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[[Sysbio:Back Door | <font face="trebuchet ms" style="color:#bcd5bc"> '''Internal''' </font>]] | [[Sysbio:Back Door | <font face="trebuchet ms" style="color:#bcd5bc"> '''Internal''' </font>]] | ||
[[Sysbio:Notebook/SysBio_notebook | <font face="trebuchet ms" style="color:#bcd5bc"> '''Lab Notebook''' </font>]] | [[Sysbio:Notebook/SysBio_notebook | <font face="trebuchet ms" style="color:#bcd5bc"> '''Lab Notebook''' </font>]] | ||
[ | [https://plus.google.com/105324148007206298526/posts <font face="trebuchet ms" style="color:#bcd5bc"> '''Lab Blog''' </font>] | ||
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==Publications== | ==Publications== | ||
'''2019''' | |||
* D.García-Morales, T. Navarro, A. Iannini, P.S. Pereira, D.G. Míguez*, F. Casares*, ''[https://dev.biologists.org/content/146/8/dev176933.abstract Dynamic Hh signalling can generate temporal information during tissue patterning]'', Development '''146''', dev176933 (2019) (*corresponding authors) | |||
* A. Núñez, G. Amo de Paz, A. Rastrojo, Z. Ferencova, A.M Gutiérrez-Bustillo, A. Alcamí, D. A. Moreno*, R. Guantes* ''[https://doi.org/10.1016/j.atmosenv.2019.116972 Temporal patterns of variability for prokaryotic and eukaryotic diversity in the urban air of Madrid (Spain)]''. Atmospheric Environment (2019) '''217''', 11697 (*corresponding authors) | |||
'''2018''' | |||
* S. Márquez-Jurado, J. Díaz-Colunga, R. Pires das Neves, A. Martínez-Lorente, F. Almazán, R. Guantes* and F.J. Iborra*, ''[http://www.nature.com/articles/s41467-017-02787-4 Mitochondrial levels determine variability in cell death by modulating apoptotic gene expression]'', Nature Communications '''9''', 389 (2018) (*corresponding authors). | |||
* V. Doldán-Martelli and D.G. Míguez, ''[https://www.nature.com/articles/s41598-018-30913-9 Drug treatment efficiency depends on the initial state of activation in nonlinear pathways]'', Scientific Reports '''8''', 1-10 (2018). | |||
* A.F. Lima, G. May, J. Díaz-Colunga, S. Pedreiro, A. Paiva, L. Ferreira, T. Enver, F. J. Iborra and R. Pires das Neves, ''[https://www.nature.com/articles/s41598-018-25517-2 Osmotic modulation of chromatin impacts on efficiency and kinetics of cell fate modulation]'', Scientific Reports '''8''',7210 (2018). | |||
* L. Marcos-Villar, J. Díaz-Colunga, J. Sandoval, N. Zamarreño, S. Landeras-Bueno, M. Esteller, A. Falcón and A. Nieto, ''[https://www.nature.com/articles/s41598-018-19370-6 Epigenetic control of influenza virus: role of H3K79 methylation in interferon-induced antiviral response]'', Scientific Reports '''8''', 1230(2018). | |||
'''2017''' | |||
* A. Aires, J. Fernández-Cadenas, R. Guantes* and A. L. Cortajarena*, ''[http://pubs.rsc.org/en/Content/ArticleLanding/2017/NR/C7NR04475E#!divAbstract An experimental and computational framework for engineering multifunctional nanoparticles: designing selective anticancer therapies]'', Nanoscale (2017) '''9''', 13760-1377 (*corresponding authors). | |||
* A. Núñez, G. Amo de Paz, Z. Ferencova, A. Rastrojo,R. Guantes, A. M. García, A. Alcamí, A.M Gutiérrez-Bustillo, D. A. Moreno, ''[http://aem.asm.org/content/83/13/e00472-17.abstract?sid=a05dcdbf-1539-420c-9a24-674aeb4f69fa Validation of the Hirst-type spore trap for simultaneous monitoring of prokaryotic and eukaryotic diversity in urban air samples by NGS]''. Appl. Environ. Microbiol. (2017) '''83''':13, e00472-17. | |||
