Sistemas complejos
The Complex Systems lab focuses on understanding the evolutionary origins of complex systems, using both mathematical models and experimental approaches based on synthetic biology. This lab has proposed and developed the concept of Major Synthetic Transitions as a framework for exploring the origins of innovation in evolution using a parallel approach, namely our potential for building or simulating synthetic systems that can recreate past evolutionary events. This includes the origin of protocells, multicellular systems, symbiosis, cognition and language. Another research area addresses Unstable Evolutionary Dynamics, namely the dynamics of biological systems (particularly RNA viruses and cancer) that exhibit a tendency towards high genetic instability as part of their adaptation potential. The Complex Systems lab also introduced the concept of "Terraforming" endangered or human-made ecosystems to avoid catastrophic shifts. The success of this proposal will require the development of a new synthesis involving multiple scales and conceptual frameworks, ranging from synthetic biology and cellular circuits to ecological communities. Finally, it also studies the evolution of artificial systems, in both silico ecosystems and technological networks, in its search for a true definition of evolutionary dynamics and technological phylogenies.
Lab website: Complex Systems Lab
Solé R, Kempes CP, Corominas-Murtra B, De Domenico M, Kolchinsky A, Lachmann M, Libby E, Saavedra S, Smith E, Wolpert D. 2024. Fundamental constraints to the logic of living systems. Interface Focus, 14(5):7-9. DOI:10.1098/rsfs.2024.0010
Solé R, Maull V, Amor DR, Mauri JP, Núria C-P. 2024. Synthetic Ecosystems: From the Test Tube to the Biosphere. ACS Synthetic Biology. DOI:10.1021/acssynbio.4c00384
Maull V, Solé R. 2024. Biodiversity as a firewall to engineered microbiomes for restoration and conservation. Royal Society Open Science, 11(6). DOI:10.1098/rsos.231526
Long C, Deng J, Nguyen J, Liu YY, Alm EJ, Solé R, Saavedra S. 2024. Structured community transitions explain the switching capacity of microbial systems. Proceedings of the National Academy of Sciences, 121(6):1-9. DOI:10.1073/pnas.2312521121
Kéfi S, Génin A, Garcia-Mayor A, Guirado E, Cabral JS, Berdugo M, Guerber J, Solé R, Maestre FT. 2024. Self-organization as a mechanism of resilience in dryland ecosystems. Proceedings of the National Academy of Sciences, 121(6):2017. DOI:10.1073/pnas.2305153121
Seoane LF, Solé R. 2023. How Turing parasites expand the computational landscape of digital life. Physical Review E, 108(4):044407. DOI:10.1103/PhysRevE.108.044407
Aguadé‐Gorgorió G, Costa J, Solé R. 2023. An oncospace for human cancers. BioEssays, 45(5). DOI:10.1002/bies.202200215
Vidiella B, Solé R. 2022. Ecological firewalls for synthetic biology. iScience, 25(7):104658. DOI:10.1016/j.isci.2022.104658
Solé R, Levin S. 2022. Ecological complexity and the biosphere: the next 30 years. Philosophical Transactions of the Royal Society B: Biological Sciences, 377(1857). DOI:10.1098/rstb.2021.0376
Solé R, Seoane LF. 2022. Evolution of Brains and Computers: The Roads Not Taken. Entropy, 24(5):665. DOI: 10.3390/e24050665.
