Institution: CBM
Research Groups: Computational biology and Bioinformatics (CBM): from Proteins to Ecosystems
Position: CT
Contact email: ubastolla@cbm.csic.es
BCB Committee: Outreach
BCB Community: No communities assigned.
BCB Tools: PC_ali, SSCPE, tnm, Zpeaks, PCA_cluster
BCB Services: No services assigned.
Research topics: Population dynamics, Ecological modelling, Evolutionary modelling, Function prediction, Functional annotation, Molecular evolution, Conservation Analysis, Evolutionary rates, Phylogenetic Analysis, Sequence Alignment, Structural bioinformatics, Molecular flexibility, Mutation Analysis and design, Structure-function relationship, Network Biology, Microbial communities
Biography: Although a physicist by training, I have always been interested in Biology, and I am convinced that only a multidisciplinary approach allow understanding the complexity of life and that biology strongly benefits from mathematical formalism resting on statistical mechanics on one side and on evolution on the other side. In this context, proteins are particularly interesting as a bridge between the two disciplines.
After my diploma work in Physics in Rome with Prof. Luca Peliti on a model of neutral evolution, I did my PhD thesis with Prof. Giorgio Parisi (2021 Physics Nobel prize), studying random Boolean networks as a null model of genetic regulation. Subsequently, I worked in Germany with Prof. Peter Grassberger, contributing to develop methods for Monte Carlo simulations of model proteins, which stimulated me to investigate protein folding stability and its relationship with protein evolution, which is now my main research interest. I developed this line as an independent researcher in the groups of Prof. Walter Knapp in FU-Berlin, Prof. Michael Lässig at the Max-Planck-Institute, Prof. Alfonso Valencia in the Center for Astrobiology in Madrid and finally in the Bioinformatics Unit of the CBMSO directed by Prof. Angel R. Ortiz, which I came to direct after he sadly and prematurely passed away.
In this field, I developed simple mathematical models that estimate the folding stability of proteins both with respect to unfolding and with respect to incorrect folding (misfolding, rarely taken into account) and I applied them to study protein evolution. I focused on the mutual relationship between folding stability and evolutionary parameters (mutation bias, population size), detecting selection for biophysical properties, and developing stability-aware substitution models that improve phylogenetic inference. I also investigated the occurrence and evolution of disordered proteins in the Centrosome.
Another subject of my interest is protein dynamics. I developed an elastic network model in torsion angle space that allows characterizing protein function by identifying conformation changes favored by natural selection and computing dynamical couplings between pairs of residues. These two lines have now merged in the structure and stability constrained protein evolution model (SSCPE) for phylogenetic inference, the subject of the present proposal.
In collaboration with experimental groups, I studied chromatin structure, developing a method for classifying chromatin states and studying their relationship with the processes of genome transcription and replication.
My other main field of interest is theoretical ecology, in particular the search of the ecosystem properties that favor the maintenance of biodiversity in the face of environmental changes. I contributed to develop structural stability as the mathematical framework that allows addressing this question, characterizing under which circumstances mutualistic interactions enhance structural stability and biodiversity. This work directed my interest to study interactions in bacterial communities, where there are many instances of cooperative interactions, and I developed a method to identify them from metagenomic data.
