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Cancer progression models and fitness landscapes: a many-to-many relationship

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OncoSimulR: genetic simulation with arbitrary epistasis and mutator genes in asexual populations

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Every which way? On predicting tumor evolution using cancer progression models

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Estimating the predictability of cancer evolution

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From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics

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Conditional prediction of consecutive tumor evolution using cancer progression models: What genotype comes next?

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Simulating Evolution in Asexual Populations with Epistasis

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EvAM-Tools: tools for evolutionary accumulation and cancer progression models

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Ten quick tips for biomarker discovery and validation analyses using machine learning

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The long and winding road to understanding organismal construction

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A picture guide to cancer progression and monotonic accumulation models: evolutionary assumptions, plausible interpretations, and alternative uses

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Global epistasis on fitness landscapes

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Adaptive therapy in cancer: the role of restrictions in the accumulation of mutations

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Evolutionary accumulation modelling in AMR: machine learning to infer and predict evolutionary dynamics of multi-drug resistance

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HyperTraPS-CT: Inference and prediction for accumulation pathways with flexible data and model structures

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A hypercubic Mk model framework for capturing reversibility in disease, cancer, and evolutionary accumulation modelling

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Evolutionary accumulation modeling in AMR: machine learning to infer and predict evolutionary dynamics of multi-drug resistance

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Spatial network structure and amphibian persistence in stochastic environments

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Habitat loss and the structure of plant-animal mutualistic networks

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Can prey behaviour induce spatially synchronic aggregation of solitary predators?

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The shape of the past in the World Wide Web: Scale-free patterns and dynamics

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The nested structure of a scavenger community

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Do scale-free regulatory networks allow more expression than random ones?

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Spatial mating networks in insect-pollinated plants

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The roosting spatial network of a bird-predator bat

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The architecture of mutualistic networks minimizes competition and increases biodiversity

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Networks of spatial genetic variation across species

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Compartments in a marine food web associated with phylogeny, body mass, and habitat structure

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Nestedness versus modularity in ecological networks: two sides of the same coin?

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Evolution of a modular software network

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Phylogenetic Signal in Module Composition and Species Connectivity in Compartmentalized Host-Parasite Networks

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Temporal dynamics of direct reciprocal and indirect effects in a host-parasite network

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Habitat loss and the disassembly of mutalistic networks

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Evolving Digital Ecological Networks

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Assessing the robustness of networks of spatial genetic variation

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Host–parasite network structure is associated with community-level immunogenetic diversity

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Community-level demographic consequences of urbanization: an ecological network approach

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Does removal of invasives restore ecological networks? An experimental approach

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Diversification and biodiversity dynamics of hot and cold spots

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Seasonal species interactions minimize the impact of species turnover on the likelihood of community persistence

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How does the functional diversity of frugivorous birds shape the spatial pattern of seed dispersal? A case study in a relict plant species

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Genetic specificity of a plant–insect food web: Implications for linking genetic variation to network complexity

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The genotype-phenotype map of an evolving digital organism

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Non-adaptive origins of evolutionary innovations increase network complexity in interacting digital organisms

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Analysis of spatial genetic variation reveals genetic divergence among populations of Primula veris associated to contrasting habitats

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Ecological succession drives the structural change of seed-rodent interaction networks in fragmented forests

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Deciphering the Interdependence between Ecological and Evolutionary Networks

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Plant interactions shape pollination networks via nonadditive effects

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Indigenous knowledge networks in the face of global change

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Coevolutionary dynamics shape the structure of bacteria‐phage infection networks

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Partner Fidelity and Asymmetric Specialization in Ecological Networks

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Mycoheterotrophic plants preferentially target arbuscular mycorrhizal fungi that are highly connected to autotrophic plants

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The phenotypic plasticity of an evolving digital organism

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Editorial: Digital evolution: Insights for biologists

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Ontology for the Avida digital evolution platform

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avidaR: an R library to perform complex queries on an ontology-based database of digital organisms

researcher

María Santos Romero

researcher

Rafael Laso Pérez

research line

Crop Genomics and Breeding Methods

project

Combining Genomic Approaches to Study Host–Pathogen Relationships in Wheat and Septoria CNS2024-154812

project

New Drought- and Heat-Tolerant Blueberry Varieties through Advanced Genomic Selection

project

Genomic Assisted breeding for SUStainable agriculture: A benchmark approach

tool

GEmetrics

An R package to calculate BLUP of the Genotype by environment metrics.

tool

TrainSel

R package for optimization of training populations in breeding programs.

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The evolutionarily conserved factor Sus1/ENY2 plays a role in telomere length maintenance

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SAGA–CORE subunit Spt7 is required for correct Ubp8 localization, chromatin association and deubiquitinase activity

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The promiscuity of the SAGA complex subunits: Multifunctional or moonlighting proteins?