Maull V, Solé R. 2022. Network-level containment of single-species bioengineering. Philosophical Transactions of the Royal Society B: Biological Sciences, 377(1857). DOI:10.1098/rstb.2021.0396
Bonforti A, Solé R. 2022. Unicellular–multicellular evolutionary branching driven by resource limitations. Journal of The Royal Society Interface, 19(191). DOI:10.1098/rsif.2022.0018
Aguadé-Gorgorió G, Kauffman S, Solé R. 2022. Transition Therapy: Tackling the Ecology of Tumor Phenotypic Plasticity. Bulletin of Mathematical Biology, 84(1):24. DOI:10.1007/s11538-021-00970-9
Vidiella B, Guillamon A, Sardanyés J, Maull V, Pla J, Conde N, Solé R. 2021. Engineering self-organized criticality in living cells. Nature Communications, 12(1):4415. DOI:10.1038/s41467-021-24695-4
Solé R, Sardanyés J, Elena SF. 2021. Phase transitions in virology. Reports on Progress in Physics, 84(11):115901. DOI:10.1088/1361-6633/ac2ab0
Solé R, Conde-Pueyo N, Guillamon A, Maull V, Pla J, Sardanyés J, Vidiella B. 2021. Synthetic criticality in cellular brains. Journal of Physics: Complexity, 2(4):041001. DOI:10.1088/2632-072X/ac35b3
Solé R, Aguadé-Gorgorió G. 2021. The ecology of cancer differentiation therapy. Journal of Theoretical Biology, 511(110552). DOI:10.1016/j.jtbi.2020.110552
Duran-Nebreda S, Pla J, Vidiella B, Piñero J, Conde-Pueyo N, Solé R. 2021. Synthetic Lateral Inhibition in Periodic Pattern Forming Microbial Colonies. ACS Synthetic Biology, 10(2): 277–285. DOI: 10.1021/acssynbio.0c00318
Vidiella B, Sardanyés J, Solé R V. 2020. Synthetic soil crusts against green-desert transitions: A spatial model: Synthetic ecosystems’ terraformation. Royal Society Open Science,7(8). DOI:10.1098/rsos.200161rsos200161
Solé R, Valverde S. 2020. Evolving complexity: how tinkering shapes cells, software and ecological networks. Philosophical Transactions of the Royal Society B: Biological Sciences, 375(1796). DOI:10.1098/rstb.2019.0325
Solé R, Valverde S. 2020. Evolving complexity: how tinkering shapes cells, software and ecological networks. The Royal Society. doi: 10.1098/rstb.2019.0325
Solé R. 2020. Using information theory to decode network coevolution. Science, 368(6497):1315-1316. DOI:10.1126/science.abc6344
Seoane LF, Solé R. 2020. Criticality in Pareto Optimal Grammars? Entropy, 22(2):165. DOI: 10.3390/e22020165.
Ollé-Vila A, Seoane LF, Solé R. 2020. Ageing, computation and the evolution of neural regeneration processes. Journal of The Royal Society Interface, 17(168). DOI:10.1098/rsif.2020.0181
Conde-Pueyo N, Vidiella B, Sardanyés J, Berdugo M, Maestre FT, Lorenzo V de, Solé R. 2020. Synthetic biology for terraformation lessons from mars, earth, and the microbiome. Life, 10(2):1–27. DOI: 10.3390/life10020014
Berdugo M, Delgado-Baquerizo M, Soliveres S, Hernández-Clemente R, Zhao Y, Gaitán JJ, Gross N, Saiz H, Maire V, Lehman A, Rillig MC, Solé RV, Maestre FT. 2020. Global ecosystem thresholds driven by aridity. Science, 367(6479):787–790. DOI: 10.1126/science.aay5958
Alsedà L, Vidiella B, Solé R, Lázaro JT, Sardanyés J. 2020. Dynamics in a time-discrete food-chain model with strong pressure on preys. Communications in Nonlinear Science and Numerical Simulation, 84:1–26. DOI:10.1016/j.cnsns.2020.105187
Aguadé-Gorgorió G, Solé R. 2020. Tumour neoantigen heterogeneity thresholds provide a time window for combination immunotherapy. Journal of the Royal Society Interface, 17(171). DOI:10.1098/rsif.2020.0736.
