1: Sheppard S, Srpan K, Lin W, Lee M, Delconte RB, Owyong M, Carmeliet P, Davis
DM, Xavier JB, Hsu KC, Sun JC. Fatty acid oxidation fuels natural killer cell
responses against infection and cancer. Proc Natl Acad Sci U S A. 2024 Mar
12;121(11):e2319254121. doi: 10.1073/pnas.2319254121. Epub 2024 Mar 5. PMID:
38442180; PMCID: PMC10945797.

2: Mathur D, Liao C, Lin W, La Ferlita A, Alaimo S, Taylor S, Zhong Y,
Iacobuzio-Donahue C, Ferro A, Xavier JB. The Ratio of Key Metabolic Transcripts
Is a Predictive Biomarker of Breast Cancer Metastasis to the Lung. Cancer Res.
2023 Oct 13;83(20):3478-3491. doi: 10.1158/0008-5472.CAN-23-0153. PMID:
37526524; PMCID: PMC10570685.

3: Xavier JB. Machine learning of cellular metabolic rewiring. bioRxiv
[Preprint]. 2023 Oct 10:2023.08.11.552957. doi: 10.1101/2023.08.11.552957. PMID:
37645838; PMCID: PMC10462012.

4: Schluter J, Djukovic A, Taylor BP, Yan J, Duan C, Hussey GA, Liao C, Sharma
S, Fontana E, Amoretti LA, Wright RJ, Dai A, Peled JU, Taur Y, Perales MA,
Siranosian BA, Bhatt AS, van den Brink MRM, Pamer EG, Xavier JB. The TaxUMAP
atlas: Efficient display of large clinical microbiome data reveals ecological
competition in protection against bacteremia. Cell Host Microbe. 2023 Jul
12;31(7):1126-1139.e6. doi: 10.1016/j.chom.2023.05.027. Epub 2023 Jun 16. PMID:
37329880; PMCID: PMC10527165.

5: Nguyen CL, Markey KA, Miltiadous O, Dai A, Waters N, Sadeghi K, Fei T,
Shouval R, Taylor BP, Liao C, Slingerland JB, Slingerland AE, Clurman AG, Maloy
MA, Bohannon L, Giardina PA, Brereton DG, Armijo GK, Fontana E, Gradissimo A,
Gyurkocza B, Sung AD, Chao NJ, Devlin SM, Taur Y, Giralt SA, Perales MA, Xavier
JB, Pamer EG, Peled JU, Gomes ALC, van den Brink MRM. High-resolution analyses
of associations between medications, microbiome, and mortality in cancer
patients. Cell. 2023 Jun 8;186(12):2705-2718.e17. doi:
10.1016/j.cell.2023.05.007. Epub 2023 Jun 8. PMID: 37295406; PMCID: PMC10390075.

6: Santamaria G, Liao C, Lindberg C, Chen Y, Wang Z, Rhee K, Pinto FR, Yan J,
Xavier JB. Evolution and regulation of microbial secondary metabolism. Elife.
2022 Nov 21;11:e76119. doi: 10.7554/eLife.76119. PMID: 36409069; PMCID:
PMC9708071.

7: Djukovic A, Garzón MJ, Canlet C, Cabral V, Lalaoui R, García-Garcerá M,
Rechenberger J, Tremblay-Franco M, Peñaranda I, Puchades-Carrasco L, Pineda-
Lucena A, González-Barberá EM, Salavert M, López-Hontangas JL, Sanz MÁ, Sanz J,
Kuster B, Rolain JM, Debrauwer L, Xavier KB, Xavier JB, Ubeda C. Lactobacillus
supports Clostridiales to restrict gut colonization by multidrug-resistant
Enterobacteriaceae. Nat Commun. 2022 Sep 24;13(1):5617. doi:
10.1038/s41467-022-33313-w. PMID: 36153315; PMCID: PMC9509339.

