubeda C, Goldberg J, Gobourne A, Lee YJ, Dubin KA, Socci ND, Viale A, Perales MA, Jenq RR, van den Brink MR, Pamer EG.

Clin Infect Dis. 2012 Oct;55(7):905-14. doi: 10.1093/cid/cis580. Epub 2012 Jun 20.


Social interaction, noise and antibiotic-mediated switches in the intestinal microbiota.

Bucci V, Bradde S, Biroli G, Xavier JB.

PLoS Comput Biol. 2012;8(4):e1002497. doi: 10.1371/journal.pcbi.1002497. Epub 2012 Apr 26.


The evolution of bacteriocin production in bacterial biofilms.

Bucci V, Nadell CD, Xavier JB.

Am Nat. 2011 Dec;178(6):E162-73. doi: 10.1086/662668. Epub 2011 Oct 26.


A quantitative test of population genetics using spatiogenetic patterns in bacterial colonies.

Korolev KS, Xavier JB, Nelson DR, Foster KR.

Am Nat. 2011 Oct;178(4):538-52. doi: 10.1086/661897. Epub 2011 Aug 19.


Social evolution in multispecies biofilms.

Mitri S, Xavier JB, Foster KR.

Proc Natl Acad Sci U S A. 2011 Jun 28;108 Suppl 2:10839-46. doi: 10.1073/pnas.1100292108. Epub 2011 Jun 20.


Social interaction in synthetic and natural microbial communities.

Xavier JB.

Mol Syst Biol. 2011 Apr 12;7:483. doi: 10.1038/msb.2011.16. Review.


A molecular mechanism that stabilizes cooperative secretions in Pseudomonas aeruginosa.

Xavier JB, Kim W, Foster KR.

Mol Microbiol. 2011 Jan;79(1):166-79. doi: 10.1111/j.1365-2958.2010.07436.x. Epub 2010 Nov 2.


Principle of system balance for drug interactions.

Xavier JB, Sander C.

N Engl J Med. 2010 Apr 8;362(14):1339-40. doi: 10.1056/NEJMcibr1001270. No abstract available.


Emergence of spatial structure in cell groups and the evolution of cooperation.

Nadell CD, Foster KR, Xavier JB.

PLoS Comput Biol. 2010 Mar 19;6(3):e1000716. doi: 10.1371/journal.pcbi.1000716.


Social evolution of spatial patterns in bacterial biofilms: when conflict drives disorder.

Xavier JB, Martinez-Garcia E, Foster KR.

Am Nat. 2009 Jul;174(1):1-12. doi: 10.1086/599297.


The sociobiology of biofilms.

Nadell CD, Xavier JB, Foster KR.

FEMS Microbiol Rev. 2009 Jan;33(1):206-24. doi: 10.1111/j.1574-6976.2008.00150.x. Epub 2008 Dec 3. Review.


The evolution of quorum sensing in bacterial biofilms.

Nadell CD, Xavier JB, Levin SA, Foster KR.

PLoS Biol. 2008 Jan;6(1):e14. doi: 10.1371/journal.pbio.0060014.


Multi-scale individual-based model of microbial and bioconversion dynamics in aerobic granular sludge.

Xavier JB, De Kreuk MK, Picioreanu C, Van Loosdrecht MC.

Environ Sci Technol. 2007 Sep 15;41(18):6410-7.


Stochastic modeling for characterisation of biofilm development with discrete detachment events (sloughing).

Bohn A, Zippel B, Almeida JS, Xavier JB.

Water Sci Technol. 2007;55(8-9):257-64.


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