Publications
Bastolla, U., Gómez-Pinto, I., Vergara, Z., Gómez, M., González, C., & Gutiérrez, C. (2024). The topography of DNA replication origins in Eukarya: GGN clusters, landmark nucleosomes, CDC6 and G4 structures. https://doi.org/10.1101/2024.01.04.574144
Lorca-Alonso, I., Arenas, M., & Bastolla, U. (2023). Site-specific structure and stability constrained substitution models improve phylogenetic inference. https://doi.org/10.1101/2023.01.22.525075
Bastolla, U., Abia, D., & Piette, O. (2023). PC_ali: a tool for improved multiple alignments and evolutionary inference based on a hybrid protein sequence and structure similarity score. Bioinformatics, 39(11). https://doi.org/10.1093/bioinformatics/btad630
Dehouck, Y., & Bastolla, U. (2021). Why are large conformational changes well described by harmonic normal modes? Biophysical Journal, 120(23), 5343–5354. https://doi.org/10.1016/j.bpj.2021.10.027
Arenas, M., & Bastolla, U. (2020). ProtASR2: Ancestral reconstruction of protein sequences accounting for folding stability. Methods in Ecology and Evolution, 11(2), 248–257. Portico. https://doi.org/10.1111/2041-210x.13341
Bastolla, U. (2020). How lethal is the novel coronavirus, and how many undetected cases there are? The importance of being tested. https://doi.org/10.1101/2020.03.27.20045062
Sequeira-Mendes, J., Vergara, Z., Peiró, R., Morata, J., Aragüez, I., Costas, C., Mendez-Giraldez, R., Casacuberta, J. M., Bastolla, U., & Gutierrez, C. (2019). Differences in firing efficiency, chromatin, and transcription underlie the developmental plasticity of the Arabidopsis DNA replication origins. Genome Research, 29(5), 784–797. https://doi.org/10.1101/gr.240986.118
Bastolla, U., & Dehouck, Y. (2019). Can Conformational Changes of Proteins Be Represented in Torsion Angle Space? A Study with Rescaled Ridge Regression. Journal of Chemical Information and Modeling, 59(11), 4929–4941. https://doi.org/10.1021/acs.jcim.9b00627
Sequeira-Mendes, J., Vergara, Z., Peiró, R., Morata, J., Aragüez, I., Costas, C., Mendez-Giraldez, R., Casacuberta, J. M., Bastolla, U., & Gutierrez, C. (2018). Differences in firing efficiency, chromatin and transcription underlie the developmental plasticity of the Arabidopsis originome. https://doi.org/10.1101/258301
Jiménez-Santos, M. J., Arenas, M., & Bastolla, U. (2018). Influence of mutation bias and hydrophobicity on the substitution rates and sequence entropies of protein evolution. https://doi.org/10.7287/peerj.preprints.26868v1
Bastolla, U., Dehouck, Y., & Echave, J. (2017). What evolution tells us about protein physics, and protein physics tells us about evolution. Current Opinion in Structural Biology, 42, 59–66. https://doi.org/10.1016/j.sbi.2016.10.020
Pascual-García, A., & Bastolla, U. (2017). Mutualism supports biodiversity when the direct competition is weak. Nature Communications, 8(1). https://doi.org/10.1038/ncomms14326
Dehouck, Y., & Bastolla, U. (2017). The maximum penalty criterion for ridge regression: application to the calibration of the force constant in elastic network models. Integrative Biology, 9(7), 627–641. https://doi.org/10.1039/c7ib00079k
Nido, G. S., Bachschmid-Romano, L., Bastolla, U., & Pascual-García, A. (2016). Learning protein folding and evolution with a snake puzzle. https://doi.org/10.7287/peerj.preprints.2201v1
Ferrera, A., Pascual-García, A., & Bastolla, U. (2016). Effective competition determines the global stability of model ecosystems. Theoretical Ecology, 10(2), 195–205. https://doi.org/10.1007/s12080-016-0322-z
Arenas, M., Sánchez-Cobos, A., & Bastolla, U. (2015). Maximum-Likelihood Phylogenetic Inference with Selection on Protein Folding Stability. Molecular Biology and Evolution, 32(8), 2195–2207. https://doi.org/10.1093/molbev/msv085
Pascual-García, A., Tamames, J., & Bastolla, U. (2014). Bacteria dialog with Santa Rosalia: Are aggregations of cosmopolitan bacteria mainly explained by habitat filtering or by ecological interactions? BMC Microbiology, 14(1). https://doi.org/10.1186/s12866-014-0284-5
Bastolla, U. (2014). Detecting Selection on Protein Stability through Statistical Mechanical Models of Folding and Evolution. Biomolecules, 4(1), 291–314. https://doi.org/10.3390/biom4010291
