Research Group

Detalle de: TheSiMBioSys (Theoretical and In Silico Modeling of Biological Systems)

Title	TheSiMBioSys (Theoretical and In Silico Modeling of Biological Systems)
Description	[EN] Our work focuses on computational, theoretical, and experimental approaches for understanding biological systems. using systems biology/biophysics approaches. The nickname of the group: The.Si.M.Bio.Sys. (Theoretical and In Silico Modeling of Biological Systems) does not reflect all our research since years ago I also started a experimental line. Our topics of interest cover quite different scales in time and space such as Cell Size Regulation in Rod-Shape Bacteria, Developmental Processes, Gene Regulatory Networks, Pattern formation, Disease Spreading...and lately space exploration. Who are we? ►Javier Buceta (P.I.): javierDOTbucetaATcsicDOTes ►Ruben Ballester (M.Sc.): rubaroDOTalumniATuvDOTes ►Oscar Delgado (intern): oscdelforDOTfaustiATgmailDOTcom ►Victor Gaya (Ph.D., co-supervised by Dr. Ana Conesa): vaDOTgayaATcsicDOTes ►Iago Grobas (Postdoc): ialogroATuvDOTes ►Marta Nadal (Ph.D.): martaDOTnadalATcsicDOTes ►Adrian Nadal (Ph.D.): adrianDOTnadalATcsicDOTes ►Raul Rodríguez González (intern): rofer4DOTalumniATuvDOTes The team is further complemented by our collaborative research with Rafael Martinez (Research Group leader of the LSyM Lab, IRTIC-UV) [ES] Nuestro trabajo se centra en enfoques computacionales, teóricos y experimentales para comprender los sistemas biológicos. utilizando enfoques de biología de sistemas/biofísica. El apodo del grupo: The.Si.M.Bio.Sys. (Modelado Teórico e In Silico de Sistemas Biológicos) no refleja toda nuestra investigación ya que hace años también inicié una línea experimental. Nuestros temas de interés cubren escalas bastante diferentes en el tiempo y el espacio, como la regulación del tamaño celular en bacterias, procesos de desarrollo, redes reguladoras de genes, formación de patrones, propagación de enfermedades...y ultimamente la exploración espacial. ¿Quienes Somos? ►Javier Buceta (P.I.): javierDOTbucetaATcsicDOTes ►Ruben Ballester (M.Sc.): rubaroDOTalumniATuvDOTes ►Oscar Delgado (intern): oscdelforDOTfaustiATgmailDOTcom ►Victor Gaya (Ph.D., co-supervised by Dr. Ana Conesa): vaDOTgayaATcsicDOTes ►Iago Grobas (Postdoc): ialogroATuvDOTes ►Marta Nadal (Ph.D.): martaDOTnadalATcsicDOTes ►Adrian Nadal (Ph.D.): adrianDOTnadalATcsicDOTes ►Raul Rodríguez González (intern): rofer4DOTalumniATuvDOTes El equipo se completa además con nuestra investigación en colaboración con Rafael Martínez (responsable del grupo de investigación del Laboratorio LSyM Lab, IRTIC-UV).
Home Page	http://www.thesimbiosys.com
Contact Email	javier.buceta@csic.es
Collaborating Companies
Spin Off
Patents
Hpc Resources
Institution	I2SYSBIO
Ontology	Computational Methods, Data Analysis, Computational models and simulations, Gene regulatory networks, Systems Biology, Statistical Methods for Biology, Bayesian statistics
Tools	APID Interactomes: protein-protein interactions database, TiFoSi, pyDockDNA, Bacteria Segmentation/Tracking Tool, ANISE
Service Units
Research Lines	Characterization of diseases from multicellularity
Funded Projects	Cells2Spine: Spatial Transcriptomics and Cell Communication Models applied to tissue regeneration and treatment in Spinal Cord Injury with Precision Nanomedicine, Conexión CSIC en Biología Computacional y Bioinformática (BCBHub), "ORIGIN AND IMPLICATIONS OF MIN AND ERK MECHANICAL WAVES IN THE GROWTH OF CELLS AND TISSUES"
Selected Publications	Spatial Dynamics and Emergent Properties of pLS20 Conjugation on Solid Surfaces Preprint · 4 Mar 2025 Mechanical strain modulates Min patterning and division inE. colifilaments Preprint · 26 Feb 2025 Apico-basal intercalations enable the integrity of curved epithelia Article · 1 Jan 2025 Stochastic analysis of Ebola infection in small zoonotic niches Article · Nov 2024 Random field calibration with data on irregular grid for regional analyses: A case study on the bare carrying capacity of bats in Africa Article · Sep 2023 View all (56 more) Developmental Pattern Formation: Spanish Contributions from a Biophysical Perspective Article · 6 May 2023 Estimation of Ebola’s spillover infection exposure in Sierra Leone based on sociodemographic and economic factors Article · 1 Sep 2022 Bacterial degrons in synthetic circuits Article · Aug 2022 ANISE: an application to design mechanobiology simulations of planar epithelia Article · 20 Jul 2022 Mechanics and self-organization in tissue development Article · Dec 2021 The complex three-dimensional organization of epithelial tissues Article · 1 Jan 2021 TiFoSi: an efficient tool for mechanobiology simulations of epithelia Software · 26 Jun 2020 A non-linear analysis of Turing pattern formation Article · 9 Aug 2019 Erratum to: Scutoids are a geometrical solution to