Joao Xavier: Publications

Joao Xavier: Publications

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Schluter J, Peled JU, Taylor BP, Markey KA, Smith M, Taur Y, Niehus R, Staffas A, Dai A, Fontana E, Amoretti LA, Wright RJ, Morjaria S, Fenelus M, Pessin MS, Chao NJ, Lew M, Bohannon L, Bush A, Sung AD, Hohl TM, Perales MA, van den Brink MRM, Xavier JB. The gut microbiota is associated with immune cell dynamics in humans. Nature. 2020 Dec;588(7837):303-307. doi: 10.1038/s41586-020-2971-8. Epub 2020 Nov 25. PMCID: PMC7725892.

Liao C, Wang T, Maslov S, Xavier JB. Modeling microbial cross-feeding at intermediate scale portrays community dynamics and species coexistence. PLoS Comput Biol. 2020 Aug 18;16(8):e1008135. doi: 10.1371/journal.pcbi.1008135. PMCID: PMC7480867.

Yan J, Estanbouli H, Liao C, Kim W, Monk JM, Rahman R, Kamboj M, Palsson BO, Qiu W, Xavier JB. Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection. PLoS Comput Biol. 2019 Dec 20;15(12):e1007562. doi: 10.1371/journal.pcbi.1007562. PMCID: PMC6944390.

Carmona-Fontaine C, Deforet M, Akkari L, Thompson CB, Joyce JA, Xavier JB. Metabolic origins of spatial organization in the tumor microenvironment. Proc Natl Acad Sci U S A. 2017 Mar 14;114(11):2934-2939. doi: 10.1073/pnas.1700600114. Epub 2017 Feb 28. PMCID: PMC5358370.

Deforet M, Carmona-Fontaine C, Korolev KS, Xavier JB. Evolution at the Edge of Expanding Populations. Am Nat. 2019 Sep;194(3):291-305. doi: 10.1086/704594. Epub 2019 Jul 24.

Morjaria S, Schluter J, Taylor BP, Littmann ER, Carter RA, Fontana E, Peled JU, van den Brink MRM, Xavier JB, Taur Y. Antibiotic-Induced Shifts in Fecal Microbiota Density and Composition during Hematopoietic Stem Cell Transplantation. Infect Immun. 2019 Aug 21;87(9). pii: e00206-19. doi: 10.1128/IAI.00206-19. Print 2019 Sep. PubMed Central PMCID: PMC6704593.

Yan J, Monaco H, Xavier JB. The Ultimate Guide to Bacterial Swarming: An Experimental Model to Study the Evolution of Cooperative Behavior. Annu Rev Microbiol. 2019 Sep 8;73:293-312. doi: 10.1146/annurev-micro-020518-120033. Epub 2019 Jun 10.

McKenney PT, Yan J, Vaubourgeix J, Becattini S, Lampen N, Motzer A, Larson PJ, Dannaoui D, Fujisawa S, Xavier JB, Pamer EG. Intestinal Bile Acids Induce a Morphotype Switch in Vancomycin-Resistant Enterococcus that Facilitates Intestinal Colonization. Cell Host Microbe. 2019 May 8;25(5):695-705.e5. doi: 10.1016/j.chom.2019.03.008. Epub 2019 Apr 25.

Dubin KA, Mathur D, McKenney PT, Taylor BP, Littmann ER, Peled JU, van den Brink MRM, Taur Y, Pamer EG, Xavier JB. Diversification and Evolution of Vancomycin-Resistant Enterococcus faecium during Intestinal Domination. Infect Immun. 2019 Jun 20;87(7). pii: e00102-19. doi: 10.1128/IAI.00102-19. Print 2019 Jul. PubMed Central PMCID: PMC6589067.

Schulfer AF, Schluter J, Zhang Y, Brown Q, Pathmasiri W, McRitchie S, Sumner S, Li H, Xavier JB, Blaser MJ. The impact of early-life sub-therapeutic antibiotic treatment (STAT) on excessive weight is robust despite transfer of intestinal microbes. ISME J. 2019 Jan 16. doi: 10.1038/s41396-019-0349-4. [Epub ahead of print].