Bastolla, U. (2014). Computing protein dynamics from protein structure with elastic network models. WIREs Computational Molecular Science, 4(5), 488–503. Portico. https://doi.org/10.1002/wcms.1186
Sequeira-Mendes, J., Aragüez, I., Peiró, R., Mendez-Giraldez, R., Zhang, X., Jacobsen, S. E., Bastolla, U., & Gutierrez, C. (2014). The Functional Topography of the Arabidopsis Genome Is Organized in a Reduced Number of Linear Motifs of Chromatin States . The Plant Cell, 26(6), 2351–2366. https://doi.org/10.1105/tpc.114.124578
Treviño, M. A., García-Mayoral, M. F., Jiménez, M. Á., Bastolla, U., & Bruix, M. (2014). Emergence of structure through protein–protein interactions and pH changes in dually predicted coiled-coil and disordered regions of centrosomal proteins. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 1844(10), 1808–1819. https://doi.org/10.1016/j.bbapap.2014.07.019
Arenas, M., Dos Santos, H. G., Posada, D., & Bastolla, U. (2013). Protein evolution along phylogenetic histories under structurally constrained substitution models. Bioinformatics, 29(23), 3020–3028. https://doi.org/10.1093/bioinformatics/btt530
Minning, J., Porto, M., & Bastolla, U. (2013). Detecting selection for negative design in proteins through an improved model of the misfolded state. Proteins: Structure, Function, and Bioinformatics, 81(7), 1102–1112. Portico. https://doi.org/10.1002/prot.24244
Bastolla, U., Porto, M., & Roman, H. E. (2013). The emerging dynamic view of proteins: Protein plasticity in allostery, evolution and self-assembly. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 1834(5), 817–819. https://doi.org/10.1016/j.bbapap.2013.03.016
Dos Santos, H. G., Klett, J., Méndez, R., & Bastolla, U. (2013). Characterizing conformation changes in proteins through the torsional elastic response. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 1834(5), 836–846. https://doi.org/10.1016/j.bbapap.2013.02.010
Dos Santos, H. G., Abia, D., Janowski, R., Mortuza, G., Bertero, M. G., Boutin, M., Guarín, N., Méndez-Giraldez, R., Nuñez, A., Pedrero, J. G., Redondo, P., Sanz, M., Speroni, S., Teichert, F., Bruix, M., Carazo, J. M., Gonzalez, C., Reina, J., Valpuesta, J. M., … Serrano, L. (2013). Structure and Non-Structure of Centrosomal Proteins. PLoS ONE, 8(5), e62633. https://doi.org/10.1371/journal.pone.0062633
Lombraña, R., Almeida, R., Revuelta, I., Madeira, S., Herranz, G., Saiz, N., Bastolla, U., & Gómez, M. (2013). High-resolution analysis of DNA synthesis start sites and nucleosome architecture at efficient mammalian replication origins. The EMBO Journal, 32(19), 2631–2644. https://doi.org/10.1038/emboj.2013.195
Nido, G. S., Méndez, R., Pascual-García, A., Abia, D., & Bastolla, U. (2012). Protein disorder in the centrosome correlates with complexity in cell types number. Mol. BioSyst., 8(1), 353–367. https://doi.org/10.1039/c1mb05199g
Bastolla, U., & Porto, M. (2012). Modeling Structural and Genomic Constraints in the Evolution of Proteins. Computational Modeling of Biological Systems, 327–345. https://doi.org/10.1007/978-1-4614-2146-7_14
Liberles, D. A., Teichmann, S. A., Bahar, I., Bastolla, U., Bloom, J., Bornberg‐Bauer, E., Colwell, L. J., de Koning, A. P. J., Dokholyan, N. V., Echave, J., Elofsson, A., Gerloff, D. L., Goldstein, R. A., Grahnen, J. A., Holder, M. T., Lakner, C., Lartillot, N., Lovell, S. C., Naylor, G., … Whelan, S. (2012). The interface of protein structure, protein biophysics, and molecular evolution. Protein Science, 21(6), 769–785. Portico. https://doi.org/10.1002/pro.2071
Bastolla, U., Bruscolini, P., & Velasco, J. L. (2012). Sequence determinants of protein folding rates: Positive correlation between contact energy and contact range indicates selection for fast folding. Proteins: Structure, Function, and Bioinformatics, 80(9), 2287–2304. Portico. https://doi.org/10.1002/prot.24118
Bastolla, U. (2011). Bioinformatics. Encyclopedia of Astrobiology, 177–178. https://doi.org/10.1007/978-3-642-11274-4_1751