three-dimensional packing of epithelia (Nature Communications, (2018), 9, 1, (2960), 10.1038/s41467-018-05376-1) Article · 8 Oct 2018 Scutoids are a geometrical solution to three-dimensional packing of epithelia Article · 27 Jul 2018 A Markovian Approach towards Bacterial Size Control and Homeostasis in Anomalous Growth Processes Article · 25 Jun 2018 A Predictive Spatial Distribution Framework for Filovirus-Infected Bats Article · 22 May 2018 Differentiation of live and heat-killed E. coli by microwave impedance spectroscopy Article · Feb 2018 Finite cell-size effects on protein variability in Turing patterned tissues Article · Aug 2017 Modeling the Ebola zoonotic dynamics: Interplay between enviroclimatic factors and bat ecology Article · 12 Jun 2017 The cellular Ising model: A framework for phase transitions in multicellular environments Article · Jun 2016 Stochastic stabilization of phenotypic States: the genetic bistable switch as a case study. Article · 11 Sep 2013 Interplay of cytoskeletal activity and lipid phase stability in dynamic protein recruitment and clustering Article · 10 Sep 2013 Sonic hedgehog signaling switches the mode of division in the developing nervous system Article · Aug 2013 Dynamics of the quorum sensing switch: Stochastic and non-stationary effects Article · 2013 Dynamics and mechanical stability of the developing dorsoventral organizer of the wing imaginal disc Article · 29 Sep 2011 Noise regulation by quorum sensing in low mRNA copy number systems Article · 20 Jan 2011 Direct mapping of nanoscale compositional connectivity on intact cell membranes Article · 16 Aug 2010 Interplay between intrinsic noise and the stochasticity of the cell cycle in bacterial colonies Article · Jun 2010 Pattern formation in nonequilibrium lipid membranes: From membrane undulations to lipid rafts Article · Mar 2010 Noise-induced coherence in multicellular circadian clocks Article · May 2009 A spatial toggle switch drives boundary formation in development Article · Dec 2008 Phase separation in three-component lipid membranes: From Monte Carlo simulations to Ginzburg-Landau equations Article · 9 Jan 2008 Robustness and stability of the gene regulatory network involved in DV boundary formation in the Drosophila wing Article · 11 Jul 2007 Noise-induced oscillatory behavior in field-dependent relaxational dynamics Article · 19 Apr 2006 Comprehensive study of pattern formation in relaxational systems Article · 8 Feb 2006 Generation of dynamic structures in nonequilibrium reactive bilayers Article · 18 Nov 2005 Nodal cilia dynamics and the specification of the left/right axis in early vertebrate embryo development Article · Oct 2005 Erratum: Nonequilibrium patterns and shape fluctuations in reactive membranes (Physical Review E (2005) 71 (051906)) Article · 14 Sep 2005 Nonequilibrium patterns and shape fluctuations in reactive membranes Article · 18 May 2005 Comments on the article "The Universal Dynamics of Tumor Growth" A. Brú et al Article · May 2005 Ratchets in homogeneous extended systems: Internal modes and the role of noise Article · Dec 2004 Effects of internal fluctuations on the spreading of Hantavirus Article · Dec 2004 Habitat size and extinction in population dynamics Conference paper · 25 May 2004 Outbreaks of Hantavirus induced by seasonality Article · 26 Feb 2004 Extinction in population dynamics Article · 26 Feb 2004 Comprehensive study of phase transitions in relaxational systems with field-dependent coefficients Article · 15 Jan 2004 Dynamics of two granules Article · 26 Aug 2003 Spatial patterns induced purely by dichotomous disorder Article · 23 Jul 2003 Patterns in reaction-diffusion systems generated by global alternation of dynamics Article · Jul 2003 Dynamical scaling analysis of plant callus growth Article · Jul 2003 Noise-driven mechanism for pattern formation Article · 27 Feb 2003 Erratum: Pattern formation induced by nonequilibrium global alternation of dynamics (Physical Review E (2002) 66 (036216)) Article · 30 Dec 2002 Switching-induced Turing instability Article · 4 Oct 2002 Pattern formation induced by nonequilibrium global alternation of dynamics Article · 24 Sep 2002 Stationary and oscillatory spatial patterns induced by global periodic switching Article · 26 Dec 2001 Negative resistance and anomalous hysteresis in a collective molecular motor Article · 1 Jun 2000 Finite resolution effects in the analysis of the scaling behavior of rough surfaces Article · 1 May 2000 Small scale properties of the stochastic stabilized Kuramoto-Sivashinsky equation Article · Mar 1998 The stochastic stabilized Kuramoto-Sivashinsky equation: A model for compact electrodeposition growth Article · Nov 1997 Noise-induced spatial patterns Article · Feb 1996
Researchers	Javier Buceta, Víctor Gaya-Martín

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