The traditional experimental approach to the study of the functioning of cells has been remarkably successful at identifying cellular components and their interactions. Current automated technologies have brought the cartoon-like representations of
cellular processes to exponentially growing webs of nodes and links that seem as close to completion as ever. The complexity of the emerging picture, however, makes it clear that all this information by itself is not enough to truly understand processes
such as cancer. In order to piece back together all the genetic, biochemical, molecular, and structural information into a physiologically relevant description of the cell, one needs "constructive" methods. Computational modeling has emerged as a
promising tool for transforming molecular detail into a more integrated form of understanding complex behavior.
We use computational and mathematical modeling to study biological networks that are relevant to cancer. We are interested, not
only in the interactions between cellular components, but also in the resulting cellular behavior and its integration into the physiological context of an organism. We study computationally how mutations affect the molecular properties of the cellular
components; how the mutated components affect different pathways; and how these modified pathways confer cell-growth advantages during tumor progression and metastasis. Having a global view of all these processes and their effects through all relevant
levels of biological organization is crucial to identify and characterize the key control elements of the system.
We are currently working on:
Gene regulation (RXR and other nuclear hormone receptors)
Signal transduction (EGF and TGF-β pathways)
Control of cell growth and death (Bcl-2/Bax in metabolism and apoptosis)
We are also developing new computational approaches to determine, capture, and use the relevant biological information. We are especially interested in stochastic analyses and in multilevel and multiscale methods.
Press on our research
Open Source Software
J. M. G. Vilar and L. Saiz (2019), Scaling and Regression over Nearest Neighbors for Single-Cell Signaling Prediction in Breast Cancer,
https://www.synapse.org/#!Synapse:syn21188145 J. M. G. Vilar (2018), Data-driven prediction of electricity grid traffic (winner solution of the European Union Big Data Technologies Horizon Prize
http://ec.europa.eu/research/horizonprize/index.cfm?prize=bigdata). Repository available at https://github.com/jmgvilar/H2020BigDataPrize/ J. M. G. Vilar and L. Saiz (2017), Combined ridge, support-vector, and random-forest regression approach for odor prediction,
https://www.synapse.org/#!Synapse:syn3794504 J. M. G. Vilar (2014), Predicting the overall survival time of AML patients using marginal probability ratios,
https://www.synapse.org/#!Synapse:syn2702223 J. M. G. Vilar (2014), Predicting remission duration in AML patients with Complete Remission using marginal probability ratios,
https://www.synapse.org/#!Synapse:syn2702224 J. M. G. Vilar (2014), Predicting Complete Remission or Primary Resistance in AML patients using marginal probability ratios,
https://www.synapse.org/#!Synapse:syn2702225 "CplexA" (released on April 19th, 2010/updated on December 12th, 2012) is a software package (available for Mathematica, Python, and Matlab) to compute probabilities and average properties of macromolecular assembly and its effects in gene regulation.
CplexA and the tutorial are available at
Articles in journals
J. A. Fernandez-Higuero, A. Muga, J. M. G. Vilar,
Extraction and Refolding Determinants of Chaperone-Driven Aggregated Protein Reactivation,
J. Mol. Biol. 432, 3239-3250 (2020). Y. Cabrera, L. Dublang, J. A. Fernandez-Higuero, D. Albesa-Jove, M. Lucas, A. R. Viguera, M. E. Guerin, J. M. G. Vilar, A. Muga, F. Moro,
Regulation of human Hsc70 ATPase and chaperone activities by Apg2: role of the acidic subdomain,
J. Mol. Biol. 431, 444-461 (2019). M. L. Fanani, J. V. Busto, J. Sot, J. Abad, G. Fabrias, L. Saiz, J. M. G. Vilar, F. M. Goni, B. Maggio, and A. Alonso,
Detectable, Kinetically Restricted Solid–Solid Phase Transition in
cis-Ceramide Monolayers, Langmuir 34, 11749-11758 (2018). J. M. G. Vilar and J. M. Rubi,
Determinants of population responses to environmental fluctuations, Scientific Reports 8: 887 (2018). J. M. G. Vilar and L. Saiz,
at the front-end by receptor networks, Cell Systems 5, 316-318 (2017). A. Keller, R.C. Gerkin, Y. Guan, A. Dhurandhar, G. Turu, B. Szalai, J.D. Mainland, Y. Ihara, C.W. Yu., R. Wolfinger, C. Vens, L. Schietgat, K. De Grave, R. Norel, DREAM Olfaction Prediction Consortium (*), G. Stolovitzky, G.A. Cecchi, L.B. Vosshall,
P. Meyer (* including J.M.G. Vilar),
human olfactory perception from chemical features of odor molecules, Science 355, 820-826 (2017). D.P. Noren, B.L. Long, R. Norel, K. Rrhissorrakrai, K. Hess, C.W. Hu, A.J. Bisberg, A. Schultz, E. Engquist, L. Liu, X. Lin, G.M. Chen, H. Xie, G.A.M. Hunter, P.C. Boutros, O. Stepanov, DREAM 9 AML-OPC Consortium (*), T. Norman, S.H. Friend, G.