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. Reconstitution of the gut microbiota of antibiotic-treated patients by autologous fecal microbiota transplant. Sci Transl Med. 2018 Sep 26;10(460). pii: eaap9489. doi:10.1126/scitranslmed.aap9489.

Logan SL, Thomas J, Yan J, Baker RP, Shields DS, Xavier JB, Hammer BK, Parthasarathy R. The Vibrio cholerae type VI secretion system can modulate host intestinal mechanics to displace gut bacterial symbionts. Proc Natl Acad Sci U S A. 2018 Apr 17;115(16):E3779-E3787. doi: 10.1073/pnas.1720133115. Epub 2018 Apr 2. PubMed Central PMCID: PMC5910850.

Yan J, Deforet M, Boyle KE, Rahman R, Liang R, Okegbe C, Dietrich LEP, Qiu W, Xavier JB. Bow-tie signaling in c-di-GMP: Machine learning in a simple biochemical network. PLoS Comput Biol. 2017 Aug 2;13(8):e1005677. doi:10.1371/journal.pcbi.1005677. eCollection 2017 Aug. PubMed Central PMCID: PMC5555705.

Boyle KE, Monaco HT, Deforet M, Yan J, Wang Z, Rhee K, Xavier JB. Metabolism and the Evolution of Social Behavior. Mol Biol Evol. 2017 Sep 1;34(9):2367-2379. doi:10.1093/molbev/msx174. PubMed Central PMCID: PMC5850603.

Yan J, Deforet M, Boyle KE, Rahman R, Liang R, Okegbe C, Dietrich LEP, Qiu W, Xavier JB. Bow-tie signaling in c-di-GMP: Machine learning in a simple biochemical network. PLoS Comput Biol. 2017 Aug 2;13(8):e1005677. doi: 10.1371/journal.pcbi.1005677. Epub 2017 Aug.

Boyle KE, Monaco HT, Deforet M, Yan J, Wang Z, Rhee K, Xavier JB. Metabolism and the Evolution of Social Behavior. Molecular biology and evolution. 2017;34(9):2367-79. Epub 2017/06/09. doi: 10.1093/molbev/msx174.

Carmona-Fontaine C, Deforet M, Akkari L, Thompson CB, Joyce JA, Xavier JB. Metabolic origins of spatial organization in the tumor microenvironment. Proc Natl Acad Sci U S A. 2017 Mar 14;114(11):2934-2939. doi: 10.1073/pnas.1700600114. Epub 2017 Feb 28.

Reviews

Xavier JB, Young VB, Skufca J, Ginty F, Testerman T, Pearson AT, Macklin P, Mitchell A, Shmulevich I, Xie L, Caporaso JG, Crandall KA, Simone NL, Godoy-Vitorino F, Griffin TJ, Whiteson KL, Gustafson HH, Slade DJ, Schmidt TM, Walther-Antonio MRS, Korem T, Webb-Robertson BM, Styczynski MP, Johnson WE, Jobin C, Ridlon JM, Koh AY, Yu M, Kelly L, Wargo JA. The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View. Trends Cancer. 2020 Mar;6(3):192-204. doi: 10.1016/j.trecan.2020.01.004. Epub 2020 Feb 7. PMCID: PMC7098063.

Yan J, Monaco H, Xavier JB. The Ultimate Guide to Bacterial Swarming: An Experimental Model to Study the Evolution of Cooperative Behavior. Annu Rev Microbiol. 2019 Sep 8;73:293-312. doi: 10.1146/annurev-micro-020518-120033. Epub 2019 Jun 10. PMCID: PMC7428860.

Korolev KS, Xavier JB, Gore J. Turning ecology and evolution against cancer. Nat Rev Cancer. 2014 May;14(5):371-80. doi: 10.1038/nrc3712. Epub 2014 Apr 17.

Bucci V, Xavier JB. Towards predictive models of the human gut microbiome. Journal of molecular biology. 2014;426(23):3907-16. Epub 2014/04/15. doi: 10.1016/j.jmb.2014.03.017.