Papers

2017

Bow-tie signaling in c-di-GMP: machine learning in a simple biochemical network
Jinyuan Yan, Maxime Deforet, Kerry E. Boyle, Rayees Rahman, Raymond Liang, Chinweike Okegbe, Lars E. P. Dietrich, Weigang Qiu and Joao B. Xavier. PLOS Computational Biology
[Open access]

Pathogenicity locus, core genome and accessory gene contributions to Clostridium difficile virulence
Brittany B. Lewis, Rebecca A. Carter, Lilan Ling, Ingrid Leiner, Ying Taur, Mini Kamboj, Erik Dubberke, Joao Xavier, Eric G. Pamer. mBio
[Open access]

Metabolism and the evolution of social behavior
Kerry E. Boyle, Hilary T. Monaco, Maxime Deforet, Jinyuan Yan, Zhe Wang, Kyu Rhee and Joao Xavier. Molecular Biology and Evolution
[Open Access]

Metabolic origins of spatial organization in the tumor microenvironment
Carlos Carmona-Fontaine, Maxime Deforet, Leila Akkari, Craig B. Thompson, Johanna A. Joyce, Joao B. Xavier. PNAS
[Open Access]

Image-Based Measurement of H2O2 Reaction-Diffusion in Wounded Zebrafish Larvae
Mark Jelcic, Balázs Enyedi, João B. Xavier and Philipp Niethammer. Biophysical Journal
[PDF]

Microenvironment-derived factors driving metastatic plasticity in melanoma
Isabella Kim, Silja Heilmann, Emily Kansler, Yan Zhang, Milena Zimmer, Kajan Ratnakumar, Robert Bowman, Theresa Simon-Vermot, Myles Fennell, Ralph Garippa, Liang Lu, William Lee, Travis Hollmann, Joao Xavier, Richard White. Nature Communications
[Open Access]

2016

Sociomicrobiology and Pathogenic Bacteria
Joao B. Xavier. ASM Spectrum
[PDF]

Human symbionts inject and neutralize antibacterial toxins to persist in the gut
Aaron G. Wexler, Yiqiao Bao, John C. Whitney, Louis-Marie Bobay, Joao B. Xavier, Whitman B. Schofield, Natasha A. Barry, Alistair B. Russell, Bao Q. Tran, Young Ah Goo, David R. Goodlett, Howard Ochman, Joseph D. Mougous, Andrew L. Goodman. PNAS
[PDF]

2015

Facultative control of matrix production optimizes competitive fitness in Pseudomonas aeruginosa PA14 biofilm models
JS Madsen, YC Lin, GR Squyres, A Price-Whelan, A de Santiago Torio, Angela Song, William C Cornell, Søren J Sørensen, Joao B Xavier, Lars EP Dietrich. Applied and environmental microbiology
[PDF]

A quantitative system for studying metastasis using transparent zebrafish
Silja Heilmann, Kajan Ratnakumar, Erin Langdon, Emily Kansler, Isabella Kim, Nathaniel R Campbell, Elizabeth Perry, Amy McMahon, Charles Kaufman, Ellen van Rooijen, William Lee, Christine Iacobuzio-Donahue, Richard Hynes, Leonard Zon, Joao Xavier, and Richard M White. Cancer Research
[PDF][cover]

Cell size homeostasis and the incremental rule in a bacterial pathogen
Maxime Deforet*, Dave van Ditmarsch* and João B. Xavier. Biophysical Journal
[PDF]

Biofilm formation as a response to ecological competition
Nuno M Oliveira, Esteban Martinez-Garcia, Joao Xavier, William M Durham, Roberto Kolter, Wook Kim, and Kevin R Foster. PLos Biology
[Open Access]

Integration of Metabolic and Quorum Sensing Signals Governing The Decision to Cooperate in a Bacterial Social Trait
Kerry E. Boyle, Hilary Monaco, Dave van Ditmarsch, Maxime Deforet and Joao B. Xavier. PLos Computational Biology
[Open Access]

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile
Charlie G. Buffie, Vanni Bucci, Richard R. Stein, Peter T. McKenney, Lilan Ling, Asia Gobourne, Daniel No, Hui Liu, Melissa Kinnebrew, Agnes Viale, Eric Littmann, Marcel R. M. van den Brink, Robert R. Jenq, Ying Taur, Chris Sander, Justin Cross, Nora C. Toussaint, Joao B. Xavier & Eric G. Pamer. Nature
[Online]

2014

Perspective: Turning ecology and evolution against cancer
Kirill S. Korolev, Joao B. Xavier & Jeff Gore. Nature Reviews Cancer
[PDF]

Review: Towards predictive models of the human gut microbiome
Bucci V and Xavier JB. Journal of Molecular Biology
[PDF]

Hyperswarming adaptations in a bacterium improve collective motility without enhancing single cell motility
Deforet M, van Ditmarsch D, Carmona-Fontaine C and Xavier JB. Soft Matter
[PDF]

Seeing is believing: what experiments with microbes reveal about evolution
van Ditmarsch D, Xavier JB. Trends in Microbiology
[PDF]

The ecological basis of morphogenesis: branching patterns in swarming colonies of bacteria
Deng P, de Vargas Roditi L, van Ditmarsch D, Xavier JB. New Journal of Physics
[Article: open access][F1000 recommended][New Journal of Physics “Highlights of 2014”]

The microbial lag phase is an evolvable trait mediating specialist and generalist strategies
A.M. New, B. Cerulus, S.K. Govers, B. Zhu, S. Boogmans, J. Xavier, and K.J. Verstrepen. PLoS Biology
[Article: open access]

2013

Emergence of spatial structure in the tumor microenvironment due to the Warburg effect
Carlos Carmona-Fontaine, Vanni Bucci, Leila Akkari, Maxime Deforet, J. A. Joyce, and Joao B. Xavier. PNAS
[PDF]

Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota
Richard R. Stein*, Vanni Bucci*, Nora C. Toussaint, Charlie G. Buffie, Gunnar Rätsch, Eric G. Pamer, Chris Sander, João B. Xavier. PLoS Computational Biology
[Article: open access]

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)

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