Sanchez Lab Publications
# Co-corresponding authors.  *Co-1st authors.   
​Sanchez lab students & postdocs
2024
[61] Global epistasis and the emergence of function in microbial consortia
Diaz-Colunga J*#, Skwara A*, Vila JCC, Bajic D# & Sanchez A#.
Cell (2024) 187(12):3108-3119.e30
[60] Diverse phage communities are maintained stably on a clonal bacterial host
Pyenson NC#, Leeks A, Nweke O, Goldford JE, Schluter, J, Turner PE, Foster KR# & Sanchez A#.
Science (2024) 386(6727) 1294-1300

​[59] Full factorial construction of synthetic microbial communities
Diaz-Colunga J, Catalan P, San Roman M, Arrabal A & Sanchez A.
eLife (2024) doi:10.7554/eLife.101906.1

[58] Global epistasis in plasmid-mediated antimicrobial resistance
De la Fuente J*, Diaz-Colunga J*, Sanchez A# & San Millan A#.
Molecular Systems Biology (2024) 20: 311-320

[57] The optimization of microbial community functions through rational environmental manipulations
Sanchez A, Arrabal A, San Roman M, Diaz-Colunga J.
Molecular Microbiology (2024) doi:10.1111/mmi.15236

[56] Assembly of gut-derived bacterial communities follows early-bird resource utilization dynamics
Aranda-Diaz A, Willis L, Nguyen T, Ho P-Y, Vila JCC, Thomsen T, Chavez T, Yan J, Yu FB, Neff N, Sanchez A, Estrela S# Huang KC#.
Cell Systems (2024) In press

[55] Predictive microbial community changes across a temperature gradient
Sun X, Folmar J, Favier A, Pyenson NC, Sanchez A, & Rebolleda-Gomez M.
American Naturalist (2024) doi:10.1086/731997

[54] Diversity begets diversity under metabolic niche construction.
Estrela S, Diaz-Colunga J, Vila JCC, Sanchez-Gorostiaga A & Sanchez A.
eLife (2024) Under revision [BioRxiv (2023) 10.1101/2022.02.13.480281]

[53] Engineering microbiomes to transform plastics
Jimenez DJ, Sanchez A, Dini-Andreote F.
Trends in Biotechnology (2023) doi:10.1016/j.tibtech.2023.09.011
2023
[52] Emergent coexistence in multispecies microbial communities
Chang CY#, Bajic D#, Vila JCC, Estrela S & Sanchez A#.
Science (2023) 381(6655) 343-348

[51] Statistically learning the functional landscape of microbial communities
Skwara A, Gowda K, Yousef M, Diaz-Colunga J, Raman A, Sanchez A, Tikhonov M & Kuehn S.
Nature Ecology & Evolution (2023) 7:1823–1833  ​
[50] Environmental modulation of global epistasis in a drug resistance fitness landscape
Diaz-Colunga J#, Sanchez A#, & Ogbunugafor CB#.
Nature Communications (2023) 14: 8055 

[49] Synthesizing microbial biodiversity
Sun X & Sanchez A.
Current Opinion in Microbiology (2023) 75:102348 ​

[48] Predictability of the community-function landscape in wine yeast ecosystems
Ruiz J, De Celis M, Diaz-Colunga J, Vila JCC, Benitez-Dominguez B, Vicente J, Santos A, Sanchez A & Belda I.
Molecular Systems Biology (2023) e11613

[47] The architecture of metabolic networks constrains the evolution of microbial resource hierarchies
Takano S, Vila JCC, Miyazaki R, Sanchez A, & Bajic D.
Molecular Biology & Evolution  (2023) msad187

[46] The community-function landscape of microbial consortia
Sanchez A #, Bajic D, Diaz-Colunga J, Skwara A, Vila JCC & Kuehn S.
Cell Systems (2023) 14 (2):122-134
​
[45] Global epistasis on fitness landscapes
Diaz-Colunga J*, Skwara A*, Gowda K, Diaz-Uriarte R, Tikhonov M, Bajic D & Sanchez A.
Philosophical Transactions of the Royal Society B (2023) 378:20220053

[44] Bacterial subcellular architecture, structural epistasis, and antibiotic resistance
Baquero F, Martinez JL, Sanchez A, Fernandez-de-Bobadilla M, San-Millán A, Rodriguez-Beltran J
Biology (2023) 12 (5) 640
PREPRINTS

[43] Macroecological laws in experimental microbial systems
Shoemaker W, Sanchez A, & Grilli J.
BioRxiv (2023) doi: 10.1101/2023.07.24.550281v1