Stolovitzky, S. Kornblau, A.A. Qutub (* including J.M.G. Vilar),
Crowdsourcing Approach to Developing and Assessing Prediction
Algorithms for AML Prognosis, PLoS Comput. Biol. 12: e1004890 (2016). J. M. G. Vilar and L. Saiz,
and enhancement of transcriptional noise by DNA looping, Phys. Rev. E 89, 062703 (2014). J. M. G. Vilar,
of Leukemia on Multidimensional Morphological and Molecular
Landscapes, Phys. Rev. X 4, 021038 (2014). J. M. G. Vilar and J. M. Rubi,
System-size scaling of Boltzmann and alternate Gibbs entropies, J. Chem. Phys. 140, 201101 (2014). J. M. G. Vilar and L. Saiz,
Biophysics of Gene Expression, Biophys. J. 104, 2574-2585 (2013). J. M. G. Vilar and L. Saiz,
prediction of complex phenotypes from a modular design in free
energy space: an extensive exploration of the lac operon, ACS Synth. Biol. 2, 576-586 (2013). N. Aghaeepour, G. Finak, The FlowCAP Consortium, The DREAM Consortium (*), H. Hoos, T.R. Mosmann, R. Brinkman, R. Gottardo, and R.H. Scheuermann (* including J. M. G. Vilar),
assessment of automated flow cytometry data analysis techniques, Nature Methods 10, 228-238 (2013). Supplementary Information [ pdf].
J. M. G. Vilar and J. M. Rubi,
processes without net thermal exchange via energy sorting, J. Chem. Phys. 136, 064115 (2012). J. M. G. Vilar and L. Saiz,
Coordinate Description of Intracellular Transport Control of
Signaling Networks, Biophys. J. 101, 2315-2323 (2011). J. M. G. Vilar and L. Saiz,
of gene expression by modulated self-assembly, Nucleic Acids Research 39, 6854-6863 (2011). J. M. G. Vilar and J. M. Rubi,
connection for anisoparametric processes in manipulated microsystems, J. Non-Equilib. Thermodyn. 36, 123-130 (2011). N. Geisel, J. M. G. Vilar, and J. M. Rubi,
Resting-Growth Strategies of Microbial Populations in Fluctuating
Environments, PLoS One 6, e18622 (2011). J. M. G. Vilar,
control of cell death, BMC Systems Biology 4, 152 (2010). J. M. G. Vilar,
Prediction of Gene Expression by Integration of DNA Sequence
Statistics with Detailed Modeling of Transcription Regulation, Biophys. J. 99, 2408-2413 (2010). J. M. G. Vilar and L. Saiz,
a Mathematica package to study macromolecular-assembly control of
gene expression, Bioinformatics 26, 2060-2061 (2010). Supplementary Information: Supplementary Data files 1 [ pdf]
and 2 [ nb]. L. Saiz and J. M. G. Vilar,
interaction networks: versatile macromolecular structures for the
control of gene expression, IET Systems Biology 2, 247-255 (2008). J. M. G. Vilar and J. M. Rubi,
of the Work-Hamiltonian Connection for Free-Energy Calculations, Phys. Rev. Lett. 100, 020601 (2008). L. Saiz and J. M. G. Vilar,
, Nucleic Acids Research Ab
initio thermodynamic modeling of distal multisite
transcription regulation 36, 726-731 (2008). M. H. Vainstein, J. M. Rubi and J. M. G. Vilar,
population dynamics in turbulent fields, Eur. Phys. J. ST 146, 177-187 (2007). L. Saiz and J. M. G. Vilar,
deconstruction of the in vivo behavior of looped DNA-protein
complexes, PLoS One 2, e355 (2007). W. Y. Shou, S. Ram, and J. M. G. Vilar,
cooperation in engineered yeast populations, Proc. Natl. Acad. Sci. USA 104, 1877-1882 (2007). J. M. G. Vilar and L. Saiz,
DNA looping, Phys. Rev. Lett. 96, 238103 (2006). L. Saiz and J. M. G. Vilar,
