Computational Systems Biophysics

Group leader
Jose M. G. Vilar
Phone
+34 946 01 3450
Address

Biofisika Institute (CSIC-UPV/EHU)
Science Park of the UPV/EHU
Barrio Sarriena s/n. 48940 Leioa, Bizkaia (Spain)

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Research goal

Our research activity is focused on computational and mathematical analysis of biological systems at their various levels of organisation, from molecular properties to cell behaviour and the role these play in the cell population dynamics. The main objective is to deepen our understanding of the underlying mechanisms and to use this information for the controlling and designing cellular processes. For this, we use the latest computational technologies with a wide range of methods including molecular dynamics, structural bioinformatics, stochastic simulation algorithms and mathematical analysis of dynamic systems.

Group members
Ikerbasque Research Professor
Publications

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Vilar JMG, Saiz L

Dynamics-informed deconvolutional neural networks for super-resolution identification of regime changes in epidemiological time series
Sci Adv. 2023 Jul 14;9(28):eadf0673
doi: 10.1126/sciadv.adf0673

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Vilar JMG, Saiz L
Multi-landmark alignment of genomic signals reveals conserved expression patterns across transcription start sites
Sci Rep. 2023 Jul 5;13(1):10835
doi: 10.1038/s41598-023-37140-x

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Chang C, Garcia-Alcala M, Saiz L, Vilar JMG, Cluzel P
Robustness of DNA looping across multiple cell divisions in individual bacteria
Proc Natl Acad Sci U S A. 2022 Aug 16;119(33):e2200061119
doi: 10.1073/pnas.2200061119

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Vilar JMG, Saiz L
Ascertaining the initiation of epidemic resurgences: an application to the COVID-19 second surges in Europe and the Northeast United States
R Soc Open Sci. 2021 Oct 6;8(10):210773
doi: 10.1098/rsos.210773

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Vilar JMG, Saiz L
Reliably quantifying the evolving worldwide dynamic state of the COVID-19 outbreak from death records, clinical parametrization, and demographic data
Sci Rep. 2021 Oct 7;11(1):19952
doi: 10.1038/s41598-021-99273-1

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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).
DOI: 10.1016/j.jmb.2020.03.002

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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).
DOI: 10.1016/j.jmb.2018.11.026

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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.

Clearly Detectable, Kinetically Restricted Solid–Solid Phase Transition in cis-Ceramide Monolayers
Langmuir 34, 11749-11758 (2018).
DOI: 10.1021/acs.langmuir.8b02198

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J. M. G. Vilar and J. M. Rubi.

Determinants of population responses to environmental fluctuations
Sci Rep. 2018 Jan 17;8(1):887
DOI: 10.1038/s41598-017-18976-6