8: Mathur D, Barnett E, Scher HI, Xavier JB. Optimizing the future: how
mathematical models inform treatment schedules for cancer. Trends Cancer. 2022
Jun;8(6):506-516. doi: 10.1016/j.trecan.2022.02.005. Epub 2022 Mar 9. PMID:
35277375; PMCID: PMC9117454.

9: Yan J, Liao C, Taylor BP, Fontana E, Amoretti LA, Wright RJ, Littmann ER, Dai
A, Waters N, Peled JU, Taur Y, Perales MA, Siranosian BA, Bhatt AS, van den
Brink MRM, Pamer EG, Schluter J, Xavier JB. A compilation of fecal microbiome
shotgun metagenomics from hematopoietic cell transplantation patients. Sci Data.
2022 May 18;9(1):219. doi: 10.1038/s41597-022-01302-9. PMID: 35585088; PMCID:
PMC9117330.

10: Mathur D, Taylor BP, Chatila WK, Scher HI, Schultz N, Razavi P, Xavier JB.
Optimal Strategy and Benefit of Pulsed Therapy Depend On Tumor Heterogeneity and
Aggressiveness at Time of Treatment Initiation. Mol Cancer Ther. 2022 May
4;21(5):831-843. doi: 10.1158/1535-7163.MCT-21-0574. PMID: 35247928; PMCID:
PMC9081172.

11: Xavier JB, Monk JM, Poudel S, Norsigian CJ, Sastry AV, Liao C, Bento J,
Suchard MA, Arrieta-Ortiz ML, Peterson EJR, Baliga NS, Stoeger T, Ruffin F,
Richardson RAK, Gao CA, Horvath TD, Haag AM, Wu Q, Savidge T, Yeaman MR.
Mathematical models to study the biology of pathogens and the infectious
diseases they cause. iScience. 2022 Mar 15;25(4):104079. doi:
10.1016/j.isci.2022.104079. PMID: 35359802; PMCID: PMC8961237.

12: Monaco H, Liu KS, Sereno T, Deforet M, Taylor BP, Chen Y, Reagor CC, Xavier
JB. Spatial-temporal dynamics of a microbial cooperative behavior resistant to
cheating. Nat Commun. 2022 Feb 7;13(1):721. doi: 10.1038/s41467-022-28321-9.
PMID: 35132084; PMCID: PMC8821651.

13: Rolling T, Zhai B, Gjonbalaj M, Tosini N, Yasuma-Mitobe K, Fontana E,
Amoretti LA, Wright RJ, Ponce DM, Perales MA, Xavier JB, van den Brink MRM,
Markey KA, Peled JU, Taur Y, Hohl TM. Haematopoietic cell transplantation
outcomes are linked to intestinal mycobiota dynamics and an expansion of Candida
parapsilosis complex species. Nat Microbiol. 2021 Dec;6(12):1505-1515. doi:
10.1038/s41564-021-00989-7. Epub 2021 Nov 11. PMID: 34764444; PMCID: PMC8939874.

14: Mishra V, Xavier JB. Unclouding Clostridiodes difficile virulence with
systems biology. Cell Host Microbe. 2021 Nov 10;29(11):1608-1610. doi:
10.1016/j.chom.2021.10.005. PMID: 34762827.

15: Campbell NR, Rao A, Hunter MV, Sznurkowska MK, Briker L, Zhang M, Baron M,
Heilmann S, Deforet M, Kenny C, Ferretti LP, Huang TH, Perlee S, Garg M,
Nsengimana J, Saini M, Montal E, Tagore M, Newton-Bishop J, Middleton MR, Corrie
P, Adams DJ, Rabbie R, Aceto N, Levesque MP, Cornell RA, Yanai I, Xavier JB,
White RM. Cooperation between melanoma cell states promotes metastasis through
heterotypic cluster formation. Dev Cell. 2021 Oct 25;56(20):2808-2825.e10. doi:
10.1016/j.devcel.2021.08.018. Epub 2021 Sep 15. PMID: 34529939; PMCID:
PMC8551056.

16: Lin W, Djukovic A, Mathur D, Xavier JB. Listening in on the conversation
between the human gut microbiome and its host. Curr Opin Microbiol. 2021
Oct;63:150-157. doi: 10.1016/j.mib.2021.07.009. Epub 2021 Aug 2. PMID: 34352595.