Mendez, R., Fritsche, M., Porto, M., & Bastolla, U. (2010). Mutation Bias Favors Protein Folding Stability in the Evolution of Small Populations. PLoS Computational Biology, 6(5), e1000767. https://doi.org/10.1371/journal.pcbi.1000767
Teichert, F., Minning, J., Bastolla, U., & Porto, M. (2010). High quality protein sequence alignment by combining structural profile prediction and profile alignment using SABERTOOTH. BMC Bioinformatics, 11(1). https://doi.org/10.1186/1471-2105-11-251
Sammet, S. G., Bastolla, U., & Porto, M. (2010). Comparison of translation loads for standard and alternative genetic codes. BMC Evolutionary Biology, 10(1). https://doi.org/10.1186/1471-2148-10-178
Mendez, R., & Bastolla, U. (2010). Torsional Network Model: Normal Modes in Torsion Angle Space Better Correlate with Conformation Changes in Proteins. Physical Review Letters, 104(22). https://doi.org/10.1103/physrevlett.104.228103
Pascual-García, A., Abia, D., Ortiz, Á. R., & Bastolla, U. (2009). Cross-Over between Discrete and Continuous Protein Structure Space: Insights into Automatic Classification and Networks of Protein Structures. PLoS Computational Biology, 5(3), e1000331. https://doi.org/10.1371/journal.pcbi.1000331
Pascual‐García, A., Abia, D., Méndez, R., Nido, G. S., & Bastolla, U. (2009). Quantifying the evolutionary divergence of protein structures: The role of function change and function conservation. Proteins: Structure, Function, and Bioinformatics, 78(1), 181–196. Portico. https://doi.org/10.1002/prot.22616
Bastolla, U., Porto, M., & Ortíz, A. R. (2008). Local interactions in protein folding determined through an inverse folding model. Proteins: Structure, Function, and Bioinformatics, 72(4), 1377–1377. Portico. https://doi.org/10.1002/prot.22152
Bastolla, U., Ortíz, A. R., Porto, M., & Teichert, F. (2008). Effective connectivity profile: A structural representation that evidences the relationship between protein structures and sequences. Proteins: Structure, Function, and Bioinformatics, 73(4), 872–888. Portico. https://doi.org/10.1002/prot.22113
Bastolla, U., Porto, M., Roman, H. E., & Vendruscolo, M. (2007). The Structurally Constrained Neutral Model of Protein Evolution. Structural Approaches to Sequence Evolution, 75–112. https://doi.org/10.1007/978-3-540-35306-5_4
Structural Approaches to Sequence Evolution. (2007). In U. Bastolla, M. Porto, H. E. Roman, & M. Vendruscolo (Eds.), Biological and Medical Physics, Biomedical Engineering. Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-540-35306-5
Teichert, F., Bastolla, U., & Porto, M. (2007). SABERTOOTH: protein structural alignment based on a vectorial structure representation. BMC Bioinformatics, 8(1). https://doi.org/10.1186/1471-2105-8-425
Han, R., Leo‐Macias, A., Zerbino, D., Bastolla, U., Contreras‐Moreira, B., & Ortiz, A. R. (2007). An efficient conformational sampling method for homology modeling. Proteins: Structure, Function, and Bioinformatics, 71(1), 175–188. Portico. https://doi.org/10.1002/prot.21672
Bastolla, U., Porto, M., Roman, H. E., & Vendruscolo, M. (2006). A protein evolution model with independent sites that reproduces site-specific amino acid distributions from the Protein Data Bank. BMC Evolutionary Biology, 6(1). https://doi.org/10.1186/1471-2148-6-43
Huedo, E., Bastolla, U., Montero, R. S., & Llorente, I. M. (2005). A framework for protein structure prediction on the grid. New Generation Computing, 23(4), 277–290. https://doi.org/10.1007/bf03037634
Briones, C., & Bastolla, U. (2005). Protein evolution in viral quasispecies under selective pressure: A thermodynamic and phylogenetic analysis. Gene, 347(2), 237–246. https://doi.org/10.1016/j.gene.2004.12.018
Bastolla, U., Porto, M., Roman, H. E., & Vendruscolo, M. (2005). Looking at structure, stability, and evolution of proteins through the principal eigenvector of contact matrices and hydrophobicity profiles. Gene, 347(2), 219–230. https://doi.org/10.1016/j.gene.2004.12.015
Bastolla, U., Lässig, M., Manrubia, S. C., & Valleriani, A. (2005). Biodiversity in model ecosystems, II: species assembly and food web structure. Journal of Theoretical Biology, 235(4), 531–539. https://doi.org/10.1016/j.jtbi.2005.02.006
