Publications

Published

  1. Global Epistasis and the emergence of ecological function. (2022). Juan Diaz-Colunga*† Abigail Skwara* , Jean C.C. Vila, Djordje Bajic† & Alvaro Sanchez#. Cell (In Press)

  2. Emergent coexistence in multispecies microbial communities. (2023). Chang-Yu Chang*†, Djordje Bajic*† , Jean C.C. Vila, Sylvie Estrela & Alvaro Sanchez*†. Science DOI: 10.1126/science.adg0727

  3. Predictability of the community‐function landscape in wine yeast ecosystems (2023) Javier Ruiz, Miguel de Celis*, Juan Diaz‐Colunga, Jean CC Vila, Belen Benitez‐Dominguez, Javier Vicente, Antonio Santos, Alvaro Sanchez, &Ignacio Belda. Molecular Systems Biology https://doi.org/10.15252/msb.202311613

  4. The architecture of metabolic networks constrains the evolution of microbial resource hierarchies (2023) Sotaro Takano†, Jean C C Vila, Ryo Miyazaki, Álvaro Sánchez, Djordje Bajić†. Molecular Biology and Evolution https://doi.org/10.1093/molbev/msad187

  5. The community function landscape of microbial consortia. (2023). Alvaro Sanchez, Djordje Bajic, Juan Diaz-Colunga Jean C C Vila & Seppe Kuehn. Cell Systems. doi:10.1016/j.cels.2022.12.011

  6. Functional Attractors in microbial community assembly. (2022) Sylvie Estrela†, Jean C. C. Vila, Nanxi Lu, Djordje Bajic, Maria Rebolleda-Gomez, Chang-Yu Chang, Joshua Goldford, Alicia Sanchez-Gorostiaga & Alvaro Sanchez†. Cell Systems https://doi.org/10.1016/j.cels.2021.09.011

  7. A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS) (2021). Ilija Dukovski*, Djordje Bajić*, Jeremy M Chacón*, Michael Quintin*, Jean CC Vila, Snorre Sulheim, Alan R Pacheco, David B Bernstein, William J Rieh, Kirill S Korolev, Alvaro Sanchez, William R Harcombe & Daniel Segrè. Nature Protocols

  8. Engineering complex communities by directed evolution (2021). Chang-Yu Chang*, Jean C.C. Vila*, Madeline Bender, Richard Li, Madeleine C. Mankowski, Molly Bassette, Julia Borden, Stefan Golfier, Paul G. Sanchez, Rachel Waymack, Xinwen Zhu, Juan Diaz-Colunga, Sylvie Estrela, Maria Rebolleda-Gomez & Alvaro Sanchez. Nature Ecology & Evolution doi:10.1038/s41559-021-01457-5 [News & Views by Silvia De Monte] [Behind the paper post]

  9. Nutrient dominance governs the assembly of microbial communities in mixed nutrient environments (2021). Sylvie Estrela*, Alicia Sanchez-Gorostiaga*, Jean C.C. Vila* & Alvaro Sanchez. eLife 10:e65948

  10. Complex yeast-bacteria interactions affect the yield of industrial ethanol fermentations. (2021). Felipe Lino, Djordje Bajic, Jean C.C. Vila, Alvaro Sanchez & Morten Sommer. Nature Communications 12, 1498, https://doi.org/10.1038/s41467-021-21844-7

  11. Directed evolution of microbial communities (2021). Alvaro Sanchez, Jean C.C. Vila, Chang-Yu Chang, Juan Diaz-Colunga, Sylvie Estrela and María Rebolleda-Gomez. Annual Review of Biophysics doi:10.1146/annurev-biophys-101220-072829

  12. Dissimilarity-Overlap Analysis of replicate enrichment communities. (2020) Jean C.C. Vila, Yang-Yu Liu & Alvaro Sanchez. ISME Journal 14: 2505–2513

  13. Uncovering the Rules of Microbial Community Invasion (2019) Jean C.C. Vila, Matt L Jones, Matishalin Patel, Tom Bell and James Rosindell. Nature Ecology & Evolution, 3, 1162–1171 . https://doi.org/10.1038/s41559-019-0952-9

  14. On the deformability of an empirical fitness landscape by microbial evolution. (2018) Djordje Bajic*†, Jean C.C. Vila*, Zachary D Blount, Alvaro Sanchez†. PNAS 115(44) 11286-91

  15. Ecological effects of cellular computing in microbial populations (2018). Maia Baskerville, Arielle Biro, Mike Blazanin, Chang-Yu Chang, Amelia Hallworth, Nicole Sonnert, Jean CC Vila, Alvaro Sanchez. Natural Computing 17(4)811–822

Preprints

  1. Metabolic similarity and the predictability of microbial community assembly (2023) Jean C.C. Vila †, Joshua Goldford, Sylvie Estrela1, Djordje Bajic, Alicia Sanchez-Gorostiaga, Alejandro Damian-Serrano, Nanxi Lu, Robert Marsland III,Maria Rebolleda-Gomez ,Pankaj Mehta and Alvaro SanchezBiorxiv

  2. Competition for shared resources increases dependence on initial population size during coalescence of gut microbial communities (2023) Doran A. Goldman,* Katherine S. Xue*†, Autumn B. Parrott, Rashi R. Jeeda, Lauryn R. Franzese, Jaime G. Lopez, Jean C. C. Vila, Dmitri A. Petrov,Benjamin H. Good,David A. Relman, and Kerwyn Casey Huang† Biorxiv

  3. Assembly of gut-derived bacterial communities follows “early-bird” resource utilization dynamic (2023) Andrés Aranda-Díaz, Lisa Willis, Taylor H Nguyen, Po-Yi Ho, Jean CC Vila, Tani Thomsen, Taylor Chavez, Rose Yan, Feiqiao Brian Yu, Norma Neff, Alvaro Sanchez, Sylvie Estrela†, Kerwyn Casey Huang†. Biorxiv

  4. Diversity begets diversity under microbial niche construction. (2022) Sylvie Estrela†, Juan Diaz-Colunga, Jean C. C. Vila, Alicia Sanchez-Gorostiaga, & Alvaro Sanchez†. Biorxiv

* Co-first authors. † Co-corresponding author