17: Liao C, Taylor BP, Ceccarani C, Fontana E, Amoretti LA, Wright RJ, Gomes
ALC, Peled JU, Taur Y, Perales MA, van den Brink MRM, Littmann E, Pamer EG,
Schluter J, Xavier JB. Author Correction: Compilation of longitudinal microbiota
data and hospitalome from hematopoietic cell transplantation patients. Sci Data.
2021 Apr 23;8(1):119. doi: 10.1038/s41597-021-00903-0. Erratum for: Sci Data.
2021 Mar 2;8(1):71. PMID: 33893321; PMCID: PMC8065137.

18: Liao C, Taylor BP, Ceccarani C, Fontana E, Amoretti LA, Wright RJ, Gomes
ALC, Peled JU, Taur Y, Perales MA, van den Brink MRM, Littmann E, Pamer EG,
Schluter J, Xavier JB. Compilation of longitudinal microbiota data and
hospitalome from hematopoietic cell transplantation patients. Sci Data. 2021 Mar
2;8(1):71. doi: 10.1038/s41597-021-00860-8. Erratum in: Sci Data. 2021 Apr
23;8(1):119. PMID: 33654104; PMCID: PMC7925583.

19: 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. PMID: 33239790; PMCID: PMC7725892.

20: 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.
PMID: 32810127; PMCID: PMC7480867.

21: Joseph TA, Shenhav L, Xavier JB, Halperin E, Pe’er I. Compositional Lotka-
Volterra describes microbial dynamics in the simplex. PLoS Comput Biol. 2020 May
29;16(5):e1007917. doi: 10.1371/journal.pcbi.1007917. PMID: 32469867; PMCID:
PMC7325845.

22: 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. PMID: 32101723; PMCID: PMC7098063.

23: Peled JU, Gomes ALC, Devlin SM, Littmann ER, Taur Y, Sung AD, Weber D,
Hashimoto D, Slingerland AE, Slingerland JB, Maloy M, Clurman AG, Stein-
Thoeringer CK, Markey KA, Docampo MD, Burgos da Silva M, Khan N, Gessner A,
Messina JA, Romero K, Lew MV, Bush A, Bohannon L, Brereton DG, Fontana E,
Amoretti LA, Wright RJ, Armijo GK, Shono Y, Sanchez-Escamilla M, Castillo Flores
N, Alarcon Tomas A, Lin RJ, Yáñez San Segundo L, Shah GL, Cho C, Scordo M,
Politikos I, Hayasaka K, Hasegawa Y, Gyurkocza B, Ponce DM, Barker JN, Perales
MA, Giralt SA, Jenq RR, Teshima T, Chao NJ, Holler E, Xavier JB, Pamer EG, van
den Brink MRM. Microbiota as Predictor of Mortality in Allogeneic Hematopoietic-
Cell Transplantation. N Engl J Med. 2020 Feb 27;382(9):822-834. doi:
10.1056/NEJMoa1900623. PMID: 32101664; PMCID: PMC7534690.

24: Laughney AM, Hu J, Campbell NR, Bakhoum SF, Setty M, Lavallée VP, Xie Y,
Masilionis I, Carr AJ, Kottapalli S, Allaj V, Mattar M, Rekhtman N, Xavier JB,
Mazutis L, Poirier JT, Rudin CM, Pe’er D, Massagué J. Regenerative lineages and
immune-mediated pruning in lung cancer metastasis. Nat Med. 2020
Feb;26(2):259-269. doi: 10.1038/s41591-019-0750-6. Epub 2020 Feb 10. PMID:
32042191; PMCID: PMC7021003.