looping: the consequences and its control, Curr. Opin. Struct. Biol. 16, 344-350 (2006). L. Saiz and J. M. G. Vilar,
dynamics of macromolecular-assembly networks, Molecular Systems Biology 2, 0024 (2006). J. M. G. Vilar,
regulation, Molecular Systems Biology 2, 0016 (2006). J. M. G. Vilar, R. Jansen, and C. Sander,
processing in the TGF-β superfamily ligand-receptor network, PLoS Comput. Biol. 2, e3 (2006). L. Saiz, J. M. Rubi, and J. M. G. Vilar,
the in vivo looping properties of DNA, Proc. Natl. Acad. Sci. USA 102, 17642-17645 (2005). D. Reguera, J. M. Rubi, and J. M. G. Vilar,
Mesoscopic Dynamics of Thermodynamic Systems, J. Phys. Chem. B 109, 21502-21515 (2005). J. M. G. Vilar and L. Saiz,
looping in gene regulation: From the assembly of macromolecular
complexes to the control of transcriptional noise, Curr. Opin. Genet. Dev. 15, 136-144 (2005). E. Korobkova, T. Emonet, J. M. G. Vilar, T. S. Shimizu, P. Cluzel,
molecular noise to behavioural variability in a single bacterium, Nature 428, 574-578 (2004). J. M. G. Vilar and S. Leibler,
looping and physical constrains on transcription regulation, J. Mol. Biol. 331, 981-989 (2003). J. M. G. Vilar, C. C. Guet, and S. Leibler,
network dynamics: the lac operon, a case study, J. Cell Biol. 161, 471-476 (2003). J. M. G. Vilar, R. V. Sole, and J. M. Rubi,
the origin of plankton patchiness, Physica A
317, 239-246 (2002). Jose M. G. Vilar, Hao Yuan Kueh, Naama Barkai, and Stanislas Leibler,
noise-resistance in genetic oscillators, Proc. Natl. Acad. Sci. USA 99, 5988-15992 (2002). J. M. G. Vilar and J. M. Rubi,
"beyond" local equilibrium, Proc. Natl. Acad. Sci. USA 98, 11081-11084 (2001). J. M. G. Vilar and J. M. Rubi,
suppression by noise, Phys. Rev. Lett. 86, 950-953 (2001). L. Saiz, J. M. G. Vilar, and J. M. Rubi,
force-suppression in ferromagnetic colloids, Physica A
293, 51-58 (2001). J. M. G. Vilar and J. M. Rubi,
periodic spatial structures by non-equilibrium fluctuations, Physica A 277, 327-334 (2000). J. M. Rubi and J. M. G. Vilar,
Rheology of Field-Responsive Suspensions, J. Phys.: Cond. Matter 12, A75-A84 (2000). A. Perez-Madrid, T. Alarcon, J.M.G. Vilar, and J. M. Rubi,
Approach to the "Negative'' Viscosity Effect in Ferrofluids, Physica A 270, 403-412 (1999). J. M. G. Vilar, R. V. Sole, and J. M. Rubi,
and Periodic Modulations in Neural Excitable Media, Phys. Rev. E 59, 5920-5928 (1999). J. M. G. Vilar and J. M. Rubi,
Concepts in Periodically Modulated Noisy Systems, Physica A
264, 1-14 (1999). J. M. G. Vilar, G. Gomila and J. M. Rubi,
Resonance in Noisy Nondynamical Systems, Phys. Rev. Lett. 81, 14-17 (1998). J. M. G. Vilar and R. V. Sole,
of Noise in Symmetric Two-Species Competition, Phys. Rev. Lett. 80, 4099-4102 (1998). J. M. G. Vilar and J. M. Rubi,
of the Output of the System in Signal Detection, Phys. Rev. E 56, 32R-35R (1997). J. M. G. Vilar and J. M. Rubi,
Multiresonance, Phys. Rev. Lett. 78, 2882-2885 (1997). J. M. G. Vilar and J. M. Rubi,
Stochastic Resonance in the Swift-Hohenberg Equation, Phys. Rev. Lett. 78, 2886-2889 (1997). Jose M. Gomez-Vilar and Ricard V. Sole,
cellular automata models for quantum systems, J. Phys. A 29, 8169 -8171 (1996). J. M. G. Vilar, A. Perez-Madrid, and J. M. Rubi,
Resonance in a Dipole, Phys. Rev. E 54, 6929-6932 (1996). J. M. G. Vilar and J. M. Rubi,