* F. Eduati, V. Doldán-Martelli, B. Klinger, T. Cokelaer, A. Sieber, F. Kogera, M. Dorel, M.J. Garnett, N. Blüthgen and J. Saez-Rodriguez ''[http://cancerres.aacrjournals.org/content/canres/77/12/3364 Drug Resistance Mechanisms in Colorectal Cancer Dissected with Cell Type–Specific Dynamic Logic Models]'', Cancer Research (2017) '''77''':12, 3364. | |||
'''2016''' | |||
* M. Bernabé-Rubio, G. Andrés, J. Casares-Arias, J. Fernández-Barrera, L. Rangel, N. Reglero-Real, D.C. Gershlick, J.J. Fernández, J. Millán, I. Correas, D.G. Miguez, M.A. Alonso, ''[http://jcb.rupress.org/content/214/3/259.long Novel role for the midbody in primary ciliogenesis by polarized epithelial cells]'', J. Cell Biology '''214''', 259–273 (2016) | |||
* A. Valencia-Expósito*, I. Grosheva*, D. G. Míguez*, A. González-Reyes, M. D. Martín-Bermudo, ''[http://www.nature.com/ncomms/2016/160218/ncomms10746/full/ncomms10746.html The Myosin Light Chain Phosphatase is required in epithelial cells to control basal actomyosin oscillations governing tissue elongation]'', Nature Communications '''7''', 10746 (2016) (*shared 1st authorship) | |||
* J. Estrada, N. Andrew, D. Gibson, F. Chang, Florian Gnad and J. Gunawardena, ''[http://http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004995 Cellular Interrogation: Exploiting Cell-to-Cell Variability to Discriminate Regulatory Mechanisms in Oscillatory Signalling.]'' PLoS Computational Biology '''12''', e1004995 (2016). | |||
* R. Guantes, I. Benedetti, R. Silva-Rocha and V. de Lorenzo, ''[http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej2015193a.html Transcription factor levels enable metabolic diversification of single cells of environmental bacteria]'', The ISME Journal (2016) | |||
* R. Guantes, J. Díaz-Colunga and F. J. Iborra, ''[http://onlinelibrary.wiley.com/doi/10.1002/bies.v38.1/issuetoc Mitochondria and the non-genetic origins of cell-to-cell variability: More is different]'', BioEssays '''38''', 64-76 (2016). | |||
'''2015''' | |||
* D. G. Míguez, ''[http://www.nature.com/articles/srep13265 A Branching Process to Characterize the Dynamics of Stem Cell Differentiation]'', Scientific Reports '''5''', 13265 (2015) | |||
* R. Guantes, A. Rastrojo, R. Neves, A. Lima, B. Aguado and F. J. Iborra, ''[http://genome.cshlp.org/content/25/5/633.abstract Global variability in gene expression and alternative splicing is modulated by mitochondrial content]'', Genome Research '''25'''(5), 633-644 (2015). | |||
* R. Guantes, S. Arganda and G. G. de Polavieja, ''Biophysics of Adaptation in a Computational Model of the Leech T Neuron'', in Jaeger D, Jung R (Eds.) Encyclopedia of Computational Neuroscience (2015). | |||
* V. Doldán-Martelli, D. G. Míguez, ''[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0117558 Synergistic Interaction between Selective Drugs in Cell Populations Models]'', PloS one '''10''' (2), e0117558 (2015). | |||
'''2014''' | |||
* S. H. Mejías, B. Sot, R. Guantes and A. L. Cortajarena , ''[http://pubs.rsc.org/en/content/articlelanding/2014/nr/c4nr01210k#!divAbstract Controlled nanometric fibers of self-assembled designed protein scaffolds]'', Nanoscale '''6''', 10982-10988 (2014). | |||