25: Djukovic A, González-Barberá EM, Sanz J, Artacho A, Peñaranda I, Herrera B,
Garzón MJ, Salavert M, López-Hontangas JL, Xavier KB, Kuster B, Debrauwer L,
Rolain JM, Sanz MA, Xavier JB, Ubeda C. High Heterogeneity of Multidrug-
Resistant <i>Enterobacteriaceae</i> Fecal Levels in Hospitalized Patients Is
Partially Driven by Intravenous β-Lactams. Antimicrob Agents Chemother. 2020 Jan
27;64(2):e01415-19. doi: 10.1128/AAC.01415-19. PMID: 31767720; PMCID:
PMC6985730.

26: Liao C, Xavier JB, Zhu Z. Enhanced inference of ecological networks by
parameterizing ensembles of population dynamics models constrained with prior
knowledge. BMC Ecol. 2020 Jan 8;20(1):3. doi: 10.1186/s12898-019-0272-6. PMID:
31914976; PMCID: PMC6950893.

27: 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. PMID:
31860667; PMCID: PMC6944390.

28: Stein-Thoeringer CK, Nichols KB, Lazrak A, Docampo MD, Slingerland AE,
Slingerland JB, Clurman AG, Armijo G, Gomes ALC, Shono Y, Staffas A, Burgos da
Silva M, Devlin SM, Markey KA, Bajic D, Pinedo R, Tsakmaklis A, Littmann ER,
Pastore A, Taur Y, Monette S, Arcila ME, Pickard AJ, Maloy M, Wright RJ,
Amoretti LA, Fontana E, Pham D, Jamal MA, Weber D, Sung AD, Hashimoto D, Scheid
C, Xavier JB, Messina JA, Romero K, Lew M, Bush A, Bohannon L, Hayasaka K,
Hasegawa Y, Vehreschild MJGT, Cross JR, Ponce DM, Perales MA, Giralt SA, Jenq
RR, Teshima T, Holler E, Chao NJ, Pamer EG, Peled JU, van den Brink MRM. Lactose
drives <i>Enterococcus</i> expansion to promote graft-versus-host disease.
Science. 2019 Nov 29;366(6469):1143-1149. doi: 10.1126/science.aax3760. PMID:
31780560; PMCID: PMC7003985.

29: 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. PMID: 31180806; PMCID: PMC7428860.

30: 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):e00206-19. doi:
10.1128/IAI.00206-19. PMID: 31262981; PMCID: PMC6704593.

31: 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):e00102-19. doi: 10.1128/IAI.00102-19. PMID: 31010813;
PMCID: PMC6589067.

32: 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. PMID: 31031170; PMCID: PMC6939634.

33: 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 May;13(5):1280-1292. doi:
10.1038/s41396-019-0349-4. Epub 2019 Jan 16. PMID: 30651608; PMCID: PMC6474226.

34: 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):eaap9489. doi:
10.1126/scitranslmed.aap9489. PMID: 30257956; PMCID: PMC6468978.

35: Logan SL, Thomas J, Yan J, Baker RP, Shields DS, Xavier JB, Hammer BK,
Parthasarathy R. The <i>Vibrio cholerae</i> 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. PMID: 29610339; PMCID: PMC5910850.

36: 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. PMID: 28595344; PMCID: PMC5850603.

37: 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. PMID: 28767643; PMCID: PMC5555705.

38: Jelcic M, Enyedi B, Xavier JB, Niethammer P. Image-Based Measurement of
H₂O₂ Reaction-Diffusion in Wounded Zebrafish Larvae.
Biophys J. 2017 May 9;112(9):2011-2018. doi: 10.1016/j.bpj.2017.03.021. PMID:
28494970; PMCID: PMC5425381.

39: 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. PMID: 28246332; PMCID: PMC5358370.

40: 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. Microenvironment-derived factors driving metastatic plasticity in melanoma.
Nat Commun. 2017 Feb 9;8:14343. doi: 10.1038/ncomms14343. PMID: 28181494; PMCID:
PMC5309794.

41: Xavier JB. Sociomicrobiology and Pathogenic Bacteria. Microbiol Spectr. 2016
Jun;4(3):10.1128/microbiolspec.VMBF-0019-2015. doi:
10.1128/microbiolspec.VMBF-0019-2015. PMID: 27337482; PMCID: PMC4920084.