Signal-to-Noise Ratio and Stochastic Resonance in Monostable Systems, Phys. Rev. Lett. 77, 2863-2866 (1996). Book chapters
D. Reguera, J. M. G. Vilar, and J. M. Rubi (eds.), Statistical Mechanics of Biocomplexity, Lecture Notes in Physics (Springer
Verlag, Berlin 1999).
Selected invited talks
Presentation of the winner solution of the European Union Big Data Technologies Horizon Prize.
European Big Data Value Forum 2018, November 2018, Vienna (Austria). Inference and prediction in molecular biological systems.
BioInformatics Conference 2018, June 2018, Belgrade (Serbia). Prediction and inference in complex biophysical systems,
International Iberian Congress of Biophysics / X Iberoamerican
Congress of Biophysics, June 2018, Castellon (Spain). Biophysical and Biomedical Applications of the Gibbs Entropy Postulate,
2018: From Physics to Information Sciences and Geometry, May 2018, Barcelona (Spain). Computational systems biophysics of cellular processes in health and disease.
BioInformatics Conference 2016, June 2016, Belgrade (Serbia). Automated diagnosis of leukemia.
Engineering Society Annual Meeting, October 2015, Tampa (Florida). Gene expression and long-range cooperativity on DNA.
Workshop on Interdisciplinary Views on Chromosome Structure and
Function, September 2014, Trieste (Italy). Gibbs entropy postulate: from thermodynamics "beyond" local equilibrium to biomedical applications.
Sitges Conference on Statistical Mechanics: New Horizons in
Statistical Physics and its Applications, June 2014, Barcelona (Spain). Systems biophysics of gene expression.
European Biophysics Congress, July 2013, Lisbon (Portugal). Computational biophysics of cellular processes in health and disease.
Congress of the Spanish Biophysical Society – SBE Barcelona 2012, July 2012, Barcelona (Spain). Submicron-scale statistical thermodynamics in living systems.
Sitges Conference on Statistical Mechanics: Understanding and
Managing Randomness in Physics, Chemistry and Biology, June 2012, Sitges, Barcelona (Spain). Computational systems biophysics at the molecular, cellular, and cell-population levels.
Cancer Institute (NCI) and National Science Foundation (NSF)
international Assessment of Physical Sciences and Engineering
Advances in Life Sciences and Oncology, May 2012, Barcelona (Spain). Multidimensional entropies for diagnosing Acute Myeloid Leukemia from patient samples using flow cytometry data,
annual meeting, October 2011, Barcelona (Spain). Signal processing in the TGF-β superfamily ligand-receptor network. Systems Biology and Connective Tissue Disorders Meeting, February 2011, Washington, DC.
From components to systems: lessons from gene regulation and synthetic cooperation.
colloquium of the Systems and Synthetic Biology Program of the CNB, November 2010, Madrid (Spain). Noise propagation across molecular, cellular, and cell-population scales.
Noise in Life 2010, October 2010, Benasque (Spain). Noise propagation across molecular, cellular, and cell-population scales.
Dynamics in Biological Systems, September 2010, Dresden (Germany). The logics of macromolecular assembly.
Processing in Cells and Tissues: From small scale dynamics to
understanding systems behavior, April 2009, Ascona (Switzerland). Intracellular noise and long-range interactions on DNA.