[42] Metabolic similarity and the predictability of microbial community assembly
Vila JCC, Goldford JE, Estrela S, Bajic D, Sanchez-Gorostiaga A, Damian-Serrano A, Marsland III R, Lu N, Rebolleda-Gomez M, Mehta P & Sanchez A.
BioRxiv (2023) 10.1101/2023.10.25.564019.v1
2022
[41] Top-down and bottom-up cohesiveness in microbial community coalescence.
Diaz-Colunga J*, Lu N*, Sanchez Gorostiaga A*, Cai H, Chang CY, Goldford J, Tikhonov M, Sanchez A
Proceedings of the National Academy of Sciences (2022) 119:6 e2111261119

[40] Functional attractors in microbial community assembly
Estrela S., Vila J.C.C., Lu N., Bajic D., Rebolleda-Gomez M., Chang C-Y., & Sanchez A.
Cell Systems (2022) 13:29-42 doi:10.1016/j.cels.2021.09.011

[39] In vitro interaction network of a synthetic gut bacterial community.
Weiss AS, Burrichter AG, Raj ACD, von Strempel A , Meng C, Kleigrewe K, Munch PC, Rossler L, Huber C, Eisenreich W, Jochum LM, Going S, Jung K, Sanchez A, Stecher B.
ISME Journal (2022) doi:10.1038/s41396-021-01153-z​
2021
[38] Functional biology in its natural context: a search for emergent simplicity
Bergelson J.*, Kreitman M.*, Petrov D.*, Sanchez A.*, Tikhonov M.*
eLife (2021) 10:e67646

[37] Engineering complex communities by directed evolution
Chang C-Y.*, Vila J.C.C.*, Bender M., Li R., Mankowski M.C., Bassette M., Borden J., Golfier S., Sanchez P.G., Waymack R., Zhu X., Diaz-Colunga J., Estrela S., Rebolleda-Gomez M. & Sanchez A.
Nature Ecology & Evolution (2021) 5:1011–1023
[36] Nutrient dominance governs the assembly of microbial communities in mixed nutrient environments
Estrela S.*#, Sanchez-Gorostiaga A.*, Vila J.C.C.*, Sanchez A.#
eLife (2021) 10:e65948
[35] A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)
Dukovski I.*, Bajic D.*, Chacón J.*, Quintin M*., Vila J.C.C., Sulheim S., Pacheco A.R., Bernstein D., Korolev K., Sanchez A. , Harcombe W. & Segre D.
Nature Protocols (2021) doi:10.1038/s41596-021-00593-3
​
[34] Complex yeast-bacteria interactions shape the yield of industrial ethanol fermentations
Lino F.S.O., Bajic D., Vila J.C.C., Sanchez A. & Sommer M.O.A.
Nature Communications (2021) 12:1498

[33] Directed evolution of microbial communities
Sanchez A., Vila J.C.C., Chang C-Y., Diaz-Colunga J., Estrela S. & Rebolleda-Gomez M.
Annual Review of Biophysics (2021) 50:323-341 

[32] Multi-replicated enrichment communities as a model system in microbial ecology
Estrela S.*, Sanchez A.*, Rebolleda-Gomez M*
Frontiers in Microbiology (2021) 12:657467

[31] The meta-gut: Hippo gut inputs lead to community coalescence of animal and environmental microbiomes.
Dutton CL, Subalusky AL, Sanchez A, Estrela S, Lu N, Hamilton SK, Njoroge L, Rosi EJ, Post DM
Scientific Reports (2021) doi:10.1038/s41396-021-01153-z

[30] The macroevolutionary consequences of niche construction in microbial metabolism.
Bajic D#, Rebolleda-Gomez M, Muñoz M & Sanchez A#
Frontiers in Microbiology (2021) doi:10.3389/fmicb.2021.718082
2020
[29] Artificially selecting microbial communities using propagule strategies
Chang, C-Y., Osborne, M.L., Bajic D. & Sanchez A.
Evolution (2020) 74 (10), 2392-2403
[28] Dissimilarity-Overlap Analysis of replicate enrichment communities
Vila J.C.C, Yang, Y-L, & Sanchez A.
ISME Journal (2020) 14:2505-13

[27] The ecology and evolution of microbial metabolic strategies.
Bajic, D. & Sanchez A.
Current Opinion in Biotechnology (2020) 62:123-128
2019
[26] Defining high-order interactions in synthetic ecology: lessons from physics and quantitative genetics
Sanchez, A
Cell Systems (2019) 9(6): 519-20

[25] High order interactions dominate the functional landscape of microbial consortia.
Sanchez-Gorostiaga, A.*, Bajic, D.*, Osborne, M.L., Poyatos, J.F., Sanchez, A.
PLoS Biology (2019) 17(12): e3000550

[24] Current state and future opportunities for prediction in microbiome research.
Sakowski, E. and 29 other authors, including Sanchez, A.
mSystems (2019) 4(5) e00392-19