42: 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.
Human symbionts inject and neutralize antibacterial toxins to persist in the
gut. Proc Natl Acad Sci U S A. 2016 Mar 29;113(13):3639-44. doi:
10.1073/pnas.1525637113. Epub 2016 Mar 8. PMID: 26957597; PMCID: PMC4822603.

43: Madsen JS, Lin YC, Squyres GR, Price-Whelan A, de Santiago Torio A, Song A,
Cornell WC, Sørensen SJ, Xavier JB, Dietrich LE. Facultative control of matrix
production optimizes competitive fitness in Pseudomonas aeruginosa PA14 biofilm
models. Appl Environ Microbiol. 2015 Dec;81(24):8414-26. doi:
10.1128/AEM.02628-15. Epub 2015 Oct 2. PMID: 26431965; PMCID: PMC4644639.

44: Deforet M, van Ditmarsch D, Xavier JB. Cell-Size Homeostasis and the
Incremental Rule in a Bacterial Pathogen. Biophys J. 2015 Aug 4;109(3):521-8.
doi: 10.1016/j.bpj.2015.07.002. PMID: 26244734; PMCID: PMC4572571.

45: Boyle KE, Monaco H, van Ditmarsch D, Deforet M, Xavier JB. Integration of
Metabolic and Quorum Sensing Signals Governing the Decision to Cooperate in a
Bacterial Social Trait. PLoS Comput Biol. 2015 Jun 23;11(5):e1004279. doi:
10.1371/journal.pcbi.1004279. PMID: 26102206; PMCID: PMC4477906.

46: 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. Precision microbiome reconstitution
restores bile acid mediated resistance to Clostridium difficile. Nature. 2015
Jan 8;517(7533):205-8. doi: 10.1038/nature13828. Epub 2014 Oct 22. PMID:
25337874; PMCID: PMC4354891.

47: Bucci V, Xavier JB. Towards predictive models of the human gut microbiome. J
Mol Biol. 2014 Nov 25;426(23):3907-16. doi: 10.1016/j.jmb.2014.03.017. Epub 2014
Apr 12. PMID: 24727124; PMCID: PMC4194272.

48: 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.
PMID: 24739582.

49: Deforet M, van Ditmarsch D, Carmona-Fontaine C, Xavier JB. Hyperswarming
adaptations in a bacterium improve collective motility without enhancing single
cell motility. Soft Matter. 2014 Apr 14;10(14):2405-13. doi: 10.1039/c3sm53127a.
PMID: 24622509; PMCID: PMC3955847.

50: Deng P, de Vargas Roditi L, van Ditmarsch D, Xavier JB. The ecological basis
of morphogenesis: branching patterns in swarming colonies of bacteria. New J
Phys. 2014 Jan;16:015006-15006. doi: 10.1088/1367-2630/16/1/015006. PMID:
24587694; PMCID: PMC3935381.

51: New AM, Cerulus B, Govers SK, Perez-Samper G, Zhu B, Boogmans S, Xavier JB,
Verstrepen KJ. Different levels of catabolite repression optimize growth in
stable and variable environments. PLoS Biol. 2014 Jan;12(1):e1001764. doi:
10.1371/journal.pbio.1001764. Epub 2014 Jan 14. PMID: 24453942; PMCID:
PMC3891604.

52: van Ditmarsch D, Xavier JB. Seeing is believing: what experiments with
microbes reveal about evolution. Trends Microbiol. 2014 Jan;22(1):2-4. doi:
10.1016/j.tim.2013.11.004. PMID: 24384383.

53: Carmona-Fontaine C, Bucci V, Akkari L, Deforet M, Joyce JA, Xavier JB.
Emergence of spatial structure in the tumor microenvironment due to the Warburg
effect. Proc Natl Acad Sci U S A. 2013 Nov 26;110(48):19402-7. doi:
10.1073/pnas.1311939110. Epub 2013 Nov 11. PMID: 24218566; PMCID: PMC3845113.

