Xavier Lab

Program for Computational Biology | Memorial Sloan-Kettering Cancer Center

Publications

2013

Convergent evolution of hyperswarming leads to impaired biofilm formation in pathogenic bacteria
van Ditmarsch D, Boyle KE, Sakhtah H, Oyler JE, Nadell CD, Deziel E, Dietrich LEP, Xavier JB. Cell Reports.
[Article: open access] [Issue cover]
[Carl Zimmer's "Matter" at the N.Y.Times] [Dave on the Radio]
[Video: 25 min talk]

Multilevel selection analysis of a microbial social trait
de Vargas Roditi L, Boyle KE, Xavier JB. Molecular Systems Biology.
[Article:Open Access]

Tumour–stromal interactions generate emergent persistence in collective cancer cell migration
Chang WK, Carmona Fontaine C, Xavier JB. Interface Focus: Theme issue on Integrated cancer biology models.
[PDF]

Review: Cutting through the complexity of cell collectives
Nadell CD, Bucci V, Drescher K, Levin SA, Bassler BL, Xavier JB. Proceedings of the Royal Society B.
[PDF]

Review: Exploiting social evolution in biofilms
Boyle KE, Heilmann S, van Ditmarsch D, Xavier JB. Current Opinion in Microbiology. 16:1–6
[PDF]

Intestinal microbiota containing Barnesiella cures vancomycin-resistant Enterococcus faecium colonization
Ubeda C, Bucci V, Caballero V, Djukovic A, Toussaint NC, Equinda M, Lipuma L Ling L, Gobourne A, No D, Taur Y, Jenq RR, van den Brink MRM, Xavier JB, Pamer EG. Infection and Immunity.
[PDF]

2012

Commentary: Altruistic cell death and collective drug resistance
Carmona Fontaine C, Xavier JB. Molecular Systems Biology.
[Article:Open Access]

Perspective: Animal Behavior and the Microbiome
Ezenwa VO, Gerardo NM, Inouye DW, Medina M, Xavier JB. Science.
[PDF]

Intestinal Domination and the Risk of Bacteremia in Patients Undergoing Allogeneic Hematopoietic Stem Cell Transplantation
Taur Y, Xavier JB, Lipuma L, Ubeda M, Goldberg J, Gobourne A, Joo Lee Y, Dubin KA, Socci ND, Viale A, Perales MA, Jenq RR, van den Brink M, Pamer EG. Clin Infect Dis.
[PDF]

Social Interaction, Noise and Antibiotic-Mediated Switches in the Intestinal Microbiota
Bucci V, Bradde S, Biroli G, Xavier JB. PLoS Computational Biology. 8(4): e1002497
[Article:Open Access]

Profound alterations of intestinal microbiota following a single dose of Clindamycin results in sustained susceptibility to C. difficile-induced colitis
Buffie C, Jarchum I, Equinda M, Lipuma L, Gobourne A, Viale A, Ubeda-Morant C, Xavier JB, Pamer E. Infection and Immunity. 80(1):63-73
[PDF][Highlight in MSKCC News| Highlight in ASM Microbe ]
[Science Translational Medicine "Editor's choice"]

2011

The evolution of bacteriocin production in bacterial biofilms
Bucci V, Nadell CD, Xavier JB. American Naturalist. 178:6 pp. E162-E173
[PDF][press release]

A quantitative test of population genetics using spatio-genetic patterns in bacterial colonies
Korolev K, Xavier JB, Nelson DR, Foster KR. American Naturalist. 178:4 pp. 538-552
[PDF]

Social evolution in multispecies biofilms
Mitri S, Xavier JB, Foster KR. Proceedings of the National Academy of Sciences. (online early)
[PDF]

High-resolution time series of Pseudomonas aeruginosa gene expression and rhamnolipid secretion through growth curve synchronization
van Ditmarsch D, Xavier JB. BMC Microbiology 2011, 11:140
[Article:Open Access]

Review: Social interaction in synthetic and natural microbial communities
Xavier JB. Molecular Systems Biology. 2011, 7:483
[Article:Open Access]

Universality in Bacterial Colonies
Bonachela JA, Nadell CD, Xavier JB, Levin SA. Journal of Statistical Physics. 2011 Mar (online early)
[PDF]

A molecular mechanism that stabilizes cooperative secretions in Pseudomonas aeruginosa
Xavier JB, Kim W, Foster KR. Mol Microbiol. 2011 Jan;79(1):166-79.
[PDF] [supporting video 1 | supporting video 2][Recipe for swarming plates]
[Science “Editor’s choice”]

2010

Commentary: Principle of system balance for drug interactions
Xavier JB, Sander C. N Engl J Med. 2010 Apr 8;362(14):1339-40.
[PDF]

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.
[Article:Open Access]
[Faculty of 1000:recommended][Quanta Magazine]

 


Selected publications before 2010

Social evolution of spatial patterns in bacterial biofilms: when conflict drives disorder
Xavier JB, Martinez-Garcia E. & Foster, KR 2009 . American Naturalist, 174: 1-12.
[PDF]
[Faculty of 1000:recommended]

The sociobiology of biofilms
Nadell CD*, Xavier JB*, & Foster, KR 2009. FEMS microbiology reviews,33: 206-224.
[PDF]

The evolution of quorum sensing in bacterial biofilms
Nadell CD*, Xavier JB*, Levin SA, & Foster, KR 2008. PLoS Biology, 6: e14
[Article:Open Access][Movie]

Cooperation and conflict in microbial biofilms
Xavier JB, and Foster KR. 2007. Proceedings of the National Academy of Sciences, 104: 876-881.
[PDF][Supplementary methods + Movies ]
["In this issue" highlight] [Carl Zimmer's Microcosm] [Faculty of 1000:recommended]

Biofilm-control strategies based on enzymic disruption of the extracellular polymeric substance matrix–a modelling study
Xavier JB, Picioreanu C, Rani SA, Van Loosdrecht M, Stewart PS 2005. Microbiology,151(12):3817.
[PDF] [Issue cover]
[Nature Reviews Microbiology highlight]

A framework for multidimensional modelling of activity and structure of multispecies biofilms
Xavier JB, Picioreanu C, van Loosdrecht MC. Environ Microbiol. 2005. 7(8):1085-103
[PDF][Support material]
[Faculty of 1000:recommended]

(See more Xavier JB publications listed at pubmed)