Ollé-Vila A, Solé R. 2019. Cellular heterogeneity results from indirect effects under metabolic tradeoffs. Royal Society Open Science, 6(9). DOI:10.1098/rsos.190281
Vidiella B, Sardanyés J, Solé R. 2018. Exploiting delayed transitions to sustain semiarid ecosystems after catastrophic shifts. Journal of The Royal Society Interface, 15(143):20180083. DOI:10.1098/rsif.2018.0083
Valverde S, Piñero J, Corominas-Murtra B, Montoya J, Joppa L, Solé R. 2018. The architecture of mutualistic networks as an evolutionary spandrel. Nature Ecology & Evolution, 2(1):94-99. DOI:10.1038/s41559-017-0383-4
Solé R. 2018. Cooperation in an RNA world. Nature Ecology & Evolution, 2(10):1527-1528. DOI:10.1038/s41559-018-0649-5
Solé R, Ollé-Vila A, Vidiella B, Duran-Nebreda S, Conde-Pueyo N. 2018. The road to synthetic multicellularity. Current Opinion in Systems Biology, 7:60-67. DOI:10.1016/j.coisb.2017.11.007
Seoane LF, Solé R V. 2018. Information theory, predictability and the emergence of complex life. Royal Society Open Science, 5(2):172221. DOI:10.1098/rsos.172221
Seoane LF, Solé R. 2018. The morphospace of language networks. Scientific Reports, 8(1):1-18. DOI:10.1038/s41598-018-28820-0
Corominas-Murtra B, Sànchez Fibla M, Valverde S, Solé R. 2018. Chromatic transitions in the emergence of syntax networks. Royal Society Open Science, 5(12):181286. DOI:10.1098/rsos.181286
Corominas-Murtra B, Seoane LF, Solé R. 2018. Zipf’s Law, unbounded complexity and open-ended evolution. Journal of The Royal Society Interface, 15(149):20180395. DOI:10.1098/rsif.2018.0395
Aguadé-Gorgorió G, Solé R. 2018. Adaptive dynamics of unstable cancer populations: The canonical equation. Evolutionary Applications, 11(8):1283-1292. DOI:10.1111/eva.12625
Valverde S. 2017. Breakdown of Modularity in Complex Networks. Frontiers in Physiology, 8:1-8. DOI:10.3389/fphys.2017.00497
Sardanyés J, Tomás Lázaro J, Guillamon A, Fontich E. 2017. Full analysis of small hypercycles with short-circuits in prebiotic evolution. Physica D: Nonlinear Phenomena, 347:90-108. DOI:10.1016/j.physd.2016.12.004
Sardanyés J, Martínez R, Simó C, Solé R. 2017. Abrupt transitions to tumor extinction: a phenotypic quasispecies model. Journal of Mathematical Biology, 74(7):1589-1609. DOI:10.1007/s00285-016-1062-9
Maestre FT, Solé R, Singh BK. 2017. Microbial biotechnology as a tool to restore degraded drylands. Microbial Biotechnology, 10(5):1250-1253. DOI:10.1111/1751-7915.12832
Macia J, Vidiella B, Solé R V. 2017. Synthetic associative learning in engineered multicellular consortia. Journal of The Royal Society Interface, 14(129):20170158. DOI:10.1098/rsif.2017.0158
Gaviria AM, Franco J, Rico G, Muntané G, Sáez C, Sánchez-Gistau V, de Pablo J, Vilella E. 2017. Noninterventional, Naturalistic, Retrospective Study to Describe Prescription Patterns of Long-Acting Injectable Antipsychotics and the Impact of Introducing a New Atypical Antipsychotic in the Spanish Province of Tarragona Catchment Area. The Primary Care Companion For CNS Disorders, 19(02):1-4. DOI:10.4088/PCC.16m02044
Castillo V, Lázaro JT, Sardanyés J. 2017. Dynamics and bifurcations in a simple quasispecies model of tumorigenesis. Computational and Applied Mathematics, 36(1):415-431. DOI:10.1007/s40314-015-0234-3
Amor DR, Montañez R, Duran-Nebreda S, Solé R. 2017. Spatial dynamics of synthetic microbial mutualists and their parasites. PLoS computational biology, 13(8):e1005689. DOI:10.1371/journal.pcbi.1005689
Aguilar D, Pinart M, Koppelman GH, Saeys Y, Nawijn MC, Postma DS, Akdis M, Auffray C, Ballereau S, Benet M, García-Aymerich J, González JR, Guerra S, Keil T, Kogevinas M, Lambrecht B, Lemonnier N, Melen E, Sunyer J, Valenta R, Valverde S, Wickman M, Bousquet J, Oliva B, Antó JM. 2017. Computational analysis of multimorbidity between asthma, eczema and rhinitis. PLoS ONE, 12(6):1-26. DOI:10.1371/journal.pone.0179125
Willemsen A, Zwart MP, Higueras P, Sardanyés J, Elena SF. 2016. Predicting the stability of homologous gene duplications in a plant RNA virus. Genome Biology and Evolution, 8(9):3065-3082. DOI:10.1093/gbe/evw219
Valverde S. 2016. Major transitions in information technology. Philosophical Transactions of the Royal Society B: Biological Sciences, 371(1701). DOI:10.1098/rstb.2015.0450
Urrios A, Macia J, Manzoni R, Conde N, Bonforti A, de Nadal E, Posas F, Solé R. 2016. A Synthetic Multicellular Memory Device. ACS Synthetic Biology, 5(8):862-873. DOI:10.1021/acssynbio.5b00252