Logic of Genomic Systems laboratory; Juan F Poyatos (CNB-CSIC)

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Recent. 
Yubero, P., and Poyatos, J. F. (2018). Large-scale analysis of the global transcriptional regulation of bacterial gene expression. Preprint [BioRxiv].
Chagoyen, M., and Poyatos, J. F. (2018). Complex genetic and epigenetic regulation deviates gene expression from a unifying global transcriptional program. Preprint [BioRxiv].
Sanchez-Gorostiaga, A., Bajic, D., Osborne, M. L., Poyatos*, J. F., and Sanchez*, A. (2018). High-order interactions dominate the functional landscape of microbial consortia. Preprint [BioRxiv]. *Both authors found guilty.
Rodrigo, G., Bajic, D., Elola, I., and Poyatos, J. F. (2017). Deconstructing a multiple antibiotic resistance regulation through the quantification of its input function. NPJ Systems Biology and Applications, 30 [PDF].
Moreno-Fenoll, C., Cavaliere, M., Martinez-Garcia, E., and Poyatos, J. F. (2017). Eco-evolutionary feedbacks can rescue cooperation in microbial populations. Scientific Reports, 7, 42561 [PDF].
Rodrigo, G., and Poyatos, J. F. (2016). Genetic redundancies enhance information transfer in noisy regulatory circuits. PLoS Computational Biology, 12, e1005156 [HTML].
Rodrigo, G., Bajic, D., Elola, I., and Poyatos, J. F. (2016). Antagonistic autoregulation speeds up a homogeneous response in Escherichia coli. Scientific Reports, 6, 36196 [PDF].
Rodrigo, G., Majer, E., Prakash, S., Daros, J.A., Jaramillo, A., and Poyatos, J. F. (2015). Exploring the dynamics and mutational landscape of riboregulation with a minimal synthetic circuit in living cells. Biophysics Journal, 109, 1070 [PDF].
Bajic, D., Moreno-Fenoll, C., and Poyatos, J. F. (2014). Rewiring of genetic networks in response to modification of genetic background. Genome Biology and Evolution, 6, 3267, [HTML].
Cavaliere, M., and Poyatos, J. F. (2013). Plasticity facilitates sustainable growth in the commons. Journal of the Royal Society Interface, 10, 20121006 [HTML].



By Topic:

Design Principles of Biological Circuits.

Rodrigo, G., Bajic, D., Elola, I., and Poyatos, J. F. (2017). Deconstructing a multiple antibiotic resistance regulation through the quantification of its input function. NPJ Systems Biology and Applications, 30 [PDF].
Rodrigo, G., and Poyatos, J. F. (2016). Genetic redundancies enhance information transfer in noisy regulatory circuits. PLoS Computational Biology, 12, e1005156 [HTML].
Rodrigo, G., Bajic, D., Elola, I., and Poyatos, J. F. (2016). Antagonistic autoregulation speeds up a homogeneous response in Escherichia coli. Scientific Reports, 6, 36196 [PDF].
Poyatos, J. F. (2012). On the search for design principles in biological systems. Adv Exp Med Biol. 751, 183-93 [PDF].
Guantes, R., Estrada, J., and Poyatos, J. F. (2010). Trade-offs and noise tolerance in signal detection by genetic circuits. PLoS ONE, 5, 8, e12314 [HTML].
Guantes R., and Poyatos, J. F. (2008). Multistable decision switches for flexible control of epigenetic differentiation. PLoS Computational Biology, 4, 11, e1000235 [HTML], [Sup].
Guantes R., and Poyatos, J. F. (2006). Dynamical principles of two-component genetic oscillators. PLoS Comput Biol, 2(3), e30 [HTML].
Camas F. M., Blazquez, J., and Poyatos, J. F. (2006). Autogenous and non autogenous control of response in a genetic network. Proceedings of the National Academy of Sciences (PNAS), 103, 12718 [PDF].


Noise and Plasticity in Gene Expression.
Bajic, D., and Poyatos, J. F. (2012). Balancing noise and plasticity in gene expression. BMC Genomics 13, 343 [HTML].
Guantes, R., Estrada, J., and Poyatos, J. F. (2010). Trade-offs and noise tolerance in signal detection by genetic circuits. PLoS ONE, 5, 8, e12314 [HTML].
Guantes R., and Poyatos, J. F. (2006). Dynamical principles of two-component genetic oscillators. PLoS Comput Biol, 2(3), e30 [HTML].