* J. Aguirre, D. Bajic and R. Guantes, Biología de Sistemas, in Sebastián A, Pascual-García A (Eds.), Bioinformática con Ñ (2014)ISBN: 978-84-617-1976-X (free textbook on bioinformatics, in Spanish). Downloadable from ''[https://es.scribd.com/doc/231270078/Bioinformatica-con-N Scribd]''. | |||
* A. L. Sanz & D. G. Míguez, ''[http://www.landesbioscience.com/journals/neurogenesis/article/29529/ Dual R-Smads interplay in the regulation of vertebrate neurogenesis]''. Neurogenesis '''1''', e29529 (2014). | |||
'''2013''' | '''2013''' | ||
* V. Doldán-Martelli, R. Guantes | * T. Ruiz-Herrero, J. Estrada, R. Guantes, D. G. Miguez, ''[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003274 A tunable coarse-grained model for ligand-receptor interaction]'', PLOS Computational Biology '''9''', e1003274 (2013). | ||
* | * D. G. Míguez*, E. Gil-Guiñón, S. Pons and E. Martí ''[http://jcs.biologists.org/content/early/2013/10/08/jcs.130435.abstract Smad2 and Smad3 cooperate and antagonize simultaneously in vertebrate neurogenesis]'', Journal Of Cell Science '''126''', 5335 (2013). '''(*First and corresponding authorship)''' | ||
* M. Saade, I. Gutiérrez-Vallejo, G. Le Dréau, M. A. Rabadán, D. G. Miguez, J. Buceta, E. Martí ''[http://www.sciencedirect.com/science/article/pii/S2211124713003306 Sonic hedgehog signaling switches the mode of division in the developing nervous system]'', Cell Reports '''4''',492 (2013). | |||
* D. G. Míguez, ''[http://link.springer.com/article/10.1007%2Fs12539-013-0165-x Network Nonlinearities in Drug Treatment]'', Interdisciplinary Sciences: Computational Life Sciences 5,85 (2013). | |||
* P. Gregorio-Godoy, D. G. Míguez, ''[http://digital-library.theiet.org/content/journals/10.1049/iet-syb.2012.0026 Synthetic approaches to study transcriptional networks and noise in mammalian systems]'', IET Systems Biology 7,11 (2013). | |||
* V. Doldán-Martelli, R. Guantes, D. G. Míguez, ''[http://www.nature.com/psp/journal/v2/n2/full/psp20132a.html A Mathematical Model for the Rational Design of Chimeric Ligands in Selective Drug Therapies]'', CPT: Pharmacometrics & Systems Pharmacology '''2''', e26 (2013). | |||
* J. Estrada and R. Guantes, ''[http://pubs.rsc.org/en/content/articlelanding/2013/mb/c2mb25243k#!divAbstract Dynamic and structural constraints in signal propagation by regulatory networks]'' Mol. BioSyst. '''9''', 268-284 (2013). | |||
'''2012''' | '''2012''' | ||
* R. Guantes, B. Cayrol, F. Busi and V. Arluison, | * R. Guantes, B. Cayrol, F. Busi and V. Arluison, ''[http://pubs.rsc.org/en/content/articlelanding/2012/mb/c2mb05479e#!divAbstract Positive Regulatory Dynamics by a small noncoding RNA: Speeding Up Responses Under Temperature Stress]'', Molecular Biosystems '''8''' , 1707-1715 (2012). | ||
* Florian Gnad , Javier Estrada and Jeremy Gunawardena , | * Florian Gnad , Javier Estrada and Jeremy Gunawardena ,''[https://bioinformatics.oxfordjournals.org/content/28/9/1284.full.pdf+html?sid=87ef4615-e74c-4704-add2-a90c7c0a1a8f Proteus: a web-based, context-specific modelling tool for molecular network]'', Bioinformatics '''28''', 1284 - 1286 (2012). | ||