54: van Ditmarsch D, Boyle KE, Sakhtah H, Oyler JE, Nadell CD, Déziel É,
Dietrich LE, Xavier JB. Convergent evolution of hyperswarming leads to impaired
biofilm formation in pathogenic bacteria. Cell Rep. 2013 Aug 29;4(4):697-708.
doi: 10.1016/j.celrep.2013.07.026. Epub 2013 Aug 15. PMID: 23954787; PMCID:
PMC3770465.

55: de Vargas Roditi L, Boyle KE, Xavier JB. Multilevel selection analysis of a
microbial social trait. Mol Syst Biol. 2013 Aug 20;9:684. doi:
10.1038/msb.2013.42. PMID: 23959025; PMCID: PMC3779802.

56: Chang WK, Carmona-Fontaine C, Xavier JB. Tumour-stromal interactions
generate emergent persistence in collective cancer cell migration. Interface
Focus. 2013 Aug 6;3(4):20130017. doi: 10.1098/rsfs.2013.0017. PMID: 24511381;
PMCID: PMC3915836.

57: Boyle KE, Heilmann S, van Ditmarsch D, Xavier JB. Exploiting social
evolution in biofilms. Curr Opin Microbiol. 2013 Apr;16(2):207-12. doi:
10.1016/j.mib.2013.01.003. Epub 2013 Jan 26. PMID: 23357558; PMCID: PMC3646963.

58: 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. Intestinal microbiota containing Barnesiella species cures vancomycin-
resistant Enterococcus faecium colonization. Infect Immun. 2013
Mar;81(3):965-73. doi: 10.1128/IAI.01197-12. Epub 2013 Jan 14. PMID: 23319552;
PMCID: PMC3584866.

59: Stein RR, Bucci V, Toussaint NC, Buffie CG, Rätsch G, Pamer EG, Sander C,
Xavier JB. Ecological modeling from time-series inference: insight into dynamics
and stability of intestinal microbiota. PLoS Comput Biol. 2013;9(12):e1003388.
doi: 10.1371/journal.pcbi.1003388. Epub 2013 Dec 12. PMID: 24348232; PMCID:
PMC3861043.

60: 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.
Intestinal domination and the risk of bacteremia in patients undergoing
allogeneic hematopoietic stem cell transplantation. Clin Infect Dis. 2012
Oct;55(7):905-14. doi: 10.1093/cid/cis580. Epub 2012 Jun 20. PMID: 22718773;
PMCID: PMC3657523.

61: Carmona-Fontaine C, Xavier JB. Altruistic cell death and collective drug
resistance. Mol Syst Biol. 2012;8:627. doi: 10.1038/msb.2012.60. PMID: 23169003;
PMCID: PMC3531905.

62: Bucci V, Bradde S, Biroli G, Xavier JB. Social interaction, noise and
antibiotic-mediated switches in the intestinal microbiota. PLoS Comput Biol.
2012;8(4):e1002497. doi: 10.1371/journal.pcbi.1002497. Epub 2012 Apr 26. PMID:
22577356; PMCID: PMC3343147.

63: Bucci V, Nadell CD, Xavier JB. The evolution of bacteriocin production in
bacterial biofilms. Am Nat. 2011 Dec;178(6):E162-73. doi: 10.1086/662668. Epub
2011 Oct 26. PMID: 22089878.

64: van Ditmarsch D, Xavier JB. High-resolution time series of Pseudomonas
aeruginosa gene expression and rhamnolipid secretion through growth curve
synchronization. BMC Microbiol. 2011 Jun 17;11:140. doi:
10.1186/1471-2180-11-140. PMID: 21682889; PMCID: PMC3152908.

65: Xavier JB. Social interaction in synthetic and natural microbial
communities. Mol Syst Biol. 2011 Apr 12;7:483. doi: 10.1038/msb.2011.16. PMID:
21487402; PMCID: PMC3101950.

66: Xavier JB, Sander C. Principle of system balance for drug interactions. N
Engl J Med. 2010 Apr 8;362(14):1339-40. doi: 10.1056/NEJMcibr1001270. PMID:
20375413.