Bastolla, U., Lässig, M., Manrubia, S. C., & Valleriani, A. (2005). Biodiversity in model ecosystems, I: coexistence conditions for competing species. Journal of Theoretical Biology, 235(4), 521–530. https://doi.org/10.1016/j.jtbi.2005.02.005
Bastolla, U., & Demetrius, L. (2005). Stability constraints and protein evolution: the role of chain length, composition and disulfide bonds. Protein Engineering, Design and Selection, 18(9), 405–415. https://doi.org/10.1093/protein/gzi045
Porto, M., Bastolla, U., Roman, H. E., & Vendruscolo, M. (2004). Reconstruction of Protein Structures from a Vectorial Representation. Physical Review Letters, 92(21). https://doi.org/10.1103/physrevlett.92.218101
Huedo, E., Bastolla, U., Montero, R. S., & Llorente, I. M. (2004). Computational proteomics on the grid. New Generation Computing, 22(2), 191–192. https://doi.org/10.1007/bf03040959
Bastolla, U., Moya, A., Viguera, E., & van Ham, R. C. H. J. (2004). Genomic Determinants of Protein Folding Thermodynamics in Prokaryotic Organisms. Journal of Molecular Biology, 343(5), 1451–1466. https://doi.org/10.1016/j.jmb.2004.08.086
Bastolla, U., Porto, M., Roman, H. E., & Vendruscolo, M. (2004). Principal eigenvector of contact matrices and hydrophobicity profiles in proteins. Proteins: Structure, Function, and Bioinformatics, 58(1), 22–30. Portico. https://doi.org/10.1002/prot.20240
Bastolla, U., Porto, M., Roman, H. E., & Vendruscolo, M. (2004). Principal eigenvector of contact matrices and hydrophobicity profiles in proteins. Proteins: Structure, Function, and Bioinformatics, 58(1), 22–30. Portico. https://doi.org/10.1002/prot.20240
Porto, M., Roman, H. E., Vendruscolo, M., & Bastolla, U. (2004). Prediction of Site-Specific Amino Acid Distributions and Limits of Divergent Evolutionary Changes in Protein Sequences. Molecular Biology and Evolution, 22(3), 630–638. https://doi.org/10.1093/molbev/msi048
van Ham, R. C. H. J., Kamerbeek, J., Palacios, C., Rausell, C., Abascal, F., Bastolla, U., Fernández, J. M., Jiménez, L., Postigo, M., Silva, F. J., Tamames, J., Viguera, E., Latorre, A., Valencia, A., Morán, F., & Moya, A. (2003). Reductive genome evolution in Buchnera aphidicola. Proceedings of the National Academy of Sciences, 100(2), 581–586. https://doi.org/10.1073/pnas.0235981100
Bastolla, U., Porto, M., Eduardo Roman, H., & Vendruscolo, M. (2003). Connectivity of Neutral Networks, Overdispersion, and Structural Conservation in Protein Evolution. Journal of Molecular Evolution, 56(3), 243–254. https://doi.org/10.1007/s00239-002-2350-0
Bastolla, U., Porto, M., Eduardo Roman, H., & Vendruscolo, M. (2003). Statistical Properties of Neutral Evolution. Journal of Molecular Evolution, 57(0), S103–S119. https://doi.org/10.1007/s00239-003-0013-4
Wallin, S., Farwer, J., & Bastolla, U. (2002). Testing similarity measures with continuous and discrete protein models. Proteins: Structure, Function, and Bioinformatics, 50(1), 144–157. Portico. https://doi.org/10.1002/prot.10271
Bastolla, U., Porto, M., Roman, H. E., & Vendruscolo, M. (2002). Lack of Self-Averaging in Neutral Evolution of Proteins. Physical Review Letters, 89(20). https://doi.org/10.1103/physrevlett.89.208101
Bastolla, U., Farwer, J., Knapp, E. W., & Vendruscolo, M. (2001). How to guarantee optimal stability for most representative structures in the protein data bank. Proteins: Structure, Function, and Bioinformatics, 44(2), 79–96. Portico. https://doi.org/10.1002/prot.1075
Bastolla, U., & Grassberger, P. (2001). Exactness of the annealed and the replica symmetric approximations for random heteropolymers. Physical Review E, 63(3). https://doi.org/10.1103/physreve.63.031901
Bastolla, U. (2001). Overlap distribution in random and designed heteropolymers. The European Physical Journal E, 4(3), 305–313. https://doi.org/10.1007/s101890170113
Lässig, M., Bastolla, U., Manrubia, S. C., & Valleriani, A. (2001). Shape of Ecological Networks. Physical Review Letters, 86(19), 4418–4421. https://doi.org/10.1103/physrevlett.86.4418
BASTOLLA, U., LÄSSIG, M., MANRUBIA, S. C., & VALLERIANI, A. (2001). Diversity Patterns from Ecological Models at Dynamical Equilibrium. Journal of Theoretical Biology, 212(1), 11–34. https://doi.org/10.1006/jtbi.2001.2324