* V. Doldán-Martelli, D. G. Míguez, ''Theoretical Approaches to Growth Hormone Signaling'', in 'Growth Hormones: Synthesis, Regulation and Health Implications', Eds. A. Andersdtr and J. Anderssen Nova Publishers ISBN 978-1-61942-681-8 (2012). | * V. Doldán-Martelli, D. G. Míguez, ''Theoretical Approaches to Growth Hormone Signaling'', in 'Growth Hormones: Synthesis, Regulation and Health Implications', Eds. A. Andersdtr and J. Anderssen Nova Publishers ISBN 978-1-61942-681-8 (2012). | ||
'''2011''' | '''2011''' | ||
* D. G. Míguez, Milos Dolnik, Irving Epstein and Alberto P. Muñuzuri, ''[http://pre.aps.org/abstract/PRE/v84/i4/e046210 Interaction Of Chemical Patterns in Coupled Layers]'', Phys. Rev. E, '''84''', 046210 (2011). | |||
* D. G. Míguez, Milos Dolnik, Irving Epstein and Alberto P. Muñuzuri, | |||
'''2010''' | '''2010''' | ||
* D. G. Míguez, | * D. G. Míguez, ''[http://www.sciencedirect.com/science/article/pii/S0301462210000402 The role of asymmetric binding in ligand-receptor systems with 1:2 interaction ratio]'' Biophys Chem '''148''', 74-81 (2010) | ||
* D.G. Míguez, "Forcing of Nonlinear Pattern Formation Systems", Lambert Academic Publishing, ISBN 9783838364223 (2010) [http://www.amazon.com/Forcing-Nonlinear-Pattern-Formation-Systems/dp/3838364228 Book] | * D.G. Míguez, "Forcing of Nonlinear Pattern Formation Systems", Lambert Academic Publishing, ISBN 9783838364223 (2010) [http://www.amazon.com/Forcing-Nonlinear-Pattern-Formation-Systems/dp/3838364228 Book] | ||
* R. Guantes, J. Estrada and J. F. Poyatos, | * R. Guantes, J. Estrada and J. F. Poyatos,''[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0012314 Trade-offs and noise tolerance in signal detection by genetic circuits]'', PLoS ONE '''5''', e12314 (2010) | ||
'''2009''' | '''2009''' | ||
* D. G. Míguez, P. McGraw, A. P. Muñuzuri and M. Menzinger, | * D. G. Míguez, P. McGraw, A. P. Muñuzuri and M. Menzinger, ''[http://pre.aps.org/abstract/PRE/v80/i2/e026208 Selection of Flow-Distributed Oscillation and Turing Patterns by Boundary Forcing in a Linearly Growing, Oscillating Medium]'', Phys. Rev. E, '''80''', 026208 (2009). | ||
'''2008''' | '''2008''' | ||
* I. A. Swinburne, D. G. Míguez, D. Landgraf, and P. A. Silver, | * I. A. Swinburne, D. G. Míguez, D. Landgraf, and P. A. Silver, ''[http://genesdev.cshlp.org/content/22/17/2342.full Intron length increases oscillatory periods of gene expression in animal cells]'', Genes & Dev., '''22''' 2008, 2342-2346 (2008). | ||
* S. Alonso, D. G. Míguez, F. Sagués, | * S. Alonso, D. G. Míguez, F. Sagués, ''[http://iopscience.iop.org/0295-5075/81/3/30006 Differential susceptibility to noise of mixed Turing and Hopf modes in a photosensitive chemical medium]'', Europhys. Lett, '''81''', 30006 (2008). | ||
* R. Guantes and J. F. Poyatos, | * R. Guantes and J. F. Poyatos,''[http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000235 Multistable decision switches for flexible control of epigenetic differentiation]'', PLoS Computational Biology '''4''', e1000235 (2008) | ||
'''2007''' | '''2007''' | ||
* D. G. Míguez, V. K. Vanag, I. R. Epstein, | * D. G. Míguez, V. K. Vanag, I. R. Epstein, ''[http://www.pnas.org/content/104/17/6992.full Fronts and pulses in an enzymatic reaction with glucose oxidase]'' P.N.A.S. '''104''', 6992 (2007). | ||
* S. Arganda, R. Guantes and G. G. de Polavieja, | * S. Arganda, R. Guantes and G. G. de Polavieja, ''[http://www.nature.com/neuro/journal/v10/n11/full/nn1982.html Sodium pumps adapt spike bursting to stimulus statistic]'', Nature Neuroscience '''10''', 1467-1473 (2007). | ||