2009, Overcoming Distance in Signaling Networks, March 2009, Maale HaChamisha (Israel). From components to systems and vice versa: lessons from gene regulation and synthetic cooperation.
Cellular Decision Making, June 2008, Toronto (Canada). Signal processing in the TGF-β superfamily ligand-receptor network.
Conference on Systems Biology of
Mammalian Cells, May 2008, Dresden (Germany). Stochastic dynamics of protein-DNA complexes.
Biochemical Networks, September 2007, Montreal (Canada). Stochastic dynamics of protein-DNA complexes.
in Cellular Signaling and Gene Regulation, August 2007, Santa Fe (New Mexico). Inferring the in vivo looping properties of DNA.
international conference on Multiscale Materials Modeling, September 2006, Freiburg (Germany). Computational Modeling of the TGF-β Superfamily Ligand-Receptor Network.
for Developmental Biology Autumn Meeting: Signal Transduction and
Integration in Embryonic Development, Sept 2006, Dundee (UK). Stochastic dynamics of protein-DNA complexes.
Nanomechanics of Biomolecules, August 2006, Ascona (Switzerland). Macromolecular assembly on looped DNA.
on "Chromatin Dynamics, Gene Regulation and Silencing", August 2006, Snowmass (Colorado). Stochastic Dynamics of Macromolecular-Assembly Networks.
Sitges Conference on Statistical Mechanics. Physical Biology: from
Molecular Interactions to Cellular Behavior, June 2006, Sitges, Barcelona (Spain). Stochastic Dynamics of Macromolecular-Assembly Networks. Systems Biology Discussion Group, New York Academy of Sciences, November 2005, New York (New York).
Stochastic Dynamics of Macromolecular-Assembly Networks. ISQBP Gilda Loew Memorial Meeting, October 2005, Staten Island (New York).
Mechanisms of Noise-resistance in Genetic Oscillators. SIAM Conference on the Life Sciences, July 2004, Portland (Oregon).
Mathematical analysis of gene circuits. Conference on Mathematical Modelling of Plant Development and Gene Networks, University of Warwick, May 2004, Coventry (United Kingdom).
Modeling the Networks of the Cell: Molecular, Cellular, and Population Levels. Workshop on Biological Information and Statistical Physics, July 2003, Dresden (Germany).
Modeling Noise, Switches and Clocks. Workshop on Dynamics, Adaptation and Fluctuations in Bio-networks, KITP, University of California, March 2003, Santa Barbara (California).
Noise in the cell: from molecular mechanisms to populations via network design. Annual American Physical Society March Meeting, March 2002, Indianapolis (Indiana).
Networking with noise at the molecular, cellular, and population level. Gordon Research Conference on Bioinformatics: From inference to Predictive Models, August 2001, Tilton (New Hampshire).
Modules of modules: from molecular interactions to cell populations. Workshop on Design and Control of Biochemical Networks, June 2001, Leiden (The Netherlands).
Ordering Periodic Spatial Structures by Noise. Workshop on Fluctuations Far From Equilibrium: Noise Induced Transport, April 1998, Dresden (Germany).
Jose Vilar (Ikerbasque Professor)
Want to join?
below! Former (VILARlab at Memorial Sloan-Kettering Cancer Center, 2004-2008)
(Visiting Investigator, 2004-2007)
Currently, Assistant Professor of Biomedical Engineering & Lab Head, University of California, Davis (2007-)
Currently, Assistant Member & Lab Head, Basic Sciences Division, Fred Hutchinson Cancer Research Center (2007-)
Anamika Sarkar (Postdoc, 2004-2005)
Currently, Assistant Scientist, Iyengar Laboratory, Mount Sinai School of Medicine (2005-)
Ori Weitz (Rotation Student, Tri-i CBM program, 2006)
Pawel Kocieniewski (Rotation Student, Tri-i CBM program, 2007)
Fan Xia (Rotation
Student, PBSB program, 2007)
Ricky Chachra (Rotation Student, PBSB program, 2008)
Igor Segota (Rotation Student, PBSB program, 2008)
There are openings for Graduate Students and Postdoctoral Researchers. To apply please contact Jose Vilar at
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