Cell Communities.
Cavaliere, M., and Poyatos, J. F. (2013). Plasticity facilitates sustainable growth in the commons. Journal of the Royal Society Interface, 10, 20121006 [HTML].
Rhiner C. Diaz B, Portela M, Poyatos J.F. et al (2009). Persistent competition among stem cells and their daughters in the Drosophila ovary germline niche. Development, 136, 6, 995 [PDF].
Moreno-Fenoll, C., Cavaliere, M., Martinez-Garcia, E., and Poyatos, J. F. (2017). Eco-evolutionary feedbacks can rescue cooperation in microbial populations. Scientific Reports, 7, 42561 [PDF].

Genetic and Biochemical Networks.
Bajic, D., Moreno-Fenoll, C., and Poyatos, J. F. (2014). Rewiring of genetic networks in response to modification of genetic background. Genome Biology and Evolution, 6, 3267, [HTML].
Poyatos, J. F. (2011). The balance of weak and strong interactions in genetic networks. PLoS ONE, 6, e14598 [HTML].
Camas, F. M., Alm, E. J., and Poyatos, J. F. (2010). Local gene regulation details a recognition code within the LacI transcriptional factor family. PLoS Computational Biology, 6, 11, e1000989 [HTML].
Camas F. M., and Poyatos, J. F. (2008). What determines the assembly of transcriptional network motifs in Escherichia coli? PLoS ONE, 3, 11, e3657 [HTML], [Sup],[Operon_names,Interactions,FFLs].
Poyatos, J. F., and Hurst, L. D. (2004). How biologically relevant are interaction-based modules in protein networks? Genome Biology, 5, R93 [HTML].
Manrubia S.C., and Poyatos J.F. (2003). Motif selection in a model of evolving replicators: The role of surfaces and limited transport in network topology. Europhysics Letters, 64, 557 [PDF].

Evolutionary Dynamics.
Cavaliere, M., and Poyatos, J. F. (2013). Plasticity facilitates sustainable growth in the commons. Journal of the Royal Society Interface, 10, 20121006 [HTML].
Poyatos, J. F., and Carnero, A. (2004). Non-neutral role of replicative senescence in tissue homeostasis and tumorigenesis. Journal of Theoretical Biology, 230, 333 [PDF].
Manrubia S.C., and Poyatos J.F. (2003). Motif selection in a model of evolving replicators: The role of surfaces and limited transport in network topology. Europhysics Letters, 64, 557 [PDF].

Genome Organization.
Camas, F. M., Alm, E. J., and Poyatos, J. F. (2010). Local gene regulation details a recognition code within the LacI transcriptional factor family. PLoS Computational Biology, 6, 11, e1000989 [HTML].
Poyatos, J. F., and Hurst, L. D. (2007). The determinants of gene order conservation in yeasts.
Genome Biology, 8, R233 [HTML].
Poyatos, J. F., and Hurst, L. D. (2006). Is optimal gene order possible? Trends in Genetics, 22,420 [PDF] [Sup].


To the quantum realm

Quantum Mechanics (selected ... and prehistoric).
My work in Quantum Mechanics focused on two basic issues: 1) how is the transition between the quantum and classical description of Nature, and 2) which computational features are specific of Quantum Systems. We provided ways to understand these questions experimentally in the trapped-ion setup. During this period, I had the privilege of working with these two virtuosos (Ignacio, Peter), and also shared very good moments in the company of this bunch (Giovanna, Thomas, Norbert, Steven, Simon, Dik).

Poyatos J. F., Cirac J. I., and Zoller P. (2000). Schemes of quantum computation with trapped ions. Fortschritte der Physik, 48, 767 [PDF].
Poyatos J. F., and Polavieja G. G. (1999). Controlling quantum transport by state synthesis in ion traps.
Physical Review Letters, 83, 3166
[PDF].
Poyatos J. F., Cirac J. I., and Zoller P. (1998).  Quantum gates with ‘hot’ trapped ions.  Physical Review Letters, 81, 1322
[PDF].
Poyatos J. F., Cirac J. I., and Zoller P. (1997). Complete characterization of a quantum process: the two-bit quantum gate. Physical Review Letters, 78, 390
[PDF].
Poyatos J. F., Cirac J. I., and Zoller P. (1996).  Quantum Reservoir Engineering with laser cooled trapped ions. Physical Review Letters, 77, 4728
[PDF].