'''2006''' | '''2006''' | ||
* V. K. Vanag, D.G. Míguez, I. R. Epstein, | * V. K. Vanag, D.G. Míguez, I. R. Epstein, ''[http://jcp.aip.org/resource/1/jcpsa6/v125/i19/p194515_s1 Designing an Enzymatic Oscillator: Bistability and Feedback Control led Oscillations with Glucose Oxidase in a CSTR]'', J. Phys. Chem. '''125''', 194515 (2006). | ||
* D.G. Míguez, S. Alonso, A.P. Muñuzuri, F. Sagués, | * D.G. Míguez, S. Alonso, A.P. Muñuzuri, F. Sagués, ''[http://prl.aps.org/abstract/PRL/v97/i17/e178301 Experimental evidence of localized oscillations in the photosensitive chlorine dioxide-iodine-malonic acid reaction]'', Phys. Rev. Lett, '''97''', 178301 (2006). | ||
* D. G. Míguez, A. P. Muñuzuri, | * D. G. Míguez, A. P. Muñuzuri, ''[http://www.sciencedirect.com/science/article/pii/S0301462206002122 On the orientation of stripes in fish skin patterning]'', Biophys. Chem. '''124''', 161 (2006). | ||
* D. G. Míguez, R. A. Satnoianu, A. P. Muñuzuri, | * D. G. Míguez, R. A. Satnoianu, A. P. Muñuzuri, ''[http://pre.aps.org/abstract/PRE/v73/i2/e025201 Experimental steady pattern formation in reaction-diffusion-advection systems]'', Phys. Rev. E '''73''', 025201 (R) (2006). | ||
* D. G. Míguez, M. Dolnik, A. P. Muñuzuri, L. Kramer, | * D. G. Míguez, M. Dolnik, A. P. Muñuzuri, L. Kramer, ''[http://prl.aps.org/abstract/PRL/v96/i4/e048304 Effect of Axial Growth on Turing Pattern Formation]''. Phys. Rev. Lett '''96''', 048304 (2006). | ||
* D. G. Míguez, G. Izús, A. P. Muñuzuri, | * D. G. Míguez, G. Izús, A. P. Muñuzuri, ''[http://pre.aps.org/abstract/PRE/v73/i1/e016207 Robustness and Stability of Flow-and-Diffusion Structures]'', Phys. Rev. E '''73''', 016207 (2006). | ||
* R. Guantes and J. F. Poyatos, | * R. Guantes and J. F. Poyatos, ''[http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.0020030 Dynamical principles of two-component genetic oscillators]'', PLoS Computational Biology '''2''', e30 (2006). | ||
'''2005''' | '''2005''' | ||
* D. G. Miguez, V. Perez-Villar, and A. P. Munuzuri, | * D. G. Miguez, V. Perez-Villar, and A. P. Munuzuri, ''[http://pre.aps.org/abstract/PRE/v71/i6/e066217 Turing instability controlled by spatiotemporal imposed dynamics]'', Phys. Rev. E '''71''', 066217 (2005). | ||
* R. Guantes and G. G. de Polavieja, "Variability in noise-driven integrator neurons", Physical Review E '''71''', 011911 (2005). | * R. Guantes and G. G. de Polavieja, "Variability in noise-driven integrator neurons", Physical Review E '''71''', 011911 (2005). | ||
* S. C. Farantos, S. Stamatiadis, L. Lathouwers and R. Guantes, "Grid enabled molecular dynamics: classical and quantum algorithms", Lecture Series on Computer and Computational Sciences '''1''', 1-16 (2005). | * S. C. Farantos, S. Stamatiadis, L. Lathouwers and R. Guantes, "Grid enabled molecular dynamics: classical and quantum algorithms", Lecture Series on Computer and Computational Sciences '''1''', 1-16 (2005). | ||
'''2004''' | '''2004''' | ||
* F. Sagués, D. G. Míguez, E. M. Nicola, A. P. Muñuzuri, J. Casademunt, L. Kramer, | * F. Sagués, D. G. Míguez, E. M. Nicola, A. P. Muñuzuri, J. Casademunt, L. Kramer, ''[http://www.sciencedirect.com/science/article/pii/S0167278904003197 Travelling-stripe forcing of Turing patterns]'', Physica D '''199''', 235 (2004). | ||