[23] Available energy fluxes drive a phase transition in the diversity, stability, and functional structure of microbial communities.
Marsland III, R.A., Cui, W., Goldford, J.E., Sanchez, A., Korolev, K.S., Mehta, P.
PLOS Computational Biology (2019) 15 (2), e1006793
2018
[22] On the deformability of an empirical adaptive landscape by microbial evolution.
Bajic, D.*, Vila, J.C.C.*, Blount, Z.D., Sanchez, A.
Proceedings of the National Academy of Sciences (2018) 115(44):11286-11291

[21] Emergent simplicity in microbial community assembly.
Goldford J*, Lu N*, Bajic D, Estrela S, Sanchez-Gorostiaga A, Tikhonov M, Segre D, Mehta P# & Sanchez A#
Science (2018) 361:469-74
[20] The ecological consequences of cellular computations.
Baskerville, M*, Biro A*, Blazanin M*, Chang C-Y.*, Hallworth, A*, Sonnert, N*, Vila, J.C.C*, Sanchez, A.
Natural Computing (2018) doi: 10.10007/s11047-018-9708-8

[19] Regulatory mechanisms are revealed by the distribution of initiation times in single microbial cells.
Choubey, S., Kondev, J., Sanchez, A.
Biophysical Journal (2018) 114(9):2072–2082
2017
[18] Cooperators trade off ecological resilience and evolutionary stability in public goods games.
Rauch, J., Kondev J., Sanchez, A.
Journal of the Royal Society Interface (2017) 14:20160967

[17] Combinatorial gene regulation through kinetic control of the transcription cycle.
Scholes, C., DePace A.H.#, Sanchez, A.#
Cell Systems (2017) 4: 97-108

[16] The evolutionary resilience of distributed cellular computation.
Cavaliere, M., & Sanchez, A.
Lecture Notes in Computer Science (2017) doi:10.1007/978-3-319-54072-6_1
2013-2015
[15] Deciphering transcriptional dynamics in vivo by counting nascent RNA molecules.
Choubey, S., Kondev, J., Sanchez, A.
PLOS Computational Biology (2015) 11(11): e1004345

[14] Eco-evolutionary dynamics of complex social strategies in microbial communities.
Harrington, K., Sanchez A.
Communicative & Integrative Biology (2014) 7 (1) e28230.

[13] Genetic determinants and physical constraints in noisy gene expression.
Sanchez, A.*, Golding, I.*
Science (2013) 342:1188-1193.
PREDOC AND POSTDOC PUBLICATIONS BY ALVARO
[12] Phenotypic states becomes increasingly sensitive to perturbations near a bifurcation in a synthetic gene network.
Axelrod, K., Sanchez, A., Gore, J.
eLife (2015) 4:e07935​

[11] Dynamics of an experimental producer-freeloader ecosystem on the brink of collapse.
Chen, A.*, Sanchez, A.*, Dai, L., Gore, J.
Nature Communications (2014) 5 – 3713.

[10] Feedback between population and evolutionary dynamics determines the fate of social microbial populations.
Sanchez, A., Gore, J.
PLoS Biology (2013) 11(4): e1001547.

[9] Regulation of noise in gene expression.
Sanchez, A., Choubey, S., Kondev, J.
Annual Review of Biophysics (2013) 42: 469–491.

[8] Stochastic models of transcriptional regulation: from single molecules to single cells.
Sanchez, A.*, Choubey, S.*, Kondev, J.
Methods (2013) 62: 23-25.

[7] Operator sequence alters gene expression independently of transcription factor occupancy in bacteria.
Garcia H.G*., Sanchez, A.*, Boedicker, J.Q.*, Osborne, M.L., Gelles, J., Kondev, J., Phillips, R.
Cell Reports (2012) 2: 150-161.

[6] Mechanism of transcriptional repression at a bacterial promoter by analysis of single molecules.
Sanchez, A., Osborne, M.L., Friedman, L.J., Kondev, J., Gelles, J.
The EMBO Journal (2011) 30: 3940-3946.

[5] Effect of promoter architecture on the cell-to-cell variability in gene expression.
Sanchez, A., Garcia, H.G., Jones, D., Phillips, R., Kondev, J.
PLOS Computational Biology (2011) 7(3):e1001100.

[4] Transcription by the numbers redux: Experiments and calculations that surprise.
Garcia, H.G., Sanchez, A., Kuhlman, T., Kondev, J., Phillips, R.
Trends in Cell Biology (2010) 20:723-733.

[3] Transcriptional control of noise in gene expression.
Sanchez, A., Kondev J.
Proceedings of the National Academy of Sciences (2008) 105(13):5081-6.

[2] Molecular brightness determined from a generalized form of Mandel's Q-parameter.
Sanchez, A., Chen, Y., Muller, J.D.
Biophysical Journal (2005) 89(5):3531-3547.

IN SPANISH

[1] Las reglas de Lewontin desde la perspectiva de los paisajes adaptativos
Sanchez, A.
eVOLUCIÓN (2024) In press.