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Transcriptional memory dampens heat shock responses in yeast: functional role of Mip6 and its interaction with Rpd3

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An exon three-way junction structure modulates splicing and degradation of the SUS1 yeast pre-mRNA

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A role for Mog1 in H2Bub1 and H3K4me3 regulation affecting RNAPII transcription and mRNA export

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Sharing Marks: H3K4 Methylation and H2B Ubiquitination as Features of Meiotic Recombination and Transcription

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Decoding Transcriptional Memory in Yeast Heat Shock and the Functional Implication of the RNA Binding Protein Mip6

orcid publication

Unraveling gene expression: a beginner’s guide from chromatin modifications to mRNA export in Saccharomyces cerevisiae

tool

Avida: a digital evolution software platform for studying evolution

Avida is the most widely used Artificial Life software platform for studying evolutionary processes, in...

project

The Coevolving Web of Life

Understanding the mechanisms driving the ongoing (co)evolution of the Web of Life is a major...

project

Harnessing evolution by engineering ecological interactions to fight human disesases

Our society faces major biomedical challenges such as cancer, antibiotic resistance, and imbalanced microbiomes. While...

project

Evolving phages by engineering ecological interactions to treat antibiotic-resistant bacterial infections

The rate at which pathogenic bacteria evolve resistance to antibiotics exceeds the pace at which...

research line

Digital evolution

Studying evolution in the lab provides valuable insights but is often constrained by long timescales...

research line

Development of efficient methods for calculating paths of minimum or maximum parameter values (e.g., minimum energy paths) through surfaces of any number of dimensions.

MEPSAnd: Minimum Energy Path Surface Analysis over n-dimensional surfaces [http://bioweb.cbm.uam.es/software/MEPSAnd/] MEPSA: Minimum Energy Pathway A...

research line

Analysis by computational simulation of enzymatic reactions catalyzed by enzymes of biomedical interest. Design of specific inhibitors.

project

New drugs to inhibit Carbapenemases. Discovery of compounds by structural design (DrugCarbapenem)

orcid publication

The African swine fever virus lectin EP153R modulates the surface membrane expression of MHC class I antigens

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Modulating the RNA Processing and Decay by the Exosome: Altering Rrp44/Dis3 Activity and End-Product (vol 8, e76504, 2013)

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A novel RAD21 p.(Gln592del) variant expands the clinical description of Cornelia de Lange syndrome type 4 – Review of the literature

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MEPSAnd: minimum energy path surface analysis over n-dimensional surfaces

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An engineered miniACE2 protein secreted by mesenchymal stromal cells effectively neutralizes multiple SARS-CoV- 2 variants in vitro

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Biallelic loss-of-function variants in ZNF142 are associated with a robust DNA methylation signature affecting a limited number of genomic loci

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Postzygotic mosaicism in SMC1A and the first reported case of a female with Cornelia de Lange syndrome

orcid publication

CONDITIONS RESTRICTING DEPOLARIZATION-DEPENDENT CALCIUM INFLUX IN SYNAPTOSOMES REVEAL A GRADED RESPONSE OF P96-DEPHOSPHORYLATION AND A TRANSIENT DEPHOSPHORYLATION OF P65

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PYRUVATE-DEHYDROGENASE DEPHOSPHORYLATION IN RAT-BRAIN SYNAPTOSOMES AND MITOCHONDRIA - EVIDENCE FOR A CALCIUM-MEDIATED EFFECT IN RESPONSE TO DEPOLARIZATION, AND VARIATIONS DUE TO AGING

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AGE-RELATED-CHANGES IN CALCIUM HOMEOSTATIC MECHANISMS IN SYNAPTOSOMES IN RELATION WITH WORKING-MEMORY DEFICIENCY

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THE ACTIVITY OF SYNAPTOSOMAL CALCIUM CHANNELS IS INVERSELY CORRELATED WITH WORKING-MEMORY PERFORMANCE IN MEMORY-IMPAIRED, AGED RATS

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IMPROVEMENT OF AFRICAN SWINE-FEVER VIRUS NEUTRALIZATION ASSAY USING RECOMBINANT VIRUSES EXPRESSING CHROMOGENIC MARKER GENES

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Neutralizing antibodies to different proteins of African swine fever virus inhibit both virus attachment and internalization

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The structural protein p54 is essential for African swine fever virus viability

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Neutralization susceptibility of African swine fever virus is dependent on the phospholipid composition of viral particles

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High level expression of the major antigenic African swine fever virus proteins p54 and p30 in baculovirus and their potential use as diagnostic reagents

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Blocking antibodies inhibit complete African swine fever virus neutralization

orcid publication

Efficient formation of influenza virus-like particles: Dependence on the expression levels of viral proteins

orcid publication

In vitro inhibition of the replication of haemorrhagic septicaemia virus (VHSV) and African swine fever virus (ASFV) by extracts from marine microalgae