* D. G. Míguez, E. M. Nicola, A. P. Muñuzuri, J. Casademunt, F. Sagués, L. Kramer, | * D. G. Míguez, E. M. Nicola, A. P. Muñuzuri, J. Casademunt, F. Sagués, L. Kramer, ''[http://prl.aps.org/abstract/PRL/v93/i4/e048303 Traveling-Stripe Forcing Generates Hexagonal Patterns]'', Phys. Rev. Lett. '''93''', 048303 (2004). | ||
* M. | * M. Kærn‡, D. G. Míguez‡, A. P. Muñuzuri, M. Menzinger, ''[http://www.sciencedirect.com/science/article/pii/S030146220400078X Control of chemical pattern formation by a clock-and-wavefront type mechanism]'', Biophys. Chem. '''110''', 231 (2004). '''Shared 1st authorship'''. | ||
* S. Sengupta, R. Guantes, S. Miret-Artés and P. Hänggi, "Controlling directed transport in two-dimensional periodic structures under crossed electric fields", Physica A '''338''', 406 (2004). | * S. Sengupta, R. Guantes, S. Miret-Artés and P. Hänggi, "Controlling directed transport in two-dimensional periodic structures under crossed electric fields", Physica A '''338''', 406 (2004). | ||
* R. Guantes, A. S. Sanz, J. Margalef-Roig and S. Miret-Artés, "Atom-surface diffraction: a trajectory description", Surface Science Reports '''53''', 199-330 (2004). | * R. Guantes, A. S. Sanz, J. Margalef-Roig and S. Miret-Artés, "Atom-surface diffraction: a trajectory description", Surface Science Reports '''53''', 199-330 (2004). | ||
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* J. L. Vega, R. Guantes, S. Miret-Artés and D. A. Micha, "Collisional lineshapes for low frequency vibrations of an atom adsorbed on a metal surface", Journal of Chemical Physics '''121''', 8580 (2004) | * J. L. Vega, R. Guantes, S. Miret-Artés and D. A. Micha, "Collisional lineshapes for low frequency vibrations of an atom adsorbed on a metal surface", Journal of Chemical Physics '''121''', 8580 (2004) | ||
'''2003''' | '''2003''' | ||
* B. Peña, C. Pérez-García, A. Sanz-Anchelergues | * B. Peña, C. Pérez-García, A. Sanz-Anchelergues, D. G. Míguez, A. P. Muñuzuri, ''[http://pre.aps.org/abstract/PRE/v68/i5/e056206 Transverse instabilities in chemical Turing patterns of stripes]'', Phys. Rev. E '''68''', 056206 (2003). | ||
* S. Rüdiger, D. G. Míguez, A. P. Muñuzuri, F. Sagués, J. Casademunt, | * S. Rüdiger, D. G. Míguez, A. P. Muñuzuri, F. Sagués, J. Casademunt, ''[http://prl.aps.org/abstract/PRL/v90/i12/e128301 Dynamics of Turing Patterns under Spatiotemporal Forcing]'', Phys. Rev. Lett '''90''', 128301 (2003). | ||
* R. Guantes and S. Miret-Artés, "Chaotic transport of particles in two-dimensional periodic potentials driven by ac forces", Physical Review E '''67''', 046212 (2003). | * R. Guantes and S. Miret-Artés, "Chaotic transport of particles in two-dimensional periodic potentials driven by ac forces", Physical Review E '''67''', 046212 (2003). | ||
* R. Guantes, J. L. Vega, S. Miret-Artés and Eli Pollak, "Kramers' turnover theory for diffusion of Na atoms on a Cu(001) surface measured by He scattering", Journal of Chemical Physics '''119''', 2780 (2003). | * R. Guantes, J. L. Vega, S. Miret-Artés and Eli Pollak, "Kramers' turnover theory for diffusion of Na atoms on a Cu(001) surface measured by He scattering", Journal of Chemical Physics '''119''', 2780 (2003). |
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