Manrubia, S. C., Bastolla, U., & Mikhailov, A. S. (2001). Replica-symmetry breaking in dynamical glasses. The European Physical Journal B, 23(4), 497–508. https://doi.org/10.1007/s100510170041
Bastolla, U., Frauenkron, H., & Grassberger, P. (2000). Phase diagram of random heteropolymers: Replica approach and application of a new Monte Carlo algorithm. Journal of Molecular Liquids, 84(1), 111–129. https://doi.org/10.1016/s0167-7322(99)00115-4
Bastolla, U., Vendruscolo, M., & Knapp, E.-W. (2000). A statistical mechanical method to optimize energy functions for protein folding. Proceedings of the National Academy of Sciences, 97(8), 3977–3981. https://doi.org/10.1073/pnas.97.8.3977
Bastolla, U., Vendruscolo, M., & Roman, H. E. (2000). Structurally constrained protein evolution: results from a lattice simulation. The European Physical Journal B, 15(2), 385–397. https://doi.org/10.1007/s100510051140
Bastolla, U., Roman, H. E., & Vendruscolo, M. (1999). Neutral Evolution of Model Proteins: Diffusion in Sequence Space and Overdispersion. Journal of Theoretical Biology, 200(1), 49–64. https://doi.org/10.1006/jtbi.1999.0975
Frauenkron, H., Bastolla, U., Gerstner, E., Grassberger, P., & Nadler, W. (1998). New Monte Carlo Algorithm for Protein Folding. Physical Review Letters, 80(14), 3149–3152. https://doi.org/10.1103/physrevlett.80.3149
Bastolla, U., & Parisi, G. (1998). The modular structure of Kauffman networks. Physica D: Nonlinear Phenomena, 115(3–4), 219–233. https://doi.org/10.1016/s0167-2789(97)00242-x
Bastolla, U., & Parisi, G. (1998). Relevant elements, magnetization and dynamical properties in Kauffman networks: A numerical study. Physica D: Nonlinear Phenomena, 115(3–4), 203–218. https://doi.org/10.1016/s0167-2789(97)00243-1
Bastolla, U., & Parisi, G. (1998). Relaxation, closing probabilities and transition from oscillatory to chaotic attractors in asymmetric neural networks. Journal of Physics A: Mathematical and General, 31(20), 4583–4602. https://doi.org/10.1088/0305-4470/31/20/003
Bastolla, U., & Grassberger, P. (1997). Phase Transitions of Single Semistiff Polymer Chains. Journal of Statistical Physics, 89(5–6), 1061–1078. https://doi.org/10.1007/bf02764222
Bastolla, U., & Parisi, G. (1997). Attraction basins in discretized maps. Journal of Physics A: Mathematical and General, 30(11), 3757–3769. https://doi.org/10.1088/0305-4470/30/11/009
Bastolla, U., & Parisi, G. (1997). A Numerical Study of the Critical Line of Kauffman Networks. Journal of Theoretical Biology, 187(1), 117–133. https://doi.org/10.1006/jtbi.1997.0423
Bastolla, U., & Parisi, G. (1997). Attractors in fully asymmetric neural networks. Journal of Physics A: Mathematical and General, 30(16), 5613–5631. https://doi.org/10.1088/0305-4470/30/16/007
Bastolla, U., & Parisi, G. (1996). Closing probabilities in the Kauffman model: An annealed computation. Physica D: Nonlinear Phenomena, 98(1), 1–25. https://doi.org/10.1016/0167-2789(96)00060-7
Error fetching reference data.
Bastolla, U., Lässig, M., Manrubia, S. C., & Valleriani, A. (n.d.). Dynamics and topology of species networks. Biological Evolution and Statistical Physics, 299–311. https://doi.org/10.1007/3-540-45692-9_17
Research lines:
There are no lines of investigation associated with this user.
Funding:
- Integrated model of protein evolution in sequence, structure and function for bioinformatics and phylogenetic applications: Agencia Española de Investigación. National. 01/09/2024-31/12/2027.
- Theoretical and computational investigation of tuberculosis antimicrobial resistance development based on extensive experimental library of mycobacterium strains: European Commission. EU. 01/01/2019-31/12/2024.
- Substitution processes with selection on protein structure and stability, for phylogenetic inference and prediction of the effects of mutations: Agencia Española de Investigación. National. 01/06/2020 - 31/05/2023.
- Angiotensin converting enzyme serum levels as predictor of infection and clinical outcome in COVID-19: CSIC. CSIC-COVID19. 01/05/2020 - 31/12/2021.